From 1c9cb877e03dc43d99b3925754dbcd263d21f985 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Thu, 17 Oct 2024 09:24:04 +0100 Subject: [PATCH 01/80] Check main rather than master when making PR for schema files --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7dea7392..c6e826a4 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -44,7 +44,7 @@ jobs: - name: Create Pull Request uses: peter-evans/create-pull-request@v6 - if: github.ref == 'refs/heads/master' + if: github.ref == 'refs/heads/main' with: token: ${{ secrets.GITHUB_TOKEN }} commit-message: Update database sql files From 6e8831fea47c48b01c5cf331e66eb16018ca36e6 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Mon, 28 Oct 2024 15:57:41 +0000 Subject: [PATCH 02/80] Add new Expeye grants (#246) (#247) Co-authored-by: Guilherme Francisco --- grants/ispyb_expeye_samples_grants.sql | 3 +++ 1 file changed, 3 insertions(+) diff --git a/grants/ispyb_expeye_samples_grants.sql b/grants/ispyb_expeye_samples_grants.sql index e2643262..2585f012 100644 --- a/grants/ispyb_expeye_samples_grants.sql +++ b/grants/ispyb_expeye_samples_grants.sql @@ -8,6 +8,8 @@ CREATE ROLE IF NOT EXISTS ispyb_expeye_samples_role; GRANT SELECT ON Proposal TO ispyb_expeye_samples_role; GRANT SELECT ON BLSession TO ispyb_expeye_samples_role; +GRANT SELECT ON DataCollectionGroup TO ispyb_expeye_samples_role; +GRANT SELECT ON DataCollection TO ispyb_expeye_samples_role; GRANT SELECT, INSERT, UPDATE, DELETE ON Shipping TO ispyb_expeye_samples_role; GRANT SELECT, INSERT, UPDATE, DELETE ON ShippingHasSession TO ispyb_expeye_samples_role; @@ -44,6 +46,7 @@ GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_BLSample TO ispyb_expeye_sam GRANT SELECT ON Protein TO ispyb_expeye_samples_role; GRANT SELECT ON Crystal TO ispyb_expeye_samples_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON XFEFluorescenceSpectrum TO ispyb_expeye_samples_role; GRANT SELECT, INSERT, UPDATE, DELETE ON DiffractionPlan TO ispyb_expeye_samples_role; From 6a760c32a343caacf77d4a0137340fd213d814d9 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Fri, 1 Nov 2024 11:59:48 +0000 Subject: [PATCH 03/80] Add roles and grants for MaxScale --- grants/maxscale.sql | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 grants/maxscale.sql diff --git a/grants/maxscale.sql b/grants/maxscale.sql new file mode 100644 index 00000000..c07bd12b --- /dev/null +++ b/grants/maxscale.sql @@ -0,0 +1,22 @@ +CREATE ROLE IF NOT EXISTS maxscale_role; +CREATE ROLE IF NOT EXISTS maxmon_role; + +-- You must also create database users and grant these roles to them, e.g. +-- CREATE USER maxscale_user@'%' IDENTIFIED BY 'the_password'; +-- CREATE USER maxmon_user@'%' IDENTIFIED BY 'the_password'; +-- GRANT maxscale_role to maxscale_user@'%'; +-- GRANT maxmon_role to maxmon_user@'%'; +-- SET DEFAULT ROLE maxscale_role FOR maxscale_user@'%'; +-- SET DEFAULT ROLE maxmon_role FOR maxmon_user@'%'; + +GRANT SHOW DATABASES ON *.* TO maxscale_role; +GRANT SELECT ON mysql.procs_priv TO maxscale_role; +GRANT SELECT ON mysql.tables_priv TO maxscale_role; +GRANT SELECT ON mysql.db TO maxscale_role; +GRANT SELECT ON mysql.roles_mapping TO maxscale_role; +GRANT SELECT ON mysql.columns_priv TO maxscale_role; +GRANT SELECT ON mysql.proxies_priv TO maxscale_role; +GRANT SELECT ON mysql.user TO maxscale_role; + +GRANT REPLICATION SLAVE, BINLOG MONITOR, SLAVE MONITOR ON *.* TO maxmon_role; +GRANT SELECT ON mysql.user TO maxmon_role; From 7543303b814f62975fa3556132935e2de4811de9 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Tue, 5 Nov 2024 13:59:11 +0000 Subject: [PATCH 04/80] Create fragment screening role with grants --- grants/ispyb_fragment_screening.sql | 32 +++++++++++++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 grants/ispyb_fragment_screening.sql diff --git a/grants/ispyb_fragment_screening.sql b/grants/ispyb_fragment_screening.sql new file mode 100644 index 00000000..fc535d9e --- /dev/null +++ b/grants/ispyb_fragment_screening.sql @@ -0,0 +1,32 @@ +-- Create the fragment screening application role. +CREATE ROLE IF NOT EXISTS ispyb_fragment_screening; + +-- You must also create a database user and grant this role to them, e.g. +-- CREATE USER fragment_screening_user@'%' IDENTIFIED BY 'the_password'; +-- GRANT ispyb_fragment_screening to fragment_screening_user@'%'; +-- SET DEFAULT ROLE ispyb_fragment_screening FOR fragment_screening_user@'%'; + +-- Grants for ispyb_fragment_screening +GRANT SELECT ON AutoProcIntegration TO 'ispyb_fragment_screening'; +GRANT SELECT ON AutoProcProgram TO 'ispyb_fragment_screening'; +GRANT SELECT ON AutoProcProgramAttachment TO 'ispyb_fragment_screening'; +GRANT SELECT ON AutoProcScaling TO 'ispyb_fragment_screening'; +GRANT SELECT ON AutoProcScalingStatistics TO 'ispyb_fragment_screening'; +GRANT SELECT ON AutoProcScaling_has_Int TO 'ispyb_fragment_screening'; +GRANT SELECT ON BLSampleImage TO 'ispyb_fragment_screening'; +GRANT SELECT ON BLSampleImageAutoScoreClass TO 'ispyb_fragment_screening'; +GRANT SELECT ON BLSampleImageScore TO 'ispyb_fragment_screening'; +GRANT SELECT ON BLSampleImage_has_AutoScoreClass TO 'ispyb_fragment_screening'; +GRANT SELECT ON BLSession TO 'ispyb_fragment_screening'; +GRANT SELECT ON BLSubSample TO 'ispyb_fragment_screening'; +GRANT SELECT ON Container TO 'ispyb_fragment_screening'; +GRANT SELECT ON ContainerInspection TO 'ispyb_fragment_screening'; +GRANT SELECT ON Crystal TO 'ispyb_fragment_screening'; +GRANT SELECT ON DataCollection TO 'ispyb_fragment_screening'; +GRANT SELECT ON ProcessingJob TO 'ispyb_fragment_screening'; +GRANT SELECT ON ProcessingJobParameter TO 'ispyb_fragment_screening'; +GRANT SELECT ON Proposal TO 'ispyb_fragment_screening'; +GRANT SELECT ON Protein TO 'ispyb_fragment_screening'; +GRANT SELECT, INSERT, UPDATE ON BLSample TO 'ispyb_fragment_screening'; +GRANT SELECT, INSERT, UPDATE ON BLSampleGroup TO 'ispyb_fragment_screening'; +GRANT SELECT, INSERT, UPDATE ON BLSampleGroup_has_BLSample TO 'ispyb_fragment_screening'; From 88e46bc46762f2b7c60c5ea8557733779ed284e0 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Thu, 14 Nov 2024 12:33:43 +0000 Subject: [PATCH 05/80] Add scripts to delete DC and DCG rows and associated rows in other tables --- .../scripts/DataCollectionGroup_delete.sql | 34 +++++++++ .../ispyb/scripts/DataCollection_delete.sql | 69 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 schemas/ispyb/scripts/DataCollectionGroup_delete.sql create mode 100644 schemas/ispyb/scripts/DataCollection_delete.sql diff --git a/schemas/ispyb/scripts/DataCollectionGroup_delete.sql b/schemas/ispyb/scripts/DataCollectionGroup_delete.sql new file mode 100644 index 00000000..ffe6c437 --- /dev/null +++ b/schemas/ispyb/scripts/DataCollectionGroup_delete.sql @@ -0,0 +1,34 @@ +-- This is a script to delete a given DataCollectionGroup (by +-- dataCollectionGroupId) and all associated rows in other tables except +-- DataCollection. +-- To delete DataCollections, run the DataCollection_delete.sql script first +-- before you run this. +-- Change the value of @dcgId and @sessionId to the values of +-- dataCollectionGroupId and sessionId you would like to delete. +-- Disclaimer: +-- This script is not extensively tested. +-- Run this at your own risk and beware of cascading deletes. + +SET @dcgId := 1000; +SET @sessionId = 999; + +DELETE XrayCentringResult +FROM XrayCentringResult + JOIN XrayCentring +WHERE XrayCentring.xrayCentringId = XrayCentringResult.xrayCentringId AND + XrayCentring.dataCollectionGroupId = @dcgId; + +DELETE +FROM XrayCentring +WHERE dataCollectionGroupId = @dcgId; + +DELETE +FROM DataCollectionGroup +WHERE dataCollectionGroupId = @dcgId; + +DELETE RobotAction +FROM RobotAction + JOIN DataCollectionGroup +WHERE RobotAction.blsessionId = @sessionId AND + DataCollectionGroup.blSampleId = RobotAction.blSampleId AND + DataCollectionGroup.dataCollectionGroupId = @dcgId; diff --git a/schemas/ispyb/scripts/DataCollection_delete.sql b/schemas/ispyb/scripts/DataCollection_delete.sql new file mode 100644 index 00000000..886486d6 --- /dev/null +++ b/schemas/ispyb/scripts/DataCollection_delete.sql @@ -0,0 +1,69 @@ +-- This is a script to delete a given DataCollection (by dataCollectionId) and +-- all associated rows in other tables. +-- Change the value of @dcId to the dataCollectionId you would like to delete. +-- Disclaimer: +-- This script is not extensively tested. It also currently will leave behind +-- some orphaned rows. +-- Run this at your own risk and beware of cascading deletes. + +SET @dcId := 1000; + +DELETE +FROM ImageQualityIndicators +WHERE dataCollectionId = @dcId; + +DELETE ProcessingJobParameter +FROM ProcessingJobParameter + JOIN ProcessingJob +WHERE ProcessingJob.processingJobId = ProcessingJobParameter.processingJobId AND + ProcessingJob.dataCollectionId = @dcId; + +DELETE ProcessingJobImageSweep +FROM ProcessingJobImageSweep + JOIN ProcessingJob +WHERE ProcessingJob.processingJobId = ProcessingJobImageSweep.processingJobId AND + ProcessingJob.dataCollectionId = @dcId; + +DELETE AutoProcProgramMessage +FROM AutoProcProgramMessage + JOIN ProcessingJob + JOIN AutoProcProgram +WHERE ProcessingJob.processingJobId = AutoProcProgram.processingJobId AND + AutoProcProgramMessage.autoProcProgramId = AutoProcProgram.autoProcProgramId AND + ProcessingJob.dataCollectionId = @dcId; + +DELETE AutoProcProgram +FROM AutoProcProgram + JOIN ProcessingJob +WHERE ProcessingJob.processingJobId = AutoProcProgram.processingJobId AND + ProcessingJob.dataCollectionId = @dcId; + +DELETE +FROM ProcessingJob +WHERE dataCollectionId = @dcId; + +DELETE AutoProcProgramMessage +FROM AutoProcProgramMessage + JOIN AutoProcProgram + JOIN AutoProcIntegration +WHERE AutoProcIntegration.autoProcProgramId = AutoProcProgram.autoProcProgramId AND + AutoProcProgramMessage.autoProcProgramId = AutoProcProgram.autoProcProgramId AND + AutoProcIntegration.dataCollectionId = @dcId; + +DELETE AutoProcProgram +FROM AutoProcProgram + JOIN AutoProcIntegration +WHERE AutoProcIntegration.autoProcProgramId = AutoProcProgram.autoProcProgramId AND + AutoProcIntegration.dataCollectionId = @dcId; + +DELETE +FROM AutoProcIntegration +WHERE dataCollectionId = @dcId; + +DELETE +FROM GridInfo +WHERE dataCollectionId = @dcId; + +DELETE +FROM DataCollection +WHERE dataCollectionId = @dcId; From c43ce45e603ec6935f421a335634dd77dbb93723 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 5 Dec 2024 13:12:16 +0000 Subject: [PATCH 06/80] Update Expeye core grants (#248) --- grants/ispyb_expeye.sql | 53 +++++++++++++++++++++++-- grants/ispyb_expeye_samples_grants.sql | 55 -------------------------- 2 files changed, 50 insertions(+), 58 deletions(-) delete mode 100644 grants/ispyb_expeye_samples_grants.sql diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 569c77c4..4b112741 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -10,9 +10,56 @@ GRANT ispyb_propagation TO ispyb_expeye_core_role; CREATE ROLE ispyb_expeye_acquisition_role; -GRANT SELECT, INSERT, UPDATE ON RobotAction TO ispyb_expeye_acquisition_role; -GRANT SELECT, INSERT, UPDATE ON GridInfo TO ispyb_expeye_acquisition_role; -GRANT SELECT, INSERT, UPDATE ON DataCollection TO ispyb_expeye_acquisition_role; +GRANT SELECT ON Proposal TO ispyb_expeye_acquisition_role; +GRANT SELECT ON BLSession TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON DataCollectionGroup TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE ON DataCollection TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON Position TO ispyb_expeye_acquisition_role; + +GRANT SELECT, INSERT, UPDATE, DELETE ON Shipping TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ShippingHasSession TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_Shipping TO ispyb_expeye_acquisition_role; + +GRANT SELECT, INSERT, UPDATE, DELETE ON LabContact TO ispyb_expeye_acquisition_role; + +GRANT SELECT, INSERT, UPDATE, DELETE ON Dewar TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON DewarLocation TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON DewarLocationList TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON DewarRegistry TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON DewarRegistry_has_Proposal TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON DewarReport TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE ON DewarTransportHistory TO ispyb_expeye_acquisition_role; + +GRANT SELECT, INSERT, UPDATE, DELETE ON Container TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerInspection TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerQueue TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerQueueSample TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerRegistry TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerRegistry_has_Proposal TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerReport TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerType TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE ON ContainerHistory TO ispyb_expeye_acquisition_role; + +GRANT SELECT ON ProcessingPipeline TO ispyb_expeye_acquisition_role; +GRANT SELECT ON ProcessingPipelineCategory TO ispyb_expeye_acquisition_role; + +GRANT SELECT, INSERT, UPDATE, DELETE ON BLSample TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup_has_BLSample TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON BLSubSample TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_BLSample TO ispyb_expeye_acquisition_role; + +GRANT SELECT ON Protein TO ispyb_expeye_acquisition_role; +GRANT SELECT ON Crystal TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON XFEFluorescenceSpectrum TO ispyb_expeye_acquisition_role; + +GRANT SELECT, INSERT, UPDATE, DELETE ON DiffractionPlan TO ispyb_expeye_acquisition_role; + +GRANT SELECT ON ComponentType TO ispyb_expeye_acquisition_role; +GRANT SELECT ON ComponentSubType TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON Component_has_SubType TO ispyb_expeye_acquisition_role; + +GRANT SELECT, INSERT, UPDATE ON RobotAction TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE ON GridInfo TO ispyb_expeye_acquisition_role; + GRANT ispyb_expeye_acquisition_role TO ispyb_expeye_core_role; diff --git a/grants/ispyb_expeye_samples_grants.sql b/grants/ispyb_expeye_samples_grants.sql deleted file mode 100644 index 2585f012..00000000 --- a/grants/ispyb_expeye_samples_grants.sql +++ /dev/null @@ -1,55 +0,0 @@ --- Create the Exp-eye Samples API role. -CREATE ROLE IF NOT EXISTS ispyb_expeye_samples_role; - --- You must also create a database user and grant this role to them, e.g. --- CREATE USER ispyb_expeye_samples@'%' IDENTIFIED BY 'the_password'; --- GRANT ispyb_expeye_samples_role to ispyb_expeye_samples@'%'; --- SET DEFAULT ROLE ispyb_expeye_samples_role FOR ispyb_expeye_core@'%'; - -GRANT SELECT ON Proposal TO ispyb_expeye_samples_role; -GRANT SELECT ON BLSession TO ispyb_expeye_samples_role; -GRANT SELECT ON DataCollectionGroup TO ispyb_expeye_samples_role; -GRANT SELECT ON DataCollection TO ispyb_expeye_samples_role; - -GRANT SELECT, INSERT, UPDATE, DELETE ON Shipping TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ShippingHasSession TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_Shipping TO ispyb_expeye_samples_role; - -GRANT SELECT, INSERT, UPDATE, DELETE ON LabContact TO ispyb_expeye_samples_role; - -GRANT SELECT, INSERT, UPDATE, DELETE ON Dewar TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON DewarLocation TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON DewarLocationList TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON DewarRegistry TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON DewarRegistry_has_Proposal TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON DewarReport TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE ON DewarTransportHistory TO ispyb_expeye_samples_role; - -GRANT SELECT, INSERT, UPDATE, DELETE ON Container TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerInspection TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerQueue TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerQueueSample TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerRegistry TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerRegistry_has_Proposal TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerReport TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON ContainerType TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE ON ContainerHistory TO ispyb_expeye_samples_role; - -GRANT SELECT ON ProcessingPipeline TO ispyb_expeye_samples_role; -GRANT SELECT ON ProcessingPipelineCategory TO ispyb_expeye_samples_role; - -GRANT SELECT, INSERT, UPDATE, DELETE ON BLSample TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup_has_BLSample TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON BLSubSample TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_BLSample TO ispyb_expeye_samples_role; - -GRANT SELECT ON Protein TO ispyb_expeye_samples_role; -GRANT SELECT ON Crystal TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON XFEFluorescenceSpectrum TO ispyb_expeye_samples_role; - -GRANT SELECT, INSERT, UPDATE, DELETE ON DiffractionPlan TO ispyb_expeye_samples_role; - -GRANT SELECT ON ComponentType TO ispyb_expeye_samples_role; -GRANT SELECT ON ComponentSubType TO ispyb_expeye_samples_role; -GRANT SELECT, INSERT, UPDATE, DELETE ON Component_has_SubType TO ispyb_expeye_samples_role; From 09e78e5514b5ce5270e94b75cd9be67361ba428d Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 5 Dec 2024 13:13:01 +0000 Subject: [PATCH 07/80] Add new boolean column "deleted" to the AutoProcProgramAttachment table (#249) --- .../2024_12_04_AutoProcProgramAttachment_deleted.sql | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 schemas/ispyb/updates/2024_12_04_AutoProcProgramAttachment_deleted.sql diff --git a/schemas/ispyb/updates/2024_12_04_AutoProcProgramAttachment_deleted.sql b/schemas/ispyb/updates/2024_12_04_AutoProcProgramAttachment_deleted.sql new file mode 100644 index 00000000..f58b535d --- /dev/null +++ b/schemas/ispyb/updates/2024_12_04_AutoProcProgramAttachment_deleted.sql @@ -0,0 +1,8 @@ +-- To undo: +-- ALTER TABLE AutoProcProgramAttachment DROP deleted, ALGORITHM=INSTANT; + +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2024_12_04_AutoProcProgramAttachment_deleted.sql', 'ONGOING'); + +ALTER TABLE AutoProcProgramAttachment ADD deleted boolean DEFAULT FALSE COMMENT '1/TRUE if the file has been deleted', ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2024_12_04_AutoProcProgramAttachment_deleted.sql'; From 29898a8ae3e8c1295ed37d3c4fc63880dfb7eb01 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 5 Dec 2024 17:14:37 +0000 Subject: [PATCH 08/80] Changes in preparation for release of v4.3.0 (#250) Changes in preparation for release of v4.3.0 * Use mariadb 10.6 (an LTS release) in CI builds as 10.8 is EOL * Updated HISTORY.md file * Tweaks to README.md * Update .sql to bump version of schema * Refreshed schema files --- .github/workflows/build.yml | 4 +- HISTORY.rst | 27 ++++++ README.md | 8 +- schemas/ispyb/data.sql | 86 ++++++++++--------- schemas/ispyb/lookups.sql | 65 +++++++------- schemas/ispyb/tables.sql | 6 +- .../2024_12_05_AdminVar_bump_version.sql | 5 ++ 7 files changed, 124 insertions(+), 77 deletions(-) create mode 100644 schemas/ispyb/updates/2024_12_05_AdminVar_bump_version.sql diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index c6e826a4..b49cb575 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest services: mariadb: - image: mariadb:10.8 + image: mariadb:10.6 env: MYSQL_USER: test MYSQL_PASSWORD: test @@ -28,7 +28,7 @@ jobs: - uses: shogo82148/actions-setup-mysql@v1 with: distribution: 'mariadb' - mysql-version: '10.8' + mysql-version: '10.6' auto-start: false - name: Build database run: | diff --git a/HISTORY.rst b/HISTORY.rst index e900af57..8995ece7 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,33 @@ History Unreleased / master ------------------- +4.3.0 (2024-12-05) +------------------- + +Note: The schema files now include a command in the first line to set the sanbox +mode which is incompatible with older clients. For more info and to disable, see: +https://mariadb.org/mariadb-dump-file-compatibility-change/ + +Admin: Changes to GitHub workflows as 'main' is now the default branch (previously 'master') + +New or modified tables and columns: + +- Add ``processingPipelineId`` column to the ``AutoProcProgram`` table +- Add new boolean column ``deleted`` to the ``AutoProcProgramAttachment`` table +- Add unique index on ``BLSample(containerId, location, subLocation)`` +- Update the ``ProcessedTomogram`` table comment + +Roles and permissions: + +- Add new grants for Expeye and combine grants into two roles instead of three +- Add roles and grants for MaxScale +- Add role with grants for fragment screening + +Scripts and data changes: + +- Trim trailing '1' in the ``SpaceGroup`` table's ``spaceGroupShortName`` column +- Add scripts that can delete ``DataCollection`` and ``DataCollectionGroup`` rows and referenced rows in other tables + 4.2.1 (2024-08-19) ------------------- diff --git a/README.md b/README.md index 4363e16d..cca80e77 100644 --- a/README.md +++ b/README.md @@ -2,19 +2,19 @@ # ispyb-database -This package provides everything needed to create the Diamond flavour of the ISPyB database schema. As the schema evolves the update scripts will also be published here, so other users of the schema should be able to stay up-to-date. +This repository provides everything needed to create the Diamond flavour of the ISPyB database schema. As the schema evolves the update scripts will also be published here, so other users of the schema should be able to stay up-to-date. ## Requirements -* Server and a client packages of MariaDB 10.3 or later. +* Server and a client packages of MariaDB 10.6 or later. * A Unix-like OS with `bash` shell. * The pandoc package (only required to build documentation at the end of the `build.sh` script.) * If binary logging is enabled in the DB system, then execute this before importing the test schema: `SET GLOBAL log_bin_trust_function_creators=ON;` ## Installation -1. Install MariaDB. See the Wiki for ideas on how to install in a particular environment. -2. Copy `.my.example.cnf` to `.my.cnf` and then edit that file to set the `user` and `password`, e.g. `user = root` and use the `password` you set when securing. Optionally, you can also set e.g. `host` and `port`. +1. Install MariaDB. Please see the Wiki for ideas on how to install in a particular environment. +2. Copy `.my.example.cnf` to `.my.cnf` and then edit that file to set the `user` and `password`, e.g. `user = root` and correspond `password`. Optionally, you can also set e.g. `host` and `port`. 3. In a test environment run the `build.sh` file. This creates the database schema and applies the grants as described in the "Schema" and "Grants" sections below. ### Schema diff --git a/schemas/ispyb/data.sql b/schemas/ispyb/data.sql index 1626a998..5e2a6f32 100644 --- a/schemas/ispyb/data.sql +++ b/schemas/ispyb/data.sql @@ -1,3 +1,4 @@ +/*M!999999\- enable the sandbox mode */ /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; @@ -49,47 +50,47 @@ INSERT INTO `AutoProcIntegration` (`autoProcIntegrationId`, `dataCollectionId`, /*!40000 ALTER TABLE `AutoProcIntegration` ENABLE KEYS */; /*!40000 ALTER TABLE `AutoProcProgram` DISABLE KEYS */; -INSERT INTO `AutoProcProgram` (`autoProcProgramId`, `processingCommandLine`, `processingPrograms`, `processingStatus`, `processingMessage`, `processingStartTime`, `processingEndTime`, `processingEnvironment`, `recordTimeStamp`, `processingJobId`) VALUES (56425592,'/dls_sw/apps/fast_dp/2395/src/fast_dp.py -a S -j 0 -J 18 /dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','fast_dp',1,NULL,NULL,NULL,NULL,'2016-01-14 12:46:22',NULL), -(56425944,'xia2 min_images=3 -3dii -xparallel -1 -atom s -blend -project cm14451v1 -crystal xtlysjan41 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-14 13:09:51',NULL), -(56425952,'xia2 min_images=3 -dials -xparallel -1 -atom s -blend -project cm14451v1 -crystal xtlysjan41 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-14 13:24:22',NULL), -(56425963,'/dls_sw/apps/GPhL/autoPROC/20151214/autoPROC/bin/linux64/process -xml -Id xtlysjan41,/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/,tlys_jan_4_1_####.cbf,1,3600 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_PROCESSORS=12 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_J','autoPROC 1.0.4 (see: http://www.globalphasing.com/autoproc/)',1,NULL,NULL,NULL,NULL,'2016-01-14 13:34:34',NULL), -(56426286,'xia2 min_images=3 -dials -atom s -blend -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/linediffraction_1_0001.cbf image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-14 14:01:57',NULL), -(56426287,'xia2 min_images=3 -3dii -atom s -blend -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/linediffraction_1_0001.cbf image=/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/tlys_jan_4_1_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-14 14:13:57',NULL), -(56983954,'/dls_sw/apps/fast_dp/2395/src/fast_dp.py -a S -j 0 -J 18 /dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','fast_dp',1,NULL,NULL,NULL,NULL,'2016-01-22 11:34:03',NULL), -(56985584,'xia2 min_images=3 -3d -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 3d',1,NULL,NULL,NULL,NULL,'2016-01-22 11:52:36',NULL), -(56985589,'/dls_sw/apps/GPhL/autoPROC/20151214/autoPROC/bin/linux64/process -xml -Id xins22,/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/,ins2_2_####.cbf,1,7200 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_PROCESSORS=12 autoPROC_XdsKeyword_MAXIMUM_NUMBER_OF_JOBS=4 Sto','autoPROC 1.0.4 (see: http://www.globalphasing.com/autoproc/)',1,NULL,NULL,NULL,NULL,'2016-01-22 11:53:38',NULL), -(56985592,'xia2 min_images=3 -3dii -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 3dii',1,NULL,NULL,NULL,NULL,'2016-01-22 11:54:01',NULL), -(56986673,'xia2 min_images=3 -dials -xparallel -1 -atom s -blend -project cm14451v1 -crystal xins22 -ispyb_xml_out ispyb.xml image=/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/ins2_2_0001.cbf','xia2 dials',1,NULL,NULL,NULL,NULL,'2016-01-22 12:01:59',5), -(56986674,'/dls_sw/apps/dimple/git-master/main.py --dls-naming --slow -fpng /dls/i24/data/2018/cm19649-3/processed/test180731/hewlmesh_1/line4/hewlmesh_1_1_/xia2/3d-run/DataFiles/cm19649v3_xhewlmesh11_free.mtz /dls/i24/data/2018/cm19649-3/tmp/hewlmesh_1.4308.pdb /d','dimple',1,'Blob scores: 78','2018-07-31 08:55:52','2018-07-31 08:57:10',NULL,'2018-07-31 08:57:10',NULL), -(56986675,NULL,'dimple',0,'Unknown error','2018-07-31 08:57:12',NULL,NULL,NULL,NULL); 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+/*!40000 ALTER TABLE `ProcessedTomogram` ENABLE KEYS */; + /*!40000 ALTER TABLE `ProcessingJob` DISABLE KEYS */; INSERT INTO `ProcessingJob` (`processingJobId`, `dataCollectionId`, `displayName`, `comments`, `recordTimestamp`, `recipe`, `automatic`) VALUES (5,1002287,'test job 01','Testing the job submission system','2017-10-16 11:02:12','DIALS/xia2',0); /*!40000 ALTER TABLE `ProcessingJob` ENABLE KEYS */; diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 6c54b6a3..3f7d45ad 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -1,3 +1,4 @@ +/*M!999999\- enable the sandbox mode */ /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; @@ -10,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.2.1'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.3.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -263,7 +264,13 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (292,'2024_07_16_ContainerType_insert_new.sql','DONE','2024-08-14 11:23:41'), (293,'2024_08_08_ProcessedTomogram.sql','DONE','2024-08-14 11:23:41'), (294,'2024_08_14_AdminVar_bump_version.sql','DONE','2024-08-14 11:23:41'), -(295,'2024_08_19_AdminVar_bump_version.sql','DONE','2024-08-19 12:17:10'); +(295,'2024_08_19_AdminVar_bump_version.sql','DONE','2024-08-19 12:17:10'), +(296,'2024_09_04_ProcessedTomogram_comment','ONGOING','2024-12-05 13:27:18'), +(297,'2024_09_17_SpaceGroup_trim','ONGOING','2024-12-05 13:27:18'), +(298,'2024_09_25_AutoProcProgram_processingPipelineId.sql','DONE','2024-12-05 13:27:18'), +(299,'2024_10_15_BLSample_unique_index.sql','DONE','2024-12-05 13:27:18'), +(300,'2024_12_04_AutoProcProgramAttachment_deleted.sql','DONE','2024-12-05 13:27:18'), +(301,'2024_12_05_AdminVar_bump_version.sql','DONE','2024-12-05 13:27:18'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; @@ -523,20 +530,20 @@ INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortNa (48,48,'Pnnn','P nn n',NULL,NULL,NULL,NULL,0), (49,49,'Pccm','P cc m',NULL,NULL,NULL,NULL,0), (50,50,'Pban','P ba n',NULL,NULL,NULL,NULL,0), -(51,51,'Pmma1','P mm a1',NULL,NULL,NULL,NULL,0), -(52,52,'Pnna1','P nn a1',NULL,NULL,NULL,NULL,0), -(53,53,'Pmna1','P mn a1',NULL,NULL,NULL,NULL,0), -(54,54,'Pcca1','P cc a1',NULL,NULL,NULL,NULL,0), -(55,55,'Pbam1','P ba m1',NULL,NULL,NULL,NULL,0), -(56,56,'Pccn1','P cc n1',NULL,NULL,NULL,NULL,0), -(57,57,'Pbcm1','P bc m1',NULL,NULL,NULL,NULL,0), -(58,58,'Pnnm1','P nn m1',NULL,NULL,NULL,NULL,0), -(59,59,'Pmmn1','P mm n1',NULL,NULL,NULL,NULL,0), -(60,60,'Pbcn1','P bc n1',NULL,NULL,NULL,NULL,0), -(61,61,'Pbca1','P bc a1',NULL,NULL,NULL,NULL,0), -(62,62,'Pnma1','P nm a1',NULL,NULL,NULL,NULL,0), -(63,63,'Cmcm1','C mc m1',NULL,NULL,NULL,NULL,0), -(64,64,'Cmca1','C mc a1',NULL,NULL,NULL,NULL,0), +(51,51,'Pmma','P mm a1',NULL,NULL,NULL,NULL,0), +(52,52,'Pnna','P nn a1',NULL,NULL,NULL,NULL,0), +(53,53,'Pmna','P mn a1',NULL,NULL,NULL,NULL,0), +(54,54,'Pcca','P cc a1',NULL,NULL,NULL,NULL,0), +(55,55,'Pbam','P ba m1',NULL,NULL,NULL,NULL,0), +(56,56,'Pccn','P cc n1',NULL,NULL,NULL,NULL,0), +(57,57,'Pbcm','P bc m1',NULL,NULL,NULL,NULL,0), +(58,58,'Pnnm','P nn m1',NULL,NULL,NULL,NULL,0), +(59,59,'Pmmn','P mm n1',NULL,NULL,NULL,NULL,0), +(60,60,'Pbcn','P bc n1',NULL,NULL,NULL,NULL,0), +(61,61,'Pbca','P bc a1',NULL,NULL,NULL,NULL,0), +(62,62,'Pnma','P nm a1',NULL,NULL,NULL,NULL,0), +(63,63,'Cmcm','C mc m1',NULL,NULL,NULL,NULL,0), +(64,64,'Cmca','C mc a1',NULL,NULL,NULL,NULL,0), (65,65,'Cmmm','C mm m',NULL,NULL,NULL,NULL,0), (66,66,'Cccm','C cc m',NULL,NULL,NULL,NULL,0), (67,67,'Cmma','C mm a',NULL,NULL,NULL,NULL,0), @@ -545,8 +552,8 @@ INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortNa (70,70,'Fddd','F dd d',NULL,NULL,NULL,NULL,0), (71,71,'Immm','I mm m',NULL,NULL,NULL,NULL,0), (72,72,'Ibam','I ba m',NULL,NULL,NULL,NULL,0), -(73,73,'Ibca1','I b c a1',NULL,NULL,NULL,NULL,0), -(74,74,'Imma1','I mm a1',NULL,NULL,NULL,NULL,0), +(73,73,'Ibca','I b c a1',NULL,NULL,NULL,NULL,0), +(74,74,'Imma','I mm a1',NULL,NULL,NULL,NULL,0), (75,75,'P4','P4','tP',NULL,NULL,NULL,1), (76,76,'P41','P41','tP',NULL,NULL,NULL,1), (77,77,'P42','P42','tP',NULL,NULL,NULL,1), @@ -599,10 +606,10 @@ INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortNa (124,124,'P4/mcc','P4/m c c',NULL,NULL,NULL,NULL,0), (125,125,'P4/nbm','P4/n b m',NULL,NULL,NULL,NULL,0), (126,126,'P4/nnc','P4/n n c',NULL,NULL,NULL,NULL,0), -(127,127,'P4/mbm1','P4/m b m1',NULL,NULL,NULL,NULL,0), -(128,128,'P4/mnc1','P4/m n c1',NULL,NULL,NULL,NULL,0), -(129,129,'P4/nmm1','P4/n m m1',NULL,NULL,NULL,NULL,0), -(130,130,'P4/ncc1','P4/n c c1',NULL,NULL,NULL,NULL,0), +(127,127,'P4/mbm','P4/m b m1',NULL,NULL,NULL,NULL,0), +(128,128,'P4/mnc','P4/m n c1',NULL,NULL,NULL,NULL,0), +(129,129,'P4/nmm','P4/n m m1',NULL,NULL,NULL,NULL,0), +(130,130,'P4/ncc','P4/n c c1',NULL,NULL,NULL,NULL,0), (131,131,'P42/mmc','P42/m m c',NULL,NULL,NULL,NULL,0), (132,132,'P42/mcm','P42/m c m',NULL,NULL,NULL,NULL,0), (133,133,'P42/nbc','P42/n b c',NULL,NULL,NULL,NULL,0), @@ -677,8 +684,8 @@ INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortNa (202,202,'Fm-3','Fm -3',NULL,NULL,NULL,NULL,0), (203,203,'Fd-3','Fd -3',NULL,NULL,NULL,NULL,0), (204,204,'Im-3','Im -3',NULL,NULL,NULL,NULL,0), -(205,205,'Pa-31','Pa -31',NULL,NULL,NULL,NULL,0), -(206,206,'Ia-31','Ia -31',NULL,NULL,NULL,NULL,0), +(205,205,'Pa-3','Pa -31',NULL,NULL,NULL,NULL,0), +(206,206,'Ia-3','Ia -31',NULL,NULL,NULL,NULL,0), (207,207,'P432','P4 3 2','cP',NULL,NULL,NULL,1), (208,208,'P4232','P42 3 2','cP',NULL,NULL,NULL,1), (209,209,'F432','F4 3 2','cF',NULL,NULL,NULL,1), @@ -695,14 +702,14 @@ INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortNa (220,220,'I-43d','I-4 3 d',NULL,NULL,NULL,NULL,0), (221,221,'Pm-3m','Pm -3 m',NULL,NULL,NULL,NULL,0), (222,222,'Pn-3n','Pn -3 n',NULL,NULL,NULL,NULL,0), -(223,223,'Pm-3n1','Pm -3 n1',NULL,NULL,NULL,NULL,0), -(224,224,'Pn-3m1','Pn -3 m1',NULL,NULL,NULL,NULL,0), +(223,223,'Pm-3n','Pm -3 n1',NULL,NULL,NULL,NULL,0), +(224,224,'Pn-3m','Pn -3 m1',NULL,NULL,NULL,NULL,0), (225,225,'Fm-3m','Fm -3 m',NULL,NULL,NULL,NULL,0), (226,226,'Fm-3c','Fm -3 c',NULL,NULL,NULL,NULL,0), -(227,227,'Fd-3m1','Fd -3 m1',NULL,NULL,NULL,NULL,0), -(228,228,'Fd-3c1','Fd -3 c1',NULL,NULL,NULL,NULL,0), +(227,227,'Fd-3m','Fd -3 m1',NULL,NULL,NULL,NULL,0), +(228,228,'Fd-3c','Fd -3 c1',NULL,NULL,NULL,NULL,0), (229,229,'Im-3m','Im -3 m',NULL,NULL,NULL,NULL,0), -(230,230,'Ia-3d1','Ia -3 d1',NULL,NULL,NULL,NULL,0); +(230,230,'Ia-3d','Ia -3 d1',NULL,NULL,NULL,NULL,0); /*!40000 ALTER TABLE `SpaceGroup` ENABLE KEYS */; /*!40000 ALTER TABLE `ProcessingPipelineCategory` DISABLE KEYS */; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index c0ef35fb..d68fca82 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -1,3 +1,4 @@ +/*M!999999\- enable the sandbox mode */ /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; @@ -124,6 +125,7 @@ CREATE TABLE `AutoProcProgram` ( `processingEnvironment` varchar(255) DEFAULT NULL COMMENT 'Cpus, Nodes,...', `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', `processingJobId` int(11) unsigned DEFAULT NULL, + `processingPipelineId` int(11) unsigned DEFAULT NULL, PRIMARY KEY (`autoProcProgramId`), KEY `AutoProcProgram_FK2` (`processingJobId`), CONSTRAINT `AutoProcProgram_FK2` FOREIGN KEY (`processingJobId`) REFERENCES `ProcessingJob` (`processingJobId`) @@ -140,6 +142,7 @@ CREATE TABLE `AutoProcProgramAttachment` ( `filePath` varchar(255) DEFAULT NULL COMMENT 'Attachment filepath to disk storage', `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', `importanceRank` tinyint(3) unsigned DEFAULT NULL COMMENT 'For the particular autoProcProgramId and fileType, indicate the importance of the attachment. Higher numbers are more important', + `deleted` tinyint(1) DEFAULT 0 COMMENT '1/TRUE if the file has been deleted', PRIMARY KEY (`autoProcProgramAttachmentId`), KEY `AutoProcProgramAttachmentIdx1` (`autoProcProgramId`), CONSTRAINT `AutoProcProgramAttachmentFk1` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE CASCADE ON UPDATE CASCADE @@ -429,6 +432,7 @@ CREATE TABLE `BLSample` ( `staffComments` varchar(255) DEFAULT NULL COMMENT 'Any staff comments on the sample', `source` varchar(50) DEFAULT current_user(), PRIMARY KEY (`blSampleId`), + UNIQUE KEY `BLSample_uidx_containerId_location_subLocation` (`containerId`,`location`,`subLocation`), KEY `BLSample_FKIndex1` (`containerId`), KEY `BLSample_FKIndex3` (`diffractionPlanId`), KEY `BLSample_FKIndex_Status` (`blSampleStatus`), @@ -2669,7 +2673,7 @@ CREATE TABLE `ProcessedTomogram` ( PRIMARY KEY (`processedTomogramId`), KEY `tomogramId` (`tomogramId`), CONSTRAINT `ProcessedTomogram_ibfk_1` FOREIGN KEY (`tomogramId`) REFERENCES `Tomogram` (`tomogramId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='References to processed tomogram paths'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Indicates the sample''s location on a multi-sample pin, where 1 is closest to the pin base or a sample''s position in a cryo-EM cassette'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingJob`; /*!40101 SET @saved_cs_client = @@character_set_client */; diff --git a/schemas/ispyb/updates/2024_12_05_AdminVar_bump_version.sql b/schemas/ispyb/updates/2024_12_05_AdminVar_bump_version.sql new file mode 100644 index 00000000..ae25d707 --- /dev/null +++ b/schemas/ispyb/updates/2024_12_05_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2024_12_05_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.3.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2024_12_05_AdminVar_bump_version.sql'; From b957b283bf3882cda623d2ca059fa9f3973e0e24 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Tue, 10 Dec 2024 16:58:32 +0000 Subject: [PATCH 09/80] Use MariaDB 10.6.19 in Dockerfile --- Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index d92144c1..92d4f9e1 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM docker.io/library/mariadb:10.10.3 +FROM docker.io/library/mariadb:10.6.19 WORKDIR /ispyb From 4ee4d83b15fc2a71151206acd37046c479a283de Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Tue, 10 Dec 2024 16:59:41 +0000 Subject: [PATCH 10/80] Specify that the Wiki has info about installing via Dockerfile --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index cca80e77..1344c761 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ This repository provides everything needed to create the Diamond flavour of the ## Installation -1. Install MariaDB. Please see the Wiki for ideas on how to install in a particular environment. +1. Install MariaDB. The Wiki has ideas on how to install in a particular environment, including OS packages or containers via the provided Dockerfile. If you use the container approach with the provided Dockerfile, then steps 2 and 3 below are done for you automatically. 2. Copy `.my.example.cnf` to `.my.cnf` and then edit that file to set the `user` and `password`, e.g. `user = root` and correspond `password`. Optionally, you can also set e.g. `host` and `port`. 3. In a test environment run the `build.sh` file. This creates the database schema and applies the grants as described in the "Schema" and "Grants" sections below. From 7a7a8463cb53625dea38002936e7df58c78ae61e Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Wed, 11 Dec 2024 11:49:40 +0000 Subject: [PATCH 11/80] Add more info, correct mistake, in "Useful scripts" README section --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 1344c761..d8a8b9c2 100644 --- a/README.md +++ b/README.md @@ -94,8 +94,8 @@ mariadb ispyb < grants/ispyb_web.sql ## Useful scripts * `build.sh`: Creates a development `ispyb_build` database and imports all the schema and grants files into it. -* `release.sh`: Makes a release, see the Releasing section. -* `bin/backup.sh`: Makes a backup of the development database. +* `release.sh`: Makes a release, see the `RELEASE.md` file for details. +* `bin/backup.sh`: Makes a backup of the development database, producing four files: `tables.sql`, `routines.sql`, `lookups.sql`, `data.sql`. * `bin/missed_updates.sh`: Generates a list of files in the `schemas/ispyb/updates/` folder that haven't been applied. * `bin/export_session.sh`: Exports a given session's database rows to SQL files. These can then easily be imported into an empty ispyb database. This can be used e.g. to create a single-session ISPyB/SynchWeb instance if combined with all the relevant data files and processing files for the session, and an instance of SynchWeb. From a5b4636c9367707106cf25ff94c5627d51b5b4e4 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Wed, 11 Dec 2024 12:34:02 +0000 Subject: [PATCH 12/80] Fix wrong scriptName in insert to SchemaStatus (#251) --- schemas/ispyb/updates/2024_09_04_ProcessedTomogram_comment.sql | 2 +- schemas/ispyb/updates/2024_09_17_SpaceGroup_trim.sql | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/schemas/ispyb/updates/2024_09_04_ProcessedTomogram_comment.sql b/schemas/ispyb/updates/2024_09_04_ProcessedTomogram_comment.sql index 85a85103..da56faa4 100644 --- a/schemas/ispyb/updates/2024_09_04_ProcessedTomogram_comment.sql +++ b/schemas/ispyb/updates/2024_09_04_ProcessedTomogram_comment.sql @@ -1,4 +1,4 @@ -INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2024_09_04_ProcessedTomogram_comment', 'ONGOING'); +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2024_09_04_ProcessedTomogram_comment.sql', 'ONGOING'); ALTER TABLE ProcessedTomogram COMMENT = 'Indicates the sample''s location on a multi-sample pin, where 1 is closest to the pin base or a sample''s position in a cryo-EM cassette'; diff --git a/schemas/ispyb/updates/2024_09_17_SpaceGroup_trim.sql b/schemas/ispyb/updates/2024_09_17_SpaceGroup_trim.sql index accbe502..d8d7cb61 100644 --- a/schemas/ispyb/updates/2024_09_17_SpaceGroup_trim.sql +++ b/schemas/ispyb/updates/2024_09_17_SpaceGroup_trim.sql @@ -1,4 +1,4 @@ -INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2024_09_17_SpaceGroup_trim', 'ONGOING'); +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2024_09_17_SpaceGroup_trim.sql', 'ONGOING'); UPDATE SpaceGroup SET spaceGroupShortName=trim(trailing '1' FROM spaceGroupShortName) WHERE spaceGroupId in (51,52,53,54,55,56,57,58,59,60,61,62,63,64,73,74,127,128,129,130,205,206,223,224,227,228,230); From 763a591324acdaaa0874155c9c6010ae761c0b0d Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Thu, 12 Dec 2024 10:19:02 +0000 Subject: [PATCH 13/80] Fix wrong scriptName values in schema lookups.sql file --- schemas/ispyb/lookups.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 3f7d45ad..2abf64aa 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -265,8 +265,8 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (293,'2024_08_08_ProcessedTomogram.sql','DONE','2024-08-14 11:23:41'), (294,'2024_08_14_AdminVar_bump_version.sql','DONE','2024-08-14 11:23:41'), (295,'2024_08_19_AdminVar_bump_version.sql','DONE','2024-08-19 12:17:10'), -(296,'2024_09_04_ProcessedTomogram_comment','ONGOING','2024-12-05 13:27:18'), -(297,'2024_09_17_SpaceGroup_trim','ONGOING','2024-12-05 13:27:18'), +(296,'2024_09_04_ProcessedTomogram_comment.sql','DONE','2024-12-05 13:27:18'), +(297,'2024_09_17_SpaceGroup_trim.sql','DONE','2024-12-05 13:27:18'), (298,'2024_09_25_AutoProcProgram_processingPipelineId.sql','DONE','2024-12-05 13:27:18'), (299,'2024_10_15_BLSample_unique_index.sql','DONE','2024-12-05 13:27:18'), (300,'2024_12_04_AutoProcProgramAttachment_deleted.sql','DONE','2024-12-05 13:27:18'), From 7050e5a15565d7989075de8e7e6f6fe62e93dbce Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Wed, 8 Jan 2025 17:07:04 +0000 Subject: [PATCH 14/80] Add binnedPixelSize column to ParticleClassificationGroup --- ...025_01_08_ParticleClassificationGroup_binnedPixelSize.sql | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 schemas/ispyb/updates/2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql diff --git a/schemas/ispyb/updates/2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql b/schemas/ispyb/updates/2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql new file mode 100644 index 00000000..dee155a0 --- /dev/null +++ b/schemas/ispyb/updates/2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql', 'ONGOING'); + +ALTER TABLE ParticleClassificationGroup ADD binnedPixelSize float COMMENT 'Binned pixel size. Unit: Angstroms', ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql'; From ff73888c9b328babf9d63414befc1ea1b9fa2e86 Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Fri, 24 Jan 2025 10:13:14 +0000 Subject: [PATCH 15/80] Add gridSquareId FK in Tomogram --- schemas/ispyb/updates/2025_01_24_Tomogram_gridSquare.sql | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 schemas/ispyb/updates/2025_01_24_Tomogram_gridSquare.sql diff --git a/schemas/ispyb/updates/2025_01_24_Tomogram_gridSquare.sql b/schemas/ispyb/updates/2025_01_24_Tomogram_gridSquare.sql new file mode 100644 index 00000000..485dae3d --- /dev/null +++ b/schemas/ispyb/updates/2025_01_24_Tomogram_gridSquare.sql @@ -0,0 +1,9 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_01_24_Tomogram_gridSquare.sql', 'ONGOING'); + +ALTER TABLE Tomogram + ADD gridSquareId int(11) unsigned COMMENT 'FK, references medium mag map in GridSquare', + ADD CONSTRAINT `Tomogram_fk_gridSquareId` + FOREIGN KEY (`gridSquareId`) + REFERENCES `GridSquare` (`gridSquareId`); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_01_24_Tomogram_gridSquare.sql'; From 163e65d06f46f13a10b2d9f6a251671a9e829c3a Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Wed, 29 Jan 2025 09:17:00 +0000 Subject: [PATCH 16/80] Bump version --- schemas/ispyb/updates/2025_01_29_AdminVar_bump_version.sql | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 schemas/ispyb/updates/2025_01_29_AdminVar_bump_version.sql diff --git a/schemas/ispyb/updates/2025_01_29_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_01_29_AdminVar_bump_version.sql new file mode 100644 index 00000000..b74beb9e --- /dev/null +++ b/schemas/ispyb/updates/2025_01_29_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_01_29_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.4.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_01_29_AdminVar_bump_version.sql'; From 55569358e24d3a4d54a69c583b551e6ce317611d Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Wed, 29 Jan 2025 11:11:57 +0000 Subject: [PATCH 17/80] Changes in preparation for release of v4.4.0 --- HISTORY.rst | 8 ++++++++ schemas/ispyb/lookups.sql | 7 +++++-- schemas/ispyb/tables.sql | 6 +++++- 3 files changed, 18 insertions(+), 3 deletions(-) diff --git a/HISTORY.rst b/HISTORY.rst index 8995ece7..24833df3 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,14 @@ History Unreleased / master ------------------- +4.4.0 (2025-29-01) +------------------- + +New or modified tables and columns: + +- Add ``binnedPixelSize`` column to the ``ParticleClassificationGroup`` table +- Add ``gridSquareId`` column to the ``Tomogram`` table + 4.3.0 (2024-12-05) ------------------- diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 2abf64aa..ca7fead7 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -11,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.3.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.4.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -270,7 +270,10 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (298,'2024_09_25_AutoProcProgram_processingPipelineId.sql','DONE','2024-12-05 13:27:18'), (299,'2024_10_15_BLSample_unique_index.sql','DONE','2024-12-05 13:27:18'), (300,'2024_12_04_AutoProcProgramAttachment_deleted.sql','DONE','2024-12-05 13:27:18'), -(301,'2024_12_05_AdminVar_bump_version.sql','DONE','2024-12-05 13:27:18'); +(301,'2024_12_05_AdminVar_bump_version.sql','DONE','2024-12-05 13:27:18'), +(302,'2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql','DONE','2025-01-29 10:29:27'), +(303,'2025_01_24_Tomogram_gridSquare.sql','DONE','2025-01-29 10:29:27'), +(304,'2025_01_29_AdminVar_bump_version.sql','DONE','2025-01-29 10:29:27'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index d68fca82..538b9336 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -2409,6 +2409,7 @@ CREATE TABLE `ParticleClassificationGroup` ( `numberOfParticlesPerBatch` int(10) unsigned DEFAULT NULL COMMENT 'total number of particles per batch (a large integer)', `numberOfClassesPerBatch` int(10) unsigned DEFAULT NULL, `symmetry` varchar(20) DEFAULT NULL, + `binnedPixelSize` float DEFAULT NULL COMMENT 'Binned pixel size. Unit: Angstroms', PRIMARY KEY (`particleClassificationGroupId`), KEY `ParticleClassificationGroup_fk_particlePickerId` (`particlePickerId`), KEY `ParticleClassificationGroup_fk_programId` (`programId`), @@ -3566,11 +3567,14 @@ CREATE TABLE `Tomogram` ( `projXZ` varchar(255) DEFAULT NULL COMMENT 'XZ projection file', `recordTimeStamp` datetime DEFAULT current_timestamp() COMMENT 'Creation or last update date/time', `globalAlignmentQuality` float DEFAULT NULL COMMENT 'Quality of fit metric for the alignment of the tilt series corresponding to this tomogram', + `gridSquareId` int(11) unsigned DEFAULT NULL COMMENT 'FK, references medium mag map in GridSquare', PRIMARY KEY (`tomogramId`), KEY `Tomogram_fk_dataCollectionId` (`dataCollectionId`), KEY `Tomogram_fk_autoProcProgramId` (`autoProcProgramId`), + KEY `Tomogram_fk_gridSquareId` (`gridSquareId`), CONSTRAINT `Tomogram_fk_autoProcProgramId` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE SET NULL ON UPDATE CASCADE, - CONSTRAINT `Tomogram_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE + CONSTRAINT `Tomogram_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE, + CONSTRAINT `Tomogram_fk_gridSquareId` FOREIGN KEY (`gridSquareId`) REFERENCES `GridSquare` (`gridSquareId`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='For storing per-sample, per-position data analysis results (reconstruction)'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup`; From 86824ccc6f80a6f86e28bc78548ec3bd247e3bef Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Fri, 14 Feb 2025 15:03:11 +0000 Subject: [PATCH 18/80] Add more processing table grants for Expeye --- grants/ispyb_expeye.sql | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 4b112741..37abe92b 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -63,3 +63,7 @@ GRANT SELECT, INSERT, UPDATE ON RobotAction TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON GridInfo TO ispyb_expeye_acquisition_role; GRANT ispyb_expeye_acquisition_role TO ispyb_expeye_core_role; + +GRANT SELECT ON AutoProcProgram TO ispyb_expeye_core_role; +GRANT SELECT, INSERT, UPDATE ON AutoProcProgramAttachment TO ispyb_expeye_core_role; +GRANT SELECT ON ProcessingJob TO ispyb_expeye_core_role; From d2a318c387959f0352c7e09dbb9ec4e71a3346e6 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Mon, 17 Feb 2025 10:50:02 +0000 Subject: [PATCH 19/80] Add bool flag to indicate purged processed folder in visit dir (#256) --- .../updates/2025_02_14_BLSession_purgedProcessedData.sql | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 schemas/ispyb/updates/2025_02_14_BLSession_purgedProcessedData.sql diff --git a/schemas/ispyb/updates/2025_02_14_BLSession_purgedProcessedData.sql b/schemas/ispyb/updates/2025_02_14_BLSession_purgedProcessedData.sql new file mode 100644 index 00000000..91f132ac --- /dev/null +++ b/schemas/ispyb/updates/2025_02_14_BLSession_purgedProcessedData.sql @@ -0,0 +1,8 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_02_14_BLSession_purgedProcessedData.sql', 'ONGOING'); + +ALTER TABLE BLSession + ADD purgedProcessedData boolean DEFAULT 0 + COMMENT 'Flag to indicate whether the processed folder in the associated visit directory has been purged', + ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_02_14_BLSession_purgedProcessedData.sql'; From 1b5695aeaddfeffda0a54ebe97fbaa51289d8ac0 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Mon, 24 Feb 2025 17:11:08 +0000 Subject: [PATCH 20/80] Add permissions for new endpoints (#257) --- grants/ispyb_expeye.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 37abe92b..9ba148f4 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -10,8 +10,8 @@ GRANT ispyb_propagation TO ispyb_expeye_core_role; CREATE ROLE ispyb_expeye_acquisition_role; -GRANT SELECT ON Proposal TO ispyb_expeye_acquisition_role; -GRANT SELECT ON BLSession TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON Proposal TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON BLSession TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON DataCollectionGroup TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON DataCollection TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON Position TO ispyb_expeye_acquisition_role; From 0ac97fa70c8fe1f5eecffd881f0aef8e8c189109 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Tue, 25 Feb 2025 16:31:53 +0000 Subject: [PATCH 21/80] Add version bump file + refresh schema files for v4.5.0 (#258) --- HISTORY.rst | 11 +- schemas/ispyb/lookups.sql | 6 +- schemas/ispyb/tables.sql | 393 +++++++++--------- .../2025_02_25_AdminVar_bump_version.sql | 5 + 4 files changed, 216 insertions(+), 199 deletions(-) create mode 100644 schemas/ispyb/updates/2025_02_25_AdminVar_bump_version.sql diff --git a/HISTORY.rst b/HISTORY.rst index 24833df3..904cb07b 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,7 +5,16 @@ History Unreleased / master ------------------- -4.4.0 (2025-29-01) +4.5.0 (2025-02-25) +------------------- + +New or modified tables and columns: + +- Add ``purgedProcessedData`` boolean column to the ``BLSession`` table. This is +a flag to indicate whether the ``processed`` folder in the associated visit +directory has been purged. + +4.4.0 (2025-01-29) ------------------- New or modified tables and columns: diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index ca7fead7..37fba1ea 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -11,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.4.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.5.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -273,7 +273,9 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (301,'2024_12_05_AdminVar_bump_version.sql','DONE','2024-12-05 13:27:18'), (302,'2025_01_08_ParticleClassificationGroup_binnedPixelSize.sql','DONE','2025-01-29 10:29:27'), (303,'2025_01_24_Tomogram_gridSquare.sql','DONE','2025-01-29 10:29:27'), -(304,'2025_01_29_AdminVar_bump_version.sql','DONE','2025-01-29 10:29:27'); +(304,'2025_01_29_AdminVar_bump_version.sql','DONE','2025-01-29 10:29:27'), +(305,'2025_02_14_BLSession_purgedProcessedData.sql','DONE','2025-02-25 15:51:29'), +(306,'2025_02_25_AdminVar_bump_version.sql','DONE','2025-02-25 15:51:30'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index 538b9336..02bb0994 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -12,7 +12,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; DROP TABLE IF EXISTS `AdminActivity`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AdminActivity` ( `adminActivityId` int(11) NOT NULL AUTO_INCREMENT, `username` varchar(45) NOT NULL DEFAULT '', @@ -26,7 +26,7 @@ CREATE TABLE `AdminActivity` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AdminVar`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AdminVar` ( `varId` int(11) NOT NULL AUTO_INCREMENT, `name` varchar(32) DEFAULT NULL, @@ -38,7 +38,7 @@ CREATE TABLE `AdminVar` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Aperture`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Aperture` ( `apertureId` int(10) unsigned NOT NULL AUTO_INCREMENT, `sizeX` float DEFAULT NULL, @@ -47,7 +47,7 @@ CREATE TABLE `Aperture` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Atlas`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Atlas` ( `atlasId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionGroupId` int(11) NOT NULL, @@ -61,7 +61,7 @@ CREATE TABLE `Atlas` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProc`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProc` ( `autoProcId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `autoProcProgramId` int(10) unsigned DEFAULT NULL COMMENT 'Related program item', @@ -80,7 +80,7 @@ CREATE TABLE `AutoProc` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcIntegration`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcIntegration` ( `autoProcIntegrationId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `dataCollectionId` int(11) unsigned NOT NULL COMMENT 'DataCollection item', @@ -113,7 +113,7 @@ CREATE TABLE `AutoProcIntegration` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcProgram`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcProgram` ( `autoProcProgramId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `processingCommandLine` varchar(255) DEFAULT NULL COMMENT 'Command line for running the automatic processing', @@ -133,7 +133,7 @@ CREATE TABLE `AutoProcProgram` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcProgramAttachment`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcProgramAttachment` ( `autoProcProgramAttachmentId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `autoProcProgramId` int(10) unsigned NOT NULL COMMENT 'Related autoProcProgram item', @@ -150,7 +150,7 @@ CREATE TABLE `AutoProcProgramAttachment` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcProgramMessage`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcProgramMessage` ( `autoProcProgramMessageId` int(10) unsigned NOT NULL AUTO_INCREMENT, `autoProcProgramId` int(10) unsigned DEFAULT NULL, @@ -165,7 +165,7 @@ CREATE TABLE `AutoProcProgramMessage` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcScaling`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcScaling` ( `autoProcScalingId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `autoProcId` int(10) unsigned DEFAULT NULL COMMENT 'Related autoProc item (used by foreign key)', @@ -178,7 +178,7 @@ CREATE TABLE `AutoProcScaling` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcScalingStatistics`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcScalingStatistics` ( `autoProcScalingStatisticsId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `autoProcScalingId` int(10) unsigned DEFAULT NULL COMMENT 'Related autoProcScaling item (used by foreign key)', @@ -212,7 +212,7 @@ CREATE TABLE `AutoProcScalingStatistics` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcScaling_has_Int`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcScaling_has_Int` ( `autoProcScaling_has_IntId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `autoProcScalingId` int(10) unsigned DEFAULT NULL COMMENT 'AutoProcScaling item', @@ -227,7 +227,7 @@ CREATE TABLE `AutoProcScaling_has_Int` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcStatus`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `AutoProcStatus` ( `autoProcStatusId` int(11) NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `autoProcIntegrationId` int(10) unsigned NOT NULL, @@ -242,7 +242,7 @@ CREATE TABLE `AutoProcStatus` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_automationError`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_automationError` ( `automationErrorId` int(10) unsigned NOT NULL AUTO_INCREMENT, `errorType` varchar(40) NOT NULL, @@ -252,7 +252,7 @@ CREATE TABLE `BF_automationError` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_automationFault`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_automationFault` ( `automationFaultId` int(10) unsigned NOT NULL AUTO_INCREMENT, `automationErrorId` int(10) unsigned DEFAULT NULL, @@ -270,7 +270,7 @@ CREATE TABLE `BF_automationFault` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_component`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_component` ( `componentId` int(10) unsigned NOT NULL AUTO_INCREMENT, `systemId` int(10) unsigned DEFAULT NULL, @@ -283,7 +283,7 @@ CREATE TABLE `BF_component` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_component_beamline`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_component_beamline` ( `component_beamlineId` int(10) unsigned NOT NULL AUTO_INCREMENT, `componentId` int(10) unsigned DEFAULT NULL, @@ -295,7 +295,7 @@ CREATE TABLE `BF_component_beamline` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_fault`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_fault` ( `faultId` int(10) unsigned NOT NULL AUTO_INCREMENT, `sessionId` int(10) unsigned NOT NULL, @@ -328,7 +328,7 @@ CREATE TABLE `BF_fault` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_subcomponent`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_subcomponent` ( `subcomponentId` int(10) unsigned NOT NULL AUTO_INCREMENT, `componentId` int(10) unsigned DEFAULT NULL, @@ -341,7 +341,7 @@ CREATE TABLE `BF_subcomponent` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_subcomponent_beamline`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_subcomponent_beamline` ( `subcomponent_beamlineId` int(10) unsigned NOT NULL AUTO_INCREMENT, `subcomponentId` int(10) unsigned DEFAULT NULL, @@ -353,7 +353,7 @@ CREATE TABLE `BF_subcomponent_beamline` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_system`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_system` ( `systemId` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(100) DEFAULT NULL, @@ -363,7 +363,7 @@ CREATE TABLE `BF_system` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_system_beamline`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BF_system_beamline` ( `system_beamlineId` int(10) unsigned NOT NULL AUTO_INCREMENT, `systemId` int(10) unsigned DEFAULT NULL, @@ -375,7 +375,7 @@ CREATE TABLE `BF_system_beamline` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BFactorFit`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BFactorFit` ( `bFactorFitId` int(11) unsigned NOT NULL AUTO_INCREMENT, `particleClassificationId` int(11) unsigned NOT NULL, @@ -389,7 +389,7 @@ CREATE TABLE `BFactorFit` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSample` ( `blSampleId` int(10) unsigned NOT NULL AUTO_INCREMENT, `diffractionPlanId` int(10) unsigned DEFAULT NULL, @@ -449,7 +449,7 @@ CREATE TABLE `BLSample` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleGroup` ( `blSampleGroupId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(100) DEFAULT NULL COMMENT 'Human-readable name', @@ -464,7 +464,7 @@ CREATE TABLE `BLSampleGroup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleGroup_has_BLSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleGroup_has_BLSample` ( `blSampleGroupId` int(11) unsigned NOT NULL, `blSampleId` int(11) unsigned NOT NULL, @@ -481,7 +481,7 @@ CREATE TABLE `BLSampleGroup_has_BLSample` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImage`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImage` ( `blSampleImageId` int(11) unsigned NOT NULL AUTO_INCREMENT, `blSampleId` int(11) unsigned NOT NULL, @@ -507,7 +507,7 @@ CREATE TABLE `BLSampleImage` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageAnalysis`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImageAnalysis` ( `blSampleImageAnalysisId` int(11) unsigned NOT NULL AUTO_INCREMENT, `blSampleImageId` int(11) unsigned DEFAULT NULL, @@ -527,7 +527,7 @@ CREATE TABLE `BLSampleImageAnalysis` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageAutoScoreClass`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImageAutoScoreClass` ( `blSampleImageAutoScoreClassId` tinyint(3) unsigned NOT NULL AUTO_INCREMENT, `blSampleImageAutoScoreSchemaId` tinyint(3) unsigned DEFAULT NULL, @@ -539,7 +539,7 @@ CREATE TABLE `BLSampleImageAutoScoreClass` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageAutoScoreSchema`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImageAutoScoreSchema` ( `blSampleImageAutoScoreSchemaId` tinyint(3) unsigned NOT NULL AUTO_INCREMENT, `schemaName` varchar(25) NOT NULL COMMENT 'Name of the schema e.g. Hampton, MARCO', @@ -549,7 +549,7 @@ CREATE TABLE `BLSampleImageAutoScoreSchema` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageMeasurement`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImageMeasurement` ( `blSampleImageMeasurementId` int(11) unsigned NOT NULL AUTO_INCREMENT, `blSampleImageId` int(11) unsigned NOT NULL, @@ -568,7 +568,7 @@ CREATE TABLE `BLSampleImageMeasurement` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageScore`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImageScore` ( `blSampleImageScoreId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) DEFAULT NULL, @@ -579,7 +579,7 @@ CREATE TABLE `BLSampleImageScore` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImage_has_AutoScoreClass`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImage_has_AutoScoreClass` ( `blSampleImageId` int(11) unsigned NOT NULL, `blSampleImageAutoScoreClassId` tinyint(3) unsigned NOT NULL, @@ -592,7 +592,7 @@ CREATE TABLE `BLSampleImage_has_AutoScoreClass` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImage_has_Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleImage_has_Positioner` ( `blSampleImageHasPositionerId` int(10) unsigned NOT NULL AUTO_INCREMENT, `blSampleImageId` int(10) unsigned NOT NULL, @@ -607,7 +607,7 @@ CREATE TABLE `BLSampleImage_has_Positioner` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleType` ( `blSampleTypeId` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(100) DEFAULT NULL, @@ -618,7 +618,7 @@ CREATE TABLE `BLSampleType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleType_has_Component`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSampleType_has_Component` ( `blSampleTypeId` int(10) unsigned NOT NULL, `componentId` int(10) unsigned NOT NULL, @@ -631,7 +631,7 @@ CREATE TABLE `BLSampleType_has_Component` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_DataCollectionPlan`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSample_has_DataCollectionPlan` ( `blSampleId` int(11) unsigned NOT NULL, `dataCollectionPlanId` int(11) unsigned NOT NULL, @@ -644,7 +644,7 @@ CREATE TABLE `BLSample_has_DataCollectionPlan` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_EnergyScan`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSample_has_EnergyScan` ( `blSampleId` int(10) unsigned NOT NULL DEFAULT 0, `energyScanId` int(10) unsigned NOT NULL DEFAULT 0, @@ -658,7 +658,7 @@ CREATE TABLE `BLSample_has_EnergyScan` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSample_has_Positioner` ( `blSampleHasPositioner` int(10) unsigned NOT NULL AUTO_INCREMENT, `blSampleId` int(10) unsigned NOT NULL, @@ -672,7 +672,7 @@ CREATE TABLE `BLSample_has_Positioner` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSession`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSession` ( `sessionId` int(10) unsigned NOT NULL AUTO_INCREMENT, `beamLineSetupId` int(10) unsigned DEFAULT NULL, @@ -692,6 +692,7 @@ CREATE TABLE `BLSession` ( `externalId` binary(16) DEFAULT NULL, `archived` tinyint(1) DEFAULT 0 COMMENT 'The data for the session is archived and no longer available on disk', `riskRating` enum('Low','Medium','High','Not Permitted') DEFAULT NULL COMMENT 'ERA in user admin system', + `purgedProcessedData` tinyint(1) DEFAULT 0 COMMENT 'Flag to indicate whether the processed folder in the associated visit directory has been purged', PRIMARY KEY (`sessionId`), UNIQUE KEY `proposalId` (`proposalId`,`visit_number`), KEY `Session_FKIndex2` (`beamLineSetupId`), @@ -706,7 +707,7 @@ CREATE TABLE `BLSession` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSession_has_SCPosition`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSession_has_SCPosition` ( `blsessionhasscpositionid` int(11) unsigned NOT NULL AUTO_INCREMENT, `blsessionid` int(11) unsigned NOT NULL, @@ -719,7 +720,7 @@ CREATE TABLE `BLSession_has_SCPosition` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSubSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSubSample` ( `blSubSampleId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `blSampleId` int(10) unsigned NOT NULL COMMENT 'sample', @@ -752,7 +753,7 @@ CREATE TABLE `BLSubSample` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSubSample_has_Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BLSubSample_has_Positioner` ( `blSubSampleHasPositioner` int(10) unsigned NOT NULL AUTO_INCREMENT, `blSubSampleId` int(10) unsigned NOT NULL, @@ -766,7 +767,7 @@ CREATE TABLE `BLSubSample_has_Positioner` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamApertures`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BeamApertures` ( `beamAperturesid` int(11) unsigned NOT NULL AUTO_INCREMENT, `beamlineStatsId` int(11) unsigned DEFAULT NULL, @@ -781,7 +782,7 @@ CREATE TABLE `BeamApertures` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamCalendar`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BeamCalendar` ( `beamCalendarId` int(10) unsigned NOT NULL AUTO_INCREMENT, `run` varchar(7) NOT NULL, @@ -793,7 +794,7 @@ CREATE TABLE `BeamCalendar` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamCentres`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BeamCentres` ( `beamCentresid` int(11) unsigned NOT NULL AUTO_INCREMENT, `beamlineStatsId` int(11) unsigned DEFAULT NULL, @@ -807,7 +808,7 @@ CREATE TABLE `BeamCentres` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamLineSetup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BeamLineSetup` ( `beamLineSetupId` int(10) unsigned NOT NULL AUTO_INCREMENT, `detectorId` int(11) DEFAULT NULL, @@ -864,7 +865,7 @@ CREATE TABLE `BeamLineSetup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamlineAction`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BeamlineAction` ( `beamlineActionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `sessionId` int(11) unsigned DEFAULT NULL, @@ -882,7 +883,7 @@ CREATE TABLE `BeamlineAction` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamlineStats`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `BeamlineStats` ( `beamlineStatsId` int(11) unsigned NOT NULL AUTO_INCREMENT, `beamline` varchar(10) DEFAULT NULL, @@ -900,7 +901,7 @@ CREATE TABLE `BeamlineStats` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CTF`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `CTF` ( `ctfId` int(11) unsigned NOT NULL AUTO_INCREMENT, `motionCorrectionId` int(11) unsigned DEFAULT NULL, @@ -929,7 +930,7 @@ CREATE TABLE `CTF` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CalendarHash`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `CalendarHash` ( `calendarHashId` int(10) unsigned NOT NULL AUTO_INCREMENT, `ckey` varchar(50) DEFAULT NULL, @@ -940,7 +941,7 @@ CREATE TABLE `CalendarHash` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Component`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Component` ( `componentId` int(11) unsigned NOT NULL AUTO_INCREMENT, `componentTypeId` int(11) unsigned NOT NULL, @@ -956,7 +957,7 @@ CREATE TABLE `Component` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ComponentLattice`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ComponentLattice` ( `componentLatticeId` int(11) unsigned NOT NULL AUTO_INCREMENT, `componentId` int(10) unsigned DEFAULT NULL, @@ -974,7 +975,7 @@ CREATE TABLE `ComponentLattice` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ComponentSubType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ComponentSubType` ( `componentSubTypeId` int(11) unsigned NOT NULL, `name` varchar(31) NOT NULL, @@ -986,7 +987,7 @@ CREATE TABLE `ComponentSubType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ComponentType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ComponentType` ( `componentTypeId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(31) NOT NULL, @@ -996,7 +997,7 @@ CREATE TABLE `ComponentType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Component_has_SubType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Component_has_SubType` ( `componentId` int(10) unsigned NOT NULL, `componentSubTypeId` int(11) unsigned NOT NULL, @@ -1008,7 +1009,7 @@ CREATE TABLE `Component_has_SubType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ConcentrationType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ConcentrationType` ( `concentrationTypeId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(31) NOT NULL, @@ -1020,7 +1021,7 @@ CREATE TABLE `ConcentrationType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Container`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Container` ( `containerId` int(10) unsigned NOT NULL AUTO_INCREMENT, `dewarId` int(10) unsigned DEFAULT NULL, @@ -1084,7 +1085,7 @@ CREATE TABLE `Container` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerHistory`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerHistory` ( `containerHistoryId` int(11) unsigned NOT NULL AUTO_INCREMENT, `containerId` int(10) unsigned DEFAULT NULL, @@ -1102,7 +1103,7 @@ CREATE TABLE `ContainerHistory` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerInspection`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerInspection` ( `containerInspectionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `containerId` int(11) unsigned NOT NULL, @@ -1129,7 +1130,7 @@ CREATE TABLE `ContainerInspection` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerQueue`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerQueue` ( `containerQueueId` int(11) unsigned NOT NULL AUTO_INCREMENT, `containerId` int(10) unsigned NOT NULL, @@ -1146,7 +1147,7 @@ CREATE TABLE `ContainerQueue` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerQueueSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerQueueSample` ( `containerQueueSampleId` int(11) unsigned NOT NULL AUTO_INCREMENT, `containerQueueId` int(11) unsigned DEFAULT NULL, @@ -1169,7 +1170,7 @@ CREATE TABLE `ContainerQueueSample` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerRegistry`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerRegistry` ( `containerRegistryId` int(11) unsigned NOT NULL AUTO_INCREMENT, `barcode` varchar(20) NOT NULL, @@ -1181,7 +1182,7 @@ CREATE TABLE `ContainerRegistry` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerRegistry_has_Proposal`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerRegistry_has_Proposal` ( `containerRegistryHasProposalId` int(11) unsigned NOT NULL AUTO_INCREMENT, `containerRegistryId` int(11) unsigned DEFAULT NULL, @@ -1199,7 +1200,7 @@ CREATE TABLE `ContainerRegistry_has_Proposal` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerReport`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerReport` ( `containerReportId` int(11) unsigned NOT NULL AUTO_INCREMENT, `containerRegistryId` int(11) unsigned DEFAULT NULL, @@ -1216,7 +1217,7 @@ CREATE TABLE `ContainerReport` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ContainerType` ( `containerTypeId` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(100) DEFAULT NULL, @@ -1236,7 +1237,7 @@ CREATE TABLE `ContainerType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CourierTermsAccepted`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `CourierTermsAccepted` ( `courierTermsAcceptedId` int(10) unsigned NOT NULL AUTO_INCREMENT, `proposalId` int(10) unsigned NOT NULL, @@ -1255,7 +1256,7 @@ CREATE TABLE `CourierTermsAccepted` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CryoemInitialModel`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `CryoemInitialModel` ( `cryoemInitialModelId` int(10) unsigned NOT NULL AUTO_INCREMENT, `resolution` float DEFAULT NULL COMMENT 'Unit: Angstroms', @@ -1265,7 +1266,7 @@ CREATE TABLE `CryoemInitialModel` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Crystal`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Crystal` ( `crystalId` int(10) unsigned NOT NULL AUTO_INCREMENT, `diffractionPlanId` int(10) unsigned DEFAULT NULL, @@ -1299,7 +1300,7 @@ CREATE TABLE `Crystal` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CrystalComposition`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `CrystalComposition` ( `crystalCompositionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `componentId` int(11) unsigned NOT NULL, @@ -1319,7 +1320,7 @@ CREATE TABLE `CrystalComposition` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Crystal_has_UUID`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Crystal_has_UUID` ( `crystal_has_UUID_Id` int(10) unsigned NOT NULL AUTO_INCREMENT, `crystalId` int(10) unsigned NOT NULL, @@ -1333,7 +1334,7 @@ CREATE TABLE `Crystal_has_UUID` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataAcquisition`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DataAcquisition` ( `dataAcquisitionId` int(10) NOT NULL AUTO_INCREMENT, `sampleCellId` int(10) NOT NULL, @@ -1346,7 +1347,7 @@ CREATE TABLE `DataAcquisition` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollection`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DataCollection` ( `dataCollectionId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `BLSAMPLEID` int(11) unsigned DEFAULT NULL, @@ -1477,7 +1478,7 @@ CREATE TABLE `DataCollection` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionComment`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DataCollectionComment` ( `dataCollectionCommentId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned NOT NULL, @@ -1494,7 +1495,7 @@ CREATE TABLE `DataCollectionComment` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionFileAttachment`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DataCollectionFileAttachment` ( `dataCollectionFileAttachmentId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned NOT NULL, @@ -1508,7 +1509,7 @@ CREATE TABLE `DataCollectionFileAttachment` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DataCollectionGroup` ( `dataCollectionGroupId` int(11) NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `sessionId` int(10) unsigned NOT NULL COMMENT 'references Session table', @@ -1537,7 +1538,7 @@ CREATE TABLE `DataCollectionGroup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionPlan_has_Detector`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DataCollectionPlan_has_Detector` ( `dataCollectionPlanHasDetectorId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionPlanId` int(11) unsigned NOT NULL, @@ -1554,7 +1555,7 @@ CREATE TABLE `DataCollectionPlan_has_Detector` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Detector`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Detector` ( `detectorId` int(11) NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `detectorType` varchar(255) DEFAULT NULL, @@ -1590,7 +1591,7 @@ CREATE TABLE `Detector` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Dewar`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Dewar` ( `dewarId` int(10) unsigned NOT NULL AUTO_INCREMENT, `shippingId` int(10) unsigned NOT NULL, @@ -1625,7 +1626,7 @@ CREATE TABLE `Dewar` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarLocation`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DewarLocation` ( `eventId` int(10) unsigned NOT NULL AUTO_INCREMENT, `dewarNumber` varchar(128) NOT NULL COMMENT 'Dewar number', @@ -1639,7 +1640,7 @@ CREATE TABLE `DewarLocation` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarLocationList`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DewarLocationList` ( `locationId` int(10) unsigned NOT NULL AUTO_INCREMENT, `locationName` varchar(128) NOT NULL DEFAULT '' COMMENT 'Location', @@ -1648,7 +1649,7 @@ CREATE TABLE `DewarLocationList` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarRegistry`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DewarRegistry` ( `dewarRegistryId` int(11) unsigned NOT NULL AUTO_INCREMENT, `facilityCode` varchar(20) NOT NULL, @@ -1667,7 +1668,7 @@ CREATE TABLE `DewarRegistry` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarRegistry_has_Proposal`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DewarRegistry_has_Proposal` ( `dewarRegistryHasProposalId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dewarRegistryId` int(11) unsigned DEFAULT NULL, @@ -1688,7 +1689,7 @@ CREATE TABLE `DewarRegistry_has_Proposal` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarReport`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DewarReport` ( `dewarReportId` int(11) unsigned NOT NULL AUTO_INCREMENT, `facilityCode` varchar(20) NOT NULL, @@ -1702,7 +1703,7 @@ CREATE TABLE `DewarReport` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarTransportHistory`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DewarTransportHistory` ( `DewarTransportHistoryId` int(10) unsigned NOT NULL AUTO_INCREMENT, `dewarId` int(10) unsigned DEFAULT NULL, @@ -1716,7 +1717,7 @@ CREATE TABLE `DewarTransportHistory` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DiffractionPlan`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `DiffractionPlan` ( `diffractionPlanId` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(20) DEFAULT NULL, @@ -1794,7 +1795,7 @@ CREATE TABLE `DiffractionPlan` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `EnergyScan`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `EnergyScan` ( `energyScanId` int(10) unsigned NOT NULL AUTO_INCREMENT, `sessionId` int(10) unsigned NOT NULL, @@ -1841,7 +1842,7 @@ CREATE TABLE `EnergyScan` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Event`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Event` ( `eventId` int(11) unsigned NOT NULL AUTO_INCREMENT, `eventChainId` int(11) unsigned NOT NULL, @@ -1863,7 +1864,7 @@ CREATE TABLE `Event` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `EventChain`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `EventChain` ( `eventChainId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned NOT NULL, @@ -1875,7 +1876,7 @@ CREATE TABLE `EventChain` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `EventType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `EventType` ( `eventTypeId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(30) NOT NULL, @@ -1885,7 +1886,7 @@ CREATE TABLE `EventType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ExperimentKindDetails`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ExperimentKindDetails` ( `experimentKindId` int(10) unsigned NOT NULL AUTO_INCREMENT, `diffractionPlanId` int(10) unsigned NOT NULL, @@ -1900,7 +1901,7 @@ CREATE TABLE `ExperimentKindDetails` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ExperimentType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ExperimentType` ( `experimentTypeId` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(100) DEFAULT NULL, @@ -1911,7 +1912,7 @@ CREATE TABLE `ExperimentType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `FoilHole`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `FoilHole` ( `foilHoleId` int(11) unsigned NOT NULL AUTO_INCREMENT, `gridSquareId` int(11) unsigned NOT NULL, @@ -1931,7 +1932,7 @@ CREATE TABLE `FoilHole` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GeometryClassname`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `GeometryClassname` ( `geometryClassnameId` int(11) unsigned NOT NULL AUTO_INCREMENT, `geometryClassname` varchar(45) DEFAULT NULL, @@ -1941,7 +1942,7 @@ CREATE TABLE `GeometryClassname` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GridImageMap`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `GridImageMap` ( `gridImageMapId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned DEFAULT NULL, @@ -1956,7 +1957,7 @@ CREATE TABLE `GridImageMap` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GridInfo`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `GridInfo` ( `gridInfoId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `xOffset` double DEFAULT NULL, @@ -1990,7 +1991,7 @@ CREATE TABLE `GridInfo` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GridSquare`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `GridSquare` ( `gridSquareId` int(11) unsigned NOT NULL AUTO_INCREMENT, `atlasId` int(11) unsigned NOT NULL, @@ -2012,7 +2013,7 @@ CREATE TABLE `GridSquare` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Image`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Image` ( `imageId` int(12) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned NOT NULL DEFAULT 0, @@ -2041,7 +2042,7 @@ CREATE TABLE `Image` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ImageQualityIndicators`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ImageQualityIndicators` ( `dataCollectionId` int(11) unsigned NOT NULL, `imageNumber` mediumint(8) unsigned NOT NULL, @@ -2066,7 +2067,7 @@ CREATE TABLE `ImageQualityIndicators` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Imager`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Imager` ( `imagerId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) NOT NULL, @@ -2078,7 +2079,7 @@ CREATE TABLE `Imager` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `InspectionType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `InspectionType` ( `inspectionTypeId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) DEFAULT NULL, @@ -2087,7 +2088,7 @@ CREATE TABLE `InspectionType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `IspybCrystalClass`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `IspybCrystalClass` ( `crystalClassId` int(11) NOT NULL AUTO_INCREMENT, `crystalClass_code` varchar(20) NOT NULL, @@ -2097,7 +2098,7 @@ CREATE TABLE `IspybCrystalClass` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `IspybReference`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `IspybReference` ( `referenceId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `referenceName` varchar(255) DEFAULT NULL COMMENT 'reference name', @@ -2109,7 +2110,7 @@ CREATE TABLE `IspybReference` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `LDAPSearchBase`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `LDAPSearchBase` ( `ldapSearchBaseId` int(11) unsigned NOT NULL AUTO_INCREMENT, `ldapSearchParametersId` int(11) unsigned NOT NULL COMMENT 'The other LDAP search parameters to be used with this search base', @@ -2122,7 +2123,7 @@ CREATE TABLE `LDAPSearchBase` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `LDAPSearchParameters`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `LDAPSearchParameters` ( `ldapSearchParametersId` int(11) unsigned NOT NULL AUTO_INCREMENT, `accountType` enum('group_member','staff_account','functional_account') NOT NULL COMMENT 'The entity type returned by the search', @@ -2136,7 +2137,7 @@ CREATE TABLE `LDAPSearchParameters` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `LabContact`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `LabContact` ( `labContactId` int(10) unsigned NOT NULL AUTO_INCREMENT, `personId` int(10) unsigned NOT NULL, @@ -2158,7 +2159,7 @@ CREATE TABLE `LabContact` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Laboratory`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Laboratory` ( `laboratoryId` int(10) unsigned NOT NULL AUTO_INCREMENT, `laboratoryUUID` varchar(45) DEFAULT NULL, @@ -2177,7 +2178,7 @@ CREATE TABLE `Laboratory` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MXMRRun`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `MXMRRun` ( `mxMRRunId` int(11) unsigned NOT NULL AUTO_INCREMENT, `autoProcScalingId` int(11) unsigned NOT NULL, @@ -2198,7 +2199,7 @@ CREATE TABLE `MXMRRun` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MXMRRunBlob`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `MXMRRunBlob` ( `mxMRRunBlobId` int(11) unsigned NOT NULL AUTO_INCREMENT, `mxMRRunId` int(11) unsigned NOT NULL, @@ -2224,7 +2225,7 @@ CREATE TABLE `MXMRRunBlob` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ModelBuilding`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ModelBuilding` ( `modelBuildingId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingAnalysisId` int(11) unsigned NOT NULL COMMENT 'Related phasing analysis item', @@ -2244,7 +2245,7 @@ CREATE TABLE `ModelBuilding` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MotionCorrection`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `MotionCorrection` ( `motionCorrectionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned DEFAULT NULL, @@ -2276,7 +2277,7 @@ CREATE TABLE `MotionCorrection` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MotorPosition`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `MotorPosition` ( `motorPositionId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phiX` double DEFAULT NULL, @@ -2296,7 +2297,7 @@ CREATE TABLE `MotorPosition` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Movie`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Movie` ( `movieId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned DEFAULT NULL, @@ -2320,7 +2321,7 @@ CREATE TABLE `Movie` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PDB`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PDB` ( `pdbId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(255) DEFAULT NULL, @@ -2332,7 +2333,7 @@ CREATE TABLE `PDB` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PDBEntry`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PDBEntry` ( `pdbEntryId` int(11) unsigned NOT NULL AUTO_INCREMENT, `autoProcProgramId` int(11) unsigned NOT NULL, @@ -2361,7 +2362,7 @@ CREATE TABLE `PDBEntry` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PDBEntry_has_AutoProcProgram`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PDBEntry_has_AutoProcProgram` ( `pdbEntryHasAutoProcId` int(11) unsigned NOT NULL AUTO_INCREMENT, `pdbEntryId` int(11) unsigned NOT NULL, @@ -2376,7 +2377,7 @@ CREATE TABLE `PDBEntry_has_AutoProcProgram` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticleClassification`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ParticleClassification` ( `particleClassificationId` int(10) unsigned NOT NULL AUTO_INCREMENT, `classNumber` int(10) unsigned DEFAULT NULL COMMENT 'Identified of the class. A unique ID given by Relion', @@ -2399,7 +2400,7 @@ CREATE TABLE `ParticleClassification` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticleClassificationGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ParticleClassificationGroup` ( `particleClassificationGroupId` int(10) unsigned NOT NULL AUTO_INCREMENT, `particlePickerId` int(10) unsigned DEFAULT NULL, @@ -2419,7 +2420,7 @@ CREATE TABLE `ParticleClassificationGroup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticleClassification_has_CryoemInitialModel`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ParticleClassification_has_CryoemInitialModel` ( `particleClassificationId` int(10) unsigned NOT NULL, `cryoemInitialModelId` int(10) unsigned NOT NULL, @@ -2431,7 +2432,7 @@ CREATE TABLE `ParticleClassification_has_CryoemInitialModel` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticlePicker`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ParticlePicker` ( `particlePickerId` int(10) unsigned NOT NULL AUTO_INCREMENT, `programId` int(10) unsigned DEFAULT NULL, @@ -2449,7 +2450,7 @@ CREATE TABLE `ParticlePicker` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Permission`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Permission` ( `permissionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `type` varchar(15) NOT NULL, @@ -2459,7 +2460,7 @@ CREATE TABLE `Permission` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Person` ( `personId` int(10) unsigned NOT NULL AUTO_INCREMENT, `laboratoryId` int(10) unsigned DEFAULT NULL, @@ -2485,7 +2486,7 @@ CREATE TABLE `Person` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Phasing`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Phasing` ( `phasingId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingAnalysisId` int(11) unsigned NOT NULL COMMENT 'Related phasing analysis item', @@ -2508,7 +2509,7 @@ CREATE TABLE `Phasing` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingAnalysis`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PhasingAnalysis` ( `phasingAnalysisId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', @@ -2517,7 +2518,7 @@ CREATE TABLE `PhasingAnalysis` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingProgramAttachment`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PhasingProgramAttachment` ( `phasingProgramAttachmentId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingProgramRunId` int(11) unsigned NOT NULL COMMENT 'Related program item', @@ -2532,7 +2533,7 @@ CREATE TABLE `PhasingProgramAttachment` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingProgramRun`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PhasingProgramRun` ( `phasingProgramRunId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingCommandLine` varchar(255) DEFAULT NULL COMMENT 'Command line for phasing', @@ -2548,7 +2549,7 @@ CREATE TABLE `PhasingProgramRun` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingStatistics`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PhasingStatistics` ( `phasingStatisticsId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingHasScalingId1` int(11) unsigned NOT NULL COMMENT 'the dataset in question', @@ -2573,7 +2574,7 @@ CREATE TABLE `PhasingStatistics` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingStep`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PhasingStep` ( `phasingStepId` int(10) unsigned NOT NULL AUTO_INCREMENT, `previousPhasingStepId` int(10) unsigned DEFAULT NULL, @@ -2600,7 +2601,7 @@ CREATE TABLE `PhasingStep` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Phasing_has_Scaling`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Phasing_has_Scaling` ( `phasingHasScalingId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingAnalysisId` int(11) unsigned NOT NULL COMMENT 'Related phasing analysis item', @@ -2616,7 +2617,7 @@ CREATE TABLE `Phasing_has_Scaling` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Position`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Position` ( `positionId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `relativePositionId` int(11) unsigned DEFAULT NULL COMMENT 'relative position, null otherwise', @@ -2635,7 +2636,7 @@ CREATE TABLE `Position` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Positioner` ( `positionerId` int(10) unsigned NOT NULL AUTO_INCREMENT, `positioner` varchar(50) NOT NULL, @@ -2645,7 +2646,7 @@ CREATE TABLE `Positioner` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PreparePhasingData`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PreparePhasingData` ( `preparePhasingDataId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingAnalysisId` int(11) unsigned NOT NULL COMMENT 'Related phasing analysis item', @@ -2665,7 +2666,7 @@ CREATE TABLE `PreparePhasingData` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessedTomogram`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ProcessedTomogram` ( `processedTomogramId` int(11) unsigned NOT NULL AUTO_INCREMENT, `tomogramId` int(11) unsigned NOT NULL COMMENT 'references Tomogram table', @@ -2678,7 +2679,7 @@ CREATE TABLE `ProcessedTomogram` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingJob`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ProcessingJob` ( `processingJobId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned DEFAULT NULL, @@ -2694,7 +2695,7 @@ CREATE TABLE `ProcessingJob` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingJobImageSweep`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ProcessingJobImageSweep` ( `processingJobImageSweepId` int(11) unsigned NOT NULL AUTO_INCREMENT, `processingJobId` int(11) unsigned DEFAULT NULL, @@ -2710,7 +2711,7 @@ CREATE TABLE `ProcessingJobImageSweep` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingJobParameter`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ProcessingJobParameter` ( `processingJobParameterId` int(11) unsigned NOT NULL AUTO_INCREMENT, `processingJobId` int(11) unsigned DEFAULT NULL, @@ -2724,7 +2725,7 @@ CREATE TABLE `ProcessingJobParameter` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingPipeline`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ProcessingPipeline` ( `processingPipelineId` int(11) unsigned NOT NULL AUTO_INCREMENT, `processingPipelineCategoryId` int(11) unsigned DEFAULT NULL, @@ -2739,7 +2740,7 @@ CREATE TABLE `ProcessingPipeline` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingPipelineCategory`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ProcessingPipelineCategory` ( `processingPipelineCategoryId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(20) NOT NULL, @@ -2748,7 +2749,7 @@ CREATE TABLE `ProcessingPipelineCategory` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project` ( `projectId` int(11) unsigned NOT NULL AUTO_INCREMENT, `personId` int(11) unsigned DEFAULT NULL, @@ -2762,7 +2763,7 @@ CREATE TABLE `Project` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_BLSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_BLSample` ( `projectId` int(11) unsigned NOT NULL, `blSampleId` int(11) unsigned NOT NULL, @@ -2774,7 +2775,7 @@ CREATE TABLE `Project_has_BLSample` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_DCGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_DCGroup` ( `projectId` int(11) unsigned NOT NULL, `dataCollectionGroupId` int(11) NOT NULL, @@ -2786,7 +2787,7 @@ CREATE TABLE `Project_has_DCGroup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_EnergyScan`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_EnergyScan` ( `projectId` int(11) unsigned NOT NULL, `energyScanId` int(11) unsigned NOT NULL, @@ -2798,7 +2799,7 @@ CREATE TABLE `Project_has_EnergyScan` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_Person` ( `projectId` int(11) unsigned NOT NULL, `personId` int(11) unsigned NOT NULL, @@ -2810,7 +2811,7 @@ CREATE TABLE `Project_has_Person` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Protein`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_Protein` ( `projectId` int(11) unsigned NOT NULL, `proteinId` int(11) unsigned NOT NULL, @@ -2822,7 +2823,7 @@ CREATE TABLE `Project_has_Protein` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Session`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_Session` ( `projectId` int(11) unsigned NOT NULL, `sessionId` int(11) unsigned NOT NULL, @@ -2834,7 +2835,7 @@ CREATE TABLE `Project_has_Session` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Shipping`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_Shipping` ( `projectId` int(11) unsigned NOT NULL, `shippingId` int(11) unsigned NOT NULL, @@ -2846,7 +2847,7 @@ CREATE TABLE `Project_has_Shipping` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_User`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_User` ( `projecthasuserid` int(11) unsigned NOT NULL AUTO_INCREMENT, `projectid` int(11) unsigned NOT NULL, @@ -2858,7 +2859,7 @@ CREATE TABLE `Project_has_User` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_XFEFSpectrum`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Project_has_XFEFSpectrum` ( `projectId` int(11) unsigned NOT NULL, `xfeFluorescenceSpectrumId` int(11) unsigned NOT NULL, @@ -2870,7 +2871,7 @@ CREATE TABLE `Project_has_XFEFSpectrum` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Proposal`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Proposal` ( `proposalId` int(10) unsigned NOT NULL AUTO_INCREMENT, `personId` int(10) unsigned NOT NULL DEFAULT 0, @@ -2889,7 +2890,7 @@ CREATE TABLE `Proposal` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProposalHasPerson`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ProposalHasPerson` ( `proposalHasPersonId` int(10) unsigned NOT NULL AUTO_INCREMENT, `proposalId` int(10) unsigned NOT NULL, @@ -2904,7 +2905,7 @@ CREATE TABLE `ProposalHasPerson` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Protein`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Protein` ( `proteinId` int(10) unsigned NOT NULL AUTO_INCREMENT, `proposalId` int(10) unsigned NOT NULL DEFAULT 0, @@ -2941,7 +2942,7 @@ CREATE TABLE `Protein` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Protein_has_PDB`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Protein_has_PDB` ( `proteinhaspdbid` int(11) unsigned NOT NULL AUTO_INCREMENT, `proteinid` int(11) unsigned NOT NULL, @@ -2955,7 +2956,7 @@ CREATE TABLE `Protein_has_PDB` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PurificationColumn`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `PurificationColumn` ( `purificationColumnId` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(100) DEFAULT NULL, @@ -2965,7 +2966,7 @@ CREATE TABLE `PurificationColumn` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `RelativeIceThickness`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `RelativeIceThickness` ( `relativeIceThicknessId` int(11) unsigned NOT NULL AUTO_INCREMENT, `motionCorrectionId` int(11) unsigned DEFAULT NULL, @@ -2984,7 +2985,7 @@ CREATE TABLE `RelativeIceThickness` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `RobotAction`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `RobotAction` ( `robotActionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `blsessionId` int(11) unsigned NOT NULL, @@ -3008,7 +3009,7 @@ CREATE TABLE `RobotAction` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SSXDataCollection`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `SSXDataCollection` ( `dataCollectionId` int(11) unsigned NOT NULL COMMENT 'Primary key is same as dataCollection (1 to 1).', `repetitionRate` float DEFAULT NULL, @@ -3027,7 +3028,7 @@ CREATE TABLE `SSXDataCollection` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SW_onceToken`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `SW_onceToken` ( `onceTokenId` int(11) unsigned NOT NULL AUTO_INCREMENT, `token` varchar(128) DEFAULT NULL, @@ -3045,7 +3046,7 @@ CREATE TABLE `SW_onceToken` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SampleComposition`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `SampleComposition` ( `sampleCompositionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `componentId` int(11) unsigned NOT NULL, @@ -3065,7 +3066,7 @@ CREATE TABLE `SampleComposition` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScanParametersModel`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScanParametersModel` ( `scanParametersModelId` int(11) unsigned NOT NULL AUTO_INCREMENT, `scanParametersServiceId` int(10) unsigned DEFAULT NULL, @@ -3085,7 +3086,7 @@ CREATE TABLE `ScanParametersModel` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScanParametersService`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScanParametersService` ( `scanParametersServiceId` int(10) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) DEFAULT NULL, @@ -3095,7 +3096,7 @@ CREATE TABLE `ScanParametersService` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Schedule`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Schedule` ( `scheduleId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) DEFAULT NULL, @@ -3104,7 +3105,7 @@ CREATE TABLE `Schedule` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScheduleComponent`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScheduleComponent` ( `scheduleComponentId` int(11) unsigned NOT NULL AUTO_INCREMENT, `scheduleId` int(11) unsigned NOT NULL, @@ -3119,7 +3120,7 @@ CREATE TABLE `ScheduleComponent` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SchemaStatus`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `SchemaStatus` ( `schemaStatusId` int(11) NOT NULL AUTO_INCREMENT, `scriptName` varchar(100) NOT NULL, @@ -3131,7 +3132,7 @@ CREATE TABLE `SchemaStatus` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Screen`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Screen` ( `screenId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) DEFAULT NULL, @@ -3147,7 +3148,7 @@ CREATE TABLE `Screen` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreenComponent`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreenComponent` ( `screenComponentId` int(11) unsigned NOT NULL AUTO_INCREMENT, `screenComponentGroupId` int(11) unsigned NOT NULL, @@ -3163,7 +3164,7 @@ CREATE TABLE `ScreenComponent` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreenComponentGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreenComponentGroup` ( `screenComponentGroupId` int(11) unsigned NOT NULL AUTO_INCREMENT, `screenId` int(11) unsigned NOT NULL, @@ -3175,7 +3176,7 @@ CREATE TABLE `ScreenComponentGroup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Screening`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Screening` ( `screeningId` int(10) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned DEFAULT NULL, @@ -3199,7 +3200,7 @@ CREATE TABLE `Screening` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningInput`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningInput` ( `screeningInputId` int(10) unsigned NOT NULL AUTO_INCREMENT, `screeningId` int(10) unsigned NOT NULL DEFAULT 0, @@ -3218,7 +3219,7 @@ CREATE TABLE `ScreeningInput` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningOutput`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningOutput` ( `screeningOutputId` int(10) unsigned NOT NULL AUTO_INCREMENT, `screeningId` int(10) unsigned NOT NULL DEFAULT 0, @@ -3254,7 +3255,7 @@ CREATE TABLE `ScreeningOutput` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningOutputLattice`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningOutputLattice` ( `screeningOutputLatticeId` int(10) unsigned NOT NULL AUTO_INCREMENT, `screeningOutputId` int(10) unsigned NOT NULL DEFAULT 0, @@ -3285,7 +3286,7 @@ CREATE TABLE `ScreeningOutputLattice` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningRank`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningRank` ( `screeningRankId` int(10) unsigned NOT NULL AUTO_INCREMENT, `screeningRankSetId` int(10) unsigned NOT NULL DEFAULT 0, @@ -3301,7 +3302,7 @@ CREATE TABLE `ScreeningRank` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningRankSet`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningRankSet` ( `screeningRankSetId` int(10) unsigned NOT NULL AUTO_INCREMENT, `rankEngine` varchar(255) DEFAULT NULL, @@ -3312,7 +3313,7 @@ CREATE TABLE `ScreeningRankSet` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningStrategy`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningStrategy` ( `screeningStrategyId` int(10) unsigned NOT NULL AUTO_INCREMENT, `screeningOutputId` int(10) unsigned NOT NULL DEFAULT 0, @@ -3334,7 +3335,7 @@ CREATE TABLE `ScreeningStrategy` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningStrategySubWedge`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningStrategySubWedge` ( `screeningStrategySubWedgeId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key', `screeningStrategyWedgeId` int(10) unsigned DEFAULT NULL COMMENT 'Foreign key to parent table', @@ -3358,7 +3359,7 @@ CREATE TABLE `ScreeningStrategySubWedge` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningStrategyWedge`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ScreeningStrategyWedge` ( `screeningStrategyWedgeId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key', `screeningStrategyId` int(10) unsigned DEFAULT NULL COMMENT 'Foreign key to parent table', @@ -3380,7 +3381,7 @@ CREATE TABLE `ScreeningStrategyWedge` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SessionType`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `SessionType` ( `sessionTypeId` int(10) unsigned NOT NULL AUTO_INCREMENT, `sessionId` int(10) unsigned NOT NULL, @@ -3392,7 +3393,7 @@ CREATE TABLE `SessionType` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Session_has_Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Session_has_Person` ( `sessionId` int(10) unsigned NOT NULL DEFAULT 0, `personId` int(10) unsigned NOT NULL DEFAULT 0, @@ -3406,7 +3407,7 @@ CREATE TABLE `Session_has_Person` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Shipping`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Shipping` ( `shippingId` int(10) unsigned NOT NULL AUTO_INCREMENT, `proposalId` int(10) unsigned NOT NULL DEFAULT 0, @@ -3459,7 +3460,7 @@ CREATE TABLE `Shipping` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ShippingHasSession`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `ShippingHasSession` ( `shippingId` int(10) unsigned NOT NULL, `sessionId` int(10) unsigned NOT NULL, @@ -3471,7 +3472,7 @@ CREATE TABLE `ShippingHasSession` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Sleeve`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Sleeve` ( `sleeveId` tinyint(3) unsigned NOT NULL COMMENT 'The unique sleeve id 1...255 which also identifies its home location in the freezer', `location` tinyint(3) unsigned DEFAULT NULL COMMENT 'NULL == freezer, 1...255 for local storage locations', @@ -3482,7 +3483,7 @@ CREATE TABLE `Sleeve` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SpaceGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `SpaceGroup` ( `spaceGroupId` int(10) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key', `spaceGroupNumber` int(10) unsigned DEFAULT NULL COMMENT 'ccp4 number pr IUCR', @@ -3501,7 +3502,7 @@ CREATE TABLE `SpaceGroup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SubstructureDetermination`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `SubstructureDetermination` ( `substructureDeterminationId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `phasingAnalysisId` int(11) unsigned NOT NULL COMMENT 'Related phasing analysis item', @@ -3522,7 +3523,7 @@ CREATE TABLE `SubstructureDetermination` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `TiltImageAlignment`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `TiltImageAlignment` ( `movieId` int(11) unsigned NOT NULL COMMENT 'FK to Movie table', `tomogramId` int(11) unsigned NOT NULL COMMENT 'FK to Tomogram table; tuple (movieID, tomogramID) is unique', @@ -3543,7 +3544,7 @@ CREATE TABLE `TiltImageAlignment` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Tomogram`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `Tomogram` ( `tomogramId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionId` int(11) unsigned DEFAULT NULL COMMENT 'FK to DataCollection table', @@ -3579,7 +3580,7 @@ CREATE TABLE `Tomogram` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `UserGroup` ( `userGroupId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(31) NOT NULL, @@ -3589,7 +3590,7 @@ CREATE TABLE `UserGroup` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup_has_LDAPSearchParameters`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `UserGroup_has_LDAPSearchParameters` ( `userGroupId` int(11) unsigned NOT NULL, `ldapSearchParametersId` int(11) unsigned NOT NULL, @@ -3602,7 +3603,7 @@ CREATE TABLE `UserGroup_has_LDAPSearchParameters` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup_has_Permission`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `UserGroup_has_Permission` ( `userGroupId` int(11) unsigned NOT NULL, `permissionId` int(11) unsigned NOT NULL, @@ -3614,7 +3615,7 @@ CREATE TABLE `UserGroup_has_Permission` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup_has_Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `UserGroup_has_Person` ( `userGroupId` int(11) unsigned NOT NULL, `personId` int(10) unsigned NOT NULL, @@ -3626,7 +3627,7 @@ CREATE TABLE `UserGroup_has_Person` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XFEFluorescenceComposite`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `XFEFluorescenceComposite` ( `xfeFluorescenceCompositeId` int(10) unsigned NOT NULL AUTO_INCREMENT, `r` int(10) unsigned NOT NULL COMMENT 'Red layer', @@ -3647,7 +3648,7 @@ CREATE TABLE `XFEFluorescenceComposite` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XFEFluorescenceSpectrum`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `XFEFluorescenceSpectrum` ( `xfeFluorescenceSpectrumId` int(10) unsigned NOT NULL AUTO_INCREMENT, `sessionId` int(10) unsigned NOT NULL, @@ -3682,7 +3683,7 @@ CREATE TABLE `XFEFluorescenceSpectrum` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XRFFluorescenceMapping`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `XRFFluorescenceMapping` ( `xrfFluorescenceMappingId` int(11) unsigned NOT NULL AUTO_INCREMENT, `xrfFluorescenceMappingROIId` int(11) unsigned NOT NULL, @@ -3706,7 +3707,7 @@ CREATE TABLE `XRFFluorescenceMapping` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XRFFluorescenceMappingROI`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `XRFFluorescenceMappingROI` ( `xrfFluorescenceMappingROIId` int(11) unsigned NOT NULL AUTO_INCREMENT, `startEnergy` float NOT NULL, @@ -3725,7 +3726,7 @@ CREATE TABLE `XRFFluorescenceMappingROI` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XrayCentring`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `XrayCentring` ( `xrayCentringId` int(11) unsigned NOT NULL AUTO_INCREMENT, `dataCollectionGroupId` int(11) NOT NULL COMMENT 'references DataCollectionGroup table', @@ -3738,7 +3739,7 @@ CREATE TABLE `XrayCentring` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XrayCentringResult`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `XrayCentringResult` ( `xrayCentringResultId` int(11) unsigned NOT NULL AUTO_INCREMENT, `xrayCentringId` int(11) unsigned NOT NULL COMMENT 'references XrayCentring table', @@ -3765,7 +3766,7 @@ CREATE TABLE `XrayCentringResult` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `v_run`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `v_run` ( `runId` int(11) unsigned NOT NULL AUTO_INCREMENT, `run` varchar(7) NOT NULL DEFAULT '', @@ -3777,7 +3778,7 @@ CREATE TABLE `v_run` ( /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `zc_ZocaloBuffer`; /*!40101 SET @saved_cs_client = @@character_set_client */; -/*!40101 SET character_set_client = utf8 */; +/*!40101 SET character_set_client = utf8mb4 */; CREATE TABLE `zc_ZocaloBuffer` ( `AutoProcProgramID` int(10) unsigned NOT NULL COMMENT 'Reference to an existing AutoProcProgram', `UUID` int(10) unsigned NOT NULL COMMENT 'AutoProcProgram-specific unique identifier', diff --git a/schemas/ispyb/updates/2025_02_25_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_02_25_AdminVar_bump_version.sql new file mode 100644 index 00000000..9c692d39 --- /dev/null +++ b/schemas/ispyb/updates/2025_02_25_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_02_25_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.5.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_02_25_AdminVar_bump_version.sql'; From 60139f8930c958405c3cacef78306cc7869a907e Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 27 Feb 2025 15:49:46 +0000 Subject: [PATCH 22/80] Add grant to AutoProcIntegration for Expeye (#259) --- grants/ispyb_expeye.sql | 2 ++ 1 file changed, 2 insertions(+) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 9ba148f4..6b61e1b3 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -66,4 +66,6 @@ GRANT ispyb_expeye_acquisition_role TO ispyb_expeye_core_role; GRANT SELECT ON AutoProcProgram TO ispyb_expeye_core_role; GRANT SELECT, INSERT, UPDATE ON AutoProcProgramAttachment TO ispyb_expeye_core_role; +GRANT SELECT ON AutoProcIntegration TO ispyb_expeye_core_role; + GRANT SELECT ON ProcessingJob TO ispyb_expeye_core_role; From 8a4c944b35276ab83e69738c9715eed2458b00fc Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Tue, 4 Mar 2025 15:35:12 +0000 Subject: [PATCH 23/80] Add atlas experiment type (#260) * Add atlas experiment type * Replace semicolon * Remove atlas from lookups file * Remove enum additions --- .../updates/2025_02_27_ExperimentType_atlas.sql.sql | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql.sql diff --git a/schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql.sql b/schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql.sql new file mode 100644 index 00000000..594cb31a --- /dev/null +++ b/schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql.sql @@ -0,0 +1,9 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_02_27_ExperimentType_atlas.sql', 'ONGOING'); + +INSERT INTO ExperimentType ( + experimentTypeId, name, proposalType, active +) VALUES ( + 44, 'Atlas', 'em', 1 +); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_02_27_ExperimentType_atlas.sql'; From 3480217df0bf0cd1fc7af75a33fd132650082d54 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Wed, 5 Mar 2025 13:01:12 +0000 Subject: [PATCH 24/80] Add a dewarRegistryId FK to the Dewar table (#261) --- .../updates/2025_03_05_Dewar_dewarRegistryId.sql | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 schemas/ispyb/updates/2025_03_05_Dewar_dewarRegistryId.sql diff --git a/schemas/ispyb/updates/2025_03_05_Dewar_dewarRegistryId.sql b/schemas/ispyb/updates/2025_03_05_Dewar_dewarRegistryId.sql new file mode 100644 index 00000000..ba7e41f9 --- /dev/null +++ b/schemas/ispyb/updates/2025_03_05_Dewar_dewarRegistryId.sql @@ -0,0 +1,11 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_03_05_Dewar_dewarRegistryId.sql', 'ONGOING'); + +ALTER TABLE Dewar + ADD dewarRegistryId int(11) unsigned COMMENT 'Reference to the registered dewar i.e. the physical item', + ADD CONSTRAINT Dewar_fk_dewarRegistryId + FOREIGN KEY (dewarRegistryId) + REFERENCES DewarRegistry(dewarRegistryId) + ON DELETE CASCADE + ON UPDATE CASCADE; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_03_05_Dewar_dewarRegistryId.sql'; From a082d141ad0462fdaff83e7bcb72dee9eeb51a41 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Wed, 5 Mar 2025 13:28:52 +0000 Subject: [PATCH 25/80] Add new proc upsert_processing_program_v2 - New procedure upsert_processing_program_v2 - grant to execute new procedure - updated routines.sql - Remove superfluous commit in procedure upsert_processing_program --- grants/ispyb_processing.sql | 1 + schemas/ispyb/routines.sql | 125 +++++++++++++++--- .../sp_upsert_processing_program.sql | 38 +++--- .../sp_upsert_processing_program_v2.sql | 84 ++++++++++++ 4 files changed, 210 insertions(+), 38 deletions(-) create mode 100644 schemas/ispyb/stored_programs/sp_upsert_processing_program_v2.sql diff --git a/grants/ispyb_processing.sql b/grants/ispyb_processing.sql index 013ea42a..b0ef0154 100644 --- a/grants/ispyb_processing.sql +++ b/grants/ispyb_processing.sql @@ -88,6 +88,7 @@ GRANT EXECUTE ON PROCEDURE `retrieve_reprocessing_by_dc` TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE `update_reprocessing_status` TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE `upsert_processing_program` TO 'ispyb_processing'; +GRANT EXECUTE ON PROCEDURE `upsert_processing_program_v2` TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE `upsert_processing_program_attachment` TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE upsert_processing_program_attachment_v2 TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE upsert_processing_program_message TO 'ispyb_processing'; diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql index c9da2dc5..7949622a 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -1,3 +1,4 @@ +/*M!999999\- enable the sandbox mode */ /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; @@ -11126,15 +11127,15 @@ CREATE PROCEDURE `upsert_processing_program`( p_recordTimestamp datetime ) MODIFIES SQL DATA - COMMENT 'If p_id is not provided, inserts new row. Otherwise updates exis' + COMMENT 'If p_id is not provided, inserts new row. Otherwise updates existing row if uts processingStatus is NULL + other conditions.' BEGIN DECLARE row_processingStatus tinyint(1) DEFAULT NULL; DECLARE row_processingEndTime datetime DEFAULT NULL; - + IF p_id IS NULL THEN - + INSERT INTO AutoProcProgram (processingStatus, processingStartTime, processingEndTime, processingMessage, processingJobId, processingCommandLine, processingPrograms, processingEnvironment, recordTimestamp) VALUES ( @@ -11146,45 +11147,43 @@ BEGIN p_commandLine, p_programs, p_environment, - + IFNULL(p_recordTimestamp, NOW()) ); SET p_id = LAST_INSERT_ID(); ELSE START TRANSACTION; - SELECT processingStatus, processingEndTime INTO row_processingStatus, row_processingEndTime + SELECT processingStatus, processingEndTime INTO row_processingStatus, row_processingEndTime FROM AutoProcProgram - WHERE autoProcProgramId = p_id; - - - - + WHERE autoProcProgramId = p_id; + + + + IF row_processingStatus IS NULL AND ( row_processingEndTime IS NULL OR p_updateTimestamp IS NULL OR row_processingEndTime <= p_updateTimestamp OR p_status IS NOT NULL) THEN UPDATE AutoProcProgram SET - + processingStatus = p_status, - - + + processingStartTime = COALESCE(processingStartTime, p_startTimestamp, NOW()), - + processingEndTime = IFNULL(p_updateTimestamp, NOW()), - + processingMessage = IFNULL(p_updateMessage, processingMessage), processingJobId = IFNULL(p_processingJobId, processingJobId), processingCommandLine = IFNULL(p_commandLine, processingCommandLine), processingPrograms = IFNULL(p_programs, processingPrograms), processingEnvironment = IFNULL(p_environment, processingEnvironment) WHERE autoProcProgramId = p_id; - END IF; - COMMIT; END IF; - COMMIT; + END IF; END ;; DELIMITER ; /*!50003 SET sql_mode = @saved_sql_mode */ ; @@ -11319,6 +11318,95 @@ DELIMITER ; /*!50003 SET collation_connection = @saved_col_connection */ ; /*!50003 SET @saved_sql_mode = @@sql_mode */ ; /*!50003 SET sql_mode = '' */ ; +/*!50003 DROP PROCEDURE IF EXISTS `upsert_processing_program_v2` */; +/*!50003 SET @saved_cs_client = @@character_set_client */ ; +/*!50003 SET @saved_cs_results = @@character_set_results */ ; +/*!50003 SET @saved_col_connection = @@collation_connection */ ; +/*!50003 SET character_set_client = utf8mb3 */ ; +/*!50003 SET character_set_results = utf8mb3 */ ; +/*!50003 SET collation_connection = utf8mb3_general_ci */ ; +DELIMITER ;; +CREATE PROCEDURE `upsert_processing_program_v2`( + INOUT p_id int(11) unsigned, + p_commandLine varchar(255), + p_programs varchar(255), + p_status int(11), + p_updateMessage varchar(80), + p_startTimestamp datetime, + p_updateTimestamp datetime, + p_environment varchar(255), + p_processingJobId int(11) unsigned, + p_processingPipelineId int(11) unsigned, + p_recordTimestamp datetime + ) + MODIFIES SQL DATA + COMMENT 'If p_id is not provided, inserts new row. Otherwise updates existing row if uts processingStatus is NULL + other conditions.' +BEGIN + DECLARE row_processingStatus tinyint(1) DEFAULT NULL; + DECLARE row_processingEndTime datetime DEFAULT NULL; + + + + IF p_id IS NULL THEN + + INSERT INTO AutoProcProgram (processingStatus, processingStartTime, processingEndTime, processingMessage, processingJobId, + processingPipelineId, processingCommandLine, processingPrograms, processingEnvironment, recordTimestamp) + VALUES ( + p_status, + p_startTimestamp, + p_updateTimestamp, + p_updateMessage, + p_processingJobId, + p_processingPipelineId, + p_commandLine, + p_programs, + p_environment, + + IFNULL(p_recordTimestamp, NOW()) + ); + SET p_id = LAST_INSERT_ID(); + ELSE + START TRANSACTION; + SELECT processingStatus, processingEndTime INTO row_processingStatus, row_processingEndTime + FROM AutoProcProgram + WHERE autoProcProgramId = p_id; + + + + + + IF row_processingStatus IS NULL AND ( + row_processingEndTime IS NULL OR p_updateTimestamp IS NULL OR + row_processingEndTime <= p_updateTimestamp OR p_status IS NOT NULL) THEN + + UPDATE AutoProcProgram + SET + + processingStatus = p_status, + + + processingStartTime = COALESCE(processingStartTime, p_startTimestamp, NOW()), + + processingEndTime = IFNULL(p_updateTimestamp, NOW()), + + processingMessage = IFNULL(p_updateMessage, processingMessage), + processingJobId = IFNULL(p_processingJobId, processingJobId), + processingPipelineId = IFNULL(p_processingPipelineId, processingPipelineId), + processingCommandLine = IFNULL(p_commandLine, processingCommandLine), + processingPrograms = IFNULL(p_programs, processingPrograms), + processingEnvironment = IFNULL(p_environment, processingEnvironment) + WHERE autoProcProgramId = p_id; + END IF; + COMMIT; + END IF; +END ;; +DELIMITER ; +/*!50003 SET sql_mode = @saved_sql_mode */ ; +/*!50003 SET character_set_client = @saved_cs_client */ ; +/*!50003 SET character_set_results = @saved_cs_results */ ; +/*!50003 SET collation_connection = @saved_col_connection */ ; +/*!50003 SET @saved_sql_mode = @@sql_mode */ ; +/*!50003 SET sql_mode = '' */ ; /*!50003 DROP PROCEDURE IF EXISTS `upsert_proposal` */; /*!50003 SET @saved_cs_client = @@character_set_client */ ; /*!50003 SET @saved_cs_results = @@character_set_results */ ; @@ -12115,6 +12203,7 @@ DELIMITER ; /*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */; /*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */; +/*M!999999\- enable the sandbox mode */ /*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */; /*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */; diff --git a/schemas/ispyb/stored_programs/sp_upsert_processing_program.sql b/schemas/ispyb/stored_programs/sp_upsert_processing_program.sql index 5cb39518..2a50a13c 100644 --- a/schemas/ispyb/stored_programs/sp_upsert_processing_program.sql +++ b/schemas/ispyb/stored_programs/sp_upsert_processing_program.sql @@ -17,19 +17,19 @@ CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `upsert_processing_program` BEGIN DECLARE row_processingStatus tinyint(1) DEFAULT NULL; DECLARE row_processingEndTime datetime DEFAULT NULL; - + -- DECLARE EXIT HANDLER FOR SQLEXCEPTION ROLLBACK; - + IF p_id IS NULL THEN -- creates a new row in AutoProcProgram with processingJobId set, and all the other values populated with the given values, INSERT INTO AutoProcProgram (processingStatus, processingStartTime, processingEndTime, processingMessage, processingJobId, processingCommandLine, processingPrograms, processingEnvironment, recordTimestamp) VALUES ( - p_status, + p_status, p_startTimestamp, p_updateTimestamp, - p_updateMessage, - p_processingJobId, + p_updateMessage, + p_processingJobId, p_commandLine, p_programs, p_environment, @@ -39,38 +39,36 @@ BEGIN SET p_id = LAST_INSERT_ID(); ELSE START TRANSACTION; - SELECT processingStatus, processingEndTime INTO row_processingStatus, row_processingEndTime - FROM AutoProcProgram - WHERE autoProcProgramId = p_id; + SELECT processingStatus, processingEndTime INTO row_processingStatus, row_processingEndTime + FROM AutoProcProgram + WHERE autoProcProgramId = p_id; -- If the existing value in processingStatus is not NULL then the row must not be updated. Stop reading here. - -- If the existing value in processingEndTime is not NULL and update time is not NULL and - -- processingEndTime is greater (>) than update time and the new status value is NULL then the row must not be + -- If the existing value in processingEndTime is not NULL and update time is not NULL and + -- processingEndTime is greater (>) than update time and the new status value is NULL then the row must not be -- updated. Stop reading here. IF row_processingStatus IS NULL AND ( - row_processingEndTime IS NULL OR p_updateTimestamp IS NULL OR - row_processingEndTime <= p_updateTimestamp OR p_status IS NOT NULL) THEN + row_processingEndTime IS NULL OR p_updateTimestamp IS NULL OR + row_processingEndTime <= p_updateTimestamp OR p_status IS NOT NULL) THEN - UPDATE AutoProcProgram - SET + UPDATE AutoProcProgram + SET -- Write status to processingStatus processingStatus = p_status, - -- If processingStartTime is NULL then write start time to processingStartTime. If start time is also NULL, + -- If processingStartTime is NULL then write start time to processingStartTime. If start time is also NULL, -- then write NOW() instead processingStartTime = COALESCE(processingStartTime, p_startTimestamp, NOW()), -- Write update time to processingEndTime. If update time is NULL then write NOW() to processingEndTime - processingEndTime = IFNULL(p_updateTimestamp, NOW()), + processingEndTime = IFNULL(p_updateTimestamp, NOW()), -- If update message is not NULL then write update message to processingMessage. - processingMessage = IFNULL(p_updateMessage, processingMessage), + processingMessage = IFNULL(p_updateMessage, processingMessage), processingJobId = IFNULL(p_processingJobId, processingJobId), processingCommandLine = IFNULL(p_commandLine, processingCommandLine), processingPrograms = IFNULL(p_programs, processingPrograms), processingEnvironment = IFNULL(p_environment, processingEnvironment) WHERE autoProcProgramId = p_id; - END IF; - COMMIT; END IF; - COMMIT; + END IF; END;; DELIMITER ; diff --git a/schemas/ispyb/stored_programs/sp_upsert_processing_program_v2.sql b/schemas/ispyb/stored_programs/sp_upsert_processing_program_v2.sql new file mode 100644 index 00000000..fba23f3a --- /dev/null +++ b/schemas/ispyb/stored_programs/sp_upsert_processing_program_v2.sql @@ -0,0 +1,84 @@ +-- Requirements for this SP described in http://jira.diamond.ac.uk/browse/SCI-6048 +-- Test: +-- set @id = NULL; +-- call upsert_processing_program_v2(@id, 'hello --dry-run --debug', 'hello', NULL, 'in progress', now(), now(), NULL, 5, 8, now()); +-- select @id; +-- call upsert_processing_program_v2(@id, NULL, NULL, 1, 'complete', NULL, NULL, NULL, NULL, NULL, NULL); +-- select * from AutoProcProgram where autoProcProgramId = @id; + +DELIMITER ;; +CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `upsert_processing_program_v2`( + INOUT p_id int(11) unsigned, + p_commandLine varchar(255), + p_programs varchar(255), + p_status int(11), + p_updateMessage varchar(80), + p_startTimestamp datetime, + p_updateTimestamp datetime, + p_environment varchar(255), + p_processingJobId int(11) unsigned, + p_processingPipelineId int(11) unsigned, + p_recordTimestamp datetime + ) + MODIFIES SQL DATA + COMMENT 'If p_id is not provided, inserts new row. Otherwise updates existing row if uts processingStatus is NULL + other conditions.' +BEGIN + DECLARE row_processingStatus tinyint(1) DEFAULT NULL; + DECLARE row_processingEndTime datetime DEFAULT NULL; + + -- DECLARE EXIT HANDLER FOR SQLEXCEPTION ROLLBACK; + + IF p_id IS NULL THEN + -- creates a new row in AutoProcProgram with processingJobId set, and all the other values populated with the given values, + INSERT INTO AutoProcProgram (processingStatus, processingStartTime, processingEndTime, processingMessage, processingJobId, + processingPipelineId, processingCommandLine, processingPrograms, processingEnvironment, recordTimestamp) + VALUES ( + p_status, + p_startTimestamp, + p_updateTimestamp, + p_updateMessage, + p_processingJobId, + p_processingPipelineId, + p_commandLine, + p_programs, + p_environment, + -- apart from recordTimeStamp, which, if given as NULL, is populated with NOW() + IFNULL(p_recordTimestamp, NOW()) + ); + SET p_id = LAST_INSERT_ID(); + ELSE + START TRANSACTION; + SELECT processingStatus, processingEndTime INTO row_processingStatus, row_processingEndTime + FROM AutoProcProgram + WHERE autoProcProgramId = p_id; + + -- If the existing value in processingStatus is not NULL then the row must not be updated. Stop reading here. + -- If the existing value in processingEndTime is not NULL and update time is not NULL and + -- processingEndTime is greater (>) than update time and the new status value is NULL then the row must not be + -- updated. Stop reading here. + IF row_processingStatus IS NULL AND ( + row_processingEndTime IS NULL OR p_updateTimestamp IS NULL OR + row_processingEndTime <= p_updateTimestamp OR p_status IS NOT NULL) THEN + + UPDATE AutoProcProgram + SET + -- Write status to processingStatus + processingStatus = p_status, + -- If processingStartTime is NULL then write start time to processingStartTime. If start time is also NULL, + -- then write NOW() instead + processingStartTime = COALESCE(processingStartTime, p_startTimestamp, NOW()), + -- Write update time to processingEndTime. If update time is NULL then write NOW() to processingEndTime + processingEndTime = IFNULL(p_updateTimestamp, NOW()), + -- If update message is not NULL then write update message to processingMessage. + processingMessage = IFNULL(p_updateMessage, processingMessage), + processingJobId = IFNULL(p_processingJobId, processingJobId), + processingPipelineId = IFNULL(p_processingPipelineId, processingPipelineId), + processingCommandLine = IFNULL(p_commandLine, processingCommandLine), + processingPrograms = IFNULL(p_programs, processingPrograms), + processingEnvironment = IFNULL(p_environment, processingEnvironment) + WHERE autoProcProgramId = p_id; + END IF; + COMMIT; + END IF; +END;; +DELIMITER ; From 2086eba7a98f1d2e4014d0717d16d0c8c44187bf Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 6 Mar 2025 12:24:20 +0000 Subject: [PATCH 26/80] Preparation for version 4.6.0 (#263) * Bump version to 4.6.0 and refresh schema files * Update HISTORY.rst with details about v4.6.0 * Rename SQL update file with double file extension --- HISTORY.rst | 21 +++++++++++++++++++ schemas/ispyb/lookups.sql | 10 ++++++--- schemas/ispyb/tables.sql | 3 +++ ...ql => 2025_02_27_ExperimentType_atlas.sql} | 0 .../2025_03_06_AdminVar_bump_version.sql | 5 +++++ 5 files changed, 36 insertions(+), 3 deletions(-) rename schemas/ispyb/updates/{2025_02_27_ExperimentType_atlas.sql.sql => 2025_02_27_ExperimentType_atlas.sql} (100%) create mode 100644 schemas/ispyb/updates/2025_03_06_AdminVar_bump_version.sql diff --git a/HISTORY.rst b/HISTORY.rst index 904cb07b..df9f3a7c 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,27 @@ History Unreleased / master ------------------- +4.6.0 (2025-03-06) +------------------- + +New columns: + +- Add a ``dewarRegistryId`` FK to the ``Dewar`` table + +Data in lookup tables: + +- Add 'Atlas' experiment type + +Stored procedures: + +- Remove superfluous commit in procedure ``upsert_processing_program`` +- New procedure ``upsert_processing_program_v2`` with additional param for pipeline ID + +Permissions: + +- Add ``SELECT`` grant for Expeye role on table ``AutoProcIntegration`` +- Add ``EXECUTE`` grant for processing role on new procedure ``upsert_processing_program_v2`` + 4.5.0 (2025-02-25) ------------------- diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 37fba1ea..c4ed6afe 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -11,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.5.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.6.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -275,7 +275,10 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (303,'2025_01_24_Tomogram_gridSquare.sql','DONE','2025-01-29 10:29:27'), (304,'2025_01_29_AdminVar_bump_version.sql','DONE','2025-01-29 10:29:27'), (305,'2025_02_14_BLSession_purgedProcessedData.sql','DONE','2025-02-25 15:51:29'), -(306,'2025_02_25_AdminVar_bump_version.sql','DONE','2025-02-25 15:51:30'); +(306,'2025_02_25_AdminVar_bump_version.sql','DONE','2025-02-25 15:51:30'), +(307,'2025_02_27_ExperimentType_atlas.sql','DONE','2025-03-06 11:58:07'), +(308,'2025_03_05_Dewar_dewarRegistryId.sql','DONE','2025-03-06 11:58:07'), +(309,'2025_03_06_AdminVar_bump_version.sql','DONE','2025-03-06 11:58:07'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; @@ -392,7 +395,8 @@ INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `activ (40,'Still','mx',1), (41,'SSX-Chip','mx',1), (42,'SSX-Jet','mx',1), -(43,'Metal ID','mx',1); +(43,'Metal ID','mx',1), +(44,'Atlas','em',1); /*!40000 ALTER TABLE `ExperimentType` ENABLE KEYS */; /*!40000 ALTER TABLE `InspectionType` DISABLE KEYS */; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index 02bb0994..e3d52447 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -1614,12 +1614,15 @@ CREATE TABLE `Dewar` ( `extra` longtext CHARACTER SET utf8mb4 COLLATE utf8mb4_bin DEFAULT NULL COMMENT 'JSON column for facility-specific or hard-to-define attributes, e.g. LN2 top-ups and contents checks' CHECK (json_valid(`extra`)), `source` varchar(50) DEFAULT current_user(), `externalShippingIdFromSynchrotron` int(11) unsigned DEFAULT NULL COMMENT 'ID for shipping from synchrotron in external application', + `dewarRegistryId` int(11) unsigned DEFAULT NULL COMMENT 'Reference to the registered dewar i.e. the physical item', PRIMARY KEY (`dewarId`), UNIQUE KEY `barCode` (`barCode`), KEY `Dewar_FKIndex1` (`shippingId`), KEY `Dewar_FKIndex2` (`firstExperimentId`), KEY `Dewar_FKIndexCode` (`code`), KEY `Dewar_FKIndexStatus` (`dewarStatus`), + KEY `Dewar_fk_dewarRegistryId` (`dewarRegistryId`), + CONSTRAINT `Dewar_fk_dewarRegistryId` FOREIGN KEY (`dewarRegistryId`) REFERENCES `DewarRegistry` (`dewarRegistryId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Dewar_fk_firstExperimentId` FOREIGN KEY (`firstExperimentId`) REFERENCES `BLSession` (`sessionId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `Dewar_ibfk_1` FOREIGN KEY (`shippingId`) REFERENCES `Shipping` (`shippingId`) ON DELETE CASCADE ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1; diff --git a/schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql.sql b/schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql similarity index 100% rename from schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql.sql rename to schemas/ispyb/updates/2025_02_27_ExperimentType_atlas.sql diff --git a/schemas/ispyb/updates/2025_03_06_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_03_06_AdminVar_bump_version.sql new file mode 100644 index 00000000..eb1af0f4 --- /dev/null +++ b/schemas/ispyb/updates/2025_03_06_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_03_06_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.6.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_03_06_AdminVar_bump_version.sql'; From ee75d199aca4a802264342ccd053f3478023548b Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 20 Mar 2025 12:25:01 +0000 Subject: [PATCH 27/80] Add new particle classification columns (#264) Add new particle classification columns --- ...rticleClassification_angularEfficiency_suggestedTilt.sql | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 schemas/ispyb/updates/2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql diff --git a/schemas/ispyb/updates/2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql b/schemas/ispyb/updates/2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql new file mode 100644 index 00000000..565eb7b0 --- /dev/null +++ b/schemas/ispyb/updates/2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql @@ -0,0 +1,6 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql', 'ONGOING'); + +ALTER TABLE ParticleClassification ADD angularEfficiency double COMMENT 'Variation in resolution across different angles, 1-2sig/mean', ALGORITHM=INSTANT; +ALTER TABLE ParticleClassification ADD suggestedTilt double COMMENT 'Suggested stage tilt angle to improve angular efficiency. Unit: degrees', ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql'; From ebeeb4d5f30efbc01ffface17ac2e4d653a3a7f4 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Wed, 2 Apr 2025 12:41:22 +0100 Subject: [PATCH 28/80] Add select grant on Container, BLSample, BLSampleImage --- grants/ispyb_scripts_processing.sql | 3 +++ 1 file changed, 3 insertions(+) diff --git a/grants/ispyb_scripts_processing.sql b/grants/ispyb_scripts_processing.sql index 8bf00a55..61f5d8c0 100644 --- a/grants/ispyb_scripts_processing.sql +++ b/grants/ispyb_scripts_processing.sql @@ -20,3 +20,6 @@ GRANT SELECT ON DataCollection TO ispyb_scripts_processing; GRANT SELECT ON Proposal TO ispyb_scripts_processing; GRANT SELECT ON ProcessingJob TO ispyb_scripts_processing; GRANT SELECT ON ProcessingJobImageSweep TO ispyb_scripts_processing; +GRANT SELECT ON Container TO ispyb_scripts_processing; +GRANT SELECT ON BLSample TO ispyb_scripts_processing; +GRANT SELECT ON BLSampleImage TO ispyb_scripts_processing; From f6b9ac5788c5067868cb4a946bacdbe4ad9c38cb Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Tue, 15 Apr 2025 15:48:17 +0100 Subject: [PATCH 29/80] Add grants for propagation role --- grants/ispyb_propagation.sql | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/grants/ispyb_propagation.sql b/grants/ispyb_propagation.sql index 83b767b4..03cbf114 100644 --- a/grants/ispyb_propagation.sql +++ b/grants/ispyb_propagation.sql @@ -22,7 +22,8 @@ GRANT SELECT ON ContainerReport TO ispyb_propagation; GRANT SELECT ON CourierTermsAccepted TO ispyb_propagation; GRANT SELECT ON DataCollectionComment TO ispyb_propagation; GRANT SELECT ON DewarRegistry_has_Proposal TO ispyb_propagation; -GRANT SELECT ON LabContact TO ispyb_propagation; +GRANT SELECT, DELETE ON LabContact TO ispyb_propagation; +GRANT SELECT, DELETE ON Laboratory TO ispyb_propagation; GRANT SELECT ON Project TO ispyb_propagation; GRANT SELECT ON DataCollectionGroup TO ispyb_propagation; GRANT SELECT ON DataCollection TO ispyb_propagation; From 7a1afaaaef6bcd024167f5f1733a949130ebede2 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 17 Apr 2025 14:36:01 +0100 Subject: [PATCH 30/80] Recreate FK constraints referencing LabContact(labContactId) with 'on delete set null' (#267) --- ...4_16_labContacts_fk_on_delete_set_null.sql | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 schemas/ispyb/updates/2025_04_16_labContacts_fk_on_delete_set_null.sql diff --git a/schemas/ispyb/updates/2025_04_16_labContacts_fk_on_delete_set_null.sql b/schemas/ispyb/updates/2025_04_16_labContacts_fk_on_delete_set_null.sql new file mode 100644 index 00000000..fae7db57 --- /dev/null +++ b/schemas/ispyb/updates/2025_04_16_labContacts_fk_on_delete_set_null.sql @@ -0,0 +1,26 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_04_16_labContacts_fk_on_delete_set_null.sql', 'ONGOING'); + +ALTER TABLE Shipping + DROP CONSTRAINT Shipping_ibfk_2, + DROP CONSTRAINT Shipping_ibfk_3; + +ALTER TABLE Shipping + ADD CONSTRAINT Shipping_ibfk_2 + FOREIGN KEY (sendingLabContactId) + REFERENCES LabContact (labContactId) + ON DELETE SET NULL ON UPDATE CASCADE, + ADD CONSTRAINT Shipping_ibfk_3 + FOREIGN KEY (returnLabContactId) + REFERENCES LabContact (labContactId) + ON DELETE SET NULL ON UPDATE CASCADE; + +ALTER TABLE DewarRegistry_has_Proposal + DROP CONSTRAINT DewarRegistry_has_Proposal_ibfk4; + +ALTER TABLE DewarRegistry_has_Proposal + ADD CONSTRAINT DewarRegistry_has_Proposal_ibfk4 + FOREIGN KEY (labContactId) + REFERENCES LabContact (labContactId) + ON DELETE SET NULL ON UPDATE CASCADE; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_04_16_labContacts_fk_on_delete_set_null.sql'; From ec4a57d3a1c2b371df430c0f1004d479e6d88b95 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Mon, 28 Apr 2025 15:11:47 +0100 Subject: [PATCH 31/80] Add reference to BLSample, describe position type (#266) --- .../2025_04_11_Position_blSampleId_positionType.sql | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 schemas/ispyb/updates/2025_04_11_Position_blSampleId_positionType.sql diff --git a/schemas/ispyb/updates/2025_04_11_Position_blSampleId_positionType.sql b/schemas/ispyb/updates/2025_04_11_Position_blSampleId_positionType.sql new file mode 100644 index 00000000..8d79c64b --- /dev/null +++ b/schemas/ispyb/updates/2025_04_11_Position_blSampleId_positionType.sql @@ -0,0 +1,10 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_04_11_Position_blSampleId_positionType.sql', 'ONGOING'); + +ALTER TABLE Position + ADD positionType varchar(45) COMMENT 'Action (type) that originated this position', + ADD blSampleId int(11) unsigned COMMENT 'FK, references parent sample', + ADD CONSTRAINT `Position_fk_blSampleId` + FOREIGN KEY (`blSampleId`) + REFERENCES `BLSample` (`blSampleId`); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_04_11_Position_blSampleId_positionType.sql'; From b7c9a4df9f7d24f18ca9629a9186186b678e82bb Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Wed, 30 Apr 2025 11:39:55 +0100 Subject: [PATCH 32/80] Make DewarRegistry.labContactId FK "on delete set null" (#269) --- ...arRegistry_fk_labContactId_on_delete_set_null.sql | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 schemas/ispyb/updates/2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql diff --git a/schemas/ispyb/updates/2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql b/schemas/ispyb/updates/2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql new file mode 100644 index 00000000..863ebac7 --- /dev/null +++ b/schemas/ispyb/updates/2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql @@ -0,0 +1,12 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql', 'ONGOING'); + +ALTER TABLE DewarRegistry + DROP CONSTRAINT DewarRegistry_ibfk_2; + +ALTER TABLE DewarRegistry + ADD CONSTRAINT DewarRegistry_ibfk_2 + FOREIGN KEY (labContactId) + REFERENCES LabContact (labContactId) + ON DELETE SET NULL ON UPDATE CASCADE; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql'; From eafe159877e99602d8e40282a4ee360dbaa2c04c Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 30 Apr 2025 11:43:08 +0100 Subject: [PATCH 33/80] Add extra grants for Expeye (#268) --- grants/ispyb_expeye.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 6b61e1b3..54a8582c 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -50,7 +50,7 @@ GRANT SELECT, INSERT, UPDATE, DELETE ON BLSubSample TO ispyb_expeye_acquisition_ GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_BLSample TO ispyb_expeye_acquisition_role; GRANT SELECT ON Protein TO ispyb_expeye_acquisition_role; -GRANT SELECT ON Crystal TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE ON Crystal TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON XFEFluorescenceSpectrum TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON DiffractionPlan TO ispyb_expeye_acquisition_role; From 0cb8da0a72282b4b553006283d25b1031f9f88d7 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Wed, 30 Apr 2025 18:05:50 +0100 Subject: [PATCH 34/80] Make Shipping FK deliveryAgent_flightCodePersonId "on delete set null" (#270) --- ...04_30_Shipping_fk_personId_on_delete_set_null.sql | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 schemas/ispyb/updates/2025_04_30_Shipping_fk_personId_on_delete_set_null.sql diff --git a/schemas/ispyb/updates/2025_04_30_Shipping_fk_personId_on_delete_set_null.sql b/schemas/ispyb/updates/2025_04_30_Shipping_fk_personId_on_delete_set_null.sql new file mode 100644 index 00000000..b9d183e3 --- /dev/null +++ b/schemas/ispyb/updates/2025_04_30_Shipping_fk_personId_on_delete_set_null.sql @@ -0,0 +1,12 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_04_30_Shipping_fk_personId_on_delete_set_null.sql', 'ONGOING'); + +ALTER TABLE Shipping + DROP CONSTRAINT Shipping_ibfk_4; + + ALTER TABLE Shipping + ADD CONSTRAINT Shipping_ibfk_4 + FOREIGN KEY (deliveryAgent_flightCodePersonId) + REFERENCES Person (personId) + ON DELETE SET NULL ON UPDATE CASCADE; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_04_30_Shipping_fk_personId_on_delete_set_null.sql'; From e28ef44ac2da9d551ce571f95883903e6eaceac3 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Thu, 1 May 2025 11:13:41 +0100 Subject: [PATCH 35/80] Add select grant for propagation role on BLSampleGroup --- grants/ispyb_propagation.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_propagation.sql b/grants/ispyb_propagation.sql index 03cbf114..2c48c093 100644 --- a/grants/ispyb_propagation.sql +++ b/grants/ispyb_propagation.sql @@ -16,6 +16,7 @@ GRANT SELECT, UPDATE, INSERT, DELETE ON ContainerRegistry_has_Proposal TO ispyb_ GRANT SELECT, UPDATE, INSERT, DELETE ON Person TO ispyb_propagation; GRANT SELECT, UPDATE, INSERT, DELETE ON UserGroup_has_Person TO ispyb_propagation; GRANT SELECT ON BF_fault TO ispyb_propagation; +GRANT SELECT ON BLSampleGroup to ispyb_propagation; GRANT SELECT ON Container TO ispyb_propagation; GRANT SELECT ON ContainerQueue TO ispyb_propagation; GRANT SELECT ON ContainerReport TO ispyb_propagation; From 6d1c3c9d0bf8dd58a87dc66f0dd5b75d4ad5f4d6 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 1 May 2025 12:43:39 +0100 Subject: [PATCH 36/80] Add blSampleId FK col in XrayCentringResult which is the actual sample to which the result belongs (#271) --- .../2025_05_01_XrayCentringResult_fk_blSampleId.sql | 11 +++++++++++ 1 file changed, 11 insertions(+) create mode 100644 schemas/ispyb/updates/2025_05_01_XrayCentringResult_fk_blSampleId.sql diff --git a/schemas/ispyb/updates/2025_05_01_XrayCentringResult_fk_blSampleId.sql b/schemas/ispyb/updates/2025_05_01_XrayCentringResult_fk_blSampleId.sql new file mode 100644 index 00000000..10108f28 --- /dev/null +++ b/schemas/ispyb/updates/2025_05_01_XrayCentringResult_fk_blSampleId.sql @@ -0,0 +1,11 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_01_XrayCentringResult_fk_blSampleId.sql', 'ONGOING'); + +ALTER TABLE XrayCentringResult + ADD blSampleId int(11) unsigned COMMENT 'The BLSample attributed for this x-ray centring result, i.e. the actual sample even for multi-pins', + ADD CONSTRAINT XrayCentringResult_fk_blSampleId + FOREIGN KEY (blSampleId) + REFERENCES BLSample(blSampleId) + ON DELETE SET NULL + ON UPDATE CASCADE; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_01_XrayCentringResult_fk_blSampleId.sql'; From 607a5c41c650355a1fba8c11ad7d7a3e74a97aee Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 1 May 2025 17:37:45 +0100 Subject: [PATCH 37/80] Add BLSamplePosition table (#272) New table BLSamplePosition with FK to BLSample, posX, posY, posZ, recordTimeStamp and positionType enum --- .../updates/2025_05_01_BLSamplePosition.sql | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 schemas/ispyb/updates/2025_05_01_BLSamplePosition.sql diff --git a/schemas/ispyb/updates/2025_05_01_BLSamplePosition.sql b/schemas/ispyb/updates/2025_05_01_BLSamplePosition.sql new file mode 100644 index 00000000..83af8715 --- /dev/null +++ b/schemas/ispyb/updates/2025_05_01_BLSamplePosition.sql @@ -0,0 +1,20 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_01_BLSamplePosition.sql', 'ONGOING'); + +ALTER TABLE Position + DROP CONSTRAINT IF EXISTS Position_fk_blSampleId, + DROP IF EXISTS positionType, + DROP IF EXISTS blSampleId; + +CREATE TABLE `BLSamplePosition` ( + `positionId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', + `blSampleId` int(11) unsigned NOT NULL COMMENT 'FK, references parent sample', + `posX` double DEFAULT NULL, + `posY` double DEFAULT NULL, + `posZ` double DEFAULT NULL, + `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', + `positionType` enum('dispensing') COMMENT 'Type of marked position (e.g.: dispensing location)', + PRIMARY KEY (`positionId`), + CONSTRAINT `BLSamplePosition_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) +); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_01_BLSamplePosition.sql'; From 6ed22fe47ab2adb9e92ef5968feb18ef3da99a7a Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Fri, 2 May 2025 09:01:19 +0100 Subject: [PATCH 38/80] Add grants for propagation role on SW_onceToken --- grants/ispyb_propagation.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_propagation.sql b/grants/ispyb_propagation.sql index 2c48c093..3e87bbe3 100644 --- a/grants/ispyb_propagation.sql +++ b/grants/ispyb_propagation.sql @@ -39,3 +39,4 @@ GRANT SELECT ON LDAPSearchBase TO ispyb_propagation; GRANT SELECT ON UserGroup TO ispyb_propagation; GRANT SELECT, UPDATE, INSERT ON BeamCalendar TO ispyb_propagation; GRANT SELECT, UPDATE, INSERT ON v_run TO ispyb_propagation; +GRANT SELECT, DELETE ON SW_onceToken TO ispyb_propagation; From 9014199a0f9bf21a46b3f3abf182fa55083848a1 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Fri, 2 May 2025 09:28:33 +0100 Subject: [PATCH 39/80] Rename BLSamplePosition PK column positionId -> blSamplePositionId (#273) --- .../updates/2025_05_02_BLSamplePosition_rename_column.sql | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 schemas/ispyb/updates/2025_05_02_BLSamplePosition_rename_column.sql diff --git a/schemas/ispyb/updates/2025_05_02_BLSamplePosition_rename_column.sql b/schemas/ispyb/updates/2025_05_02_BLSamplePosition_rename_column.sql new file mode 100644 index 00000000..c5b022e6 --- /dev/null +++ b/schemas/ispyb/updates/2025_05_02_BLSamplePosition_rename_column.sql @@ -0,0 +1,6 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_02_BLSamplePosition_rename_column.sql', 'ONGOING'); + +ALTER TABLE BLSamplePosition + RENAME COLUMN `positionId` TO `blSamplePositionId`; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_02_BLSamplePosition_rename_column.sql'; From ba88503c7759b7c571f5668abe829b495c20498b Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 8 May 2025 17:12:51 +0100 Subject: [PATCH 40/80] SP update_container_assign: also return sample locations (#274) --- .../stored_programs/sp_update_container_assign.sql | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/schemas/ispyb/stored_programs/sp_update_container_assign.sql b/schemas/ispyb/stored_programs/sp_update_container_assign.sql index 6650b3b3..4a1ac941 100644 --- a/schemas/ispyb/stored_programs/sp_update_container_assign.sql +++ b/schemas/ispyb/stored_programs/sp_update_container_assign.sql @@ -20,6 +20,7 @@ BEGIN DECLARE row_proposalCode varchar(45) DEFAULT NULL; DECLARE row_proposalNumber varchar(45) DEFAULT NULL; DECLARE row_queuedCount int(11) unsigned DEFAULT NULL; + DECLARE row_samples varchar(255) DEFAULT NULL; IF p_beamline IS NULL THEN SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_beamline is NULL'; @@ -50,7 +51,7 @@ BEGIN INNER JOIN ContainerRegistry cr ON c.containerRegistryId = cr.containerRegistryId INNER JOIN Dewar d ON d.dewarId = c.dewarId INNER JOIN Shipping s ON s.shippingId = d.shippingId - INNER JOIN Proposal p ON p.proposalId = s.proposalId + INNER JOIN Proposal p ON p.proposalId = s.proposalId LEFT OUTER JOIN ContainerQueue cq ON cq.containerId = c.containerId WHERE cr.barcode = p_registry_barcode GROUP BY c.containerId, @@ -116,10 +117,18 @@ BEGIN ELSE SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_registry_barcode is NULL'; END IF; + + SELECT group_concat(location ORDER BY cast(location AS integer) SEPARATOR ',') + INTO row_samples + FROM BLSample + WHERE containerId = row_containerId + GROUP BY containerId; + SELECT row_containerId as "containerId", currentContainerStatus as "containerStatus", row_proposalCode as "proposalCode", row_proposalNumber as "proposalNumber", - row_queuedCount as "queuedCount"; + row_queuedCount as "queuedCount", + row_samples as "samples"; END ;; DELIMITER ; From 22e9d5bd48045c2ef0c714b4762aaa9e68d3d97f Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Mon, 12 May 2025 08:43:14 +0100 Subject: [PATCH 41/80] Preparations for release 4.7.0 (#275) --- schemas/ispyb/lookups.sql | 13 +++- schemas/ispyb/routines.sql | 61 ++++++++++++++++--- schemas/ispyb/tables.sql | 29 +++++++-- .../2025_05_12_AdminVar_bump_version.sql | 5 ++ 4 files changed, 92 insertions(+), 16 deletions(-) create mode 100644 schemas/ispyb/updates/2025_05_12_AdminVar_bump_version.sql diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index c4ed6afe..ab7080fd 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -11,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.6.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.7.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -278,7 +278,16 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (306,'2025_02_25_AdminVar_bump_version.sql','DONE','2025-02-25 15:51:30'), (307,'2025_02_27_ExperimentType_atlas.sql','DONE','2025-03-06 11:58:07'), (308,'2025_03_05_Dewar_dewarRegistryId.sql','DONE','2025-03-06 11:58:07'), -(309,'2025_03_06_AdminVar_bump_version.sql','DONE','2025-03-06 11:58:07'); +(309,'2025_03_06_AdminVar_bump_version.sql','DONE','2025-03-06 11:58:07'), +(310,'2025_03_20_ParticleClassification_angularEfficiency_suggestedTilt.sql','DONE','2025-05-09 15:21:06'), +(311,'2025_04_11_Position_blSampleId_positionType.sql','DONE','2025-05-09 15:21:06'), +(312,'2025_04_16_labContacts_fk_on_delete_set_null.sql','DONE','2025-05-09 15:21:06'), +(313,'2025_04_29_DewarRegistry_fk_labContactId_on_delete_set_null.sql','DONE','2025-05-09 15:21:06'), +(314,'2025_04_30_Shipping_fk_personId_on_delete_set_null.sql','DONE','2025-05-09 15:21:06'), +(315,'2025_05_01_BLSamplePosition.sql','DONE','2025-05-09 15:21:06'), +(316,'2025_05_01_XrayCentringResult_fk_blSampleId.sql','DONE','2025-05-09 15:21:06'), +(317,'2025_05_02_BLSamplePosition_rename_column.sql','DONE','2025-05-09 15:21:06'), +(318,'2025_05_12_AdminVar_bump_version.sql','DONE','2025-05-09 15:21:06'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql index 7949622a..335dede8 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -7456,30 +7456,61 @@ BEGIN DECLARE row_beamlineLocation varchar(20) DEFAULT NULL; DECLARE row_sampleChangerLocation varchar(20) DEFAULT NULL; DECLARE row_proposalId int(10) unsigned DEFAULT NULL; + DECLARE row_proposalCode varchar(45) DEFAULT NULL; + DECLARE row_proposalNumber varchar(45) DEFAULT NULL; DECLARE row_queuedCount int(11) unsigned DEFAULT NULL; + DECLARE row_samples varchar(255) DEFAULT NULL; + + IF p_beamline IS NULL THEN + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_beamline is NULL'; + END IF; IF NOT (p_registry_barcode IS NULL) THEN START TRANSACTION; - SELECT c.containerId, c.containerStatus, c.dewarId, c.beamlineLocation, c.sampleChangerLocation, s.proposalId, count(cq.containerQueueId) - INTO row_containerId, row_containerStatus, row_dewarId, row_beamlineLocation, row_sampleChangerLocation, row_proposalId, row_queuedCount + SELECT c.containerId, + c.containerStatus, + c.dewarId, + c.beamlineLocation, + c.sampleChangerLocation, + p.proposalId, + p.proposalCode, + p.proposalNumber, + count(cq.containerQueueId) + INTO row_containerId, + row_containerStatus, + row_dewarId, + row_beamlineLocation, + row_sampleChangerLocation, + row_proposalId, + row_proposalCode, + row_proposalNumber, + row_queuedCount FROM Container c INNER JOIN ContainerRegistry cr ON c.containerRegistryId = cr.containerRegistryId INNER JOIN Dewar d ON d.dewarId = c.dewarId INNER JOIN Shipping s ON s.shippingId = d.shippingId + INNER JOIN Proposal p ON p.proposalId = s.proposalId LEFT OUTER JOIN ContainerQueue cq ON cq.containerId = c.containerId WHERE cr.barcode = p_registry_barcode - GROUP BY c.containerId, c.containerStatus, c.dewarId, c.beamlineLocation, c.sampleChangerLocation, s.proposalId + GROUP BY c.containerId, + c.containerStatus, + c.dewarId, + c.beamlineLocation, + c.sampleChangerLocation, + p.proposalId, + p.proposalCode, + p.proposalNumber ORDER BY c.containerId DESC LIMIT 1; SELECT row_containerStatus INTO currentContainerStatus; - + IF NOT row_containerId IS NULL THEN IF (NOT row_containerStatus <=> 'processing') OR (row_beamlineLocation = p_beamline AND row_sampleChangerLocation = p_position) THEN - + UPDATE Container c INNER JOIN Dewar d ON d.dewarId = c.dewarId INNER JOIN Shipping s ON s.shippingId = d.shippingId @@ -7496,8 +7527,8 @@ BEGIN SELECT IF(row_containerStatus<=>'processing', 'at facility', 'processing') INTO currentContainerStatus; IF NOT row_containerStatus <=> 'processing' THEN - - + + UPDATE Container c INNER JOIN Dewar d ON d.dewarId = c.dewarId INNER JOIN Shipping s ON s.shippingId = d.shippingId @@ -7506,12 +7537,12 @@ BEGIN WHERE s.proposalId = row_proposalId AND c.beamlineLocation = p_beamline AND c.sampleChangerLocation = p_position AND c.containerId <> row_containerId; - + INSERT INTO DewarTransportHistory (dewarId, dewarStatus, storageLocation, arrivalDate) VALUES (row_dewarId, 'processing', p_beamline, NOW()); END IF; - + INSERT INTO ContainerHistory (containerId, location, status, beamlineName, currentDewarId) SELECT row_containerId, p_position, IF(row_containerStatus<=>'processing', 'at facility', 'processing'), p_beamline, currentDewarId FROM Container @@ -7525,9 +7556,19 @@ BEGIN ELSE SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_registry_barcode is NULL'; END IF; + + SELECT group_concat(location ORDER BY cast(location AS integer) SEPARATOR ',') + INTO row_samples + FROM BLSample + WHERE containerId = row_containerId + GROUP BY containerId; + SELECT row_containerId as "containerId", currentContainerStatus as "containerStatus", - row_queuedCount as "queuedCount"; + row_proposalCode as "proposalCode", + row_proposalNumber as "proposalNumber", + row_queuedCount as "queuedCount", + row_samples as "samples"; END ;; DELIMITER ; /*!50003 SET sql_mode = @saved_sql_mode */ ; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index e3d52447..0b8b6ffc 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -605,6 +605,22 @@ CREATE TABLE `BLSampleImage_has_Positioner` ( CONSTRAINT `BLSampleImageHasPositioner_ibfk2` FOREIGN KEY (`positionerId`) REFERENCES `Positioner` (`positionerId`) ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Allows a BLSampleImage to store motor positions along with the image'; /*!40101 SET character_set_client = @saved_cs_client */; +DROP TABLE IF EXISTS `BLSamplePosition`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8mb4 */; +CREATE TABLE `BLSamplePosition` ( + `blSamplePositionId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', + `blSampleId` int(11) unsigned NOT NULL COMMENT 'FK, references parent sample', + `posX` double DEFAULT NULL, + `posY` double DEFAULT NULL, + `posZ` double DEFAULT NULL, + `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', + `positionType` enum('dispensing') DEFAULT NULL COMMENT 'Type of marked position (e.g.: dispensing location)', + PRIMARY KEY (`blSamplePositionId`), + KEY `BLSamplePosition_fk_blSampleId` (`blSampleId`), + CONSTRAINT `BLSamplePosition_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci; +/*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleType`; /*!40101 SET @saved_cs_client = @@character_set_client */; /*!40101 SET character_set_client = utf8mb4 */; @@ -1687,7 +1703,7 @@ CREATE TABLE `DewarRegistry_has_Proposal` ( CONSTRAINT `DewarRegistry_has_Proposal_ibfk1` FOREIGN KEY (`dewarRegistryId`) REFERENCES `DewarRegistry` (`dewarRegistryId`), CONSTRAINT `DewarRegistry_has_Proposal_ibfk2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`), CONSTRAINT `DewarRegistry_has_Proposal_ibfk3` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`), - CONSTRAINT `DewarRegistry_has_Proposal_ibfk4` FOREIGN KEY (`labContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE NO ACTION ON UPDATE CASCADE + CONSTRAINT `DewarRegistry_has_Proposal_ibfk4` FOREIGN KEY (`labContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarReport`; @@ -2396,6 +2412,8 @@ CREATE TABLE `ParticleClassification` ( `bFactorFitIntercept` float DEFAULT NULL COMMENT 'Intercept of quadratic fit to refinement resolution against the logarithm of the number of particles', `bFactorFitLinear` float DEFAULT NULL COMMENT 'Linear coefficient of quadratic fit to refinement resolution against the logarithm of the number of particles, equal to half of the B factor', `bFactorFitQuadratic` float DEFAULT NULL COMMENT 'Quadratic coefficient of quadratic fit to refinement resolution against the logarithm of the number of particles', + `angularEfficiency` double DEFAULT NULL COMMENT 'Variation in resolution across different angles, 1-2sig/mean', + `suggestedTilt` double DEFAULT NULL COMMENT 'Suggested stage tilt angle to improve angular efficiency. Unit: degrees', PRIMARY KEY (`particleClassificationId`), KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`), CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE @@ -3456,9 +3474,9 @@ CREATE TABLE `Shipping` ( KEY `Shipping_FKIndexStatus` (`shippingStatus`), KEY `Shipping_ibfk_4` (`deliveryAgent_flightCodePersonId`), CONSTRAINT `Shipping_ibfk_1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE, - CONSTRAINT `Shipping_ibfk_2` FOREIGN KEY (`sendingLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE CASCADE ON UPDATE CASCADE, - CONSTRAINT `Shipping_ibfk_3` FOREIGN KEY (`returnLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE CASCADE ON UPDATE CASCADE, - CONSTRAINT `Shipping_ibfk_4` FOREIGN KEY (`deliveryAgent_flightCodePersonId`) REFERENCES `Person` (`personId`) + CONSTRAINT `Shipping_ibfk_2` FOREIGN KEY (`sendingLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE, + CONSTRAINT `Shipping_ibfk_3` FOREIGN KEY (`returnLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE, + CONSTRAINT `Shipping_ibfk_4` FOREIGN KEY (`deliveryAgent_flightCodePersonId`) REFERENCES `Person` (`personId`) ON DELETE SET NULL ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ShippingHasSession`; @@ -3762,8 +3780,11 @@ CREATE TABLE `XrayCentringResult` ( `boundingBoxMaxZ` float DEFAULT NULL COMMENT 'Maximum z-coordinate of the bounding box containing the crystal (in voxels)', `status` enum('success','failure','pending') DEFAULT NULL COMMENT 'to be removed', `gridInfoId` int(11) unsigned DEFAULT NULL COMMENT 'to be removed', + `blSampleId` int(11) unsigned DEFAULT NULL COMMENT 'The BLSample attributed for this x-ray centring result, i.e. the actual sample even for multi-pins', PRIMARY KEY (`xrayCentringResultId`), KEY `xrayCentringId` (`xrayCentringId`), + KEY `XrayCentringResult_fk_blSampleId` (`blSampleId`), + CONSTRAINT `XrayCentringResult_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `XrayCentringResult_ibfk_1` FOREIGN KEY (`xrayCentringId`) REFERENCES `XrayCentring` (`xrayCentringId`) ON DELETE CASCADE ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Xray Centring result.'; /*!40101 SET character_set_client = @saved_cs_client */; diff --git a/schemas/ispyb/updates/2025_05_12_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_05_12_AdminVar_bump_version.sql new file mode 100644 index 00000000..bd1302d0 --- /dev/null +++ b/schemas/ispyb/updates/2025_05_12_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_12_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.7.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_12_AdminVar_bump_version.sql'; From c2a65cad426ce35e67f4a6a861183b52869926e1 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Mon, 12 May 2025 09:41:59 +0100 Subject: [PATCH 42/80] Update HISTORY.rst --- HISTORY.rst | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/HISTORY.rst b/HISTORY.rst index df9f3a7c..8043d616 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,27 @@ History Unreleased / master ------------------- +4.7.0 (2025-05-12) +------------------- + +New or modified tables, columns, lookup values: + +- New table ``BLSamplePosition`` +- Add a ``blSampleId`` FK to the ``XrayCentringResult`` table +- Add ``angularEfficiency`` and ``suggestedTilt`` columns to ``ParticleClassification`` +- Recreate FK constraints referencing ``LabContact(labContactId)`` with 'on delete set null +- Make ``Shipping`` FK ``deliveryAgent_flightCodePersonId`` "on delete set null" + +Roles and permissions: + +- Add new grants for Expeye +- Add new permissions for ``ispyb_propagation`` +- Add new permissions for ``ispyb_scripts_processing.sql`` + +Stored procedures: + +- Also return sample locations for ``update_container_assign`` + 4.6.0 (2025-03-06) ------------------- From 436fff0e67aa1e28c42c08be56b668cc3b03c5c3 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 15 May 2025 11:57:42 +0100 Subject: [PATCH 43/80] Allow Expeye to query BLSamplePosition (#277) --- grants/ispyb_expeye.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 54a8582c..ade2285f 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -48,6 +48,7 @@ GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup TO ispyb_expeye_acquisitio GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup_has_BLSample TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSubSample TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_BLSample TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE ON BLSamplePosition TO ispyb_expeye_acquisition_role; GRANT SELECT ON Protein TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON Crystal TO ispyb_expeye_acquisition_role; From a1e1f306fb9d1bce32edba33814ceeb19289584b Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 15 May 2025 11:57:50 +0100 Subject: [PATCH 44/80] Allow Expeye to select on SpaceGroup (#276) --- grants/ispyb_expeye.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index ade2285f..0bebdb3a 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -50,6 +50,7 @@ GRANT SELECT, INSERT, UPDATE, DELETE ON BLSubSample TO ispyb_expeye_acquisition_ GRANT SELECT, INSERT, UPDATE, DELETE ON Project_has_BLSample TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON BLSamplePosition TO ispyb_expeye_acquisition_role; +GRANT SELECT ON SpaceGroup TO ispyb_expeye_acquisition_role; GRANT SELECT ON Protein TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE ON Crystal TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON XFEFluorescenceSpectrum TO ispyb_expeye_acquisition_role; From 7fe5ffc93f3f5895cc60bf840c9e252a416811ba Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Mon, 19 May 2025 23:57:12 +0100 Subject: [PATCH 45/80] Allow ispyb-processing to modify BLSamplePosition (#279) --- grants/ispyb_processing.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_processing.sql b/grants/ispyb_processing.sql index b0ef0154..918ae0ac 100644 --- a/grants/ispyb_processing.sql +++ b/grants/ispyb_processing.sql @@ -9,6 +9,7 @@ CREATE ROLE IF NOT EXISTS ispyb_processing; -- Grants for ispyb_processing GRANT SELECT ON AdminVar TO 'ispyb_processing'; -- Hack TO allow ispyb_processing to connect through MaxScale GRANT SELECT,INSERT ON ImageQualityIndicators TO 'ispyb_processing'; -- Needed for bulk insertion of aggregated IQIs +GRANT SELECT,INSERT,UPDATE ON BLSamplePosition TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON BLSampleImage TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON BLSampleImageAnalysis TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON BLSampleImage_has_AutoScoreClass TO 'ispyb_processing'; From 863b9839b7d2b74865bb9336d92cd09d913a3fd3 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Tue, 27 May 2025 10:17:27 +0100 Subject: [PATCH 46/80] Add table Ligand w/ junction tables BLSample_has_Ligand, Ligand_has_PDB (#280) --- .../2025_05_23_Ligand_and_junction_tables.sql | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 schemas/ispyb/updates/2025_05_23_Ligand_and_junction_tables.sql diff --git a/schemas/ispyb/updates/2025_05_23_Ligand_and_junction_tables.sql b/schemas/ispyb/updates/2025_05_23_Ligand_and_junction_tables.sql new file mode 100644 index 00000000..f62fadea --- /dev/null +++ b/schemas/ispyb/updates/2025_05_23_Ligand_and_junction_tables.sql @@ -0,0 +1,58 @@ +-- To undo: +-- drop table BLSample_has_Ligand; +-- drop table Ligand_has_PDB +-- drop table Ligand; +-- delete from SchemaStatus where scriptName = '2025_05_23_Ligand_and_junction_tables.sql'; + + +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_23_Ligand_and_junction_tables.sql', 'ONGOING'); + +CREATE TABLE Ligand ( + ligandId int(11) unsigned PRIMARY KEY AUTO_INCREMENT, + proposalId int(10) unsigned NOT NULL COMMENT 'References Proposal table', + name varchar(30) NOT NULL COMMENT 'Ligand name', + SMILES varchar(400) COMMENT 'Chemical structure', + libraryName varchar(30) COMMENT 'Name of ligand library, to preserve provenance', + libraryBatchNumber varchar(30) COMMENT 'Batch number of library, to preserve provenance', + plateBarcode varchar(30) COMMENT 'Specific barcode of the plate it came from, to preserve provenance', + sourceWell varchar(30) COMMENT 'Location within that plate, to preserve provenance', + CONSTRAINT `Ligand_fk_proposalId` + FOREIGN KEY (proposalId) + REFERENCES Proposal (proposalId) + ON DELETE CASCADE + ON UPDATE CASCADE +) COMMENT = 'Ligands in biochemistry are substances that bind to biomolecules'; + +CREATE TABLE BLSample_has_Ligand ( + blSampleId int(10) unsigned, + ligandId int(11) unsigned, + PRIMARY KEY (blSampleId, ligandId), + CONSTRAINT BLSample_has_Ligand_fk1 + FOREIGN KEY (blSampleId) + REFERENCES BLSample (blSampleId) + ON DELETE CASCADE + ON UPDATE CASCADE, + CONSTRAINT BLSample_has_Ligand_fk2 + FOREIGN KEY (ligandId) + REFERENCES Ligand (ligandId) + ON DELETE CASCADE + ON UPDATE CASCADE +) COMMENT = 'Junction table for BLSample and Ligand'; + +CREATE TABLE Ligand_has_PDB ( + ligandId int(11) unsigned, + pdbId int(11) unsigned, + PRIMARY KEY (ligandId, pdbId), + CONSTRAINT Ligand_Has_PDB_fk1 + FOREIGN KEY (ligandId) + REFERENCES Ligand (ligandId) + ON DELETE CASCADE + ON UPDATE CASCADE, + CONSTRAINT Ligand_Has_PDB_fk2 + FOREIGN KEY (pdbid) + REFERENCES PDB (pdbId) + ON DELETE CASCADE + ON UPDATE CASCADE +) COMMENT = 'Junction table for Ligand and PDB'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_23_Ligand_and_junction_tables.sql'; From b2543031fef7d2ab3aa36a2b4a1ecd7f80c4c27f Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Tue, 27 May 2025 10:18:30 +0100 Subject: [PATCH 47/80] Inlcude all + fix order of grant files in build.sh (#281) --- build.sh | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/build.sh b/build.sh index 245f6ba3..ff6cebf7 100755 --- a/build.sh +++ b/build.sh @@ -26,14 +26,18 @@ function exec_schema { function exec_grants { mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_acquisition.sql + mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_propagation.sql + mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_expeye.sql + mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_fragment_screening.sql mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_import.sql mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_processing.sql mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_ro_nopii.sql mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_scripts_processing.sql + mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_ssx_writer.sql mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_touchscreen.sql - mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_web.sql mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_web_verify_tests.sql - mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_ssx_writer.sql + mariadb --defaults-file=.my.cnf -D $1 < grants/ispyb_web.sql + mariadb --defaults-file=.my.cnf -D $1 < grants/maxscale.sql } function exec_missed_updates { From 593bb8c26121244a19652ed06ec34896f222757b Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Tue, 27 May 2025 10:23:22 +0100 Subject: [PATCH 48/80] Set recordTimeStamp default to current timestamp (#278) --- .../2025_05_14_BLSamplePosition_recordTimeStamp_default.sql | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 schemas/ispyb/updates/2025_05_14_BLSamplePosition_recordTimeStamp_default.sql diff --git a/schemas/ispyb/updates/2025_05_14_BLSamplePosition_recordTimeStamp_default.sql b/schemas/ispyb/updates/2025_05_14_BLSamplePosition_recordTimeStamp_default.sql new file mode 100644 index 00000000..9d54a1fa --- /dev/null +++ b/schemas/ispyb/updates/2025_05_14_BLSamplePosition_recordTimeStamp_default.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_14_BLSamplePosition_recordTimeStamp_default.sql', 'ONGOING'); + +ALTER TABLE BLSamplePosition MODIFY COLUMN recordTimeStamp datetime DEFAULT current_timestamp; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_14_BLSamplePosition_recordTimeStamp_default.sql'; From 659c283951b8f19f1ba8c69aa204f5a4536ded58 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 29 May 2025 16:45:38 +0100 Subject: [PATCH 49/80] Add new col BLSession.icatId for the internal ICAT visit ID (#282) --- schemas/ispyb/updates/2025_05_28_BLSession_icatId.sql | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 schemas/ispyb/updates/2025_05_28_BLSession_icatId.sql diff --git a/schemas/ispyb/updates/2025_05_28_BLSession_icatId.sql b/schemas/ispyb/updates/2025_05_28_BLSession_icatId.sql new file mode 100644 index 00000000..eea68d91 --- /dev/null +++ b/schemas/ispyb/updates/2025_05_28_BLSession_icatId.sql @@ -0,0 +1,6 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_05_28_BLSession_icatId.sql', 'ONGOING'); + +ALTER TABLE BLSession + ADD icatId int(11) unsigned COMMENT 'The internal ICAT ID for this BLSession'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_05_28_BLSession_icatId.sql'; From 7dd87e87829cca218b6287962a489d05c7d50bce Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Fri, 6 Jun 2025 09:19:59 +0100 Subject: [PATCH 50/80] Add new DewarRegistry column enum and stop using Dewar.type is sprocs (#283) * Add DewarRegistry column enum and stop using Dewar.type is sprocs * Add a new `type` column which is an enum in the DewarRegistry table * Add enum option 'Thermal Shipper' to `type` column * In sproc retrieve_dewars_for_proposal_code_number_v2: Use DR.type instead of D.type * In sproc upsert_dewar_v3: Remove param p_type and don't write to D.type --- ...eve_dewars_for_proposal_code_number_v2.sql | 16 +-- .../stored_programs/sp_upsert_dewar_v3.sql | 100 ++++++++++++++++++ .../updates/2025_06_02_DewarRegistry_type.sql | 6 ++ 3 files changed, 115 insertions(+), 7 deletions(-) create mode 100644 schemas/ispyb/stored_programs/sp_upsert_dewar_v3.sql create mode 100644 schemas/ispyb/updates/2025_06_02_DewarRegistry_type.sql diff --git a/schemas/ispyb/stored_programs/sp_retrieve_dewars_for_proposal_code_number_v2.sql b/schemas/ispyb/stored_programs/sp_retrieve_dewars_for_proposal_code_number_v2.sql index f81b0f05..c6c5ec24 100644 --- a/schemas/ispyb/stored_programs/sp_retrieve_dewars_for_proposal_code_number_v2.sql +++ b/schemas/ispyb/stored_programs/sp_retrieve_dewars_for_proposal_code_number_v2.sql @@ -1,7 +1,7 @@ DELIMITER ;; CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE retrieve_dewars_for_proposal_code_number_v2( - p_proposalCode varchar(3), - p_proposalNumber int unsigned, + p_proposalCode varchar(3), + p_proposalNumber int unsigned, p_authLogin varchar(45)) READS SQL DATA COMMENT 'Return multi-row result-set with dewar ID + other dewar info associated with shipments in a given proposal specified by proposal code, proposal_number' @@ -12,25 +12,27 @@ BEGIN SELECT d.dewarId "id", d.shippingId "shippingId", d.code "name", d.comments "comments", d.storageLocation "storageLocation", d.dewarStatus "status", d.isStorageDewar "isStorageDewar", d.barCode "barCode", d.firstExperimentId "firstSessionId", - d.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" + dr.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" FROM Dewar d + LEFT JOIN DewarRegistry dr ON dr.facilityCode = d.facilityCode INNER JOIN Shipping s ON s.shippingId = d.shippingId - INNER JOIN Proposal p ON p.proposalId = s.proposalId + INNER JOIN Proposal p ON p.proposalId = s.proposalId INNER JOIN BLSession bs ON bs.proposalId = s.proposalId INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId INNER JOIN Person per ON per.personId = shp.personId WHERE per.login = p_authLogin AND p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber GROUP BY d.dewarId, d.shippingId, d.code, d.comments, d.storageLocation, d.dewarStatus, d.isStorageDewar, d.barCode, d.firstExperimentId, - d.type, d.facilityCode, d.weight, d.deliveryAgent_barcode; + dr.type, d.facilityCode, d.weight, d.deliveryAgent_barcode; ELSE SELECT d.dewarId "id", d.shippingId "shippingId", d.code "name", d.comments "comments", d.storageLocation "storageLocation", d.dewarStatus "status", d.isStorageDewar "isStorageDewar", d.barCode "barCode", d.firstExperimentId "firstSessionId", - d.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" + dr.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" FROM Dewar d + LEFT JOIN DewarRegistry dr ON dr.facilityCode = d.facilityCode INNER JOIN Shipping s ON s.shippingId = d.shippingId - INNER JOIN Proposal p ON p.proposalId = s.proposalId + INNER JOIN Proposal p ON p.proposalId = s.proposalId WHERE p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber; END IF; diff --git a/schemas/ispyb/stored_programs/sp_upsert_dewar_v3.sql b/schemas/ispyb/stored_programs/sp_upsert_dewar_v3.sql new file mode 100644 index 00000000..f84bda34 --- /dev/null +++ b/schemas/ispyb/stored_programs/sp_upsert_dewar_v3.sql @@ -0,0 +1,100 @@ +-- Note: upsert_dewar_v3 is the same as upsert_dewar_v2 except it doesn't set the deprecated type column +-- Test: +-- SET @id = NULL; +-- CALL upsert_dewar_v3(@id, 'boaty', 6988, 'boatys dewar', NULL, '1', 'at facility', 0, 'DLS-MX-00101', NULL, 0, 0, NULL, NULL, 'DLS-MX-00101', 5, NULL); +-- + +DELIMITER ;; + +CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `upsert_dewar_v3`( + + INOUT p_id int(10) unsigned, + p_authLogin varchar(45), + p_shippingId int(10) unsigned, + p_name varchar(45), + p_comments tinytext, + p_storageLocation varchar(45), + p_status varchar(45), + p_isStorageDewar tinyint(1), + p_barcode varchar(45), + p_firstSessionId int(10) unsigned, + p_customsValue int(11) unsigned, + p_transportValue int(11) unsigned, + p_trackingNumberToSynchrotron varchar(30), + p_trackingNumberFromSynchrotron varchar(30), + p_facilityCode varchar(20), + p_weight float, + p_deliveryAgentBarcode varchar(30) + ) + MODIFIES SQL DATA + COMMENT 'Inserts or updates info about a dewar/parcel (p_id).\nMandatory columns:\nFor insert: none\nFor update: p_id \nReturns: Record ID in p_id.' +BEGIN + DECLARE row_storageLocation varchar(45) DEFAULT NULL; + DECLARE row_dewarStatus varchar(45) DEFAULT NULL; + DECLARE row_count int unsigned DEFAULT 0; + + IF p_storageLocation IS NULL THEN + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_storageLocation is NULL'; + END IF; + + IF p_authLogin IS NOT NULL AND p_shippingId IS NOT NULL THEN + + -- Authorise only if the person (p_authLogin) is a member of a session on the proposal of the shipping that the dewar belongs to. + -- If the dewar doesn't have a shipping this will fail. + SELECT count(*) INTO row_count + FROM Shipping s + INNER JOIN BLSession bs ON bs.proposalId = s.proposalId + INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId + INNER JOIN Person p ON p.personId = shp.personId + WHERE p.login = p_authLogin AND s.shippingId = p_shippingId; + + IF row_count = 0 THEN + SIGNAL SQLSTATE '02000' + SET MYSQL_ERRNO=1643, MESSAGE_TEXT = 'Dewar not in a shipping belonging to one of the p_authLogin Person sessions'; + END IF; + END IF; + + IF p_id IS NULL THEN + INSERT INTO Dewar(dewarId,shippingId,code,comments,storageLocation,dewarStatus,isStorageDewar,barCode,firstExperimentId,customsValue,transportValue, + trackingNumberToSynchrotron,trackingNumberFromSynchrotron,FACILITYCODE,weight,deliveryAgent_barcode) + VALUES (p_id, p_shippingId, p_name, p_comments, p_storageLocation, p_status, p_isStorageDewar, p_barcode, p_firstSessionId, p_customsValue, p_transportValue, + p_trackingNumberToSynchrotron, p_trackingNumberFromSynchrotron, p_facilityCode, p_weight, p_deliveryAgentBarcode); + SET p_id = LAST_INSERT_ID(); + ELSE + + SELECT storageLocation, dewarStatus INTO row_storageLocation, row_dewarStatus FROM Dewar WHERE dewarId = p_id; + + UPDATE Dewar + SET shippingId = IFNULL(p_shippingId, shippingId), + code = IFNULL(p_name, code), + comments = IFNULL(p_comments, comments), + storageLocation = IFNULL(p_storageLocation, storageLocation), + dewarStatus = IFNULL(p_status, dewarStatus), + isStorageDewar = IFNULL(p_isStorageDewar, isStorageDewar), + barCode = IFNULL(p_barcode, barCode), + firstExperimentId = IFNULL(p_firstSessionId, firstExperimentId), + customsValue = IFNULL(p_customsValue, customsValue), + transportValue = IFNULL(p_transportValue, transportValue), + trackingNumberToSynchrotron = IFNULL(p_trackingNumberToSynchrotron, trackingNumberToSynchrotron), + trackingNumberFromSynchrotron = IFNULL(p_trackingNumberFromSynchrotron, trackingNumberFromSynchrotron), + FACILITYCODE = IFNULL(p_facilityCode, FACILITYCODE), + weight = IFNULL(p_weight, weight), + deliveryAgent_barcode = IFNULL(p_deliveryAgentBarcode, deliveryAgent_barcode) + WHERE dewarId = p_id; + + -- If a dewar is moved or the status has changed then ... + IF row_storageLocation <> p_storageLocation OR row_dewarStatus <> p_status THEN + INSERT INTO DewarTransportHistory (dewarId, dewarStatus, storageLocation, arrivalDate) + VALUES (p_id, p_status, p_storageLocation, NOW()); + END IF; + + -- If a dewar is moved then ... + IF row_storageLocation <> p_storageLocation THEN + -- any pucks within the dewar should have sampleChangerLocation set to blank and the containerStatus field set to "at facility" + UPDATE Container + SET sampleChangerLocation = '', containerStatus = 'at facility' + WHERE dewarId = p_id; + END IF; + END IF; +END;; +DELIMITER ; diff --git a/schemas/ispyb/updates/2025_06_02_DewarRegistry_type.sql b/schemas/ispyb/updates/2025_06_02_DewarRegistry_type.sql new file mode 100644 index 00000000..96f06150 --- /dev/null +++ b/schemas/ispyb/updates/2025_06_02_DewarRegistry_type.sql @@ -0,0 +1,6 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_06_02_DewarRegistry_type.sql', 'ONGOING'); + +ALTER TABLE DewarRegistry + ADD `type` enum('Dewar','Toolbox','Thermal Shipper') NOT NULL DEFAULT 'Dewar'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_06_02_DewarRegistry_type.sql'; From 966fd1c0ce4c046e683292d5354933cff244bb79 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Mon, 23 Jun 2025 16:28:41 +0100 Subject: [PATCH 51/80] Grant permissions on BLSamplePosition to ispyb-web (#284) --- grants/ispyb_web.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_web.sql b/grants/ispyb_web.sql index 9e1e32ea..ea6b81e3 100644 --- a/grants/ispyb_web.sql +++ b/grants/ispyb_web.sql @@ -105,6 +105,7 @@ GRANT INSERT, UPDATE, DELETE ON ConcentrationType TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON BLSampleImageScore TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON BLSampleImage TO 'ispyb_web'; +GRANT SELECT, INSERT, UPDATE, DELETE ON BLSamplePosition TO 'ispyb_web'; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleImageMeasurement TO 'ispyb_web'; GRANT SELECT, INSERT, UPDATE, DELETE ON SW_onceToken TO 'ispyb_web'; From 52111de8b6030ea40663e1f86ff98c57dfd9e4d7 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Fri, 27 Jun 2025 09:31:28 +0100 Subject: [PATCH 52/80] Add new ContainerType 'Cryo-EM Puck' (#285) --- .../updates/2025_06_26_ContainerType_cryoem_puck.sql | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 schemas/ispyb/updates/2025_06_26_ContainerType_cryoem_puck.sql diff --git a/schemas/ispyb/updates/2025_06_26_ContainerType_cryoem_puck.sql b/schemas/ispyb/updates/2025_06_26_ContainerType_cryoem_puck.sql new file mode 100644 index 00000000..12b18d80 --- /dev/null +++ b/schemas/ispyb/updates/2025_06_26_ContainerType_cryoem_puck.sql @@ -0,0 +1,9 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_06_26_ContainerType_cryoem_puck.sql', 'ONGOING'); + +INSERT INTO ContainerType ( + containerTypeId, name, proposalType, active, capacity +) VALUES ( + 38, 'Cryo-EM Puck', 'mx', 1, 12 +); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_06_26_ContainerType_cryoem_puck.sql'; From 7344af7ab77ffb63e2cb0ce1d14babd0e43240f3 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Fri, 27 Jun 2025 14:01:14 +0100 Subject: [PATCH 53/80] Add pixel location columns to tomogram table (#286) --- schemas/ispyb/updates/2025_06_27_Tomogram_pixelLocation.sql | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 schemas/ispyb/updates/2025_06_27_Tomogram_pixelLocation.sql diff --git a/schemas/ispyb/updates/2025_06_27_Tomogram_pixelLocation.sql b/schemas/ispyb/updates/2025_06_27_Tomogram_pixelLocation.sql new file mode 100644 index 00000000..93bd724b --- /dev/null +++ b/schemas/ispyb/updates/2025_06_27_Tomogram_pixelLocation.sql @@ -0,0 +1,6 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_06_27_Tomogram_pixelLocation.sql', 'ONGOING'); + +ALTER TABLE ParticleClassification ADD pixelLocationX int COMMENT 'pixel location of tomogram centre on search map image (x)', ALGORITHM=INSTANT; +ALTER TABLE ParticleClassification ADD pixelLocationY int COMMENT 'pixel location of tomogram centre on search map image (y)', ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_06_27_Tomogram_pixelLocation.sql'; From 36db516e9a0033d243b48efb6cde35231e364ada Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Fri, 27 Jun 2025 17:35:45 +0100 Subject: [PATCH 54/80] Refresh schema files and fix minor bug in grants file (#288) * Use 'if not exists' when creating role * Refresh schema files --- grants/ispyb_expeye.sql | 2 +- schemas/ispyb/lookups.sql | 11 +++- schemas/ispyb/routines.sql | 118 +++++++++++++++++++++++++++++++++++-- schemas/ispyb/tables.sql | 49 ++++++++++++++- 4 files changed, 170 insertions(+), 10 deletions(-) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 0bebdb3a..359d91f5 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -8,7 +8,7 @@ CREATE ROLE IF NOT EXISTS ispyb_expeye_core_role; GRANT ispyb_propagation TO ispyb_expeye_core_role; -CREATE ROLE ispyb_expeye_acquisition_role; +CREATE ROLE IF NOT EXISTS ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON Proposal TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSession TO ispyb_expeye_acquisition_role; diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index ab7080fd..48671a59 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -287,7 +287,13 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (315,'2025_05_01_BLSamplePosition.sql','DONE','2025-05-09 15:21:06'), (316,'2025_05_01_XrayCentringResult_fk_blSampleId.sql','DONE','2025-05-09 15:21:06'), (317,'2025_05_02_BLSamplePosition_rename_column.sql','DONE','2025-05-09 15:21:06'), -(318,'2025_05_12_AdminVar_bump_version.sql','DONE','2025-05-09 15:21:06'); +(318,'2025_05_12_AdminVar_bump_version.sql','DONE','2025-05-09 15:21:06'), +(319,'2025_05_14_BLSamplePosition_recordTimeStamp_default.sql','DONE','2025-06-27 16:04:05'), +(320,'2025_05_23_Ligand_and_junction_tables.sql','DONE','2025-06-27 16:04:05'), +(321,'2025_05_28_BLSession_icatId.sql','DONE','2025-06-27 16:04:05'), +(322,'2025_06_02_DewarRegistry_type.sql','DONE','2025-06-27 16:04:05'), +(323,'2025_06_26_ContainerType_cryoem_puck.sql','DONE','2025-06-27 16:04:05'), +(324,'2025_06_27_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:04:05'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; @@ -358,7 +364,8 @@ INSERT INTO `ContainerType` (`containerTypeId`, `name`, `proposalType`, `active` (34,'I22_Grid_81','saxs',1,81,9,1,1,1,1,0,0,-1), (35,'I22_Capillary_Rack_25','saxs',1,25,25,1,1,1,1,0,0,-1), (36,'VMXm-Cartridge','mx',1,5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(37,'VMXm-GridBox','mx',1,4,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); +(37,'VMXm-GridBox','mx',1,4,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), +(38,'Cryo-EM Puck','mx',1,12,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `ContainerType` ENABLE KEYS */; /*!40000 ALTER TABLE `ExperimentType` DISABLE KEYS */; diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql index 335dede8..00420fa4 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -4190,25 +4190,27 @@ BEGIN SELECT d.dewarId "id", d.shippingId "shippingId", d.code "name", d.comments "comments", d.storageLocation "storageLocation", d.dewarStatus "status", d.isStorageDewar "isStorageDewar", d.barCode "barCode", d.firstExperimentId "firstSessionId", - d.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" + dr.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" FROM Dewar d + LEFT JOIN DewarRegistry dr ON dr.facilityCode = d.facilityCode INNER JOIN Shipping s ON s.shippingId = d.shippingId - INNER JOIN Proposal p ON p.proposalId = s.proposalId + INNER JOIN Proposal p ON p.proposalId = s.proposalId INNER JOIN BLSession bs ON bs.proposalId = s.proposalId INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId INNER JOIN Person per ON per.personId = shp.personId WHERE per.login = p_authLogin AND p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber GROUP BY d.dewarId, d.shippingId, d.code, d.comments, d.storageLocation, d.dewarStatus, d.isStorageDewar, d.barCode, d.firstExperimentId, - d.type, d.facilityCode, d.weight, d.deliveryAgent_barcode; + dr.type, d.facilityCode, d.weight, d.deliveryAgent_barcode; ELSE SELECT d.dewarId "id", d.shippingId "shippingId", d.code "name", d.comments "comments", d.storageLocation "storageLocation", d.dewarStatus "status", d.isStorageDewar "isStorageDewar", d.barCode "barCode", d.firstExperimentId "firstSessionId", - d.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" + dr.type "type", d.facilityCode "facilityCode", d.weight "weight", d.deliveryAgent_barcode "deliveryAgentBarcode" FROM Dewar d + LEFT JOIN DewarRegistry dr ON dr.facilityCode = d.facilityCode INNER JOIN Shipping s ON s.shippingId = d.shippingId - INNER JOIN Proposal p ON p.proposalId = s.proposalId + INNER JOIN Proposal p ON p.proposalId = s.proposalId WHERE p.proposalCode = p_proposalCode AND p.proposalNumber = p_proposalNumber; END IF; @@ -9996,6 +9998,112 @@ DELIMITER ; /*!50003 SET character_set_results = @saved_cs_results */ ; /*!50003 SET collation_connection = @saved_col_connection */ ; /*!50003 SET @saved_sql_mode = @@sql_mode */ ; +/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ; +/*!50003 DROP PROCEDURE IF EXISTS `upsert_dewar_v3` */; +/*!50003 SET @saved_cs_client = @@character_set_client */ ; +/*!50003 SET @saved_cs_results = @@character_set_results */ ; +/*!50003 SET @saved_col_connection = @@collation_connection */ ; +/*!50003 SET character_set_client = utf8mb3 */ ; +/*!50003 SET character_set_results = utf8mb3 */ ; +/*!50003 SET collation_connection = utf8mb3_general_ci */ ; +DELIMITER ;; +CREATE PROCEDURE `upsert_dewar_v3`( + + INOUT p_id int(10) unsigned, + p_authLogin varchar(45), + p_shippingId int(10) unsigned, + p_name varchar(45), + p_comments tinytext, + p_storageLocation varchar(45), + p_status varchar(45), + p_isStorageDewar tinyint(1), + p_barcode varchar(45), + p_firstSessionId int(10) unsigned, + p_customsValue int(11) unsigned, + p_transportValue int(11) unsigned, + p_trackingNumberToSynchrotron varchar(30), + p_trackingNumberFromSynchrotron varchar(30), + p_facilityCode varchar(20), + p_weight float, + p_deliveryAgentBarcode varchar(30) + ) + MODIFIES SQL DATA + COMMENT 'Inserts or updates info about a dewar/parcel (p_id).\nMandatory columns:\nFor insert: none\nFor update: p_id \nReturns: Record ID in p_id.' +BEGIN + DECLARE row_storageLocation varchar(45) DEFAULT NULL; + DECLARE row_dewarStatus varchar(45) DEFAULT NULL; + DECLARE row_count int unsigned DEFAULT 0; + + IF p_storageLocation IS NULL THEN + SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory argument p_storageLocation is NULL'; + END IF; + + IF p_authLogin IS NOT NULL AND p_shippingId IS NOT NULL THEN + + + + SELECT count(*) INTO row_count + FROM Shipping s + INNER JOIN BLSession bs ON bs.proposalId = s.proposalId + INNER JOIN Session_has_Person shp ON bs.sessionId = shp.sessionId + INNER JOIN Person p ON p.personId = shp.personId + WHERE p.login = p_authLogin AND s.shippingId = p_shippingId; + + IF row_count = 0 THEN + SIGNAL SQLSTATE '02000' + SET MYSQL_ERRNO=1643, MESSAGE_TEXT = 'Dewar not in a shipping belonging to one of the p_authLogin Person sessions'; + END IF; + END IF; + + IF p_id IS NULL THEN + INSERT INTO Dewar(dewarId,shippingId,code,comments,storageLocation,dewarStatus,isStorageDewar,barCode,firstExperimentId,customsValue,transportValue, + trackingNumberToSynchrotron,trackingNumberFromSynchrotron,FACILITYCODE,weight,deliveryAgent_barcode) + VALUES (p_id, p_shippingId, p_name, p_comments, p_storageLocation, p_status, p_isStorageDewar, p_barcode, p_firstSessionId, p_customsValue, p_transportValue, + p_trackingNumberToSynchrotron, p_trackingNumberFromSynchrotron, p_facilityCode, p_weight, p_deliveryAgentBarcode); + SET p_id = LAST_INSERT_ID(); + ELSE + + SELECT storageLocation, dewarStatus INTO row_storageLocation, row_dewarStatus FROM Dewar WHERE dewarId = p_id; + + UPDATE Dewar + SET shippingId = IFNULL(p_shippingId, shippingId), + code = IFNULL(p_name, code), + comments = IFNULL(p_comments, comments), + storageLocation = IFNULL(p_storageLocation, storageLocation), + dewarStatus = IFNULL(p_status, dewarStatus), + isStorageDewar = IFNULL(p_isStorageDewar, isStorageDewar), + barCode = IFNULL(p_barcode, barCode), + firstExperimentId = IFNULL(p_firstSessionId, firstExperimentId), + customsValue = IFNULL(p_customsValue, customsValue), + transportValue = IFNULL(p_transportValue, transportValue), + trackingNumberToSynchrotron = IFNULL(p_trackingNumberToSynchrotron, trackingNumberToSynchrotron), + trackingNumberFromSynchrotron = IFNULL(p_trackingNumberFromSynchrotron, trackingNumberFromSynchrotron), + FACILITYCODE = IFNULL(p_facilityCode, FACILITYCODE), + weight = IFNULL(p_weight, weight), + deliveryAgent_barcode = IFNULL(p_deliveryAgentBarcode, deliveryAgent_barcode) + WHERE dewarId = p_id; + + + IF row_storageLocation <> p_storageLocation OR row_dewarStatus <> p_status THEN + INSERT INTO DewarTransportHistory (dewarId, dewarStatus, storageLocation, arrivalDate) + VALUES (p_id, p_status, p_storageLocation, NOW()); + END IF; + + + IF row_storageLocation <> p_storageLocation THEN + + UPDATE Container + SET sampleChangerLocation = '', containerStatus = 'at facility' + WHERE dewarId = p_id; + END IF; + END IF; +END ;; +DELIMITER ; +/*!50003 SET sql_mode = @saved_sql_mode */ ; +/*!50003 SET character_set_client = @saved_cs_client */ ; +/*!50003 SET character_set_results = @saved_cs_results */ ; +/*!50003 SET collation_connection = @saved_col_connection */ ; +/*!50003 SET @saved_sql_mode = @@sql_mode */ ; /*!50003 SET sql_mode = '' */ ; /*!50003 DROP PROCEDURE IF EXISTS `upsert_energy_scan` */; /*!50003 SET @saved_cs_client = @@character_set_client */ ; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index 0b8b6ffc..ac9021af 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -614,12 +614,12 @@ CREATE TABLE `BLSamplePosition` ( `posX` double DEFAULT NULL, `posY` double DEFAULT NULL, `posZ` double DEFAULT NULL, - `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', + `recordTimeStamp` datetime DEFAULT current_timestamp(), `positionType` enum('dispensing') DEFAULT NULL COMMENT 'Type of marked position (e.g.: dispensing location)', PRIMARY KEY (`blSamplePositionId`), KEY `BLSamplePosition_fk_blSampleId` (`blSampleId`), CONSTRAINT `BLSamplePosition_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -672,6 +672,18 @@ CREATE TABLE `BLSample_has_EnergyScan` ( CONSTRAINT `BLSample_has_EnergyScan_ibfk_2` FOREIGN KEY (`energyScanId`) REFERENCES `EnergyScan` (`energyScanId`) ON DELETE CASCADE ON UPDATE CASCADE ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; +DROP TABLE IF EXISTS `BLSample_has_Ligand`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8mb4 */; +CREATE TABLE `BLSample_has_Ligand` ( + `blSampleId` int(10) unsigned NOT NULL, + `ligandId` int(11) unsigned NOT NULL, + PRIMARY KEY (`blSampleId`,`ligandId`), + KEY `BLSample_has_Ligand_fk2` (`ligandId`), + CONSTRAINT `BLSample_has_Ligand_fk1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE CASCADE ON UPDATE CASCADE, + CONSTRAINT `BLSample_has_Ligand_fk2` FOREIGN KEY (`ligandId`) REFERENCES `Ligand` (`ligandId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Junction table for BLSample and Ligand'; +/*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; /*!40101 SET character_set_client = utf8mb4 */; @@ -709,6 +721,7 @@ CREATE TABLE `BLSession` ( `archived` tinyint(1) DEFAULT 0 COMMENT 'The data for the session is archived and no longer available on disk', `riskRating` enum('Low','Medium','High','Not Permitted') DEFAULT NULL COMMENT 'ERA in user admin system', `purgedProcessedData` tinyint(1) DEFAULT 0 COMMENT 'Flag to indicate whether the processed folder in the associated visit directory has been purged', + `icatId` int(11) unsigned DEFAULT NULL COMMENT 'The internal ICAT ID for this BLSession', PRIMARY KEY (`sessionId`), UNIQUE KEY `proposalId` (`proposalId`,`visit_number`), KEY `Session_FKIndex2` (`beamLineSetupId`), @@ -1677,6 +1690,7 @@ CREATE TABLE `DewarRegistry` ( `purchaseDate` datetime DEFAULT NULL, `bltimestamp` datetime NOT NULL DEFAULT current_timestamp(), `manufacturerSerialNumber` varchar(15) DEFAULT NULL COMMENT 'Dewar serial number as given by manufacturer. Used to be typically 5 or 6 digits, more likely to be 11 alphanumeric chars in future', + `type` enum('Dewar','Toolbox','Thermal Shipper') NOT NULL DEFAULT 'Dewar', PRIMARY KEY (`dewarRegistryId`), UNIQUE KEY `facilityCode` (`facilityCode`), KEY `DewarRegistry_ibfk_1` (`proposalId`), @@ -2195,6 +2209,35 @@ CREATE TABLE `Laboratory` ( PRIMARY KEY (`laboratoryId`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1; /*!40101 SET character_set_client = @saved_cs_client */; +DROP TABLE IF EXISTS `Ligand`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8mb4 */; +CREATE TABLE `Ligand` ( + `ligandId` int(11) unsigned NOT NULL AUTO_INCREMENT, + `proposalId` int(10) unsigned NOT NULL COMMENT 'References Proposal table', + `name` varchar(30) NOT NULL COMMENT 'Ligand name', + `SMILES` varchar(400) DEFAULT NULL COMMENT 'Chemical structure', + `libraryName` varchar(30) DEFAULT NULL COMMENT 'Name of ligand library, to preserve provenance', + `libraryBatchNumber` varchar(30) DEFAULT NULL COMMENT 'Batch number of library, to preserve provenance', + `plateBarcode` varchar(30) DEFAULT NULL COMMENT 'Specific barcode of the plate it came from, to preserve provenance', + `sourceWell` varchar(30) DEFAULT NULL COMMENT 'Location within that plate, to preserve provenance', + PRIMARY KEY (`ligandId`), + KEY `Ligand_fk_proposalId` (`proposalId`), + CONSTRAINT `Ligand_fk_proposalId` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Ligands in biochemistry are substances that bind to biomolecules'; +/*!40101 SET character_set_client = @saved_cs_client */; +DROP TABLE IF EXISTS `Ligand_has_PDB`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8mb4 */; +CREATE TABLE `Ligand_has_PDB` ( + `ligandId` int(11) unsigned NOT NULL, + `pdbId` int(11) unsigned NOT NULL, + PRIMARY KEY (`ligandId`,`pdbId`), + KEY `Ligand_Has_PDB_fk2` (`pdbId`), + CONSTRAINT `Ligand_Has_PDB_fk1` FOREIGN KEY (`ligandId`) REFERENCES `Ligand` (`ligandId`) ON DELETE CASCADE ON UPDATE CASCADE, + CONSTRAINT `Ligand_Has_PDB_fk2` FOREIGN KEY (`pdbId`) REFERENCES `PDB` (`pdbId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Junction table for Ligand and PDB'; +/*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MXMRRun`; /*!40101 SET @saved_cs_client = @@character_set_client */; /*!40101 SET character_set_client = utf8mb4 */; @@ -2414,6 +2457,8 @@ CREATE TABLE `ParticleClassification` ( `bFactorFitQuadratic` float DEFAULT NULL COMMENT 'Quadratic coefficient of quadratic fit to refinement resolution against the logarithm of the number of particles', `angularEfficiency` double DEFAULT NULL COMMENT 'Variation in resolution across different angles, 1-2sig/mean', `suggestedTilt` double DEFAULT NULL COMMENT 'Suggested stage tilt angle to improve angular efficiency. Unit: degrees', + `pixelLocationX` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (x)', + `pixelLocationY` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (y)', PRIMARY KEY (`particleClassificationId`), KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`), CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE From b2c809be92b691a43c17b39c61fe0af009daa3f6 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Fri, 27 Jun 2025 17:38:37 +0100 Subject: [PATCH 55/80] Tomogram pixel location (#287) Undo columns in ParticleClassification, create them in Tomogram --- ...ParticleClassification_set_Tomogram_pixelLocation.sql | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 schemas/ispyb/updates/2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql diff --git a/schemas/ispyb/updates/2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql b/schemas/ispyb/updates/2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql new file mode 100644 index 00000000..f4cdfec3 --- /dev/null +++ b/schemas/ispyb/updates/2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql @@ -0,0 +1,9 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql', 'ONGOING'); + +ALTER TABLE ParticleClassification DROP COLUMN IF EXISTS pixelLocationX; +ALTER TABLE ParticleClassification DROP COLUMN IF EXISTS pixelLocationY; + +ALTER TABLE Tomogram ADD pixelLocationX int COMMENT 'pixel location of tomogram centre on search map image (x)', ALGORITHM=INSTANT; +ALTER TABLE Tomogram ADD pixelLocationY int COMMENT 'pixel location of tomogram centre on search map image (y)', ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql'; From 438defe3214e815f084044415f367773d0c3df57 Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Fri, 27 Jun 2025 17:57:08 +0100 Subject: [PATCH 56/80] Refresh schema files tables.sql and lookups.sql --- schemas/ispyb/lookups.sql | 3 ++- schemas/ispyb/tables.sql | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 48671a59..22c8e0ad 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -293,7 +293,8 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (321,'2025_05_28_BLSession_icatId.sql','DONE','2025-06-27 16:04:05'), (322,'2025_06_02_DewarRegistry_type.sql','DONE','2025-06-27 16:04:05'), (323,'2025_06_26_ContainerType_cryoem_puck.sql','DONE','2025-06-27 16:04:05'), -(324,'2025_06_27_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:04:05'); +(324,'2025_06_27_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:04:05'), +(325,'2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:40:00'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index ac9021af..0a4575ac 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -2457,8 +2457,6 @@ CREATE TABLE `ParticleClassification` ( `bFactorFitQuadratic` float DEFAULT NULL COMMENT 'Quadratic coefficient of quadratic fit to refinement resolution against the logarithm of the number of particles', `angularEfficiency` double DEFAULT NULL COMMENT 'Variation in resolution across different angles, 1-2sig/mean', `suggestedTilt` double DEFAULT NULL COMMENT 'Suggested stage tilt angle to improve angular efficiency. Unit: degrees', - `pixelLocationX` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (x)', - `pixelLocationY` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (y)', PRIMARY KEY (`particleClassificationId`), KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`), CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE @@ -3635,6 +3633,8 @@ CREATE TABLE `Tomogram` ( `recordTimeStamp` datetime DEFAULT current_timestamp() COMMENT 'Creation or last update date/time', `globalAlignmentQuality` float DEFAULT NULL COMMENT 'Quality of fit metric for the alignment of the tilt series corresponding to this tomogram', `gridSquareId` int(11) unsigned DEFAULT NULL COMMENT 'FK, references medium mag map in GridSquare', + `pixelLocationX` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (x)', + `pixelLocationY` int(11) DEFAULT NULL COMMENT 'pixel location of tomogram centre on search map image (y)', PRIMARY KEY (`tomogramId`), KEY `Tomogram_fk_dataCollectionId` (`dataCollectionId`), KEY `Tomogram_fk_autoProcProgramId` (`autoProcProgramId`), From c7b059536444486d9044c9cdc0f6ae505e35f763 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Tue, 1 Jul 2025 10:51:35 +0100 Subject: [PATCH 57/80] Add extra grants for ispyb_processing (#289) --- grants/ispyb_processing.sql | 2 ++ 1 file changed, 2 insertions(+) diff --git a/grants/ispyb_processing.sql b/grants/ispyb_processing.sql index 918ae0ac..03f43003 100644 --- a/grants/ispyb_processing.sql +++ b/grants/ispyb_processing.sql @@ -15,6 +15,7 @@ GRANT SELECT,INSERT,UPDATE ON BLSampleImageAnalysis TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON BLSampleImage_has_AutoScoreClass TO 'ispyb_processing'; GRANT SELECT,INSERT ON PDB TO 'ispyb_processing'; GRANT SELECT,INSERT ON Protein_has_PDB TO 'ispyb_processing'; +GRANT SELECT,INSERT,UPDATE ON Container TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON AutoProcProgram TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON AutoProcProgramAttachment TO 'ispyb_processing'; @@ -31,6 +32,7 @@ GRANT SELECT,INSERT,UPDATE ON RelativeIceThickness TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON CTF TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON Movie TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON BFactorFit TO 'ispyb_processing'; +GRANT SELECT,INSERT,UPDATE ON DataCollectionFileAttachment TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON Tomogram TO 'ispyb_processing'; GRANT SELECT,INSERT,UPDATE ON ProcessedTomogram TO 'ispyb_processing'; From 64b82d26a36ee261262b3cd9500ee5a218bdd7de Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 2 Jul 2025 09:26:14 +0100 Subject: [PATCH 58/80] Grant ligand-related permissions to ispyb_web (#290) Grant ligand-related permissions to ispyb_web --- grants/ispyb_web.sql | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/grants/ispyb_web.sql b/grants/ispyb_web.sql index ea6b81e3..45321594 100644 --- a/grants/ispyb_web.sql +++ b/grants/ispyb_web.sql @@ -56,6 +56,10 @@ GRANT INSERT, UPDATE, DELETE ON Project_has_Shipping TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON Project_has_User TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON Project_has_XFEFSpectrum TO 'ispyb_web'; +GRANT INSERT, UPDATE ON Ligand TO 'ispyb_web'; +GRANT INSERT, UPDATE ON Ligand_has_PDB TO 'ispyb_web'; +GRANT INSERT, UPDATE ON BLSample_has_Ligand TO 'ispyb_web'; + GRANT INSERT, UPDATE, DELETE ON UserGroup_has_Permission TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON Permission TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON UserGroup_has_Person TO 'ispyb_web'; From 947a0ee738975dab5d0d21b35d21bf4035859dae Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Mon, 7 Jul 2025 11:28:06 +0100 Subject: [PATCH 59/80] Allow ispyb_web to remove ligand references (#291) --- grants/ispyb_web.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/grants/ispyb_web.sql b/grants/ispyb_web.sql index 45321594..1c8290cb 100644 --- a/grants/ispyb_web.sql +++ b/grants/ispyb_web.sql @@ -57,8 +57,8 @@ GRANT INSERT, UPDATE, DELETE ON Project_has_User TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON Project_has_XFEFSpectrum TO 'ispyb_web'; GRANT INSERT, UPDATE ON Ligand TO 'ispyb_web'; -GRANT INSERT, UPDATE ON Ligand_has_PDB TO 'ispyb_web'; -GRANT INSERT, UPDATE ON BLSample_has_Ligand TO 'ispyb_web'; +GRANT INSERT, UPDATE, DELETE ON Ligand_has_PDB TO 'ispyb_web'; +GRANT INSERT, UPDATE, DELETE ON BLSample_has_Ligand TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON UserGroup_has_Permission TO 'ispyb_web'; GRANT INSERT, UPDATE, DELETE ON Permission TO 'ispyb_web'; From d2b518e6a90a08ca2b9d20447234bf08e64bba41 Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Thu, 17 Jul 2025 13:15:03 +0100 Subject: [PATCH 60/80] Preparations for release 4.8.0 --- schemas/ispyb/data.sql | 38 ++++++++++++------- .../2025_07_17_AdminVar_bump_version.sql | 5 +++ 2 files changed, 30 insertions(+), 13 deletions(-) create mode 100644 schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql diff --git a/schemas/ispyb/data.sql b/schemas/ispyb/data.sql index 5e2a6f32..9ce10b65 100644 --- a/schemas/ispyb/data.sql +++ b/schemas/ispyb/data.sql @@ -256,6 +256,9 @@ INSERT INTO `BLSampleImageScore` (`blSampleImageScoreId`, `name`, `score`, `colo /*!40000 ALTER TABLE `BLSampleImage_has_Positioner` DISABLE KEYS */; /*!40000 ALTER TABLE `BLSampleImage_has_Positioner` ENABLE KEYS */; +/*!40000 ALTER TABLE `BLSamplePosition` DISABLE KEYS */; +/*!40000 ALTER TABLE `BLSamplePosition` ENABLE KEYS */; + /*!40000 ALTER TABLE `BLSampleType_has_Component` DISABLE KEYS */; /*!40000 ALTER TABLE `BLSampleType_has_Component` ENABLE KEYS */; @@ -267,16 +270,19 @@ INSERT INTO `BLSample_has_DataCollectionPlan` (`blSampleId`, `dataCollectionPlan /*!40000 ALTER TABLE `BLSample_has_EnergyScan` DISABLE KEYS */; /*!40000 ALTER TABLE `BLSample_has_EnergyScan` ENABLE KEYS */; +/*!40000 ALTER TABLE `BLSample_has_Ligand` DISABLE KEYS */; +/*!40000 ALTER TABLE `BLSample_has_Ligand` ENABLE KEYS */; + /*!40000 ALTER TABLE `BLSample_has_Positioner` DISABLE KEYS */; /*!40000 ALTER TABLE `BLSample_has_Positioner` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSession` DISABLE KEYS */; -INSERT INTO `BLSession` (`sessionId`, `beamLineSetupId`, `proposalId`, `beamCalendarId`, `startDate`, `endDate`, `beamLineName`, `scheduled`, `nbShifts`, `comments`, `beamLineOperator`, `bltimeStamp`, `visit_number`, `usedFlag`, `lastUpdate`, `externalId`, `archived`, `riskRating`) VALUES (55167,1,37027,NULL,'2016-01-01 09:00:00','2016-01-01 17:00:00','i03',NULL,NULL,'ghfg',NULL,'2015-12-21 15:20:43',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL), -(55168,1,37027,NULL,'2016-03-11 09:00:00','2016-03-11 17:00:00','i03',NULL,NULL,'jhgjh',NULL,'2015-12-21 15:20:44',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL), -(339525,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-16 16:08:29',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL), -(339528,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:07:42',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL), -(339531,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:08:09',3,NULL,'0000-00-00 00:00:00',NULL,0,NULL), -(339535,NULL,37027,NULL,'2018-03-27 09:00:00','2018-07-27 09:00:00','i02-2',NULL,NULL,NULL,NULL,'2018-04-05 15:48:37',99,NULL,'0000-00-00 00:00:00',NULL,0,NULL); +INSERT INTO `BLSession` (`sessionId`, `beamLineSetupId`, `proposalId`, `beamCalendarId`, `startDate`, `endDate`, `beamLineName`, `scheduled`, `nbShifts`, `comments`, `beamLineOperator`, `bltimeStamp`, `visit_number`, `usedFlag`, `lastUpdate`, `externalId`, `archived`, `riskRating`, `purgedProcessedData`, `icatId`) VALUES (55167,1,37027,NULL,'2016-01-01 09:00:00','2016-01-01 17:00:00','i03',NULL,NULL,'ghfg',NULL,'2015-12-21 15:20:43',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), +(55168,1,37027,NULL,'2016-03-11 09:00:00','2016-03-11 17:00:00','i03',NULL,NULL,'jhgjh',NULL,'2015-12-21 15:20:44',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), +(339525,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-16 16:08:29',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), +(339528,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:07:42',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), +(339531,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:08:09',3,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), +(339535,NULL,37027,NULL,'2018-03-27 09:00:00','2018-07-27 09:00:00','i02-2',NULL,NULL,NULL,NULL,'2018-04-05 15:48:37',99,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL); /*!40000 ALTER TABLE `BLSession` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSession_has_SCPosition` DISABLE KEYS */; @@ -435,13 +441,13 @@ INSERT INTO `DataCollectionPlan_has_Detector` (`dataCollectionPlanHasDetectorId` /*!40000 ALTER TABLE `DataCollectionPlan_has_Detector` ENABLE KEYS */; /*!40000 ALTER TABLE `Dewar` DISABLE KEYS */; -INSERT INTO `Dewar` (`dewarId`, `shippingId`, `code`, `comments`, `storageLocation`, `dewarStatus`, `bltimeStamp`, `isStorageDewar`, `barCode`, `firstExperimentId`, `customsValue`, `transportValue`, `trackingNumberToSynchrotron`, `trackingNumberFromSynchrotron`, `type`, `facilityCode`, `weight`, `deliveryAgent_barcode`, `extra`, `source`, `externalShippingIdFromSynchrotron`) VALUES (573,474,'Dewar-1-cm0001-1',NULL,NULL,'processing',NULL,0,'dewar-cm0001-1-0000001',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL), -(576,474,'Dewar-2-cm0001-1',NULL,NULL,'at DLS',NULL,0,'dewar-cm0001-1-0000002',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL), -(579,477,'Dewar-3-cm0001-2',NULL,NULL,'processing',NULL,0,'dewar-cm0001-2-0000477',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL), -(582,480,'Dewar-4-cm0001-3',NULL,NULL,'processing',NULL,0,'dewar-cm0001-3-0000480',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL), -(8287,6988,'Default Dewar:cm14451-1',NULL,NULL,'processing',NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL), -(8572,7227,'cm14451-2_Dewar1',NULL,NULL,'processing','2016-02-10 13:03:07',0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL), -(8578,7231,'Dewar_1',NULL,NULL,'opened',NULL,0,'cm14451-12345',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL); +INSERT INTO `Dewar` (`dewarId`, `shippingId`, `code`, `comments`, `storageLocation`, `dewarStatus`, `bltimeStamp`, `isStorageDewar`, `barCode`, `firstExperimentId`, `customsValue`, `transportValue`, `trackingNumberToSynchrotron`, `trackingNumberFromSynchrotron`, `type`, `facilityCode`, `weight`, `deliveryAgent_barcode`, `extra`, `source`, `externalShippingIdFromSynchrotron`, `dewarRegistryId`) VALUES (573,474,'Dewar-1-cm0001-1',NULL,NULL,'processing',NULL,0,'dewar-cm0001-1-0000001',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), +(576,474,'Dewar-2-cm0001-1',NULL,NULL,'at DLS',NULL,0,'dewar-cm0001-1-0000002',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), +(579,477,'Dewar-3-cm0001-2',NULL,NULL,'processing',NULL,0,'dewar-cm0001-2-0000477',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), +(582,480,'Dewar-4-cm0001-3',NULL,NULL,'processing',NULL,0,'dewar-cm0001-3-0000480',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), +(8287,6988,'Default Dewar:cm14451-1',NULL,NULL,'processing',NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), +(8572,7227,'cm14451-2_Dewar1',NULL,NULL,'processing','2016-02-10 13:03:07',0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), +(8578,7231,'Dewar_1',NULL,NULL,'opened',NULL,0,'cm14451-12345',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL); /*!40000 ALTER TABLE `Dewar` ENABLE KEYS */; /*!40000 ALTER TABLE `DewarLocation` DISABLE KEYS */; @@ -554,6 +560,12 @@ INSERT INTO `ImageQualityIndicators` (`dataCollectionId`, `imageNumber`, `imageI /*!40000 ALTER TABLE `Laboratory` DISABLE KEYS */; /*!40000 ALTER TABLE `Laboratory` ENABLE KEYS */; +/*!40000 ALTER TABLE `Ligand` DISABLE KEYS */; +/*!40000 ALTER TABLE `Ligand` ENABLE KEYS */; + +/*!40000 ALTER TABLE `Ligand_has_PDB` DISABLE KEYS */; +/*!40000 ALTER TABLE `Ligand_has_PDB` ENABLE KEYS */; + /*!40000 ALTER TABLE `MXMRRun` DISABLE KEYS */; INSERT INTO `MXMRRun` (`mxMRRunId`, `autoProcScalingId`, `rValueStart`, `rValueEnd`, `rFreeValueStart`, `rFreeValueEnd`, `LLG`, `TFZ`, `spaceGroup`, `autoProcProgramId`) VALUES (672897,603470,0.1812,0.1682,0.1896,0.1888,NULL,NULL,NULL,56986674), (672900,603470,NULL,NULL,NULL,NULL,NULL,NULL,NULL,56986675); diff --git a/schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql new file mode 100644 index 00000000..916751db --- /dev/null +++ b/schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_17_07_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.8.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_17_07_AdminVar_bump_version.sql'; From 8e4891730c3d44a3d1efda8255c2d9e8fffba061 Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Thu, 17 Jul 2025 14:16:58 +0100 Subject: [PATCH 61/80] Include all files in released archive file --- release.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/release.sh b/release.sh index a613bc8c..a7b26d9c 100755 --- a/release.sh +++ b/release.sh @@ -40,7 +40,7 @@ fi echo "Creating archive file" mkdir -p dist -tar cvfz ${archive} build.sh grants/ispyb_*.sql schemas/ispyb/*.sql schemas/ispyb/updates/*.sql schemas/ispyb_analytics/* schemas/xchem_db/*.sql schemas/xchem_db/*.sql bin/* +tar cvfz ${archive} build.sh grants/*.sql schemas/ispyb/*.sql schemas/ispyb/updates/*.sql schemas/ispyb_analytics/* schemas/xchem_db/*.sql schemas/xchem_db/*.sql bin/* echo "Creating tag v${schema_version}" git tag -a v${schema_version} -m v${schema_version} From 55f34dc2e5ce9e84f152a74618ba7e913899f590 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 17 Jul 2025 14:35:24 +0100 Subject: [PATCH 62/80] Update HISTORY.rst --- HISTORY.rst | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/HISTORY.rst b/HISTORY.rst index 8043d616..be0fd1b9 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,20 @@ History Unreleased / master ------------------- +4.8.0 (2025-07-17) +------------------- + +New or modified tables, columns, lookup values: + +- New table ``Ligand`` +- New table ``BLSample_has_Ligand`` +- New table ``Ligand_has_PDB`` +- Add ``pixelLocationX`` and ``pixelLocationY`` columns to ``Tomogram`` table +- Add ``cryoEM`` container type to ``ContainerType`` +- Add ``type`` enum column to ``DewarRegistry`` +- Add ``icatId`` column to ``BLSession`` +- Set ``recordTimeStamp`` column in ``BLSamplePosition`` to default to current time + 4.7.0 (2025-05-12) ------------------- From 90423bb7c15c1c3f183ce9f7b3d6b2f2b73fb0dc Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Thu, 17 Jul 2025 15:06:58 +0100 Subject: [PATCH 63/80] Fix date --- schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql index 916751db..9a0ce446 100644 --- a/schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql +++ b/schemas/ispyb/updates/2025_07_17_AdminVar_bump_version.sql @@ -1,5 +1,5 @@ -INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_17_07_AdminVar_bump_version.sql', 'ONGOING'); +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_07_17_AdminVar_bump_version.sql', 'ONGOING'); UPDATE AdminVar SET `value` = '4.8.0' WHERE `name` = 'schemaVersion'; -UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_17_07_AdminVar_bump_version.sql'; +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_07_17_AdminVar_bump_version.sql'; From 68888e3445b33372e72321f96076cfb15449dc8b Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Tue, 22 Jul 2025 13:41:51 +0100 Subject: [PATCH 64/80] Update maximum string length for p_status (#292) --- .../sp_retrieve_containers_on_beamline_with_status.sql | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql b/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql index 6fc0117e..8d637bb6 100644 --- a/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql +++ b/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql @@ -1,5 +1,5 @@ DELIMITER ;; -CREATE DEFINER=`ispyb_root`@`%` PROCEDURE `retrieve_containers_on_beamline_with_status`(IN p_beamline varchar(20), IN p_status varchar(40)) +CREATE DEFINER=`ispyb_root`@`%` PROCEDURE `retrieve_containers_on_beamline_with_status`(IN p_beamline varchar(20), IN p_status varchar(45)) READS SQL DATA COMMENT 'Returns a multi-row result-set with info about when containers on beamline p_beamline last had status p_status' BEGIN From ef4ef3fdb589f006893806c1bc5deeb7f9479cb1 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Tue, 22 Jul 2025 13:55:32 +0100 Subject: [PATCH 65/80] Use CREATE OR REPLACE ... PROCEDURE syntax (#293) --- .../sp_retrieve_containers_on_beamline_with_status.sql | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql b/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql index 8d637bb6..0656bb26 100644 --- a/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql +++ b/schemas/ispyb/stored_programs/sp_retrieve_containers_on_beamline_with_status.sql @@ -1,5 +1,5 @@ DELIMITER ;; -CREATE DEFINER=`ispyb_root`@`%` PROCEDURE `retrieve_containers_on_beamline_with_status`(IN p_beamline varchar(20), IN p_status varchar(45)) +CREATE OR REPLACE DEFINER=`ispyb_root`@`%` PROCEDURE `retrieve_containers_on_beamline_with_status`(IN p_beamline varchar(20), IN p_status varchar(45)) READS SQL DATA COMMENT 'Returns a multi-row result-set with info about when containers on beamline p_beamline last had status p_status' BEGIN @@ -7,10 +7,10 @@ BEGIN SELECT c.barcode "barcode", c.sampleChangerLocation "location", max(ch.blTimeStamp) "added" FROM Container c LEFT OUTER JOIN ContainerHistory ch ON c.containerId = ch.containerId AND ch.status = p_status - WHERE c.containerStatus = p_status AND ch.beamlineName = p_beamline + WHERE c.containerStatus = p_status AND ch.beamlineName = p_beamline GROUP BY c.barcode, c.sampleChangerLocation ORDER BY ch.blTimeStamp ASC; - ELSE + ELSE SIGNAL SQLSTATE '45000' SET MYSQL_ERRNO=1644, MESSAGE_TEXT='Mandatory arguments p_status and/or p_beamline are NULL'; END IF; END ;; From dc9e06cd6f23abe13f242c9e9c1caad091e089ad Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 24 Jul 2025 11:29:57 +0100 Subject: [PATCH 66/80] Grants to the Ligand tables for the expeye role (#294) --- grants/ispyb_expeye.sql | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 359d91f5..5f9fa9cf 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -71,3 +71,7 @@ GRANT SELECT, INSERT, UPDATE ON AutoProcProgramAttachment TO ispyb_expeye_core_r GRANT SELECT ON AutoProcIntegration TO ispyb_expeye_core_role; GRANT SELECT ON ProcessingJob TO ispyb_expeye_core_role; + +GRANT SELECT, INSERT, UPDATE ON Ligand TO ispyb_expeye_core_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON Ligand_has_PDB TO ispyb_expeye_core_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON BLSample_has_Ligand TO ispyb_expeye_core_role; From ca39aa949b1fb7c3a69dcf13962be3b8b531e0e5 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 24 Jul 2025 17:36:09 +0100 Subject: [PATCH 67/80] Add grants on Protein_has_PDB for expeye role (#295) --- grants/ispyb_expeye.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index 5f9fa9cf..cd1510b2 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -75,3 +75,4 @@ GRANT SELECT ON ProcessingJob TO ispyb_expeye_core_role; GRANT SELECT, INSERT, UPDATE ON Ligand TO ispyb_expeye_core_role; GRANT SELECT, INSERT, UPDATE, DELETE ON Ligand_has_PDB TO ispyb_expeye_core_role; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSample_has_Ligand TO ispyb_expeye_core_role; +GRANT SELECT, INSERT, UPDATE, DELETE ON Protein_has_PDB TO ispyb_expeye_core_role; From 5ff39ac8c6cb3cdeee003547de169b453e7f97f5 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Fri, 25 Jul 2025 15:32:28 +0100 Subject: [PATCH 68/80] Grant BLSampleImage perms to Expeye (#297) --- grants/ispyb_expeye.sql | 1 + 1 file changed, 1 insertion(+) diff --git a/grants/ispyb_expeye.sql b/grants/ispyb_expeye.sql index cd1510b2..65e59a2b 100644 --- a/grants/ispyb_expeye.sql +++ b/grants/ispyb_expeye.sql @@ -44,6 +44,7 @@ GRANT SELECT ON ProcessingPipeline TO ispyb_expeye_acquisition_role; GRANT SELECT ON ProcessingPipelineCategory TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSample TO ispyb_expeye_acquisition_role; +GRANT SELECT, INSERT, UPDATE, DELETE on BLSampleImage TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSampleGroup_has_BLSample TO ispyb_expeye_acquisition_role; GRANT SELECT, INSERT, UPDATE, DELETE ON BLSubSample TO ispyb_expeye_acquisition_role; From 6464aca9e15359b80a745d80eee88fb2390ea480 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Fri, 25 Jul 2025 21:14:23 +0100 Subject: [PATCH 69/80] Add new column Container.parentContainerLocation (#296) --- .../2025_07_25_Container_parentContainerLocation.sql | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 schemas/ispyb/updates/2025_07_25_Container_parentContainerLocation.sql diff --git a/schemas/ispyb/updates/2025_07_25_Container_parentContainerLocation.sql b/schemas/ispyb/updates/2025_07_25_Container_parentContainerLocation.sql new file mode 100644 index 00000000..bf23e79a --- /dev/null +++ b/schemas/ispyb/updates/2025_07_25_Container_parentContainerLocation.sql @@ -0,0 +1,7 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_07_25_Container_parentContainerLocation.sql', 'ONGOING'); + +ALTER TABLE Container + ADD parentContainerLocation int unsigned + COMMENT 'Indicates where inside the parent container this container is located', ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_07_25_Container_parentContainerLocation.sql'; From d0cdd52437ecdd07449ad3e3d7af8cbfd53f690f Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Wed, 24 Sep 2025 13:03:12 +0100 Subject: [PATCH 70/80] New proc insert_screening_v2 with grant and updated routines.sql (#300) --- grants/ispyb_processing.sql | 1 + schemas/ispyb/routines.sql | 45 +++++++++++++++++-- .../sp_insert_screening_v2.sql | 30 +++++++++++++ 3 files changed, 73 insertions(+), 3 deletions(-) create mode 100644 schemas/ispyb/stored_programs/sp_insert_screening_v2.sql diff --git a/grants/ispyb_processing.sql b/grants/ispyb_processing.sql index 03f43003..c1964c2a 100644 --- a/grants/ispyb_processing.sql +++ b/grants/ispyb_processing.sql @@ -77,6 +77,7 @@ GRANT EXECUTE ON PROCEDURE retrieve_most_recent_session TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE retrieve_containers_submitted_non_ls TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE `insert_screening` TO 'ispyb_processing'; +GRANT EXECUTE ON PROCEDURE `insert_screening_v2` TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE insert_screening_input TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE `insert_screening_output` TO 'ispyb_processing'; GRANT EXECUTE ON PROCEDURE `insert_screening_output_v2` TO 'ispyb_processing'; diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql index 00420fa4..e3de2590 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -131,7 +131,7 @@ DELIMITER ; /*!50003 SET character_set_results = utf8mb3 */ ; /*!50003 SET collation_connection = utf8mb3_general_ci */ ; DELIMITER ;; -CREATE FUNCTION `retrieve_proposal_title`(p_proposal_code varchar(5), p_proposal_number int) RETURNS varchar(255) CHARSET latin1 +CREATE FUNCTION `retrieve_proposal_title`(p_proposal_code varchar(5), p_proposal_number int) RETURNS varchar(255) CHARSET latin1 COLLATE latin1_swedish_ci READS SQL DATA BEGIN DECLARE ret_title varchar(255); @@ -156,7 +156,7 @@ DELIMITER ; /*!50003 SET character_set_results = utf8mb3 */ ; /*!50003 SET collation_connection = utf8mb3_general_ci */ ; DELIMITER ;; -CREATE FUNCTION `retrieve_proposal_title_v2`(p_proposalCode varchar(5), p_proposalNumber int) RETURNS varchar(255) CHARSET latin1 +CREATE FUNCTION `retrieve_proposal_title_v2`(p_proposalCode varchar(5), p_proposalNumber int) RETURNS varchar(255) CHARSET latin1 COLLATE latin1_swedish_ci READS SQL DATA COMMENT 'Retrieve the title for a given proposal code and number.' BEGIN @@ -207,7 +207,7 @@ DELIMITER ; /*!50003 SET character_set_results = utf8mb3 */ ; /*!50003 SET collation_connection = utf8mb3_general_ci */ ; DELIMITER ;; -CREATE FUNCTION `root_replace`(p_str varchar(255), p_oldroot varchar(255), p_newroot varchar(255)) RETURNS varchar(255) CHARSET latin1 +CREATE FUNCTION `root_replace`(p_str varchar(255), p_oldroot varchar(255), p_newroot varchar(255)) RETURNS varchar(255) CHARSET latin1 COLLATE latin1_swedish_ci COMMENT 'Returns a varchar where the old root p_oldroot (the leftmost part) of p_str has been replaced with a new root p_newroot' BEGIN DECLARE path_len smallint unsigned DEFAULT LENGTH(p_oldroot); @@ -2334,6 +2334,45 @@ BEGIN SET p_id = LAST_INSERT_ID(); END IF; +END ;; +DELIMITER ; +/*!50003 SET sql_mode = @saved_sql_mode */ ; +/*!50003 SET character_set_client = @saved_cs_client */ ; +/*!50003 SET character_set_results = @saved_cs_results */ ; +/*!50003 SET collation_connection = @saved_col_connection */ ; +/*!50003 SET @saved_sql_mode = @@sql_mode */ ; +/*!50003 SET sql_mode = 'STRICT_TRANS_TABLES,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION' */ ; +/*!50003 DROP PROCEDURE IF EXISTS `insert_screening_v2` */; +/*!50003 SET @saved_cs_client = @@character_set_client */ ; +/*!50003 SET @saved_cs_results = @@character_set_results */ ; +/*!50003 SET @saved_col_connection = @@collation_connection */ ; +/*!50003 SET character_set_client = utf8mb3 */ ; +/*!50003 SET character_set_results = utf8mb3 */ ; +/*!50003 SET collation_connection = utf8mb3_general_ci */ ; +DELIMITER ;; +CREATE PROCEDURE `insert_screening_v2`( + OUT p_id int(11) unsigned, + p_dcgId int(11) unsigned, + p_dcId int(11) unsigned, + p_programVersion varchar(45), + p_shortComments varchar(20), + p_comments varchar(255), + p_autoProcProgramId int(10) unsigned +) + MODIFIES SQL DATA + COMMENT 'Insert a row with info about a screening. Returns the ID in p_id.' +BEGIN + IF p_dcgId IS NULL AND p_dcId IS NOT NULL THEN + SELECT dataCollectionGroupId INTO p_dcgId FROM DataCollection WHERE dataCollectionId = p_dcId; + END IF; + + INSERT INTO Screening (dataCollectionGroupId, dataCollectionId, programVersion, shortComments, comments, autoProcProgramId) + VALUES (p_dcgId, p_dcId, p_programVersion, p_shortComments, p_comments, p_autoProcProgramId); + + IF LAST_INSERT_ID() <> 0 THEN + SET p_id = LAST_INSERT_ID(); + END IF; + END ;; DELIMITER ; /*!50003 SET sql_mode = @saved_sql_mode */ ; diff --git a/schemas/ispyb/stored_programs/sp_insert_screening_v2.sql b/schemas/ispyb/stored_programs/sp_insert_screening_v2.sql new file mode 100644 index 00000000..45378b9f --- /dev/null +++ b/schemas/ispyb/stored_programs/sp_insert_screening_v2.sql @@ -0,0 +1,30 @@ +-- To test: +-- SET @id = NULL; +-- CALL insert_screening_v2(@id, NULL, 6017416, 'EDNA MXv1', 'EDNAStrategy2', 'Standard Anomalous Dataset Multiplicity=3 I/sig=2 Maxlifespan=4034 s', 56986688); + +DELIMITER ;; +CREATE OR REPLACE PROCEDURE `insert_screening_v2`( + OUT p_id int(11) unsigned, + p_dcgId int(11) unsigned, + p_dcId int(11) unsigned, + p_programVersion varchar(45), + p_shortComments varchar(20), + p_comments varchar(255), + p_autoProcProgramId int(10) unsigned +) +MODIFIES SQL DATA +COMMENT 'Insert a row with info about a screening. Returns the ID in p_id.' +BEGIN + IF p_dcgId IS NULL AND p_dcId IS NOT NULL THEN + SELECT dataCollectionGroupId INTO p_dcgId FROM DataCollection WHERE dataCollectionId = p_dcId; + END IF; + + INSERT INTO Screening (dataCollectionGroupId, dataCollectionId, programVersion, shortComments, comments, autoProcProgramId) + VALUES (p_dcgId, p_dcId, p_programVersion, p_shortComments, p_comments, p_autoProcProgramId); + + IF LAST_INSERT_ID() <> 0 THEN + SET p_id = LAST_INSERT_ID(); + END IF; + +END;; +DELIMITER ; From aef84778acb6e9ca4c1d3703c1b45dc75ce0baf9 Mon Sep 17 00:00:00 2001 From: Karl Levik Date: Thu, 25 Sep 2025 16:51:19 +0100 Subject: [PATCH 71/80] Add start and end date columns to Proposal table, update relevant schema files (#301) Add start+end date cols to Proposal, refresh schema files --- schemas/ispyb/lookups.sql | 7 +- schemas/ispyb/tables.sql | 403 +++++++++--------- .../2025_09_24_Proposal_start_end_date.sql | 10 + 3 files changed, 218 insertions(+), 202 deletions(-) create mode 100644 schemas/ispyb/updates/2025_09_24_Proposal_start_end_date.sql diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 22c8e0ad..f8e6b06c 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -11,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.7.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.8.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -294,7 +294,10 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (322,'2025_06_02_DewarRegistry_type.sql','DONE','2025-06-27 16:04:05'), (323,'2025_06_26_ContainerType_cryoem_puck.sql','DONE','2025-06-27 16:04:05'), (324,'2025_06_27_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:04:05'), -(325,'2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:40:00'); +(325,'2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:40:00'), +(326,'2025_07_17_AdminVar_bump_version.sql','DONE','2025-09-24 11:36:21'), +(327,'2025_07_25_Container_parentContainerLocation.sql','DONE','2025-09-24 11:36:21'), +(328,'2025_09_24_Proposal_start_end_date.sql','DONE','2025-09-24 15:56:17'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index 0a4575ac..90683460 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -22,7 +22,7 @@ CREATE TABLE `AdminActivity` ( PRIMARY KEY (`adminActivityId`), UNIQUE KEY `username` (`username`), KEY `AdminActivity_FKAction` (`action`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AdminVar`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -34,7 +34,7 @@ CREATE TABLE `AdminVar` ( PRIMARY KEY (`varId`), KEY `AdminVar_FKIndexName` (`name`), KEY `AdminVar_FKIndexValue` (`value`(767)) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='ISPyB administration values'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='ISPyB administration values'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Aperture`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -43,7 +43,7 @@ CREATE TABLE `Aperture` ( `apertureId` int(10) unsigned NOT NULL AUTO_INCREMENT, `sizeX` float DEFAULT NULL, PRIMARY KEY (`apertureId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Atlas`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -57,7 +57,7 @@ CREATE TABLE `Atlas` ( PRIMARY KEY (`atlasId`), KEY `Atlas_fk_dataCollectionGroupId` (`dataCollectionGroupId`), CONSTRAINT `Atlas_fk_dataCollectionGroupId` FOREIGN KEY (`dataCollectionGroupId`) REFERENCES `DataCollectionGroup` (`dataCollectionGroupId`) ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Atlas of a Cryo-EM grid'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Atlas of a Cryo-EM grid'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProc`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -76,7 +76,7 @@ CREATE TABLE `AutoProc` ( PRIMARY KEY (`autoProcId`), KEY `AutoProc_FKIndex1` (`autoProcProgramId`), KEY `AutoProc_refined_unit_cell` (`refinedCell_a`,`refinedCell_b`,`refinedCell_c`,`refinedCell_alpha`,`refinedCell_beta`,`refinedCell_gamma`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcIntegration`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -109,7 +109,7 @@ CREATE TABLE `AutoProcIntegration` ( KEY `AutoProcIntegration_FKIndex1` (`autoProcProgramId`), CONSTRAINT `AutoProcIntegration_ibfk_1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `AutoProcIntegration_ibfk_2` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcProgram`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -129,7 +129,7 @@ CREATE TABLE `AutoProcProgram` ( PRIMARY KEY (`autoProcProgramId`), KEY `AutoProcProgram_FK2` (`processingJobId`), CONSTRAINT `AutoProcProgram_FK2` FOREIGN KEY (`processingJobId`) REFERENCES `ProcessingJob` (`processingJobId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcProgramAttachment`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -146,7 +146,7 @@ CREATE TABLE `AutoProcProgramAttachment` ( PRIMARY KEY (`autoProcProgramAttachmentId`), KEY `AutoProcProgramAttachmentIdx1` (`autoProcProgramId`), CONSTRAINT `AutoProcProgramAttachmentFk1` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcProgramMessage`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -161,7 +161,7 @@ CREATE TABLE `AutoProcProgramMessage` ( PRIMARY KEY (`autoProcProgramMessageId`), KEY `AutoProcProgramMessage_fk1` (`autoProcProgramId`), CONSTRAINT `AutoProcProgramMessage_fk1` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcScaling`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -174,7 +174,7 @@ CREATE TABLE `AutoProcScaling` ( KEY `AutoProcScalingFk1` (`autoProcId`), KEY `AutoProcScalingIdx1` (`autoProcScalingId`,`autoProcId`), CONSTRAINT `AutoProcScalingFk1` FOREIGN KEY (`autoProcId`) REFERENCES `AutoProc` (`autoProcId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcScalingStatistics`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -208,7 +208,7 @@ CREATE TABLE `AutoProcScalingStatistics` ( KEY `AutoProcScalingStatistics_FKindexType` (`scalingStatisticsType`), KEY `AutoProcScalingStatistics_scalingId_statisticsType` (`autoProcScalingId`,`scalingStatisticsType`), CONSTRAINT `_AutoProcScalingStatisticsFk1` FOREIGN KEY (`autoProcScalingId`) REFERENCES `AutoProcScaling` (`autoProcScalingId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcScaling_has_Int`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -223,7 +223,7 @@ CREATE TABLE `AutoProcScaling_has_Int` ( KEY `AutoProcScal_has_IntIdx2` (`autoProcIntegrationId`), CONSTRAINT `AutoProcScaling_has_IntFk1` FOREIGN KEY (`autoProcScalingId`) REFERENCES `AutoProcScaling` (`autoProcScalingId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `AutoProcScaling_has_IntFk2` FOREIGN KEY (`autoProcIntegrationId`) REFERENCES `AutoProcIntegration` (`autoProcIntegrationId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `AutoProcStatus`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -238,7 +238,7 @@ CREATE TABLE `AutoProcStatus` ( PRIMARY KEY (`autoProcStatusId`), KEY `AutoProcStatus_FKIndex1` (`autoProcIntegrationId`), CONSTRAINT `AutoProcStatus_ibfk_1` FOREIGN KEY (`autoProcIntegrationId`) REFERENCES `AutoProcIntegration` (`autoProcIntegrationId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='AutoProcStatus table is linked to AutoProcIntegration'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='AutoProcStatus table is linked to AutoProcIntegration'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_automationError`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -248,7 +248,7 @@ CREATE TABLE `BF_automationError` ( `errorType` varchar(40) NOT NULL, `solution` text DEFAULT NULL, PRIMARY KEY (`automationErrorId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_automationFault`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -266,7 +266,7 @@ CREATE TABLE `BF_automationFault` ( KEY `BF_automationFault_ibfk2` (`containerId`), CONSTRAINT `BF_automationFault_ibfk1` FOREIGN KEY (`automationErrorId`) REFERENCES `BF_automationError` (`automationErrorId`), CONSTRAINT `BF_automationFault_ibfk2` FOREIGN KEY (`containerId`) REFERENCES `Container` (`containerId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_component`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -279,7 +279,7 @@ CREATE TABLE `BF_component` ( PRIMARY KEY (`componentId`), KEY `bf_component_FK1` (`systemId`), CONSTRAINT `bf_component_FK1` FOREIGN KEY (`systemId`) REFERENCES `BF_system` (`systemId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_component_beamline`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -291,7 +291,7 @@ CREATE TABLE `BF_component_beamline` ( PRIMARY KEY (`component_beamlineId`), KEY `bf_component_beamline_FK1` (`componentId`), CONSTRAINT `bf_component_beamline_FK1` FOREIGN KEY (`componentId`) REFERENCES `BF_component` (`componentId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_fault`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -324,7 +324,7 @@ CREATE TABLE `BF_fault` ( CONSTRAINT `bf_fault_FK2` FOREIGN KEY (`subcomponentId`) REFERENCES `BF_subcomponent` (`subcomponentId`), CONSTRAINT `bf_fault_FK3` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`), CONSTRAINT `bf_fault_FK4` FOREIGN KEY (`assigneeId`) REFERENCES `Person` (`personId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_subcomponent`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -337,7 +337,7 @@ CREATE TABLE `BF_subcomponent` ( PRIMARY KEY (`subcomponentId`), KEY `bf_subcomponent_FK1` (`componentId`), CONSTRAINT `bf_subcomponent_FK1` FOREIGN KEY (`componentId`) REFERENCES `BF_component` (`componentId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_subcomponent_beamline`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -349,7 +349,7 @@ CREATE TABLE `BF_subcomponent_beamline` ( PRIMARY KEY (`subcomponent_beamlineId`), KEY `bf_subcomponent_beamline_FK1` (`subcomponentId`), CONSTRAINT `bf_subcomponent_beamline_FK1` FOREIGN KEY (`subcomponentId`) REFERENCES `BF_subcomponent` (`subcomponentId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_system`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -359,7 +359,7 @@ CREATE TABLE `BF_system` ( `name` varchar(100) DEFAULT NULL, `description` varchar(200) DEFAULT NULL, PRIMARY KEY (`systemId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BF_system_beamline`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -371,7 +371,7 @@ CREATE TABLE `BF_system_beamline` ( PRIMARY KEY (`system_beamlineId`), KEY `bf_system_beamline_FK1` (`systemId`), CONSTRAINT `bf_system_beamline_FK1` FOREIGN KEY (`systemId`) REFERENCES `BF_system` (`systemId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BFactorFit`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -385,7 +385,7 @@ CREATE TABLE `BFactorFit` ( PRIMARY KEY (`bFactorFitId`), KEY `BFactorFit_fk_particleClassificationId` (`particleClassificationId`), CONSTRAINT `BFactorFit_fk_particleClassificationId` FOREIGN KEY (`particleClassificationId`) REFERENCES `ParticleClassification` (`particleClassificationId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='CryoEM reconstruction resolution as a function of the number of particles for the creation of a Rosenthal-Henderson plot and the calculation of B-factors'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='CryoEM reconstruction resolution as a function of the number of particles for the creation of a Rosenthal-Henderson plot and the calculation of B-factors'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -445,7 +445,7 @@ CREATE TABLE `BLSample` ( CONSTRAINT `BLSample_ibfk_1` FOREIGN KEY (`containerId`) REFERENCES `Container` (`containerId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSample_ibfk_2` FOREIGN KEY (`crystalId`) REFERENCES `Crystal` (`crystalId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSample_ibfk_3` FOREIGN KEY (`diffractionPlanId`) REFERENCES `DiffractionPlan` (`diffractionPlanId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -460,7 +460,7 @@ CREATE TABLE `BLSampleGroup` ( KEY `BLSampleGroup_fk_ownerId` (`ownerId`), CONSTRAINT `BLSampleGroup_fk_ownerId` FOREIGN KEY (`ownerId`) REFERENCES `Person` (`personId`) ON UPDATE CASCADE, CONSTRAINT `BLSampleGroup_fk_proposalId` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE SET NULL ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleGroup_has_BLSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -477,7 +477,7 @@ CREATE TABLE `BLSampleGroup_has_BLSample` ( CONSTRAINT `BLSampleGroup_has_BLSample_ibfk1` FOREIGN KEY (`blSampleGroupId`) REFERENCES `BLSampleGroup` (`blSampleGroupId`), CONSTRAINT `BLSampleGroup_has_BLSample_ibfk2` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`), CONSTRAINT `BLSampleGroup_has_BLSample_ibfk3` FOREIGN KEY (`blSampleTypeId`) REFERENCES `BLSampleType` (`blSampleTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImage`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -503,7 +503,7 @@ CREATE TABLE `BLSampleImage` ( CONSTRAINT `BLSampleImage_fk1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `BLSampleImage_fk2` FOREIGN KEY (`containerInspectionId`) REFERENCES `ContainerInspection` (`containerInspectionId`), CONSTRAINT `BLSampleImage_fk3` FOREIGN KEY (`blSampleImageScoreId`) REFERENCES `BLSampleImageScore` (`blSampleImageScoreId`) ON DELETE NO ACTION ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageAnalysis`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -523,7 +523,7 @@ CREATE TABLE `BLSampleImageAnalysis` ( PRIMARY KEY (`blSampleImageAnalysisId`), KEY `BLSampleImageAnalysis_ibfk1` (`blSampleImageId`), CONSTRAINT `BLSampleImageAnalysis_ibfk1` FOREIGN KEY (`blSampleImageId`) REFERENCES `BLSampleImage` (`blSampleImageId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageAutoScoreClass`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -535,7 +535,7 @@ CREATE TABLE `BLSampleImageAutoScoreClass` ( PRIMARY KEY (`blSampleImageAutoScoreClassId`), KEY `BLSampleImageAutoScoreClass_fk1` (`blSampleImageAutoScoreSchemaId`), CONSTRAINT `BLSampleImageAutoScoreClass_fk1` FOREIGN KEY (`blSampleImageAutoScoreSchemaId`) REFERENCES `BLSampleImageAutoScoreSchema` (`blSampleImageAutoScoreSchemaId`) ON DELETE NO ACTION ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='The automated scoring classes - the thing being scored'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='The automated scoring classes - the thing being scored'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageAutoScoreSchema`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -545,7 +545,7 @@ CREATE TABLE `BLSampleImageAutoScoreSchema` ( `schemaName` varchar(25) NOT NULL COMMENT 'Name of the schema e.g. Hampton, MARCO', `enabled` tinyint(1) DEFAULT 1 COMMENT 'Whether this schema is enabled (could be configurable in the UI)', PRIMARY KEY (`blSampleImageAutoScoreSchemaId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Scoring schema name and whether it is enabled'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Scoring schema name and whether it is enabled'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageMeasurement`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -564,7 +564,7 @@ CREATE TABLE `BLSampleImageMeasurement` ( KEY `BLSampleImageMeasurement_ibfk_2` (`blSubSampleId`), CONSTRAINT `BLSampleImageMeasurement_ibfk_1` FOREIGN KEY (`blSampleImageId`) REFERENCES `BLSampleImage` (`blSampleImageId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSampleImageMeasurement_ibfk_2` FOREIGN KEY (`blSubSampleId`) REFERENCES `BLSubSample` (`blSubSampleId`) ON DELETE NO ACTION ON UPDATE NO ACTION -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='For measuring crystal growth over time'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='For measuring crystal growth over time'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImageScore`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -575,7 +575,7 @@ CREATE TABLE `BLSampleImageScore` ( `score` float DEFAULT NULL, `colour` varchar(15) DEFAULT NULL, PRIMARY KEY (`blSampleImageScoreId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImage_has_AutoScoreClass`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -588,7 +588,7 @@ CREATE TABLE `BLSampleImage_has_AutoScoreClass` ( KEY `BLSampleImage_has_AutoScoreClass_fk2` (`blSampleImageAutoScoreClassId`), CONSTRAINT `BLSampleImage_has_AutoScoreClass_fk1` FOREIGN KEY (`blSampleImageId`) REFERENCES `BLSampleImage` (`blSampleImageId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSampleImage_has_AutoScoreClass_fk2` FOREIGN KEY (`blSampleImageAutoScoreClassId`) REFERENCES `BLSampleImageAutoScoreClass` (`blSampleImageAutoScoreClassId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Many-to-many relationship between drop images and thing being scored, as well as the actual probability (score) that the drop image contains that thing'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Many-to-many relationship between drop images and thing being scored, as well as the actual probability (score) that the drop image contains that thing'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleImage_has_Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -603,7 +603,7 @@ CREATE TABLE `BLSampleImage_has_Positioner` ( KEY `BLSampleImageHasPositioner_ibfk2` (`positionerId`), CONSTRAINT `BLSampleImageHasPositioner_ibfk1` FOREIGN KEY (`blSampleImageId`) REFERENCES `BLSampleImage` (`blSampleImageId`), CONSTRAINT `BLSampleImageHasPositioner_ibfk2` FOREIGN KEY (`positionerId`) REFERENCES `Positioner` (`positionerId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Allows a BLSampleImage to store motor positions along with the image'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Allows a BLSampleImage to store motor positions along with the image'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSamplePosition`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -619,7 +619,7 @@ CREATE TABLE `BLSamplePosition` ( PRIMARY KEY (`blSamplePositionId`), KEY `BLSamplePosition_fk_blSampleId` (`blSampleId`), CONSTRAINT `BLSamplePosition_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -630,7 +630,7 @@ CREATE TABLE `BLSampleType` ( `proposalType` varchar(10) DEFAULT NULL, `active` tinyint(1) DEFAULT 1 COMMENT '1=active, 0=inactive', PRIMARY KEY (`blSampleTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSampleType_has_Component`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -643,7 +643,7 @@ CREATE TABLE `BLSampleType_has_Component` ( KEY `blSampleType_has_Component_fk2` (`componentId`), CONSTRAINT `blSampleType_has_Component_fk1` FOREIGN KEY (`blSampleTypeId`) REFERENCES `Crystal` (`crystalId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `blSampleType_has_Component_fk2` FOREIGN KEY (`componentId`) REFERENCES `Protein` (`proteinId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_DataCollectionPlan`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -656,7 +656,7 @@ CREATE TABLE `BLSample_has_DataCollectionPlan` ( KEY `BLSample_has_DataCollectionPlan_ibfk2` (`dataCollectionPlanId`), CONSTRAINT `BLSample_has_DataCollectionPlan_ibfk1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`), CONSTRAINT `BLSample_has_DataCollectionPlan_ibfk2` FOREIGN KEY (`dataCollectionPlanId`) REFERENCES `DiffractionPlan` (`diffractionPlanId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_EnergyScan`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -670,7 +670,7 @@ CREATE TABLE `BLSample_has_EnergyScan` ( KEY `BLSample_has_EnergyScan_FKIndex2` (`energyScanId`), CONSTRAINT `BLSample_has_EnergyScan_ibfk_1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSample_has_EnergyScan_ibfk_2` FOREIGN KEY (`energyScanId`) REFERENCES `EnergyScan` (`energyScanId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_Ligand`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -682,7 +682,7 @@ CREATE TABLE `BLSample_has_Ligand` ( KEY `BLSample_has_Ligand_fk2` (`ligandId`), CONSTRAINT `BLSample_has_Ligand_fk1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSample_has_Ligand_fk2` FOREIGN KEY (`ligandId`) REFERENCES `Ligand` (`ligandId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Junction table for BLSample and Ligand'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Junction table for BLSample and Ligand'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSample_has_Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -696,7 +696,7 @@ CREATE TABLE `BLSample_has_Positioner` ( KEY `BLSampleHasPositioner_ibfk2` (`positionerId`), CONSTRAINT `BLSampleHasPositioner_ibfk1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`), CONSTRAINT `BLSampleHasPositioner_ibfk2` FOREIGN KEY (`positionerId`) REFERENCES `Positioner` (`positionerId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSession`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -732,7 +732,7 @@ CREATE TABLE `BLSession` ( CONSTRAINT `BLSession_fk_beamCalendarId` FOREIGN KEY (`beamCalendarId`) REFERENCES `BeamCalendar` (`beamCalendarId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `BLSession_ibfk_1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSession_ibfk_2` FOREIGN KEY (`beamLineSetupId`) REFERENCES `BeamLineSetup` (`beamLineSetupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSession_has_SCPosition`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -745,7 +745,7 @@ CREATE TABLE `BLSession_has_SCPosition` ( PRIMARY KEY (`blsessionhasscpositionid`), KEY `blsession_has_scposition_FK1` (`blsessionid`), CONSTRAINT `blsession_has_scposition_FK1` FOREIGN KEY (`blsessionid`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSubSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -778,7 +778,7 @@ CREATE TABLE `BLSubSample` ( CONSTRAINT `BLSubSample_motorPositionfk_1` FOREIGN KEY (`motorPositionId`) REFERENCES `MotorPosition` (`motorPositionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSubSample_positionfk_1` FOREIGN KEY (`positionId`) REFERENCES `Position` (`positionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `BLSubSample_positionfk_2` FOREIGN KEY (`position2Id`) REFERENCES `Position` (`positionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BLSubSample_has_Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -792,7 +792,7 @@ CREATE TABLE `BLSubSample_has_Positioner` ( KEY `BLSubSampleHasPositioner_ibfk2` (`positionerId`), CONSTRAINT `BLSubSampleHasPositioner_ibfk1` FOREIGN KEY (`blSubSampleId`) REFERENCES `BLSubSample` (`blSubSampleId`), CONSTRAINT `BLSubSampleHasPositioner_ibfk2` FOREIGN KEY (`positionerId`) REFERENCES `Positioner` (`positionerId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamApertures`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -807,7 +807,7 @@ CREATE TABLE `BeamApertures` ( PRIMARY KEY (`beamAperturesid`), KEY `beamapertures_FK1` (`beamlineStatsId`), CONSTRAINT `beamapertures_FK1` FOREIGN KEY (`beamlineStatsId`) REFERENCES `BeamlineStats` (`beamlineStatsId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamCalendar`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -819,7 +819,7 @@ CREATE TABLE `BeamCalendar` ( `startDate` datetime NOT NULL, `endDate` datetime NOT NULL, PRIMARY KEY (`beamCalendarId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamCentres`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -833,7 +833,7 @@ CREATE TABLE `BeamCentres` ( PRIMARY KEY (`beamCentresid`), KEY `beamCentres_FK1` (`beamlineStatsId`), CONSTRAINT `beamCentres_FK1` FOREIGN KEY (`beamlineStatsId`) REFERENCES `BeamlineStats` (`beamlineStatsId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamLineSetup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -890,7 +890,7 @@ CREATE TABLE `BeamLineSetup` ( PRIMARY KEY (`beamLineSetupId`), KEY `BeamLineSetup_ibfk_1` (`detectorId`), CONSTRAINT `BeamLineSetup_ibfk_1` FOREIGN KEY (`detectorId`) REFERENCES `Detector` (`detectorId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamlineAction`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -908,7 +908,7 @@ CREATE TABLE `BeamlineAction` ( PRIMARY KEY (`beamlineActionId`), KEY `BeamlineAction_ibfk1` (`sessionId`), CONSTRAINT `BeamlineAction_ibfk1` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `BeamlineStats`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -926,7 +926,7 @@ CREATE TABLE `BeamlineStats` ( `scanFileW` varchar(255) DEFAULT NULL, `scanFileH` varchar(255) DEFAULT NULL, PRIMARY KEY (`beamlineStatsId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CTF`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -955,7 +955,7 @@ CREATE TABLE `CTF` ( KEY `CTF_ibfk2` (`autoProcProgramId`), CONSTRAINT `CTF_ibfk1` FOREIGN KEY (`motionCorrectionId`) REFERENCES `MotionCorrection` (`motionCorrectionId`), CONSTRAINT `CTF_ibfk2` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CalendarHash`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -966,7 +966,7 @@ CREATE TABLE `CalendarHash` ( `hash` varchar(128) DEFAULT NULL, `beamline` tinyint(1) DEFAULT NULL, PRIMARY KEY (`calendarHashId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Lets people get to their calendars without logging in using a private (hash) url'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Lets people get to their calendars without logging in using a private (hash) url'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Component`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -982,7 +982,7 @@ CREATE TABLE `Component` ( KEY `proposalId` (`proposalId`), CONSTRAINT `Component_ibfk_1` FOREIGN KEY (`componentTypeId`) REFERENCES `ComponentType` (`componentTypeId`), CONSTRAINT `Component_ibfk_2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Description of a component that can be used inside a crystal or a sample.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Description of a component that can be used inside a crystal or a sample.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ComponentLattice`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1000,7 +1000,7 @@ CREATE TABLE `ComponentLattice` ( PRIMARY KEY (`componentLatticeId`), KEY `ComponentLattice_ibfk1` (`componentId`), CONSTRAINT `ComponentLattice_ibfk1` FOREIGN KEY (`componentId`) REFERENCES `Protein` (`proteinId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ComponentSubType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1012,7 +1012,7 @@ CREATE TABLE `ComponentSubType` ( `proposalType` varchar(10) DEFAULT NULL, `active` tinyint(1) DEFAULT 1 COMMENT '1=active, 0=inactive', PRIMARY KEY (`componentSubTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ComponentType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1022,7 +1022,7 @@ CREATE TABLE `ComponentType` ( `name` varchar(31) NOT NULL, PRIMARY KEY (`componentTypeId`), UNIQUE KEY `name` (`name`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Component_has_SubType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1034,7 +1034,7 @@ CREATE TABLE `Component_has_SubType` ( KEY `component_has_SubType_fk2` (`componentSubTypeId`), CONSTRAINT `component_has_SubType_fk1` FOREIGN KEY (`componentId`) REFERENCES `Protein` (`proteinId`) ON DELETE CASCADE, CONSTRAINT `component_has_SubType_fk2` FOREIGN KEY (`componentSubTypeId`) REFERENCES `ComponentSubType` (`componentSubTypeId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ConcentrationType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1046,7 +1046,7 @@ CREATE TABLE `ConcentrationType` ( `proposalType` varchar(10) DEFAULT NULL, `active` tinyint(1) DEFAULT 1 COMMENT '1=active, 0=inactive', PRIMARY KEY (`concentrationTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Container`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1080,6 +1080,7 @@ CREATE TABLE `Container` ( `currentDewarId` int(10) unsigned DEFAULT NULL COMMENT 'The dewar with which the container is currently associated', `parentContainerId` int(10) unsigned DEFAULT NULL, `source` varchar(50) DEFAULT current_user(), + `parentContainerLocation` int(10) unsigned DEFAULT NULL COMMENT 'Indicates where inside the parent container this container is located', PRIMARY KEY (`containerId`), UNIQUE KEY `Container_UNIndex1` (`barcode`), KEY `Container_FKIndex` (`beamlineLocation`), @@ -1110,7 +1111,7 @@ CREATE TABLE `Container` ( CONSTRAINT `Container_ibfk8` FOREIGN KEY (`containerRegistryId`) REFERENCES `ContainerRegistry` (`containerRegistryId`), CONSTRAINT `Container_ibfk9` FOREIGN KEY (`priorityPipelineId`) REFERENCES `ProcessingPipeline` (`processingPipelineId`), CONSTRAINT `Container_ibfk_1` FOREIGN KEY (`dewarId`) REFERENCES `Dewar` (`dewarId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerHistory`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1128,7 +1129,7 @@ CREATE TABLE `ContainerHistory` ( KEY `ContainerHistory_fk_dewarId` (`currentDewarId`), CONSTRAINT `ContainerHistory_fk_dewarId` FOREIGN KEY (`currentDewarId`) REFERENCES `Dewar` (`dewarId`), CONSTRAINT `ContainerHistory_ibfk1` FOREIGN KEY (`containerId`) REFERENCES `Container` (`containerId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerInspection`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1155,7 +1156,7 @@ CREATE TABLE `ContainerInspection` ( CONSTRAINT `ContainerInspection_fk2` FOREIGN KEY (`inspectionTypeId`) REFERENCES `InspectionType` (`inspectionTypeId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `ContainerInspection_fk3` FOREIGN KEY (`imagerId`) REFERENCES `Imager` (`imagerId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `ContainerInspection_fk4` FOREIGN KEY (`scheduleComponentid`) REFERENCES `ScheduleComponent` (`scheduleComponentId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerQueue`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1172,7 +1173,7 @@ CREATE TABLE `ContainerQueue` ( KEY `ContainerQueue_idx1` (`containerId`,`completedTimeStamp`), CONSTRAINT `ContainerQueue_ibfk1` FOREIGN KEY (`containerId`) REFERENCES `Container` (`containerId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ContainerQueue_ibfk2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerQueueSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1195,7 +1196,7 @@ CREATE TABLE `ContainerQueueSample` ( CONSTRAINT `ContainerQueueSample_dataCollectionPlanId` FOREIGN KEY (`dataCollectionPlanId`) REFERENCES `DiffractionPlan` (`diffractionPlanId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `ContainerQueueSample_ibfk1` FOREIGN KEY (`containerQueueId`) REFERENCES `ContainerQueue` (`containerQueueId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ContainerQueueSample_ibfk2` FOREIGN KEY (`blSubSampleId`) REFERENCES `BLSubSample` (`blSubSampleId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerRegistry`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1207,7 +1208,7 @@ CREATE TABLE `ContainerRegistry` ( `recordTimestamp` datetime DEFAULT current_timestamp(), PRIMARY KEY (`containerRegistryId`), UNIQUE KEY `ContainerRegistry_uniq_barcode` (`barcode`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerRegistry_has_Proposal`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1225,7 +1226,7 @@ CREATE TABLE `ContainerRegistry_has_Proposal` ( CONSTRAINT `ContainerRegistry_has_Proposal_ibfk1` FOREIGN KEY (`containerRegistryId`) REFERENCES `ContainerRegistry` (`containerRegistryId`), CONSTRAINT `ContainerRegistry_has_Proposal_ibfk2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`), CONSTRAINT `ContainerRegistry_has_Proposal_ibfk3` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerReport`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1242,7 +1243,7 @@ CREATE TABLE `ContainerReport` ( KEY `ContainerReport_ibfk2` (`personId`), CONSTRAINT `ContainerReport_ibfk1` FOREIGN KEY (`containerRegistryId`) REFERENCES `ContainerRegistry` (`containerRegistryId`), CONSTRAINT `ContainerReport_ibfk2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ContainerType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1262,7 +1263,7 @@ CREATE TABLE `ContainerType` ( `dropOffsetY` float DEFAULT NULL, `wellDrop` smallint(6) DEFAULT NULL, PRIMARY KEY (`containerTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='A lookup table for different types of containers'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='A lookup table for different types of containers'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CourierTermsAccepted`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1281,7 +1282,7 @@ CREATE TABLE `CourierTermsAccepted` ( CONSTRAINT `CourierTermsAccepted_ibfk_1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`), CONSTRAINT `CourierTermsAccepted_ibfk_2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`), CONSTRAINT `CourierTermsAccepted_ibfk_3` FOREIGN KEY (`shippingId`) REFERENCES `Shipping` (`shippingId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Records acceptances of the courier T and C'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Records acceptances of the courier T and C'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CryoemInitialModel`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1291,7 +1292,7 @@ CREATE TABLE `CryoemInitialModel` ( `resolution` float DEFAULT NULL COMMENT 'Unit: Angstroms', `numberOfParticles` int(10) unsigned DEFAULT NULL, PRIMARY KEY (`cryoemInitialModelId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Initial cryo-EM model generation results'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Initial cryo-EM model generation results'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Crystal`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1325,7 +1326,7 @@ CREATE TABLE `Crystal` ( KEY `Crystal_FKIndex2` (`diffractionPlanId`), CONSTRAINT `Crystal_ibfk_1` FOREIGN KEY (`proteinId`) REFERENCES `Protein` (`proteinId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Crystal_ibfk_2` FOREIGN KEY (`diffractionPlanId`) REFERENCES `DiffractionPlan` (`diffractionPlanId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `CrystalComposition`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1345,7 +1346,7 @@ CREATE TABLE `CrystalComposition` ( CONSTRAINT `CrystalComposition_ibfk_1` FOREIGN KEY (`componentId`) REFERENCES `Component` (`componentId`), CONSTRAINT `CrystalComposition_ibfk_2` FOREIGN KEY (`crystalId`) REFERENCES `Crystal` (`crystalId`), CONSTRAINT `CrystalComposition_ibfk_3` FOREIGN KEY (`concentrationTypeId`) REFERENCES `ConcentrationType` (`concentrationTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Links a crystal to its components with a specified abundance or ratio.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Links a crystal to its components with a specified abundance or ratio.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Crystal_has_UUID`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1359,7 +1360,7 @@ CREATE TABLE `Crystal_has_UUID` ( KEY `Crystal_has_UUID_FKIndex1` (`crystalId`), KEY `Crystal_has_UUID_FKIndex2` (`UUID`), CONSTRAINT `ibfk_1` FOREIGN KEY (`crystalId`) REFERENCES `Crystal` (`crystalId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataAcquisition`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1372,7 +1373,7 @@ CREATE TABLE `DataAcquisition` ( `waitTime` varchar(45) DEFAULT NULL, `detectorDistance` varchar(45) DEFAULT NULL, PRIMARY KEY (`dataAcquisitionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollection`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1503,7 +1504,7 @@ CREATE TABLE `DataCollection` ( CONSTRAINT `DataCollection_ibfk_6` FOREIGN KEY (`startPositionId`) REFERENCES `MotorPosition` (`motorPositionId`), CONSTRAINT `DataCollection_ibfk_7` FOREIGN KEY (`endPositionId`) REFERENCES `MotorPosition` (`motorPositionId`), CONSTRAINT `DataCollection_ibfk_8` FOREIGN KEY (`blSubSampleId`) REFERENCES `BLSubSample` (`blSubSampleId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionComment`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1520,7 +1521,7 @@ CREATE TABLE `DataCollectionComment` ( KEY `dataCollectionComment_fk2` (`personId`), CONSTRAINT `dataCollectionComment_fk1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `dataCollectionComment_fk2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionFileAttachment`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1534,7 +1535,7 @@ CREATE TABLE `DataCollectionFileAttachment` ( PRIMARY KEY (`dataCollectionFileAttachmentId`), KEY `_dataCollectionFileAttachmentId_fk1` (`dataCollectionId`), CONSTRAINT `_dataCollectionFileAttachmentId_fk1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1563,7 +1564,7 @@ CREATE TABLE `DataCollectionGroup` ( CONSTRAINT `DataCollectionGroup_ibfk_1` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `DataCollectionGroup_ibfk_2` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `DataCollectionGroup_ibfk_4` FOREIGN KEY (`experimentTypeId`) REFERENCES `ExperimentType` (`experimentTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='a dataCollectionGroup is a group of dataCollection for a spe'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='a dataCollectionGroup is a group of dataCollection for a spe'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DataCollectionPlan_has_Detector`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1580,7 +1581,7 @@ CREATE TABLE `DataCollectionPlan_has_Detector` ( KEY `DataCollectionPlan_has_Detector_ibfk2` (`detectorId`), CONSTRAINT `DataCollectionPlan_has_Detector_ibfk1` FOREIGN KEY (`dataCollectionPlanId`) REFERENCES `DiffractionPlan` (`diffractionPlanId`), CONSTRAINT `DataCollectionPlan_has_Detector_ibfk2` FOREIGN KEY (`detectorId`) REFERENCES `Detector` (`detectorId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Detector`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1616,7 +1617,7 @@ CREATE TABLE `Detector` ( PRIMARY KEY (`detectorId`), UNIQUE KEY `Detector_ibuk1` (`detectorSerialNumber`), KEY `Detector_FKIndex1` (`detectorType`,`detectorManufacturer`,`detectorModel`,`detectorPixelSizeHorizontal`,`detectorPixelSizeVertical`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Detector table is linked to a dataCollection'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Detector table is linked to a dataCollection'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Dewar`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1654,7 +1655,7 @@ CREATE TABLE `Dewar` ( CONSTRAINT `Dewar_fk_dewarRegistryId` FOREIGN KEY (`dewarRegistryId`) REFERENCES `DewarRegistry` (`dewarRegistryId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Dewar_fk_firstExperimentId` FOREIGN KEY (`firstExperimentId`) REFERENCES `BLSession` (`sessionId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `Dewar_ibfk_1` FOREIGN KEY (`shippingId`) REFERENCES `Shipping` (`shippingId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarLocation`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1668,7 +1669,7 @@ CREATE TABLE `DewarLocation` ( `courierName` varchar(128) DEFAULT NULL COMMENT 'Carrier name who''s shipping back the dewar', `courierTrackingNumber` varchar(128) DEFAULT NULL COMMENT 'Tracking number of the shippment', PRIMARY KEY (`eventId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='ISPyB Dewar location table'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='ISPyB Dewar location table'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarLocationList`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1677,7 +1678,7 @@ CREATE TABLE `DewarLocationList` ( `locationId` int(10) unsigned NOT NULL AUTO_INCREMENT, `locationName` varchar(128) NOT NULL DEFAULT '' COMMENT 'Location', PRIMARY KEY (`locationId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='List of locations for dewars'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='List of locations for dewars'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarRegistry`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1697,7 +1698,7 @@ CREATE TABLE `DewarRegistry` ( KEY `DewarRegistry_ibfk_2` (`labContactId`), CONSTRAINT `DewarRegistry_ibfk_1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE NO ACTION ON UPDATE CASCADE, CONSTRAINT `DewarRegistry_ibfk_2` FOREIGN KEY (`labContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarRegistry_has_Proposal`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1718,7 +1719,7 @@ CREATE TABLE `DewarRegistry_has_Proposal` ( CONSTRAINT `DewarRegistry_has_Proposal_ibfk2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`), CONSTRAINT `DewarRegistry_has_Proposal_ibfk3` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`), CONSTRAINT `DewarRegistry_has_Proposal_ibfk4` FOREIGN KEY (`labContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarReport`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1732,7 +1733,7 @@ CREATE TABLE `DewarReport` ( PRIMARY KEY (`dewarReportId`), KEY `DewarReportIdx1` (`facilityCode`), CONSTRAINT `DewarReport_ibfk_1` FOREIGN KEY (`facilityCode`) REFERENCES `DewarRegistry` (`facilityCode`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DewarTransportHistory`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1746,7 +1747,7 @@ CREATE TABLE `DewarTransportHistory` ( PRIMARY KEY (`DewarTransportHistoryId`), KEY `DewarTransportHistory_FKIndex1` (`dewarId`), CONSTRAINT `DewarTransportHistory_ibfk_1` FOREIGN KEY (`dewarId`) REFERENCES `Dewar` (`dewarId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `DiffractionPlan`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1824,7 +1825,7 @@ CREATE TABLE `DiffractionPlan` ( CONSTRAINT `DiffractionPlan_ibfk1` FOREIGN KEY (`presetForProposalId`) REFERENCES `Proposal` (`proposalId`), CONSTRAINT `DiffractionPlan_ibfk2` FOREIGN KEY (`purificationColumnId`) REFERENCES `PurificationColumn` (`purificationColumnId`), CONSTRAINT `DiffractionPlan_ibfk3` FOREIGN KEY (`experimentTypeId`) REFERENCES `ExperimentType` (`experimentTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `EnergyScan`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1871,7 +1872,7 @@ CREATE TABLE `EnergyScan` ( CONSTRAINT `ES_ibfk_1` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ES_ibfk_2` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`), CONSTRAINT `ES_ibfk_3` FOREIGN KEY (`blSubSampleId`) REFERENCES `BLSubSample` (`blSubSampleId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Event`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1893,7 +1894,7 @@ CREATE TABLE `Event` ( CONSTRAINT `Event_ibfk_1` FOREIGN KEY (`eventChainId`) REFERENCES `EventChain` (`eventChainId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Event_ibfk_2` FOREIGN KEY (`componentId`) REFERENCES `Component` (`componentId`), CONSTRAINT `Event_ibfk_3` FOREIGN KEY (`eventTypeId`) REFERENCES `EventType` (`eventTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Describes an event that occurred during a data collection and should be taken into account for data analysis. Can optionally be repeated at a specified frequency.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Describes an event that occurred during a data collection and should be taken into account for data analysis. Can optionally be repeated at a specified frequency.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `EventChain`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1905,7 +1906,7 @@ CREATE TABLE `EventChain` ( PRIMARY KEY (`eventChainId`), KEY `dataCollectionId` (`dataCollectionId`), CONSTRAINT `EventChain_ibfk_1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Groups events together in a data collection.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Groups events together in a data collection.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `EventType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1915,7 +1916,7 @@ CREATE TABLE `EventType` ( `name` varchar(30) NOT NULL, PRIMARY KEY (`eventTypeId`), UNIQUE KEY `name` (`name`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Defines the list of event types which can occur during a data collection.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Defines the list of event types which can occur during a data collection.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ExperimentKindDetails`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1930,7 +1931,7 @@ CREATE TABLE `ExperimentKindDetails` ( PRIMARY KEY (`experimentKindId`), KEY `ExperimentKindDetails_FKIndex1` (`diffractionPlanId`), CONSTRAINT `EKD_ibfk_1` FOREIGN KEY (`diffractionPlanId`) REFERENCES `DiffractionPlan` (`diffractionPlanId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ExperimentType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1941,7 +1942,7 @@ CREATE TABLE `ExperimentType` ( `proposalType` varchar(10) DEFAULT NULL, `active` tinyint(1) DEFAULT 1 COMMENT '1=active, 0=inactive', PRIMARY KEY (`experimentTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='A lookup table for different types of experients'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='A lookup table for different types of experients'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `FoilHole`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1961,7 +1962,7 @@ CREATE TABLE `FoilHole` ( PRIMARY KEY (`foilHoleId`), KEY `FoilHole_fk_gridSquareId` (`gridSquareId`), CONSTRAINT `FoilHole_fk_gridSquareId` FOREIGN KEY (`gridSquareId`) REFERENCES `GridSquare` (`gridSquareId`) ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Details of a Cryo-EM foil hole within a grid square including image captured at foil hole magnification if applicable'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Details of a Cryo-EM foil hole within a grid square including image captured at foil hole magnification if applicable'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GeometryClassname`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1971,7 +1972,7 @@ CREATE TABLE `GeometryClassname` ( `geometryClassname` varchar(45) DEFAULT NULL, `geometryOrder` int(2) NOT NULL, PRIMARY KEY (`geometryClassnameId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GridImageMap`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -1986,7 +1987,7 @@ CREATE TABLE `GridImageMap` ( PRIMARY KEY (`gridImageMapId`), KEY `_GridImageMap_ibfk1` (`dataCollectionId`), CONSTRAINT `_GridImageMap_ibfk1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GridInfo`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2020,7 +2021,7 @@ CREATE TABLE `GridInfo` ( KEY `GridInfo_fk_dataCollectionId` (`dataCollectionId`), CONSTRAINT `GridInfo_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `GridInfo_ibfk_2` FOREIGN KEY (`dataCollectionGroupId`) REFERENCES `DataCollectionGroup` (`dataCollectionGroupId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `GridSquare`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2042,7 +2043,7 @@ CREATE TABLE `GridSquare` ( PRIMARY KEY (`gridSquareId`), KEY `GridSquare_fk_atlasId` (`atlasId`), CONSTRAINT `GridSquare_fk_atlasId` FOREIGN KEY (`atlasId`) REFERENCES `Atlas` (`atlasId`) ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Details of a Cryo-EM grid square including image captured at grid square magnification'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Details of a Cryo-EM grid square including image captured at grid square magnification'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Image`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2071,7 +2072,7 @@ CREATE TABLE `Image` ( KEY `motorPositionId` (`motorPositionId`), CONSTRAINT `Image_ibfk_1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Image_ibfk_2` FOREIGN KEY (`motorPositionId`) REFERENCES `MotorPosition` (`motorPositionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ImageQualityIndicators`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2096,7 +2097,7 @@ CREATE TABLE `ImageQualityIndicators` ( `dozor_score` double DEFAULT NULL COMMENT 'dozor_score', `driftFactor` float DEFAULT NULL COMMENT 'EM movie drift factor', PRIMARY KEY (`dataCollectionId`,`imageNumber`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Imager`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2108,7 +2109,7 @@ CREATE TABLE `Imager` ( `serial` varchar(45) DEFAULT NULL, `capacity` smallint(6) DEFAULT NULL, PRIMARY KEY (`imagerId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `InspectionType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2117,7 +2118,7 @@ CREATE TABLE `InspectionType` ( `inspectionTypeId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) DEFAULT NULL, PRIMARY KEY (`inspectionTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `IspybCrystalClass`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2127,7 +2128,7 @@ CREATE TABLE `IspybCrystalClass` ( `crystalClass_code` varchar(20) NOT NULL, `crystalClass_name` varchar(255) NOT NULL, PRIMARY KEY (`crystalClassId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='ISPyB crystal class values'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='ISPyB crystal class values'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `IspybReference`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2139,7 +2140,7 @@ CREATE TABLE `IspybReference` ( `referenceBibtext` blob DEFAULT NULL COMMENT 'bibtext value of the reference', `beamline` enum('All','ID14-4','ID23-1','ID23-2','ID29','XRF','AllXRF','Mesh') DEFAULT NULL COMMENT 'beamline involved', PRIMARY KEY (`referenceId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `LDAPSearchBase`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2152,7 +2153,7 @@ CREATE TABLE `LDAPSearchBase` ( PRIMARY KEY (`ldapSearchBaseId`), KEY `LDAPSearchBase_fk_ldapSearchParametersId` (`ldapSearchParametersId`), CONSTRAINT `LDAPSearchBase_fk_ldapSearchParametersId` FOREIGN KEY (`ldapSearchParametersId`) REFERENCES `LDAPSearchParameters` (`ldapSearchParametersId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='LDAP search base and the sequence number in which it should be attempted'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='LDAP search base and the sequence number in which it should be attempted'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `LDAPSearchParameters`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2166,7 +2167,7 @@ CREATE TABLE `LDAPSearchParameters` ( `filter` varchar(200) DEFAULT NULL COMMENT 'A filter string for the search', `attributes` varchar(255) NOT NULL COMMENT 'Comma-separated list of search attributes', PRIMARY KEY (`ldapSearchParametersId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='All necessary parameters to run an LDAP search, except the search base'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='All necessary parameters to run an LDAP search, except the search base'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `LabContact`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2188,7 +2189,7 @@ CREATE TABLE `LabContact` ( KEY `LabContact_FKIndex1` (`proposalId`), CONSTRAINT `LabContact_ibfk_1` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `LabContact_ibfk_2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Laboratory`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2207,7 +2208,7 @@ CREATE TABLE `Laboratory` ( `postcode` varchar(15) DEFAULT NULL, `EORINumber` varchar(17) DEFAULT NULL COMMENT 'An EORI number consists of an ISO Country code from an EU Member State (2 characters) + a maximum of 15 characters', PRIMARY KEY (`laboratoryId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Ligand`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2224,7 +2225,7 @@ CREATE TABLE `Ligand` ( PRIMARY KEY (`ligandId`), KEY `Ligand_fk_proposalId` (`proposalId`), CONSTRAINT `Ligand_fk_proposalId` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Ligands in biochemistry are substances that bind to biomolecules'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Ligands in biochemistry are substances that bind to biomolecules'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Ligand_has_PDB`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2236,7 +2237,7 @@ CREATE TABLE `Ligand_has_PDB` ( KEY `Ligand_Has_PDB_fk2` (`pdbId`), CONSTRAINT `Ligand_Has_PDB_fk1` FOREIGN KEY (`ligandId`) REFERENCES `Ligand` (`ligandId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Ligand_Has_PDB_fk2` FOREIGN KEY (`pdbId`) REFERENCES `PDB` (`pdbId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Junction table for Ligand and PDB'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Junction table for Ligand and PDB'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MXMRRun`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2257,7 +2258,7 @@ CREATE TABLE `MXMRRun` ( KEY `mxMRRun_FK2` (`autoProcProgramId`), CONSTRAINT `mxMRRun_FK1` FOREIGN KEY (`autoProcScalingId`) REFERENCES `AutoProcScaling` (`autoProcScalingId`), CONSTRAINT `mxMRRun_FK2` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MXMRRunBlob`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2283,7 +2284,7 @@ CREATE TABLE `MXMRRunBlob` ( PRIMARY KEY (`mxMRRunBlobId`), KEY `mxMRRunBlob_FK1` (`mxMRRunId`), CONSTRAINT `mxMRRunBlob_FK1` FOREIGN KEY (`mxMRRunId`) REFERENCES `MXMRRun` (`mxMRRunId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ModelBuilding`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2303,7 +2304,7 @@ CREATE TABLE `ModelBuilding` ( CONSTRAINT `ModelBuilding_phasingAnalysisfk_1` FOREIGN KEY (`phasingAnalysisId`) REFERENCES `PhasingAnalysis` (`phasingAnalysisId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ModelBuilding_phasingProgramRunfk_1` FOREIGN KEY (`phasingProgramRunId`) REFERENCES `PhasingProgramRun` (`phasingProgramRunId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ModelBuilding_spaceGroupfk_1` FOREIGN KEY (`spaceGroupId`) REFERENCES `SpaceGroup` (`spaceGroupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MotionCorrection`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2335,7 +2336,7 @@ CREATE TABLE `MotionCorrection` ( CONSTRAINT `MotionCorrection_ibfk2` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`), CONSTRAINT `MotionCorrection_ibfk3` FOREIGN KEY (`movieId`) REFERENCES `Movie` (`movieId`), CONSTRAINT `_MotionCorrection_ibfk1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `MotorPosition`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2355,7 +2356,7 @@ CREATE TABLE `MotorPosition` ( `gridIndexZ` int(11) DEFAULT NULL, `recordTimeStamp` timestamp NOT NULL DEFAULT current_timestamp() COMMENT 'Creation or last update date/time', PRIMARY KEY (`motorPositionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Movie`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2379,7 +2380,7 @@ CREATE TABLE `Movie` ( KEY `Movie_fk_foilHoleId` (`foilHoleId`), CONSTRAINT `Movie_fk_foilHoleId` FOREIGN KEY (`foilHoleId`) REFERENCES `FoilHole` (`foilHoleId`) ON DELETE NO ACTION ON UPDATE CASCADE, CONSTRAINT `Movie_ibfk1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PDB`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2387,11 +2388,11 @@ DROP TABLE IF EXISTS `PDB`; CREATE TABLE `PDB` ( `pdbId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(255) DEFAULT NULL, - `contents` mediumtext /*!100301 COMPRESSED*/ CHARACTER SET utf8mb3 DEFAULT NULL, + `contents` mediumtext /*M!100301 COMPRESSED*/ CHARACTER SET utf8mb3 COLLATE utf8mb3_general_ci DEFAULT NULL, `code` varchar(4) DEFAULT NULL, `source` varchar(30) DEFAULT NULL COMMENT 'Could be e.g. AlphaFold or RoseTTAFold', PRIMARY KEY (`pdbId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PDBEntry`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2420,7 +2421,7 @@ CREATE TABLE `PDBEntry` ( PRIMARY KEY (`pdbEntryId`), KEY `pdbEntryIdx1` (`autoProcProgramId`), CONSTRAINT `pdbEntry_FK1` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PDBEntry_has_AutoProcProgram`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2435,7 +2436,7 @@ CREATE TABLE `PDBEntry_has_AutoProcProgram` ( KEY `pdbEntry_AutoProcProgramIdx2` (`autoProcProgramId`), CONSTRAINT `pdbEntry_AutoProcProgram_FK1` FOREIGN KEY (`pdbEntryId`) REFERENCES `PDBEntry` (`pdbEntryId`) ON DELETE CASCADE, CONSTRAINT `pdbEntry_AutoProcProgram_FK2` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticleClassification`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2460,7 +2461,7 @@ CREATE TABLE `ParticleClassification` ( PRIMARY KEY (`particleClassificationId`), KEY `ParticleClassification_fk_particleClassificationGroupId` (`particleClassificationGroupId`), CONSTRAINT `ParticleClassification_fk_particleClassificationGroupId` FOREIGN KEY (`particleClassificationGroupId`) REFERENCES `ParticleClassificationGroup` (`particleClassificationGroupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Results of 2D or 2D classification'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Results of 2D or 2D classification'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticleClassificationGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2480,7 +2481,7 @@ CREATE TABLE `ParticleClassificationGroup` ( KEY `ParticleClassificationGroup_fk_programId` (`programId`), CONSTRAINT `ParticleClassificationGroup_fk_particlePickerId` FOREIGN KEY (`particlePickerId`) REFERENCES `ParticlePicker` (`particlePickerId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ParticleClassificationGroup_fk_programId` FOREIGN KEY (`programId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE NO ACTION ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticleClassification_has_CryoemInitialModel`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2492,7 +2493,7 @@ CREATE TABLE `ParticleClassification_has_CryoemInitialModel` ( KEY `ParticleClassification_has_InitialModel_fk2` (`cryoemInitialModelId`), CONSTRAINT `ParticleClassification_has_CryoemInitialModel_fk1` FOREIGN KEY (`particleClassificationId`) REFERENCES `ParticleClassification` (`particleClassificationId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ParticleClassification_has_InitialModel_fk2` FOREIGN KEY (`cryoemInitialModelId`) REFERENCES `CryoemInitialModel` (`cryoemInitialModelId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ParticlePicker`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2510,7 +2511,7 @@ CREATE TABLE `ParticlePicker` ( KEY `ParticlePicker_fk_motionCorrectionId` (`firstMotionCorrectionId`), CONSTRAINT `ParticlePicker_fk_motionCorrectionId` FOREIGN KEY (`firstMotionCorrectionId`) REFERENCES `MotionCorrection` (`motionCorrectionId`) ON DELETE NO ACTION ON UPDATE CASCADE, CONSTRAINT `ParticlePicker_fk_programId` FOREIGN KEY (`programId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE NO ACTION ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='An instance of a particle picker program that was run'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='An instance of a particle picker program that was run'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Permission`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2520,7 +2521,7 @@ CREATE TABLE `Permission` ( `type` varchar(15) NOT NULL, `description` varchar(100) DEFAULT NULL, PRIMARY KEY (`permissionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2546,7 +2547,7 @@ CREATE TABLE `Person` ( KEY `Person_FKIndexFamilyName` (`familyName`), KEY `siteId` (`siteId`), CONSTRAINT `Person_ibfk_1` FOREIGN KEY (`laboratoryId`) REFERENCES `Laboratory` (`laboratoryId`) ON DELETE NO ACTION ON UPDATE NO ACTION -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Phasing`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2569,7 +2570,7 @@ CREATE TABLE `Phasing` ( CONSTRAINT `Phasing_phasingAnalysisfk_1` FOREIGN KEY (`phasingAnalysisId`) REFERENCES `PhasingAnalysis` (`phasingAnalysisId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Phasing_phasingProgramRunfk_1` FOREIGN KEY (`phasingProgramRunId`) REFERENCES `PhasingProgramRun` (`phasingProgramRunId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Phasing_spaceGroupfk_1` FOREIGN KEY (`spaceGroupId`) REFERENCES `SpaceGroup` (`spaceGroupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingAnalysis`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2578,7 +2579,7 @@ CREATE TABLE `PhasingAnalysis` ( `phasingAnalysisId` int(11) unsigned NOT NULL AUTO_INCREMENT COMMENT 'Primary key (auto-incremented)', `recordTimeStamp` datetime DEFAULT NULL COMMENT 'Creation or last update date/time', PRIMARY KEY (`phasingAnalysisId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingProgramAttachment`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2593,7 +2594,7 @@ CREATE TABLE `PhasingProgramAttachment` ( PRIMARY KEY (`phasingProgramAttachmentId`), KEY `PhasingProgramAttachment_FKIndex1` (`phasingProgramRunId`), CONSTRAINT `Phasing_phasingProgramAttachmentfk_1` FOREIGN KEY (`phasingProgramRunId`) REFERENCES `PhasingProgramRun` (`phasingProgramRunId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingProgramRun`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2609,7 +2610,7 @@ CREATE TABLE `PhasingProgramRun` ( `phasingEnvironment` varchar(255) DEFAULT NULL COMMENT 'Cpus, Nodes,...', `recordTimeStamp` datetime DEFAULT current_timestamp(), PRIMARY KEY (`phasingProgramRunId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingStatistics`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2634,7 +2635,7 @@ CREATE TABLE `PhasingStatistics` ( CONSTRAINT `PhasingStatistics_phasingHasScalingfk_1` FOREIGN KEY (`phasingHasScalingId1`) REFERENCES `Phasing_has_Scaling` (`phasingHasScalingId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `PhasingStatistics_phasingHasScalingfk_2` FOREIGN KEY (`phasingHasScalingId2`) REFERENCES `Phasing_has_Scaling` (`phasingHasScalingId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `fk_PhasingStatistics_phasingStep` FOREIGN KEY (`phasingStepId`) REFERENCES `PhasingStep` (`phasingStepId`) ON DELETE NO ACTION ON UPDATE NO ACTION -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PhasingStep`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2661,7 +2662,7 @@ CREATE TABLE `PhasingStep` ( CONSTRAINT `FK_autoprocScaling` FOREIGN KEY (`autoProcScalingId`) REFERENCES `AutoProcScaling` (`autoProcScalingId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `FK_program` FOREIGN KEY (`programRunId`) REFERENCES `PhasingProgramRun` (`phasingProgramRunId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `FK_spacegroup` FOREIGN KEY (`spaceGroupId`) REFERENCES `SpaceGroup` (`spaceGroupId`) ON DELETE NO ACTION ON UPDATE NO ACTION -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Phasing_has_Scaling`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2677,7 +2678,7 @@ CREATE TABLE `Phasing_has_Scaling` ( KEY `PhasingHasScaling_FKIndex2` (`autoProcScalingId`), CONSTRAINT `PhasingHasScaling_autoProcScalingfk_1` FOREIGN KEY (`autoProcScalingId`) REFERENCES `AutoProcScaling` (`autoProcScalingId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `PhasingHasScaling_phasingAnalysisfk_1` FOREIGN KEY (`phasingAnalysisId`) REFERENCES `PhasingAnalysis` (`phasingAnalysisId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Position`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2696,7 +2697,7 @@ CREATE TABLE `Position` ( PRIMARY KEY (`positionId`), KEY `Position_FKIndex1` (`relativePositionId`), CONSTRAINT `Position_relativePositionfk_1` FOREIGN KEY (`relativePositionId`) REFERENCES `Position` (`positionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Positioner`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2706,7 +2707,7 @@ CREATE TABLE `Positioner` ( `positioner` varchar(50) NOT NULL, `value` float NOT NULL, PRIMARY KEY (`positionerId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='An arbitrary positioner and its value, could be e.g. a motor. Allows for instance to store some positions with a sample or subsample'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='An arbitrary positioner and its value, could be e.g. a motor. Allows for instance to store some positions with a sample or subsample'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PreparePhasingData`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2726,7 +2727,7 @@ CREATE TABLE `PreparePhasingData` ( CONSTRAINT `PreparePhasingData_phasingAnalysisfk_1` FOREIGN KEY (`phasingAnalysisId`) REFERENCES `PhasingAnalysis` (`phasingAnalysisId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `PreparePhasingData_phasingProgramRunfk_1` FOREIGN KEY (`phasingProgramRunId`) REFERENCES `PhasingProgramRun` (`phasingProgramRunId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `PreparePhasingData_spaceGroupfk_1` FOREIGN KEY (`spaceGroupId`) REFERENCES `SpaceGroup` (`spaceGroupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessedTomogram`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2739,7 +2740,7 @@ CREATE TABLE `ProcessedTomogram` ( PRIMARY KEY (`processedTomogramId`), KEY `tomogramId` (`tomogramId`), CONSTRAINT `ProcessedTomogram_ibfk_1` FOREIGN KEY (`tomogramId`) REFERENCES `Tomogram` (`tomogramId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Indicates the sample''s location on a multi-sample pin, where 1 is closest to the pin base or a sample''s position in a cryo-EM cassette'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Indicates the sample''s location on a multi-sample pin, where 1 is closest to the pin base or a sample''s position in a cryo-EM cassette'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingJob`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2755,7 +2756,7 @@ CREATE TABLE `ProcessingJob` ( PRIMARY KEY (`processingJobId`), KEY `ProcessingJob_ibfk1` (`dataCollectionId`), CONSTRAINT `ProcessingJob_ibfk1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='From this we get both job times and lag times'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='From this we get both job times and lag times'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingJobImageSweep`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2771,7 +2772,7 @@ CREATE TABLE `ProcessingJobImageSweep` ( KEY `ProcessingJobImageSweep_ibfk2` (`dataCollectionId`), CONSTRAINT `ProcessingJobImageSweep_ibfk1` FOREIGN KEY (`processingJobId`) REFERENCES `ProcessingJob` (`processingJobId`), CONSTRAINT `ProcessingJobImageSweep_ibfk2` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='This allows multiple sweeps per processing job for multi-xia2'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='This allows multiple sweeps per processing job for multi-xia2'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingJobParameter`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2785,7 +2786,7 @@ CREATE TABLE `ProcessingJobParameter` ( KEY `ProcessingJobParameter_ibfk1` (`processingJobId`), KEY `ProcessingJobParameter_idx_paramKey_procJobId` (`parameterKey`,`processingJobId`), CONSTRAINT `ProcessingJobParameter_ibfk1` FOREIGN KEY (`processingJobId`) REFERENCES `ProcessingJob` (`processingJobId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingPipeline`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2800,7 +2801,7 @@ CREATE TABLE `ProcessingPipeline` ( PRIMARY KEY (`processingPipelineId`), KEY `ProcessingPipeline_fk1` (`processingPipelineCategoryId`), CONSTRAINT `ProcessingPipeline_fk1` FOREIGN KEY (`processingPipelineCategoryId`) REFERENCES `ProcessingPipelineCategory` (`processingPipelineCategoryId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='A lookup table for different processing pipelines and their categories'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='A lookup table for different processing pipelines and their categories'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProcessingPipelineCategory`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2809,7 +2810,7 @@ CREATE TABLE `ProcessingPipelineCategory` ( `processingPipelineCategoryId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(20) NOT NULL, PRIMARY KEY (`processingPipelineCategoryId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='A lookup table for the category of processing pipeline'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='A lookup table for the category of processing pipeline'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2823,7 +2824,7 @@ CREATE TABLE `Project` ( PRIMARY KEY (`projectId`), KEY `Project_FK1` (`personId`), CONSTRAINT `Project_FK1` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_BLSample`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2835,7 +2836,7 @@ CREATE TABLE `Project_has_BLSample` ( KEY `Project_has_BLSample_FK2` (`blSampleId`), CONSTRAINT `Project_has_BLSample_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Project_has_BLSample_FK2` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_DCGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2847,7 +2848,7 @@ CREATE TABLE `Project_has_DCGroup` ( KEY `Project_has_DCGroup_FK2` (`dataCollectionGroupId`), CONSTRAINT `Project_has_DCGroup_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Project_has_DCGroup_FK2` FOREIGN KEY (`dataCollectionGroupId`) REFERENCES `DataCollectionGroup` (`dataCollectionGroupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_EnergyScan`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2859,7 +2860,7 @@ CREATE TABLE `Project_has_EnergyScan` ( KEY `project_has_energyscan_FK2` (`energyScanId`), CONSTRAINT `project_has_energyscan_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `project_has_energyscan_FK2` FOREIGN KEY (`energyScanId`) REFERENCES `EnergyScan` (`energyScanId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2871,7 +2872,7 @@ CREATE TABLE `Project_has_Person` ( KEY `project_has_person_FK2` (`personId`), CONSTRAINT `project_has_person_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE, CONSTRAINT `project_has_person_FK2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Protein`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2883,7 +2884,7 @@ CREATE TABLE `Project_has_Protein` ( KEY `project_has_protein_FK2` (`proteinId`), CONSTRAINT `project_has_protein_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE, CONSTRAINT `project_has_protein_FK2` FOREIGN KEY (`proteinId`) REFERENCES `Protein` (`proteinId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Session`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2895,7 +2896,7 @@ CREATE TABLE `Project_has_Session` ( KEY `project_has_session_FK2` (`sessionId`), CONSTRAINT `project_has_session_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `project_has_session_FK2` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_Shipping`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2907,7 +2908,7 @@ CREATE TABLE `Project_has_Shipping` ( KEY `project_has_shipping_FK2` (`shippingId`), CONSTRAINT `project_has_shipping_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE, CONSTRAINT `project_has_shipping_FK2` FOREIGN KEY (`shippingId`) REFERENCES `Shipping` (`shippingId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_User`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2919,7 +2920,7 @@ CREATE TABLE `Project_has_User` ( PRIMARY KEY (`projecthasuserid`), KEY `Project_Has_user_FK1` (`projectid`), CONSTRAINT `Project_Has_user_FK1` FOREIGN KEY (`projectid`) REFERENCES `Project` (`projectId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Project_has_XFEFSpectrum`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2931,7 +2932,7 @@ CREATE TABLE `Project_has_XFEFSpectrum` ( KEY `project_has_xfefspectrum_FK2` (`xfeFluorescenceSpectrumId`), CONSTRAINT `project_has_xfefspectrum_FK1` FOREIGN KEY (`projectId`) REFERENCES `Project` (`projectId`) ON DELETE CASCADE, CONSTRAINT `project_has_xfefspectrum_FK2` FOREIGN KEY (`xfeFluorescenceSpectrumId`) REFERENCES `XFEFluorescenceSpectrum` (`xfeFluorescenceSpectrumId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Proposal`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2946,11 +2947,13 @@ CREATE TABLE `Proposal` ( `proposalType` varchar(2) DEFAULT NULL COMMENT 'Proposal type: MX, BX', `externalId` binary(16) DEFAULT NULL, `state` enum('Open','Closed','Cancelled') DEFAULT 'Open', + `startDate` datetime DEFAULT NULL COMMENT 'Start of the allocation period', + `endDate` datetime DEFAULT NULL COMMENT 'End of the allocation period', PRIMARY KEY (`proposalId`), UNIQUE KEY `Proposal_FKIndexCodeNumber` (`proposalCode`,`proposalNumber`), KEY `Proposal_FKIndex1` (`personId`), CONSTRAINT `Proposal_ibfk_1` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ProposalHasPerson`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2965,7 +2968,7 @@ CREATE TABLE `ProposalHasPerson` ( KEY `fk_ProposalHasPerson_Personal` (`personId`), CONSTRAINT `fk_ProposalHasPerson_Personal` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `fk_ProposalHasPerson_Proposal` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE NO ACTION ON UPDATE NO ACTION -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Protein`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3002,7 +3005,7 @@ CREATE TABLE `Protein` ( CONSTRAINT `Protein_ibfk_1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `protein_fk3` FOREIGN KEY (`componentTypeId`) REFERENCES `ComponentType` (`componentTypeId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `protein_fk4` FOREIGN KEY (`concentrationTypeId`) REFERENCES `ConcentrationType` (`concentrationTypeId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Protein_has_PDB`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3016,7 +3019,7 @@ CREATE TABLE `Protein_has_PDB` ( KEY `Protein_Has_PDB_fk2` (`pdbid`), CONSTRAINT `Protein_Has_PDB_fk1` FOREIGN KEY (`proteinid`) REFERENCES `Protein` (`proteinId`), CONSTRAINT `Protein_Has_PDB_fk2` FOREIGN KEY (`pdbid`) REFERENCES `PDB` (`pdbId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `PurificationColumn`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3026,7 +3029,7 @@ CREATE TABLE `PurificationColumn` ( `name` varchar(100) DEFAULT NULL, `active` tinyint(1) DEFAULT 1 COMMENT '1=active, 0=inactive', PRIMARY KEY (`purificationColumnId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Size exclusion chromotography (SEC) lookup table for BioSAXS'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Size exclusion chromotography (SEC) lookup table for BioSAXS'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `RelativeIceThickness`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3069,7 +3072,7 @@ CREATE TABLE `RobotAction` ( KEY `RobotAction_FK2` (`blsampleId`), CONSTRAINT `RobotAction_FK1` FOREIGN KEY (`blsessionId`) REFERENCES `BLSession` (`sessionId`), CONSTRAINT `RobotAction_FK2` FOREIGN KEY (`blsampleId`) REFERENCES `BLSample` (`blSampleId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Robot actions as reported by GDA'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Robot actions as reported by GDA'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SSXDataCollection`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3088,7 +3091,7 @@ CREATE TABLE `SSXDataCollection` ( `experimentName` varchar(255) DEFAULT NULL, PRIMARY KEY (`dataCollectionId`), CONSTRAINT `SSXDataCollection_ibfk_1` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Extends DataCollection with SSX-specific fields.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Extends DataCollection with SSX-specific fields.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SW_onceToken`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3106,7 +3109,7 @@ CREATE TABLE `SW_onceToken` ( KEY `SW_onceToken_recordTimeStamp_idx` (`recordTimeStamp`), CONSTRAINT `SW_onceToken_fk1` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`), CONSTRAINT `SW_onceToken_fk2` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='One-time use tokens needed for token auth in order to grant access to file downloads and webcams (and some images)'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='One-time use tokens needed for token auth in order to grant access to file downloads and webcams (and some images)'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SampleComposition`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3126,7 +3129,7 @@ CREATE TABLE `SampleComposition` ( CONSTRAINT `SampleComposition_ibfk_1` FOREIGN KEY (`componentId`) REFERENCES `Component` (`componentId`), CONSTRAINT `SampleComposition_ibfk_2` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`), CONSTRAINT `SampleComposition_ibfk_3` FOREIGN KEY (`concentrationTypeId`) REFERENCES `ConcentrationType` (`concentrationTypeId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Links a sample to its components with a specified abundance or ratio.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Links a sample to its components with a specified abundance or ratio.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScanParametersModel`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3146,7 +3149,7 @@ CREATE TABLE `ScanParametersModel` ( KEY `PDF_Model_ibfk2` (`dataCollectionPlanId`), CONSTRAINT `PDF_Model_ibfk1` FOREIGN KEY (`scanParametersServiceId`) REFERENCES `ScanParametersService` (`scanParametersServiceId`) ON UPDATE CASCADE, CONSTRAINT `PDF_Model_ibfk2` FOREIGN KEY (`dataCollectionPlanId`) REFERENCES `DiffractionPlan` (`diffractionPlanId`) ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScanParametersService`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3156,7 +3159,7 @@ CREATE TABLE `ScanParametersService` ( `name` varchar(45) DEFAULT NULL, `description` varchar(45) DEFAULT NULL, PRIMARY KEY (`scanParametersServiceId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Schedule`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3165,7 +3168,7 @@ CREATE TABLE `Schedule` ( `scheduleId` int(11) unsigned NOT NULL AUTO_INCREMENT, `name` varchar(45) DEFAULT NULL, PRIMARY KEY (`scheduleId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScheduleComponent`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3180,7 +3183,7 @@ CREATE TABLE `ScheduleComponent` ( KEY `ScheduleComponent_fk2` (`inspectionTypeId`), CONSTRAINT `ScheduleComponent_fk1` FOREIGN KEY (`scheduleId`) REFERENCES `Schedule` (`scheduleId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ScheduleComponent_fk2` FOREIGN KEY (`inspectionTypeId`) REFERENCES `InspectionType` (`inspectionTypeId`) ON DELETE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SchemaStatus`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3192,7 +3195,7 @@ CREATE TABLE `SchemaStatus` ( `recordTimeStamp` timestamp NOT NULL DEFAULT current_timestamp(), PRIMARY KEY (`schemaStatusId`), UNIQUE KEY `scriptName` (`scriptName`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Screen`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3208,7 +3211,7 @@ CREATE TABLE `Screen` ( KEY `Screen_fk_containerTypeId` (`containerTypeId`), CONSTRAINT `Screen_fk1` FOREIGN KEY (`proposalId`) REFERENCES `Proposal` (`proposalId`), CONSTRAINT `Screen_fk_containerTypeId` FOREIGN KEY (`containerTypeId`) REFERENCES `ContainerType` (`containerTypeId`) ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreenComponent`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3224,7 +3227,7 @@ CREATE TABLE `ScreenComponent` ( KEY `ScreenComponent_fk2` (`componentId`), CONSTRAINT `ScreenComponent_fk1` FOREIGN KEY (`screenComponentGroupId`) REFERENCES `ScreenComponentGroup` (`screenComponentGroupId`), CONSTRAINT `ScreenComponent_fk2` FOREIGN KEY (`componentId`) REFERENCES `Protein` (`proteinId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreenComponentGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3236,7 +3239,7 @@ CREATE TABLE `ScreenComponentGroup` ( PRIMARY KEY (`screenComponentGroupId`), KEY `ScreenComponentGroup_fk1` (`screenId`), CONSTRAINT `ScreenComponentGroup_fk1` FOREIGN KEY (`screenId`) REFERENCES `Screen` (`screenId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Screening`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3260,7 +3263,7 @@ CREATE TABLE `Screening` ( CONSTRAINT `Screening_fk_autoProcProgramId` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `Screening_ibfk_1` FOREIGN KEY (`dataCollectionGroupId`) REFERENCES `DataCollectionGroup` (`dataCollectionGroupId`) ON DELETE NO ACTION ON UPDATE NO ACTION, CONSTRAINT `_Screening_ibfk2` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningInput`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3279,7 +3282,7 @@ CREATE TABLE `ScreeningInput` ( PRIMARY KEY (`screeningInputId`), KEY `ScreeningInput_FKIndex1` (`screeningId`), CONSTRAINT `ScreeningInput_ibfk_1` FOREIGN KEY (`screeningId`) REFERENCES `Screening` (`screeningId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningOutput`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3315,7 +3318,7 @@ CREATE TABLE `ScreeningOutput` ( PRIMARY KEY (`screeningOutputId`), KEY `ScreeningOutput_FKIndex1` (`screeningId`), CONSTRAINT `ScreeningOutput_ibfk_1` FOREIGN KEY (`screeningId`) REFERENCES `Screening` (`screeningId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningOutputLattice`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3346,7 +3349,7 @@ CREATE TABLE `ScreeningOutputLattice` ( PRIMARY KEY (`screeningOutputLatticeId`), KEY `ScreeningOutputLattice_FKIndex1` (`screeningOutputId`), CONSTRAINT `ScreeningOutputLattice_ibfk_1` FOREIGN KEY (`screeningOutputId`) REFERENCES `ScreeningOutput` (`screeningOutputId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningRank`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3362,7 +3365,7 @@ CREATE TABLE `ScreeningRank` ( KEY `ScreeningRank_FKIndex2` (`screeningRankSetId`), CONSTRAINT `ScreeningRank_ibfk_1` FOREIGN KEY (`screeningId`) REFERENCES `Screening` (`screeningId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ScreeningRank_ibfk_2` FOREIGN KEY (`screeningRankSetId`) REFERENCES `ScreeningRankSet` (`screeningRankSetId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningRankSet`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3373,7 +3376,7 @@ CREATE TABLE `ScreeningRankSet` ( `rankingProjectFileName` varchar(255) DEFAULT NULL, `rankingSummaryFileName` varchar(255) DEFAULT NULL, PRIMARY KEY (`screeningRankSetId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningStrategy`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3395,7 +3398,7 @@ CREATE TABLE `ScreeningStrategy` ( PRIMARY KEY (`screeningStrategyId`), KEY `ScreeningStrategy_FKIndex1` (`screeningOutputId`), CONSTRAINT `ScreeningStrategy_ibfk_1` FOREIGN KEY (`screeningOutputId`) REFERENCES `ScreeningOutput` (`screeningOutputId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningStrategySubWedge`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3419,7 +3422,7 @@ CREATE TABLE `ScreeningStrategySubWedge` ( PRIMARY KEY (`screeningStrategySubWedgeId`), KEY `ScreeningStrategySubWedge_FK1` (`screeningStrategyWedgeId`), CONSTRAINT `ScreeningStrategySubWedge_FK1` FOREIGN KEY (`screeningStrategyWedgeId`) REFERENCES `ScreeningStrategyWedge` (`screeningStrategyWedgeId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ScreeningStrategyWedge`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3441,7 +3444,7 @@ CREATE TABLE `ScreeningStrategyWedge` ( PRIMARY KEY (`screeningStrategyWedgeId`), KEY `ScreeningStrategyWedge_IBFK_1` (`screeningStrategyId`), CONSTRAINT `ScreeningStrategyWedge_IBFK_1` FOREIGN KEY (`screeningStrategyId`) REFERENCES `ScreeningStrategy` (`screeningStrategyId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SessionType`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3453,7 +3456,7 @@ CREATE TABLE `SessionType` ( PRIMARY KEY (`sessionTypeId`), KEY `SessionType_FKIndex1` (`sessionId`), CONSTRAINT `SessionType_ibfk_1` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Session_has_Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3467,7 +3470,7 @@ CREATE TABLE `Session_has_Person` ( KEY `Session_has_Person_FKIndex2` (`personId`), CONSTRAINT `Session_has_Person_ibfk_1` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Session_has_Person_ibfk_2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Shipping`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3520,7 +3523,7 @@ CREATE TABLE `Shipping` ( CONSTRAINT `Shipping_ibfk_2` FOREIGN KEY (`sendingLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `Shipping_ibfk_3` FOREIGN KEY (`returnLabContactId`) REFERENCES `LabContact` (`labContactId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `Shipping_ibfk_4` FOREIGN KEY (`deliveryAgent_flightCodePersonId`) REFERENCES `Person` (`personId`) ON DELETE SET NULL ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `ShippingHasSession`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3532,7 +3535,7 @@ CREATE TABLE `ShippingHasSession` ( KEY `ShippingHasSession_FKIndex2` (`sessionId`), CONSTRAINT `ShippingHasSession_ibfk_1` FOREIGN KEY (`shippingId`) REFERENCES `Shipping` (`shippingId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `ShippingHasSession_ibfk_2` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Sleeve`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3543,7 +3546,7 @@ CREATE TABLE `Sleeve` ( `lastMovedToFreezer` timestamp NOT NULL DEFAULT current_timestamp(), `lastMovedFromFreezer` timestamp NULL DEFAULT current_timestamp(), PRIMARY KEY (`sleeveId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Registry of ice-filled sleeves used to cool plates whilst on the goniometer'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='Registry of ice-filled sleeves used to cool plates whilst on the goniometer'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SpaceGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3562,7 +3565,7 @@ CREATE TABLE `SpaceGroup` ( KEY `geometryClassnameId` (`geometryClassnameId`), KEY `SpaceGroup_FKShortName` (`spaceGroupShortName`), CONSTRAINT `SpaceGroup_ibfk_1` FOREIGN KEY (`geometryClassnameId`) REFERENCES `GeometryClassname` (`geometryClassnameId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `SubstructureDetermination`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3583,7 +3586,7 @@ CREATE TABLE `SubstructureDetermination` ( CONSTRAINT `SubstructureDetermination_phasingAnalysisfk_1` FOREIGN KEY (`phasingAnalysisId`) REFERENCES `PhasingAnalysis` (`phasingAnalysisId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `SubstructureDetermination_phasingProgramRunfk_1` FOREIGN KEY (`phasingProgramRunId`) REFERENCES `PhasingProgramRun` (`phasingProgramRunId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `SubstructureDetermination_spaceGroupfk_1` FOREIGN KEY (`spaceGroupId`) REFERENCES `SpaceGroup` (`spaceGroupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `TiltImageAlignment`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3604,7 +3607,7 @@ CREATE TABLE `TiltImageAlignment` ( KEY `TiltImageAlignment_fk_tomogramId` (`tomogramId`), CONSTRAINT `TiltImageAlignment_fk_movieId` FOREIGN KEY (`movieId`) REFERENCES `Movie` (`movieId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `TiltImageAlignment_fk_tomogramId` FOREIGN KEY (`tomogramId`) REFERENCES `Tomogram` (`tomogramId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='For storing per-movie analysis results (reconstruction)'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='For storing per-movie analysis results (reconstruction)'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Tomogram`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3642,7 +3645,7 @@ CREATE TABLE `Tomogram` ( CONSTRAINT `Tomogram_fk_autoProcProgramId` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `Tomogram_fk_dataCollectionId` FOREIGN KEY (`dataCollectionId`) REFERENCES `DataCollection` (`dataCollectionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `Tomogram_fk_gridSquareId` FOREIGN KEY (`gridSquareId`) REFERENCES `GridSquare` (`gridSquareId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='For storing per-sample, per-position data analysis results (reconstruction)'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='For storing per-sample, per-position data analysis results (reconstruction)'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3652,7 +3655,7 @@ CREATE TABLE `UserGroup` ( `name` varchar(31) NOT NULL, PRIMARY KEY (`userGroupId`), UNIQUE KEY `UserGroup_idx1` (`name`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup_has_LDAPSearchParameters`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3665,7 +3668,7 @@ CREATE TABLE `UserGroup_has_LDAPSearchParameters` ( KEY `UserGroup_has_LDAPSearchParameters_fk2` (`ldapSearchParametersId`), CONSTRAINT `UserGroup_has_LDAPSearchParameters_fk1` FOREIGN KEY (`userGroupId`) REFERENCES `UserGroup` (`userGroupId`), CONSTRAINT `UserGroup_has_LDAPSearchParameters_fk2` FOREIGN KEY (`ldapSearchParametersId`) REFERENCES `LDAPSearchParameters` (`ldapSearchParametersId`) -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Gives the LDAP search parameters needed to find a set of usergroup members'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Gives the LDAP search parameters needed to find a set of usergroup members'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup_has_Permission`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3677,7 +3680,7 @@ CREATE TABLE `UserGroup_has_Permission` ( KEY `UserGroup_has_Permission_fk2` (`permissionId`), CONSTRAINT `UserGroup_has_Permission_fk1` FOREIGN KEY (`userGroupId`) REFERENCES `UserGroup` (`userGroupId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `UserGroup_has_Permission_fk2` FOREIGN KEY (`permissionId`) REFERENCES `Permission` (`permissionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `UserGroup_has_Person`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3689,7 +3692,7 @@ CREATE TABLE `UserGroup_has_Person` ( KEY `userGroup_has_Person_fk2` (`personId`), CONSTRAINT `userGroup_has_Person_fk1` FOREIGN KEY (`userGroupId`) REFERENCES `UserGroup` (`userGroupId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `userGroup_has_Person_fk2` FOREIGN KEY (`personId`) REFERENCES `Person` (`personId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XFEFluorescenceComposite`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3710,7 +3713,7 @@ CREATE TABLE `XFEFluorescenceComposite` ( CONSTRAINT `XFEFluorescenceComposite_ibfk1` FOREIGN KEY (`r`) REFERENCES `XRFFluorescenceMapping` (`xrfFluorescenceMappingId`), CONSTRAINT `XFEFluorescenceComposite_ibfk2` FOREIGN KEY (`g`) REFERENCES `XRFFluorescenceMapping` (`xrfFluorescenceMappingId`), CONSTRAINT `XFEFluorescenceComposite_ibfk3` FOREIGN KEY (`b`) REFERENCES `XRFFluorescenceMapping` (`xrfFluorescenceMappingId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='A composite XRF map composed of three XRFFluorescenceMapping entries creating r, g, b layers'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='A composite XRF map composed of three XRFFluorescenceMapping entries creating r, g, b layers'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XFEFluorescenceSpectrum`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3745,7 +3748,7 @@ CREATE TABLE `XFEFluorescenceSpectrum` ( CONSTRAINT `XFE_ibfk_1` FOREIGN KEY (`sessionId`) REFERENCES `BLSession` (`sessionId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `XFE_ibfk_2` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `XFE_ibfk_3` FOREIGN KEY (`blSubSampleId`) REFERENCES `BLSubSample` (`blSubSampleId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XRFFluorescenceMapping`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3769,7 +3772,7 @@ CREATE TABLE `XRFFluorescenceMapping` ( CONSTRAINT `XRFFluorescenceMapping_ibfk1` FOREIGN KEY (`xrfFluorescenceMappingROIId`) REFERENCES `XRFFluorescenceMappingROI` (`xrfFluorescenceMappingROIId`) ON DELETE CASCADE ON UPDATE CASCADE, CONSTRAINT `XRFFluorescenceMapping_ibfk2` FOREIGN KEY (`gridInfoId`) REFERENCES `GridInfo` (`gridInfoId`), CONSTRAINT `XRFFluorescenceMapping_ibfk3` FOREIGN KEY (`autoProcProgramId`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='An XRF map generated from an XRF Mapping ROI based on data from a gridscan of a sample'; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci COMMENT='An XRF map generated from an XRF Mapping ROI based on data from a gridscan of a sample'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XRFFluorescenceMappingROI`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3788,7 +3791,7 @@ CREATE TABLE `XRFFluorescenceMappingROI` ( PRIMARY KEY (`xrfFluorescenceMappingROIId`), KEY `XRFFluorescenceMappingROI_FKblSampleId` (`blSampleId`), CONSTRAINT `XRFFluorescenceMappingROI_FKblSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XrayCentring`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3801,7 +3804,7 @@ CREATE TABLE `XrayCentring` ( PRIMARY KEY (`xrayCentringId`), KEY `dataCollectionGroupId` (`dataCollectionGroupId`), CONSTRAINT `XrayCentring_ibfk_1` FOREIGN KEY (`dataCollectionGroupId`) REFERENCES `DataCollectionGroup` (`dataCollectionGroupId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Xray Centring analysis associated with one or more grid scans.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Xray Centring analysis associated with one or more grid scans.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `XrayCentringResult`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3831,7 +3834,7 @@ CREATE TABLE `XrayCentringResult` ( KEY `XrayCentringResult_fk_blSampleId` (`blSampleId`), CONSTRAINT `XrayCentringResult_fk_blSampleId` FOREIGN KEY (`blSampleId`) REFERENCES `BLSample` (`blSampleId`) ON DELETE SET NULL ON UPDATE CASCADE, CONSTRAINT `XrayCentringResult_ibfk_1` FOREIGN KEY (`xrayCentringId`) REFERENCES `XrayCentring` (`xrayCentringId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COMMENT='Xray Centring result.'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Xray Centring result.'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `v_run`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3843,7 +3846,7 @@ CREATE TABLE `v_run` ( `endDate` datetime DEFAULT NULL, PRIMARY KEY (`runId`), KEY `v_run_idx1` (`startDate`,`endDate`) -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `zc_ZocaloBuffer`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -3854,7 +3857,7 @@ CREATE TABLE `zc_ZocaloBuffer` ( `Reference` int(10) unsigned DEFAULT NULL COMMENT 'Context-dependent reference to primary key IDs in other ISPyB tables', PRIMARY KEY (`AutoProcProgramID`,`UUID`), CONSTRAINT `AutoProcProgram_fk_AutoProcProgramId` FOREIGN KEY (`AutoProcProgramID`) REFERENCES `AutoProcProgram` (`autoProcProgramId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=latin1; +) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; /*!40103 SET TIME_ZONE=@OLD_TIME_ZONE */; diff --git a/schemas/ispyb/updates/2025_09_24_Proposal_start_end_date.sql b/schemas/ispyb/updates/2025_09_24_Proposal_start_end_date.sql new file mode 100644 index 00000000..f1ed488b --- /dev/null +++ b/schemas/ispyb/updates/2025_09_24_Proposal_start_end_date.sql @@ -0,0 +1,10 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_09_24_Proposal_start_end_date.sql', 'ONGOING'); + +ALTER TABLE Proposal + ADD startDate datetime + COMMENT 'Start of the allocation period', + ADD endDate datetime + COMMENT 'End of the allocation period', + ALGORITHM=INSTANT; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_09_24_Proposal_start_end_date.sql'; From fff554bd674316c30074fd0a7a67be0d07a4cf42 Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 1 Oct 2025 16:48:16 +0100 Subject: [PATCH 72/80] Update sp_update_container_status.sql (#298) --- schemas/ispyb/stored_programs/sp_update_container_status.sql | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/schemas/ispyb/stored_programs/sp_update_container_status.sql b/schemas/ispyb/stored_programs/sp_update_container_status.sql index 40ab960e..b2683cce 100644 --- a/schemas/ispyb/stored_programs/sp_update_container_status.sql +++ b/schemas/ispyb/stored_programs/sp_update_container_status.sql @@ -7,7 +7,8 @@ BEGIN DECLARE row_scLoc varchar(20) DEFAULT NULL; IF NOT (p_barcode IS NULL) AND p_status IN ('in_storage', 'in_localstorage', 'processing', 'disposed', - 'in_transit_to_localstorage', 'in_transit_to_storage', 'in_transit_loading', 'in_transit_unloading', 'in_loadlock', 'in_transit_to_loadlock') THEN + 'in_transit_to_localstorage', 'in_transit_to_storage', 'in_transit_loading', 'in_transit_unloading', 'in_loadlock', 'in_transit_to_loadlock', + 'in_transit_to_loadlock_from_hotel', 'in_transit_to_loadlock_from_local_storage') THEN SELECT containerId, sampleChangerLocation INTO row_containerId, row_scLoc FROM Container From 88c888da8cc25dfc4c931f623ca3c20dd350100f Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Wed, 1 Oct 2025 16:50:33 +0100 Subject: [PATCH 73/80] Add new SWISSCI plate (#299) --- .../2025_07_29_ContainerType_insert.sql | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 schemas/ispyb/updates/2025_07_29_ContainerType_insert.sql diff --git a/schemas/ispyb/updates/2025_07_29_ContainerType_insert.sql b/schemas/ispyb/updates/2025_07_29_ContainerType_insert.sql new file mode 100644 index 00000000..3d55372e --- /dev/null +++ b/schemas/ispyb/updates/2025_07_29_ContainerType_insert.sql @@ -0,0 +1,33 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_07_29_ContainerType_insert.sql', 'ONGOING'); + +INSERT + INTO + ContainerType (containerTypeId, + name, + capacity, + wellPerRow, + dropPerWellX, + dropPerWellY, + dropHeight, + dropWidth, + dropOffsetX, + dropOffsetY, + wellDrop, + proposalType, + active) +VALUES + (39, +'SWISSCI 2 Drop', +192, +12, +1, +2, +1, +1, +0, +0, +1, +'mx', +1); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_07_29_ContainerType_insert.sql'; From a2c4bb19242ee95a5abfff31dd46aaf8839be14f Mon Sep 17 00:00:00 2001 From: KarlLevik Date: Wed, 1 Oct 2025 17:04:28 +0100 Subject: [PATCH 74/80] Preparations for v4.9.0 --- HISTORY.rst | 29 ++++++++++++++++++- schemas/ispyb/lookups.sql | 9 ++++-- schemas/ispyb/routines.sql | 3 +- .../2025_10_01_AdminVar_bump_version.sql | 5 ++++ 4 files changed, 41 insertions(+), 5 deletions(-) create mode 100644 schemas/ispyb/updates/2025_10_01_AdminVar_bump_version.sql diff --git a/HISTORY.rst b/HISTORY.rst index be0fd1b9..2935fb5c 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,33 @@ History Unreleased / master ------------------- +4.9.0 (2025-10-01) +------------------- + +New columns: + +- Add ``startDate`` and ``endDate`` columns to the ``Proposal`` table +- Add ``parentContainerLocation`` column to the ``Container`` table + +Table permissions for the expeye role: + +- ``BLSampleImage`` +- ``Protein_has_PDB`` +- The ``Ligand`` tables + +Stored procedures: + +- Updated procedure ``update_container_status`` to allow more statuses +- New procedure ``insert_screening_v2`` with relevant grants +- In source file for procedure ``retrieve_containers_on_beamline_with_status``: + + - Use ``CREATE OR REPLACE ... PROCEDURE`` syntax + - Update maximum string length for ``p_status`` parameter + +Lookups: + +- A new type "SWISSCI 2 Drop" was added to ``ContainerType`` + 4.8.0 (2025-07-17) ------------------- @@ -32,7 +59,7 @@ New or modified tables, columns, lookup values: Roles and permissions: -- Add new grants for Expeye +- Add new grants for Expeye - Add new permissions for ``ispyb_propagation`` - Add new permissions for ``ispyb_scripts_processing.sql`` diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index f8e6b06c..417686c7 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -11,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.8.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.9.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -297,7 +297,9 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (325,'2025_06_27_undo_ParticleClassification_set_Tomogram_pixelLocation.sql','DONE','2025-06-27 16:40:00'), (326,'2025_07_17_AdminVar_bump_version.sql','DONE','2025-09-24 11:36:21'), (327,'2025_07_25_Container_parentContainerLocation.sql','DONE','2025-09-24 11:36:21'), -(328,'2025_09_24_Proposal_start_end_date.sql','DONE','2025-09-24 15:56:17'); +(328,'2025_09_24_Proposal_start_end_date.sql','DONE','2025-09-24 15:56:17'), +(329,'2025_10_01_AdminVar_bump_version.sql','DONE','2025-10-01 15:40:02'), +(330,'2025_07_29_ContainerType_insert.sql','DONE','2025-10-01 15:51:03'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; @@ -369,7 +371,8 @@ INSERT INTO `ContainerType` (`containerTypeId`, `name`, `proposalType`, `active` (35,'I22_Capillary_Rack_25','saxs',1,25,25,1,1,1,1,0,0,-1), (36,'VMXm-Cartridge','mx',1,5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), (37,'VMXm-GridBox','mx',1,4,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(38,'Cryo-EM Puck','mx',1,12,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); +(38,'Cryo-EM Puck','mx',1,12,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), +(39,'SWISSCI 2 Drop','mx',1,192,12,1,2,1,1,0,0,1); /*!40000 ALTER TABLE `ContainerType` ENABLE KEYS */; /*!40000 ALTER TABLE `ExperimentType` DISABLE KEYS */; diff --git a/schemas/ispyb/routines.sql b/schemas/ispyb/routines.sql index e3de2590..e969ba74 100644 --- a/schemas/ispyb/routines.sql +++ b/schemas/ispyb/routines.sql @@ -7827,7 +7827,8 @@ BEGIN DECLARE row_scLoc varchar(20) DEFAULT NULL; IF NOT (p_barcode IS NULL) AND p_status IN ('in_storage', 'in_localstorage', 'processing', 'disposed', - 'in_transit_to_localstorage', 'in_transit_to_storage', 'in_transit_loading', 'in_transit_unloading', 'in_loadlock', 'in_transit_to_loadlock') THEN + 'in_transit_to_localstorage', 'in_transit_to_storage', 'in_transit_loading', 'in_transit_unloading', 'in_loadlock', 'in_transit_to_loadlock', + 'in_transit_to_loadlock_from_hotel', 'in_transit_to_loadlock_from_local_storage') THEN SELECT containerId, sampleChangerLocation INTO row_containerId, row_scLoc FROM Container diff --git a/schemas/ispyb/updates/2025_10_01_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_10_01_AdminVar_bump_version.sql new file mode 100644 index 00000000..6bec0f37 --- /dev/null +++ b/schemas/ispyb/updates/2025_10_01_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_10_01_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.9.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_10_01_AdminVar_bump_version.sql'; From a55c52603777049e4c0b24d76b21dd4e25acfa7c Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Thu, 13 Nov 2025 15:23:18 +0000 Subject: [PATCH 75/80] Add new experiment types --- .../updates/2025_11_13_ExperimentType_clem_and_fib.sql | 10 ++++++++++ 1 file changed, 10 insertions(+) create mode 100644 schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql diff --git a/schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql b/schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql new file mode 100644 index 00000000..4c51882f --- /dev/null +++ b/schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql @@ -0,0 +1,10 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_11_13_ExperimentType_clem_and_fib.sql', 'ONGOING'); + +INSERT INTO ExperimentType ( + experimentTypeId, name, proposalType, active +) VALUES ( + 45, 'CLEM', 'em', 1, + 46, 'FIB', 'em', 1 +); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_11_13_ExperimentType_clem_and_fib.sql'; From 23899f2bc47d3fe673591c009995e0acee37339a Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 20 Nov 2025 15:26:32 +0000 Subject: [PATCH 76/80] Add new experiment types (#303) * Add new experiment types * Fix syntax --- .../updates/2025_11_13_ExperimentType_clem_and_fib.sql | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql diff --git a/schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql b/schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql new file mode 100644 index 00000000..8e204f31 --- /dev/null +++ b/schemas/ispyb/updates/2025_11_13_ExperimentType_clem_and_fib.sql @@ -0,0 +1,7 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_11_13_ExperimentType_clem_and_fib.sql', 'ONGOING'); + +INSERT INTO ExperimentType ( + experimentTypeId, name, proposalType, active +) VALUES (45, 'CLEM', 'em', 1), (46, 'FIB', 'em', 1); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_11_13_ExperimentType_clem_and_fib.sql'; From 4c178d56cc85e6341bc519082a277e8c674697dd Mon Sep 17 00:00:00 2001 From: Guilherme Francisco Date: Thu, 20 Nov 2025 15:26:38 +0000 Subject: [PATCH 77/80] Add laser parameters tables (#302) * Add laser parameters tables * Add enum value to RobotAction actionType --- .../2025_11_03_LaserParameters_tables.sql | 40 +++++++++++++++++++ .../2025_11_05_RobotAction_new_type.sql | 5 +++ 2 files changed, 45 insertions(+) create mode 100644 schemas/ispyb/updates/2025_11_03_LaserParameters_tables.sql create mode 100644 schemas/ispyb/updates/2025_11_05_RobotAction_new_type.sql diff --git a/schemas/ispyb/updates/2025_11_03_LaserParameters_tables.sql b/schemas/ispyb/updates/2025_11_03_LaserParameters_tables.sql new file mode 100644 index 00000000..24d24a3c --- /dev/null +++ b/schemas/ispyb/updates/2025_11_03_LaserParameters_tables.sql @@ -0,0 +1,40 @@ +-- To undo: +-- drop table LaserPoint; +-- drop table LaserParameters; +-- delete from SchemaStatus where scriptName = '2025_11_03_LaserParameters_tables.sql'; + + +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_11_03_LaserParameters_tables.sql', 'ONGOING'); + +CREATE TABLE LaserParameters ( + laserParametersId int(11) unsigned PRIMARY KEY AUTO_INCREMENT, + robotActionId int(11) unsigned, + laserRepetitionRate float COMMENT 'Laser repetition rate, in kHz', + scanheadMoveSpeed float COMMENT 'Scanhead move speed, in m/s', + laserTransmission float COMMENT 'Laser transmission, in %', + numberOfPasses int(10) unsigned, + gonioRotationSpeed int(10) COMMENT 'Goniometer rotation speed, in deg/s', + totalMarkingTime float COMMENT 'Total marking time, in s', + CONSTRAINT `LaserParameters_fk_robotActionId` + FOREIGN KEY (robotActionId) + REFERENCES RobotAction (robotActionId) + ON DELETE CASCADE + ON UPDATE CASCADE +) COMMENT = 'Laser parameters'; + +CREATE TABLE LaserPoint ( + laserPointId int(11) unsigned PRIMARY KEY AUTO_INCREMENT, + laserParametersId int(11) unsigned, + x int(10) unsigned NOT NULL COMMENT 'X coordinate of point, in microns', + y int(10) unsigned NOT NULL COMMENT 'Y coordinate of point, in microns', + pointIndex int(10) NOT NULL COMMENT 'Index of point, expresses ordinality', + radius int(10) unsigned COMMENT 'Radius of point, in microns', + laserOn tinyint(1) DEFAULT 0, + CONSTRAINT LaserPoint_fk_laserParametersId + FOREIGN KEY (laserParametersId) + REFERENCES LaserParameters (laserParametersId) + ON DELETE CASCADE + ON UPDATE CASCADE +) COMMENT = 'Laser points'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_11_03_LaserParameters_tables.sql'; diff --git a/schemas/ispyb/updates/2025_11_05_RobotAction_new_type.sql b/schemas/ispyb/updates/2025_11_05_RobotAction_new_type.sql new file mode 100644 index 00000000..ce09f264 --- /dev/null +++ b/schemas/ispyb/updates/2025_11_05_RobotAction_new_type.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_11_05_RobotAction_new_type.sql', 'ONGOING'); + +ALTER TABLE RobotAction MODIFY COLUMN actionType ENUM('LOAD', 'UNLOAD', 'DISPOSE', 'STORE', 'WASH', 'ANNEAL', 'MOSAIC', 'LASER'); + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_11_05_RobotAction_new_type.sql'; From 460e78e94b03e0747cf9e9980ac1d98c96a1584f Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Thu, 20 Nov 2025 15:52:18 +0000 Subject: [PATCH 78/80] Preparations for 4.9.0 release --- HISTORY.rst | 16 ++++ schemas/ispyb/data.sql | 44 ++++++---- schemas/ispyb/lookups.sql | 86 ++++++++++--------- schemas/ispyb/tables.sql | 35 +++++++- .../2025_11_20_AdminVar_bump_version.sql | 5 ++ 5 files changed, 126 insertions(+), 60 deletions(-) create mode 100644 schemas/ispyb/updates/2025_11_20_AdminVar_bump_version.sql diff --git a/HISTORY.rst b/HISTORY.rst index 2935fb5c..c5f0b89f 100644 --- a/HISTORY.rst +++ b/HISTORY.rst @@ -5,6 +5,22 @@ History Unreleased / master ------------------- +4.10.0 (2025-11-20) +------------------- + +Thank you so much, Karl! / Tusen takk, Karl! + +Lookups: + +- Add ``CLEM`` experiment type +- Add ``FIB`` experiment type + +New or modified tables, columns, lookup values: + +- New table ``LaserParameters`` +- New table ``LaserPoint`` +- Add ``LASER`` to ``RobotAction`` ``actionType`` column + 4.9.0 (2025-10-01) ------------------- diff --git a/schemas/ispyb/data.sql b/schemas/ispyb/data.sql index 9ce10b65..f8c51f63 100644 --- a/schemas/ispyb/data.sql +++ b/schemas/ispyb/data.sql @@ -332,19 +332,19 @@ INSERT INTO `ComponentLattice` (`componentLatticeId`, `componentId`, `spaceGroup /*!40000 ALTER TABLE `Component_has_SubType` ENABLE KEYS */; /*!40000 ALTER TABLE `Container` DISABLE KEYS */; -INSERT INTO `Container` (`containerId`, `dewarId`, `code`, `containerType`, `capacity`, `sampleChangerLocation`, `containerStatus`, `bltimeStamp`, `beamlineLocation`, `screenId`, `scheduleId`, `barcode`, `imagerId`, `sessionId`, `ownerId`, `requestedImagerId`, `requestedReturn`, `comments`, `experimentType`, `storageTemperature`, `containerRegistryId`, `scLocationUpdated`, `priorityPipelineId`, `experimentTypeId`, `containerTypeId`, `currentDewarId`, `parentContainerId`, `source`) VALUES (1326,573,'Container-1-cm0001-1','Puck-16',16,'3','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000001',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,4,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(1329,573,'Container-2-cm0001-1','Puck-16',16,'4','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000002',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(1332,576,'Container-3-cm0001-1','Puck-16',16,'5','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000003',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(1335,579,'Container-4-cm0001-2','Puck-16',16,'6','processing',NULL,'i03',NULL,NULL,'container-cm0001-2-0001335',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(1338,582,'Container-5-cm0001-3','Puck-16',16,'7','processing',NULL,'i03',NULL,NULL,'container-cm0001-3-0001338',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(1341,573,'Manual',NULL,NULL,'9',NULL,NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(33049,8287,'cm14451-1_i03r-002','Puck',16,NULL,'at DLS',NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(34864,8572,'I03R-001','Puck',16,'29','processing','2016-02-24 12:13:05','i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(34874,8572,'test_plate2','CrystalQuickX',192,'3','in_storage','2016-02-12 09:20:44','i03',NULL,2,'test_plate2',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(34877,8572,'test_plate3','CrystalQuickX',192,'3','in_storage','2016-10-04 10:50:05','i03',NULL,2,'test_plate3',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(34879,8572,'test_plate4','CrystalQuickX',192,'4','processing',NULL,'i02-2',NULL,2,'test_plate4',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(34883,NULL,'XPDF-container-1','XPDF container',NULL,NULL,'processing',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(34888,8578,'TestSim01','CrystalQuickX',192,'1','in_storage',NULL,'i02-2',NULL,2,'VMXiSim-001',7,339535,1,7,0,NULL,NULL,NULL,5,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'); +INSERT INTO `Container` (`containerId`, `dewarId`, `code`, `containerType`, `capacity`, `sampleChangerLocation`, `containerStatus`, `bltimeStamp`, `beamlineLocation`, `screenId`, `scheduleId`, `barcode`, `imagerId`, `sessionId`, `ownerId`, `requestedImagerId`, `requestedReturn`, `comments`, `experimentType`, `storageTemperature`, `containerRegistryId`, `scLocationUpdated`, `priorityPipelineId`, `experimentTypeId`, `containerTypeId`, `currentDewarId`, `parentContainerId`, `source`, `parentContainerLocation`) VALUES (1326,573,'Container-1-cm0001-1','Puck-16',16,'3','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000001',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,4,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(1329,573,'Container-2-cm0001-1','Puck-16',16,'4','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000002',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(1332,576,'Container-3-cm0001-1','Puck-16',16,'5','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000003',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(1335,579,'Container-4-cm0001-2','Puck-16',16,'6','processing',NULL,'i03',NULL,NULL,'container-cm0001-2-0001335',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(1338,582,'Container-5-cm0001-3','Puck-16',16,'7','processing',NULL,'i03',NULL,NULL,'container-cm0001-3-0001338',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(1341,573,'Manual',NULL,NULL,'9',NULL,NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(33049,8287,'cm14451-1_i03r-002','Puck',16,NULL,'at DLS',NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(34864,8572,'I03R-001','Puck',16,'29','processing','2016-02-24 12:13:05','i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(34874,8572,'test_plate2','CrystalQuickX',192,'3','in_storage','2016-02-12 09:20:44','i03',NULL,2,'test_plate2',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(34877,8572,'test_plate3','CrystalQuickX',192,'3','in_storage','2016-10-04 10:50:05','i03',NULL,2,'test_plate3',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(34879,8572,'test_plate4','CrystalQuickX',192,'4','processing',NULL,'i02-2',NULL,2,'test_plate4',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(34883,NULL,'XPDF-container-1','XPDF container',NULL,NULL,'processing',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), +(34888,8578,'TestSim01','CrystalQuickX',192,'1','in_storage',NULL,'i02-2',NULL,2,'VMXiSim-001',7,339535,1,7,0,NULL,NULL,NULL,5,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL); /*!40000 ALTER TABLE `Container` ENABLE KEYS */; /*!40000 ALTER TABLE `ContainerHistory` DISABLE KEYS */; @@ -560,6 +560,12 @@ INSERT INTO `ImageQualityIndicators` (`dataCollectionId`, `imageNumber`, `imageI /*!40000 ALTER TABLE `Laboratory` DISABLE KEYS */; /*!40000 ALTER TABLE `Laboratory` ENABLE KEYS */; +/*!40000 ALTER TABLE `LaserParameters` DISABLE KEYS */; +/*!40000 ALTER TABLE `LaserParameters` ENABLE KEYS */; + +/*!40000 ALTER TABLE `LaserPoint` DISABLE KEYS */; +/*!40000 ALTER TABLE `LaserPoint` ENABLE KEYS */; + /*!40000 ALTER TABLE `Ligand` DISABLE KEYS */; /*!40000 ALTER TABLE `Ligand` ENABLE KEYS */; @@ -694,8 +700,8 @@ INSERT INTO `ProcessingJobParameter` (`processingJobParameterId`, `processingJob /*!40000 ALTER TABLE `Project_has_XFEFSpectrum` ENABLE KEYS */; /*!40000 ALTER TABLE `Proposal` DISABLE KEYS */; -INSERT INTO `Proposal` (`proposalId`, `personId`, `title`, `proposalCode`, `proposalNumber`, `bltimeStamp`, `proposalType`, `externalId`, `state`) VALUES (37027,1,'I03 Commissioning Directory 2016','cm','14451','2015-12-21 15:20:43',NULL,NULL,'Open'), -(141666,46266,'Test Proposal cm-0001','cm','1','2016-03-16 16:01:34',NULL,NULL,'Open'); +INSERT INTO `Proposal` (`proposalId`, `personId`, `title`, `proposalCode`, `proposalNumber`, `bltimeStamp`, `proposalType`, `externalId`, `state`, `startDate`, `endDate`) VALUES (37027,1,'I03 Commissioning Directory 2016','cm','14451','2015-12-21 15:20:43',NULL,NULL,'Open',NULL,NULL), +(141666,46266,'Test Proposal cm-0001','cm','1','2016-03-16 16:01:34',NULL,NULL,'Open',NULL,NULL); /*!40000 ALTER TABLE `Proposal` ENABLE KEYS */; /*!40000 ALTER TABLE `ProposalHasPerson` DISABLE KEYS */; @@ -944,11 +950,11 @@ INSERT INTO `Shipping` (`shippingId`, `proposalId`, `shippingName`, `deliveryAge /*!40000 ALTER TABLE `Shipping` ENABLE KEYS */; /*!40000 ALTER TABLE `ShippingHasSession` DISABLE KEYS */; -INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (474,339525), +INSERT INTO `ShippingHasSession` (`shippingId`, `sessionId`) VALUES (6988,55167), +(7227,55168), +(474,339525), (477,339528), -(480,339531), -(6988,55167), -(7227,55168); +(480,339531); /*!40000 ALTER TABLE `ShippingHasSession` ENABLE KEYS */; /*!40000 ALTER TABLE `Sleeve` DISABLE KEYS */; diff --git a/schemas/ispyb/lookups.sql b/schemas/ispyb/lookups.sql index 417686c7..ad3b3583 100644 --- a/schemas/ispyb/lookups.sql +++ b/schemas/ispyb/lookups.sql @@ -11,7 +11,7 @@ /*!40111 SET @OLD_SQL_NOTES=@@SQL_NOTES, SQL_NOTES=0 */; /*!40000 ALTER TABLE `AdminVar` DISABLE KEYS */; -INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.9.0'); +INSERT INTO `AdminVar` (`varId`, `name`, `value`) VALUES (4,'schemaVersion','4.10.0'); /*!40000 ALTER TABLE `AdminVar` ENABLE KEYS */; /*!40000 ALTER TABLE `SchemaStatus` DISABLE KEYS */; @@ -299,7 +299,11 @@ INSERT INTO `SchemaStatus` (`schemaStatusId`, `scriptName`, `schemaStatus`, `rec (327,'2025_07_25_Container_parentContainerLocation.sql','DONE','2025-09-24 11:36:21'), (328,'2025_09_24_Proposal_start_end_date.sql','DONE','2025-09-24 15:56:17'), (329,'2025_10_01_AdminVar_bump_version.sql','DONE','2025-10-01 15:40:02'), -(330,'2025_07_29_ContainerType_insert.sql','DONE','2025-10-01 15:51:03'); +(330,'2025_07_29_ContainerType_insert.sql','DONE','2025-10-01 15:51:03'), +(331,'2025_11_03_LaserParameters_tables.sql','DONE','2025-11-20 15:47:48'), +(332,'2025_11_05_RobotAction_new_type.sql','DONE','2025-11-20 15:47:48'), +(333,'2025_11_13_ExperimentType_clem_and_fib.sql','DONE','2025-11-20 15:47:48'), +(334,'2025_11_20_AdminVar_bump_version.sql','DONE','2025-11-20 15:47:48'); /*!40000 ALTER TABLE `SchemaStatus` ENABLE KEYS */; /*!40000 ALTER TABLE `ComponentType` DISABLE KEYS */; @@ -419,7 +423,9 @@ INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `activ (41,'SSX-Chip','mx',1), (42,'SSX-Jet','mx',1), (43,'Metal ID','mx',1), -(44,'Atlas','em',1); +(44,'Atlas','em',1), +(45,'CLEM','em',1), +(46,'FIB','em',1); /*!40000 ALTER TABLE `ExperimentType` ENABLE KEYS */; /*!40000 ALTER TABLE `InspectionType` DISABLE KEYS */; @@ -849,63 +855,63 @@ INSERT INTO `Permission` (`permissionId`, `type`, `description`) VALUES (1,'mx_a /*!40000 ALTER TABLE `UserGroup_has_Permission` DISABLE KEYS */; INSERT INTO `UserGroup_has_Permission` (`userGroupId`, `permissionId`) VALUES (1,1), -(1,7), -(1,8), -(1,9), -(1,10), -(1,11), -(1,18), -(1,20), -(1,23), -(1,49), (2,1), -(2,6), -(2,23), -(2,80), -(3,7), -(3,23), -(4,20), -(5,10), -(6,8), -(6,23), (8,1), +(9,1), +(14,1), +(24,1), (8,2), (8,4), +(2,6), (8,6), +(9,6), +(1,7), +(3,7), (8,7), +(1,8), +(6,8), (8,8), +(1,9), (8,9), +(1,10), +(5,10), (8,10), +(1,11), (8,11), -(8,18), -(8,20), -(8,23), -(8,26), -(8,29), -(8,37), -(8,49), -(9,1), -(9,6), (10,12), -(10,77), (11,13), (11,15), (11,16), (11,17), -(11,32), -(11,43), -(11,55), -(11,58), -(11,64), +(1,18), +(8,18), (12,18), -(14,1), +(1,20), +(4,20), +(8,20), +(1,23), +(2,23), +(3,23), +(6,23), +(8,23), +(28,23), +(8,26), (17,26), +(8,29), (20,29), -(24,1), -(28,23), +(11,32), +(8,37), (28,37), +(11,43), +(1,49), +(8,49), (34,49), -(39,69); +(11,55), +(11,58), +(11,64), +(39,69), +(10,77), +(2,80); /*!40000 ALTER TABLE `UserGroup_has_Permission` ENABLE KEYS */; /*!40000 ALTER TABLE `ScanParametersService` DISABLE KEYS */; diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index 90683460..6eb13e2d 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -2210,6 +2210,39 @@ CREATE TABLE `Laboratory` ( PRIMARY KEY (`laboratoryId`) ) ENGINE=InnoDB DEFAULT CHARSET=latin1 COLLATE=latin1_swedish_ci; /*!40101 SET character_set_client = @saved_cs_client */; +DROP TABLE IF EXISTS `LaserParameters`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8mb4 */; +CREATE TABLE `LaserParameters` ( + `laserParametersId` int(11) unsigned NOT NULL AUTO_INCREMENT, + `robotActionId` int(11) unsigned DEFAULT NULL, + `laserRepetitionRate` float DEFAULT NULL COMMENT 'Laser repetition rate, in kHz', + `scanheadMoveSpeed` float DEFAULT NULL COMMENT 'Scanhead move speed, in m/s', + `laserTransmission` float DEFAULT NULL COMMENT 'Laser transmission, in %', + `numberOfPasses` int(10) unsigned DEFAULT NULL, + `gonioRotationSpeed` int(10) DEFAULT NULL COMMENT 'Goniometer rotation speed, in deg/s', + `totalMarkingTime` float DEFAULT NULL COMMENT 'Total marking time, in s', + PRIMARY KEY (`laserParametersId`), + KEY `LaserParameters_fk_robotActionId` (`robotActionId`), + CONSTRAINT `LaserParameters_fk_robotActionId` FOREIGN KEY (`robotActionId`) REFERENCES `RobotAction` (`robotActionId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_ai_ci COMMENT='Laser parameters'; +/*!40101 SET character_set_client = @saved_cs_client */; +DROP TABLE IF EXISTS `LaserPoint`; +/*!40101 SET @saved_cs_client = @@character_set_client */; +/*!40101 SET character_set_client = utf8mb4 */; +CREATE TABLE `LaserPoint` ( + `laserPointId` int(11) unsigned NOT NULL AUTO_INCREMENT, + `laserParametersId` int(11) unsigned DEFAULT NULL, + `x` int(10) unsigned NOT NULL COMMENT 'X coordinate of point, in microns', + `y` int(10) unsigned NOT NULL COMMENT 'Y coordinate of point, in microns', + `pointIndex` int(10) NOT NULL COMMENT 'Index of point, expresses ordinality', + `radius` int(10) unsigned DEFAULT NULL COMMENT 'Radius of point, in microns', + `laserOn` tinyint(1) DEFAULT 0, + PRIMARY KEY (`laserPointId`), + KEY `LaserPoint_fk_laserParametersId` (`laserParametersId`), + CONSTRAINT `LaserPoint_fk_laserParametersId` FOREIGN KEY (`laserParametersId`) REFERENCES `LaserParameters` (`laserParametersId`) ON DELETE CASCADE ON UPDATE CASCADE +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_ai_ci COMMENT='Laser points'; +/*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Ligand`; /*!40101 SET @saved_cs_client = @@character_set_client */; /*!40101 SET character_set_client = utf8mb4 */; @@ -3057,7 +3090,7 @@ CREATE TABLE `RobotAction` ( `robotActionId` int(11) unsigned NOT NULL AUTO_INCREMENT, `blsessionId` int(11) unsigned NOT NULL, `blsampleId` int(11) unsigned DEFAULT NULL, - `actionType` enum('LOAD','UNLOAD','DISPOSE','STORE','WASH','ANNEAL','MOSAIC') DEFAULT NULL, + `actionType` enum('LOAD','UNLOAD','DISPOSE','STORE','WASH','ANNEAL','MOSAIC','LASER') DEFAULT NULL, `startTimestamp` timestamp NOT NULL DEFAULT current_timestamp() ON UPDATE current_timestamp(), `endTimestamp` timestamp NOT NULL DEFAULT '0000-00-00 00:00:00', `status` enum('SUCCESS','ERROR','CRITICAL','WARNING','EPICSFAIL','COMMANDNOTSENT') DEFAULT NULL, diff --git a/schemas/ispyb/updates/2025_11_20_AdminVar_bump_version.sql b/schemas/ispyb/updates/2025_11_20_AdminVar_bump_version.sql new file mode 100644 index 00000000..3fd5b92d --- /dev/null +++ b/schemas/ispyb/updates/2025_11_20_AdminVar_bump_version.sql @@ -0,0 +1,5 @@ +INSERT IGNORE INTO SchemaStatus (scriptName, schemaStatus) VALUES ('2025_11_20_AdminVar_bump_version.sql', 'ONGOING'); + +UPDATE AdminVar SET `value` = '4.10.0' WHERE `name` = 'schemaVersion'; + +UPDATE SchemaStatus SET schemaStatus = 'DONE' WHERE scriptName = '2025_11_20_AdminVar_bump_version.sql'; From cf847b0e722b9a1cd599ac503a6f71b89a4b91d5 Mon Sep 17 00:00:00 2001 From: Guilherme de Freitas Date: Thu, 20 Nov 2025 15:56:31 +0000 Subject: [PATCH 79/80] Fix collation --- schemas/ispyb/tables.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/schemas/ispyb/tables.sql b/schemas/ispyb/tables.sql index 6eb13e2d..2da7b7d0 100644 --- a/schemas/ispyb/tables.sql +++ b/schemas/ispyb/tables.sql @@ -2225,7 +2225,7 @@ CREATE TABLE `LaserParameters` ( PRIMARY KEY (`laserParametersId`), KEY `LaserParameters_fk_robotActionId` (`robotActionId`), CONSTRAINT `LaserParameters_fk_robotActionId` FOREIGN KEY (`robotActionId`) REFERENCES `RobotAction` (`robotActionId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_ai_ci COMMENT='Laser parameters'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Laser parameters'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `LaserPoint`; /*!40101 SET @saved_cs_client = @@character_set_client */; @@ -2241,7 +2241,7 @@ CREATE TABLE `LaserPoint` ( PRIMARY KEY (`laserPointId`), KEY `LaserPoint_fk_laserParametersId` (`laserParametersId`), CONSTRAINT `LaserPoint_fk_laserParametersId` FOREIGN KEY (`laserParametersId`) REFERENCES `LaserParameters` (`laserParametersId`) ON DELETE CASCADE ON UPDATE CASCADE -) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_ai_ci COMMENT='Laser points'; +) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_general_ci COMMENT='Laser points'; /*!40101 SET character_set_client = @saved_cs_client */; DROP TABLE IF EXISTS `Ligand`; /*!40101 SET @saved_cs_client = @@character_set_client */; From 05c875eb41059f85821220a15450536eb3a3b48d Mon Sep 17 00:00:00 2001 From: gfrn <12566585+gfrn@users.noreply.github.com> Date: Thu, 20 Nov 2025 15:58:06 +0000 Subject: [PATCH 80/80] Update database sql files --- schemas/ispyb/data.sql | 643 +++------------------------- schemas/ispyb/lookups.sql | 854 +------------------------------------- 2 files changed, 70 insertions(+), 1427 deletions(-) diff --git a/schemas/ispyb/data.sql b/schemas/ispyb/data.sql index f8c51f63..e4d55c0c 100644 --- a/schemas/ispyb/data.sql +++ b/schemas/ispyb/data.sql @@ -20,146 +20,34 @@ /*!40000 ALTER TABLE `Atlas` ENABLE KEYS */; /*!40000 ALTER TABLE `AutoProc` DISABLE KEYS */; -INSERT INTO `AutoProc` (`autoProcId`, `autoProcProgramId`, `spaceGroup`, `refinedCell_a`, `refinedCell_b`, `refinedCell_c`, `refinedCell_alpha`, `refinedCell_beta`, `refinedCell_gamma`, `recordTimeStamp`) VALUES (596406,56425592,'P 6 2 2',92.5546,92.5546,129.784,90,90,120,'2016-01-14 12:46:22'), -(596411,56425944,'P 63 2 2',92.53,92.53,129.75,90,90,120,'2016-01-14 13:09:51'), -(596418,56425952,'P 61 2 2',92.6461,92.6461,129.879,90,90,120,'2016-01-14 13:24:22'), -(596419,56425963,'P 63 2 2',92.511,92.511,129.722,90,90,120,'2016-01-14 13:34:34'), -(596420,56426286,'P 61 2 2',92.693,92.693,129.839,90,90,120,'2016-01-14 14:01:57'), -(596421,56426287,'P 63 2 2',92.64,92.64,129.77,90,90,120,'2016-01-14 14:13:57'), -(603708,56983954,'I 2 3',78.1548,78.1548,78.1548,90,90,90,'2016-01-22 11:34:03'), -(603731,56985584,'I 2 3',78.15,78.15,78.15,90,90,90,'2016-01-22 11:52:36'), -(603732,56985589,'I 2 3',78.157,78.157,78.157,90,90,90,'2016-01-22 11:53:38'), -(603735,56985592,'I 2 3',78.15,78.15,78.15,90,90,90,'2016-01-22 11:54:01'), -(603744,56986673,'I 2 3',78.1381,78.1381,78.1381,90,90,90,'2016-01-22 12:01:59'); +INSERT INTO `AutoProc` (`autoProcId`, `autoProcProgramId`, `spaceGroup`, `refinedCell_a`, `refinedCell_b`, `refinedCell_c`, `refinedCell_alpha`, `refinedCell_beta`, `refinedCell_gamma`, `recordTimeStamp`) VALUES (596406,56425592,'P 6 2 2',92.5546,92.5546,129.784,90,90,120,'2016-01-14 12:46:22'),(596411,56425944,'P 63 2 2',92.53,92.53,129.75,90,90,120,'2016-01-14 13:09:51'),(596418,56425952,'P 61 2 2',92.6461,92.6461,129.879,90,90,120,'2016-01-14 13:24:22'),(596419,56425963,'P 63 2 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`rPimWithinIPlusIMinus`, `rPimAllIPlusIMinus`, `fractionalPartialBias`, `nTotalObservations`, `nTotalUniqueObservations`, `meanIOverSigI`, `completeness`, `multiplicity`, `anomalousCompleteness`, `anomalousMultiplicity`, `recordTimeStamp`, `anomalous`, `ccHalf`, `ccAnomalous`, `resIOverSigI2`) VALUES (1770617,596133,'outerShell',NULL,1.65,1.61,0.766,NULL,0.789,NULL,NULL,NULL,105090,3089,5.5,97.8,34,96.8,17.8,'2016-01-14 12:46:22',0,91.7,15.8,NULL),(1770618,596133,'innerShell',NULL,29.5,7.18,0.061,NULL,0.063,NULL,NULL,NULL,17093,593,61.7,98.6,28.8,100,19.5,'2016-01-14 12:46:22',0,99.9,73.4,NULL),(1770619,596133,'overall',NULL,29.5,1.61,0.106,NULL,0.109,NULL,NULL,NULL,1588225,43478,30.2,99.8,36.5,99.8,19.4,'2016-01-14 12:46:22',0,99.9,60.5,NULL),(1770632,596138,'outerShell',NULL,1.49,1.45,1.326,NULL,1.419,0.506,0.365,NULL,61482,4245,2,99.8,14.5,99.5,7.4,'2016-01-14 13:09:51',0,0.584,-0.059,NULL),(1770633,596138,'innerShell',NULL,68.18,6.48,0.064,NULL,0.07,0.015,0.012,NULL,23609,800,58.6,99.8,29.5,100,19.7,'2016-01-14 13:09:51',0,0.998,0.732,NULL),(1770634,596138,'overall',NULL,68.18,1.45,0.116,NULL,0.123,0.028,0.021,NULL,1942930,58601,22.9,99.9,33.2,99.9,17.4,'2016-01-14 13:09:51',0,0.999,0.592,NULL),(1770653,596145,'outerShell',NULL,1.46,1.42,3.758,NULL,4.107,1.67,1.216,NULL,42977,4422,2.2,97.9,9.7,96.3,5,'2016-01-14 13:24:22',0,0.497,-0.012,NULL),(1770654,596145,'innerShell',NULL,129.88,6.35,0.09,NULL,0.095,0.02,0.017,NULL,28041,858,32,100,32.7,100,21.3,'2016-01-14 13:24:22',0,0.996,0.556,NULL),(1770655,596145,'overall',NULL,129.88,1.42,0.177,NULL,0.184,0.045,0.033,NULL,1942399,62483,16.4,99.8,31.1,99.7,16.2,'2016-01-14 13:24:22',0,0.999,0.343,NULL),(1770656,596146,'outerShell',NULL,1.476,1.451,1.268,1.314,1.312,0.459,0.33,NULL,42945,2859,2.4,99.2,15,98.9,7.8,'2016-01-14 13:34:35',0,0.633,-0.059,NULL),(1770657,596146,'innerShell',NULL,129.722,3.938,0.08,0.078,0.081,0.017,0.014,NULL,103297,3251,50.7,100,31.8,99.7,19.1,'2016-01-14 13:34:35',0,0.993,-0.169,NULL),(1770658,596146,'overall',NULL,129.722,1.451,0.138,0.141,0.141,0.032,0.024,NULL,1953227,58523,22.5,100,33.4,100,17.8,'2016-01-14 13:34:35',0,0.996,0.035,NULL),(1770659,596147,'outerShell',NULL,1.47,1.43,3.442,NULL,3.711,1.471,1.058,NULL,46996,4388,1.6,99,10.7,97.8,5.5,'2016-01-14 14:01:57',0,0.627,-0.004,NULL),(1770660,596147,'innerShell',NULL,129.84,6.4,0.124,NULL,0.129,0.023,0.019,NULL,41147,842,27,100,48.9,100,31.8,'2016-01-14 14:01:57',0,0.996,0.532,NULL),(1770661,596147,'overall',NULL,129.84,1.43,0.707,NULL,0.719,0.156,0.114,NULL,2865527,61286,14.1,99.9,46.8,99.8,24.3,'2016-01-14 14:01:57',0,0.998,0.175,NULL),(1770662,596148,'outerShell',NULL,1.47,1.43,1.278,NULL,1.362,0.447,0.326,NULL,66780,4414,1.7,99.2,15.1,97,7.8,'2016-01-14 14:13:57',0,0.564,-0.056,NULL),(1770663,596148,'innerShell',NULL,80.23,6.4,0.106,NULL,0.112,0.02,0.017,NULL,36380,837,58.7,100,43.5,100,28.9,'2016-01-14 14:13:57',0,0.987,0.717,NULL),(1770664,596148,'overall',NULL,80.23,1.43,0.166,NULL,0.172,0.032,0.024,NULL,2926200,61215,22.9,99.9,47.8,99.8,25,'2016-01-14 14:13:57',0,0.997,0.589,NULL),(1792520,603434,'outerShell',NULL,1.57,1.53,0.765,NULL,0.775,NULL,NULL,NULL,64789,889,7.4,97.6,72.9,97.3,37,'2016-01-22 11:34:03',0,97.7,-4.8,NULL),(1792521,603434,'innerShell',NULL,27.63,6.84,0.043,NULL,0.044,NULL,NULL,NULL,10404,156,144.1,98.6,66.7,99,39.5,'2016-01-22 11:34:03',0,100,74.1,NULL),(1792522,603434,'overall',NULL,27.63,1.53,0.073,NULL,0.074,NULL,NULL,NULL,946151,12186,50.8,99.8,77.6,99.8,40,'2016-01-22 11:34:03',0,100,41.3,NULL),(1792589,603457,'outerShell',NULL,1.38,1.34,3.435,NULL,3.586,0.744,0.543,NULL,57789,1347,1.2,100,42.9,100,21.2,'2016-01-22 11:52:36',0,0.622,-0.017,NULL),(1792590,603457,'innerShell',NULL,31.9,6,0.044,NULL,0.046,0.007,0.006,NULL,15766,225,131.3,99.6,70.1,100,40.5,'2016-01-22 11:52:36',0,1,0.665,NULL),(1792591,603457,'overall',NULL,31.9,1.34,0.08,NULL,0.082,0.013,0.009,NULL,1309987,17989,34.2,100,72.8,100,37.2,'2016-01-22 11:52:36',0,1,0.484,NULL),(1792592,603458,'outerShell',NULL,1.4,1.376,2.142,2.136,2.156,0.345,0.249,NULL,60591,813,2.4,100,74.5,100,38.1,'2016-01-22 11:53:38',0,0.908,0.059,NULL),(1792593,603458,'innerShell',NULL,39.079,3.735,0.045,0.044,0.045,0.007,0.005,NULL,64542,887,114,99.9,72.8,99.9,40.2,'2016-01-22 11:53:38',0,1,0.267,NULL),(1792594,603458,'overall',NULL,39.079,1.376,0.083,0.084,0.083,0.013,0.009,NULL,1275766,16626,35,100,76.7,100,39.9,'2016-01-22 11:53:38',0,1,0.217,NULL),(1792601,603461,'outerShell',NULL,1.38,1.34,3.444,NULL,3.597,0.746,0.545,NULL,57746,1347,1.2,100,42.9,100,21.2,'2016-01-22 11:54:01',0,0.647,0.002,NULL),(1792602,603461,'innerShell',NULL,31.9,6,0.044,NULL,0.046,0.007,0.006,NULL,15773,225,131.2,99.6,70.1,100,40.5,'2016-01-22 11:54:01',0,1,0.654,NULL),(1792603,603461,'overall',NULL,31.9,1.34,0.08,NULL,0.082,0.013,0.009,NULL,1314502,17989,34.2,100,73.1,100,37.3,'2016-01-22 11:54:01',0,1,0.469,NULL),(1792628,603470,'outerShell',NULL,1.36,1.33,3.124,NULL,3.246,0.711,0.515,NULL,53402,1370,1.3,100,39,100,19.2,'2016-01-22 12:01:59',0,0.703,0.017,NULL),(1792629,603470,'innerShell',NULL,39.07,5.95,0.051,NULL,0.053,0.008,0.006,NULL,16799,235,117.7,99.7,71.5,100,41.9,'2016-01-22 12:01:59',0,1,0.654,NULL),(1792630,603470,'overall',NULL,39.07,1.33,0.08,NULL,0.082,0.013,0.009,NULL,1305126,18395,30.9,100,71,100,36.1,'2016-01-22 12:01:59',0,1,0.482,NULL); /*!40000 ALTER TABLE `AutoProcScalingStatistics` ENABLE KEYS */; /*!40000 ALTER TABLE `AutoProcScaling_has_Int` DISABLE KEYS */; -INSERT INTO `AutoProcScaling_has_Int` (`autoProcScaling_has_IntId`, `autoProcScalingId`, `autoProcIntegrationId`, `recordTimeStamp`) VALUES (592507,596133,592508,'2016-01-14 12:46:22'), -(592512,596138,592513,'2016-01-14 13:09:51'), -(592519,596145,592520,'2016-01-14 13:24:22'), -(592520,596146,592521,'2016-01-14 13:34:35'), -(592521,596147,592522,'2016-01-14 14:01:57'), -(592522,596147,592523,'2016-01-14 14:01:57'), -(592523,596148,592524,'2016-01-14 14:13:57'), -(592524,596148,592525,'2016-01-14 14:13:57'), -(600338,603434,600339,'2016-01-22 11:34:03'), -(600361,603457,600362,'2016-01-22 11:52:36'), -(600362,603458,600363,'2016-01-22 11:53:38'), -(600365,603461,600366,'2016-01-22 11:54:01'), -(600375,603470,600376,'2016-01-22 12:01:59'); +INSERT INTO `AutoProcScaling_has_Int` (`autoProcScaling_has_IntId`, `autoProcScalingId`, `autoProcIntegrationId`, `recordTimeStamp`) VALUES (592507,596133,592508,'2016-01-14 12:46:22'),(592512,596138,592513,'2016-01-14 13:09:51'),(592519,596145,592520,'2016-01-14 13:24:22'),(592520,596146,592521,'2016-01-14 13:34:35'),(592521,596147,592522,'2016-01-14 14:01:57'),(592522,596147,592523,'2016-01-14 14:01:57'),(592523,596148,592524,'2016-01-14 14:13:57'),(592524,596148,592525,'2016-01-14 14:13:57'),(600338,603434,600339,'2016-01-22 11:34:03'),(600361,603457,600362,'2016-01-22 11:52:36'),(600362,603458,600363,'2016-01-22 11:53:38'),(600365,603461,600366,'2016-01-22 11:54:01'),(600375,603470,600376,'2016-01-22 12:01:59'); /*!40000 ALTER TABLE `AutoProcScaling_has_Int` ENABLE KEYS */; /*!40000 ALTER TABLE `AutoProcStatus` DISABLE KEYS */; @@ -187,47 +75,19 @@ INSERT INTO `AutoProcScaling_has_Int` (`autoProcScaling_has_IntId`, `autoProcSca /*!40000 ALTER TABLE `BFactorFit` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSample` DISABLE KEYS */; -INSERT INTO `BLSample` (`blSampleId`, `diffractionPlanId`, `crystalId`, `containerId`, `name`, `code`, `location`, `holderLength`, `loopLength`, `loopType`, `wireWidth`, `comments`, `completionStage`, `structureStage`, `publicationStage`, `publicationComments`, `blSampleStatus`, `isInSampleChanger`, `lastKnownCenteringPosition`, `POSITIONID`, `recordTimeStamp`, `SMILES`, `blSubSampleId`, `lastImageURL`, `screenComponentGroupId`, `volume`, `dimension1`, `dimension2`, `dimension3`, `shape`, `packingFraction`, `preparationTemeprature`, `preparationHumidity`, `blottingTime`, `blottingForce`, `blottingDrainTime`, `support`, `subLocation`, `staffComments`, `source`) VALUES (11550,NULL,3918,1326,'Sample-001','SAM-011550','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:16:11',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11553,NULL,3921,1326,'Sample-002','SAM-011553','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:21:43',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11556,NULL,3924,1326,'Sample-003','SAM-011556','3',NULL,NULL,NULL,NULL,'',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11559,NULL,3927,1329,'Sample-004','SAM-011559','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11562,NULL,3930,1329,'Sample-005','SAM-011562','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11565,NULL,3933,1329,'Sample-006','SAM-011565','3',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11568,NULL,3936,1332,'Sample-007','SAM-011568','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11571,NULL,3939,1332,'Sample-008','SAM-011571','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11574,NULL,3942,1332,'Sample-009','SAM-011574','3',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11577,NULL,3942,1335,'Sample-010','SAM-011577','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11580,NULL,3942,1335,'Sample-011','SAM-011580','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11583,NULL,3951,1335,'Sample-012','SAM-011583','3',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11586,NULL,3954,NULL,'Sample-013','SAM-011586',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11589,NULL,3957,NULL,'Sample-014','SAM-011589',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(11592,NULL,3960,NULL,'Sample-015','SAM-011592',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(374695,NULL,310037,33049,'tlys_jan_4','HA00AU3712','4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:57:04',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(398810,197784,333301,34864,'thau8','HA00AK8934','8',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:57:05',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(398816,197784,310037,34874,'thau88','HH00AU3788','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-09-30 14:21:28',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(398819,197784,310037,34877,'thau99','HH00AU3799','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-05 10:15:47',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(398824,NULL,333308,34883,'XPDF-1','XPDF-0001',NULL,NULL,NULL,NULL,NULL,'Test sample for XPDF',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-26 14:47:58',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(398827,NULL,333308,34883,'XPDF-2','XPDF-0002',NULL,NULL,NULL,NULL,NULL,'Test sample for XPDF',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-26 14:51:23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'), -(398828,NULL,NULL,34888,'hello','hello','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2020-10-14 18:33:06',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'); +INSERT INTO `BLSample` (`blSampleId`, `diffractionPlanId`, `crystalId`, `containerId`, `name`, `code`, `location`, `holderLength`, `loopLength`, `loopType`, `wireWidth`, `comments`, `completionStage`, `structureStage`, `publicationStage`, `publicationComments`, `blSampleStatus`, `isInSampleChanger`, `lastKnownCenteringPosition`, `POSITIONID`, `recordTimeStamp`, `SMILES`, `blSubSampleId`, `lastImageURL`, `screenComponentGroupId`, `volume`, `dimension1`, `dimension2`, `dimension3`, `shape`, `packingFraction`, `preparationTemeprature`, `preparationHumidity`, `blottingTime`, `blottingForce`, `blottingDrainTime`, `support`, `subLocation`, `staffComments`, `source`) VALUES (11550,NULL,3918,1326,'Sample-001','SAM-011550','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:16:11',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11553,NULL,3921,1326,'Sample-002','SAM-011553','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:21:43',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11556,NULL,3924,1326,'Sample-003','SAM-011556','3',NULL,NULL,NULL,NULL,'',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11559,NULL,3927,1329,'Sample-004','SAM-011559','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11562,NULL,3930,1329,'Sample-005','SAM-011562','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11565,NULL,3933,1329,'Sample-006','SAM-011565','3',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11568,NULL,3936,1332,'Sample-007','SAM-011568','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11571,NULL,3939,1332,'Sample-008','SAM-011571','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11574,NULL,3942,1332,'Sample-009','SAM-011574','3',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11577,NULL,3942,1335,'Sample-010','SAM-011577','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11580,NULL,3942,1335,'Sample-011','SAM-011580','2',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11583,NULL,3951,1335,'Sample-012','SAM-011583','3',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11586,NULL,3954,NULL,'Sample-013','SAM-011586',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11589,NULL,3957,NULL,'Sample-014','SAM-011589',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(11592,NULL,3960,NULL,'Sample-015','SAM-011592',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:27:25',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(374695,NULL,310037,33049,'tlys_jan_4','HA00AU3712','4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:57:04',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(398810,197784,333301,34864,'thau8','HA00AK8934','8',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:57:05',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(398816,197784,310037,34874,'thau88','HH00AU3788','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-09-30 14:21:28',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(398819,197784,310037,34877,'thau99','HH00AU3799','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-05 10:15:47',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(398824,NULL,333308,34883,'XPDF-1','XPDF-0001',NULL,NULL,NULL,NULL,NULL,'Test sample for XPDF',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-26 14:47:58',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(398827,NULL,333308,34883,'XPDF-2','XPDF-0002',NULL,NULL,NULL,NULL,NULL,'Test sample for XPDF',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-26 14:51:23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'),(398828,NULL,NULL,34888,'hello','hello','1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2020-10-14 18:33:06',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%'); /*!40000 ALTER TABLE `BLSample` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleGroup` DISABLE KEYS */; -INSERT INTO `BLSampleGroup` (`blSampleGroupId`, `name`, `proposalId`, `ownerId`) VALUES (5,NULL,37027,NULL), -(6,'foo',37027,NULL), -(7,'bar',37027,NULL); +INSERT INTO `BLSampleGroup` (`blSampleGroupId`, `name`, `proposalId`, `ownerId`) VALUES (5,NULL,37027,NULL),(6,'foo',37027,NULL),(7,'bar',37027,NULL); /*!40000 ALTER TABLE `BLSampleGroup` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleGroup_has_BLSample` DISABLE KEYS */; -INSERT INTO `BLSampleGroup_has_BLSample` (`blSampleGroupId`, `blSampleId`, `groupOrder`, `type`, `blSampleTypeId`) VALUES (5,398824,1,'background',NULL), -(5,398827,2,'sample',NULL), -(6,398810,NULL,NULL,NULL), -(7,374695,NULL,NULL,NULL), -(7,398810,NULL,NULL,NULL); +INSERT INTO `BLSampleGroup_has_BLSample` (`blSampleGroupId`, `blSampleId`, `groupOrder`, `type`, `blSampleTypeId`) VALUES (5,398824,1,'background',NULL),(5,398827,2,'sample',NULL),(6,398810,NULL,NULL,NULL),(7,374695,NULL,NULL,NULL),(7,398810,NULL,NULL,NULL); /*!40000 ALTER TABLE `BLSampleGroup_has_BLSample` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleImage` DISABLE KEYS */; -INSERT INTO `BLSampleImage` (`blSampleImageId`, `blSampleId`, `micronsPerPixelX`, `micronsPerPixelY`, `imageFullPath`, `blSampleImageScoreId`, `comments`, `blTimeStamp`, `containerInspectionId`, `modifiedTimeStamp`, `offsetX`, `offsetY`) VALUES (2,398819,NULL,NULL,'/dls/i03/data/2016/cm1234-5/something.jpg',NULL,NULL,'2016-10-05 11:23:33',NULL,NULL,0,0), -(5,398816,1.1,1.2,'/dls/i03/data/2016/cm1234-5/something-else.jpg',NULL,NULL,'2016-10-10 14:31:06',4,NULL,0,0); +INSERT INTO `BLSampleImage` (`blSampleImageId`, `blSampleId`, `micronsPerPixelX`, `micronsPerPixelY`, `imageFullPath`, `blSampleImageScoreId`, `comments`, `blTimeStamp`, `containerInspectionId`, `modifiedTimeStamp`, `offsetX`, `offsetY`) VALUES (2,398819,NULL,NULL,'/dls/i03/data/2016/cm1234-5/something.jpg',NULL,NULL,'2016-10-05 11:23:33',NULL,NULL,0,0),(5,398816,1.1,1.2,'/dls/i03/data/2016/cm1234-5/something-else.jpg',NULL,NULL,'2016-10-10 14:31:06',4,NULL,0,0); /*!40000 ALTER TABLE `BLSampleImage` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleImageAnalysis` DISABLE KEYS */; @@ -238,16 +98,7 @@ INSERT INTO `BLSampleImageAnalysis` (`blSampleImageAnalysisId`, `blSampleImageId /*!40000 ALTER TABLE `BLSampleImageMeasurement` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleImageScore` DISABLE KEYS */; -INSERT INTO `BLSampleImageScore` (`blSampleImageScoreId`, `name`, `score`, `colour`) VALUES (1,'Clear',0,'#cccccc'), -(2,'Contaminated',1,'#fffd96'), -(3,'Light Precipitate',2,'#fdfd96'), -(4,'Phase Separation',4,'#fdfd96'), -(5,'Spherulites',5,'#ffb347'), -(6,'Microcrystals',6,'#ffb347'), -(7,'1D Crystals',7,'#87ceeb'), -(8,'2D Crystals',8,'#77dd77'), -(9,'3D Crystals',9,'#77dd77'), -(10,'Heavy Precipitate',3,'#ff6961'); +INSERT INTO `BLSampleImageScore` (`blSampleImageScoreId`, `name`, `score`, `colour`) VALUES (1,'Clear',0,'#cccccc'),(2,'Contaminated',1,'#fffd96'),(3,'Light Precipitate',2,'#fdfd96'),(4,'Phase Separation',4,'#fdfd96'),(5,'Spherulites',5,'#ffb347'),(6,'Microcrystals',6,'#ffb347'),(7,'1D Crystals',7,'#87ceeb'),(8,'2D Crystals',8,'#77dd77'),(9,'3D Crystals',9,'#77dd77'),(10,'Heavy Precipitate',3,'#ff6961'); /*!40000 ALTER TABLE `BLSampleImageScore` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleImage_has_AutoScoreClass` DISABLE KEYS */; @@ -263,8 +114,7 @@ INSERT INTO `BLSampleImageScore` (`blSampleImageScoreId`, `name`, `score`, `colo /*!40000 ALTER TABLE `BLSampleType_has_Component` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSample_has_DataCollectionPlan` DISABLE KEYS */; -INSERT INTO `BLSample_has_DataCollectionPlan` (`blSampleId`, `dataCollectionPlanId`, `planOrder`) VALUES (398824,197792,1), -(398827,197792,2); +INSERT INTO `BLSample_has_DataCollectionPlan` (`blSampleId`, `dataCollectionPlanId`, `planOrder`) VALUES (398824,197792,1),(398827,197792,2); /*!40000 ALTER TABLE `BLSample_has_DataCollectionPlan` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSample_has_EnergyScan` DISABLE KEYS */; @@ -277,20 +127,14 @@ INSERT INTO `BLSample_has_DataCollectionPlan` (`blSampleId`, `dataCollectionPlan /*!40000 ALTER TABLE `BLSample_has_Positioner` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSession` DISABLE KEYS */; -INSERT INTO `BLSession` (`sessionId`, `beamLineSetupId`, `proposalId`, `beamCalendarId`, `startDate`, `endDate`, `beamLineName`, `scheduled`, `nbShifts`, `comments`, `beamLineOperator`, `bltimeStamp`, `visit_number`, `usedFlag`, `lastUpdate`, `externalId`, `archived`, `riskRating`, `purgedProcessedData`, `icatId`) VALUES (55167,1,37027,NULL,'2016-01-01 09:00:00','2016-01-01 17:00:00','i03',NULL,NULL,'ghfg',NULL,'2015-12-21 15:20:43',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), -(55168,1,37027,NULL,'2016-03-11 09:00:00','2016-03-11 17:00:00','i03',NULL,NULL,'jhgjh',NULL,'2015-12-21 15:20:44',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), -(339525,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-16 16:08:29',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), -(339528,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:07:42',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), -(339531,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:08:09',3,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL), -(339535,NULL,37027,NULL,'2018-03-27 09:00:00','2018-07-27 09:00:00','i02-2',NULL,NULL,NULL,NULL,'2018-04-05 15:48:37',99,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL); +INSERT INTO `BLSession` (`sessionId`, `beamLineSetupId`, `proposalId`, `beamCalendarId`, `startDate`, `endDate`, `beamLineName`, `scheduled`, `nbShifts`, `comments`, `beamLineOperator`, `bltimeStamp`, `visit_number`, `usedFlag`, `lastUpdate`, `externalId`, `archived`, `riskRating`, `purgedProcessedData`, `icatId`) VALUES (55167,1,37027,NULL,'2016-01-01 09:00:00','2016-01-01 17:00:00','i03',NULL,NULL,'ghfg',NULL,'2015-12-21 15:20:43',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL),(55168,1,37027,NULL,'2016-03-11 09:00:00','2016-03-11 17:00:00','i03',NULL,NULL,'jhgjh',NULL,'2015-12-21 15:20:44',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL),(339525,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-16 16:08:29',1,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL),(339528,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:07:42',2,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL),(339531,NULL,141666,NULL,NULL,NULL,'i03',NULL,NULL,NULL,NULL,'2016-03-17 15:08:09',3,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL),(339535,NULL,37027,NULL,'2018-03-27 09:00:00','2018-07-27 09:00:00','i02-2',NULL,NULL,NULL,NULL,'2018-04-05 15:48:37',99,NULL,'0000-00-00 00:00:00',NULL,0,NULL,0,NULL); /*!40000 ALTER TABLE `BLSession` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSession_has_SCPosition` DISABLE KEYS */; /*!40000 ALTER TABLE `BLSession_has_SCPosition` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSubSample` DISABLE KEYS */; -INSERT INTO `BLSubSample` (`blSubSampleId`, `blSampleId`, `diffractionPlanId`, `blSampleImageId`, `positionId`, `position2Id`, `motorPositionId`, `blSubSampleUUID`, `imgFileName`, `imgFilePath`, `comments`, `recordTimeStamp`, `source`, `type`) VALUES (2,398816,197784,NULL,2,5,NULL,NULL,NULL,NULL,NULL,'2016-09-30 14:25:19','manual',NULL), -(5,398819,197784,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-05 10:16:44','manual',NULL); +INSERT INTO `BLSubSample` (`blSubSampleId`, `blSampleId`, `diffractionPlanId`, `blSampleImageId`, `positionId`, `position2Id`, `motorPositionId`, `blSubSampleUUID`, `imgFileName`, `imgFilePath`, `comments`, `recordTimeStamp`, `source`, `type`) VALUES (2,398816,197784,NULL,2,5,NULL,NULL,NULL,NULL,NULL,'2016-09-30 14:25:19','manual',NULL),(5,398819,197784,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-05 10:16:44','manual',NULL); /*!40000 ALTER TABLE `BLSubSample` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSubSample_has_Positioner` DISABLE KEYS */; @@ -332,24 +176,11 @@ INSERT INTO `ComponentLattice` (`componentLatticeId`, `componentId`, `spaceGroup /*!40000 ALTER TABLE `Component_has_SubType` ENABLE KEYS */; /*!40000 ALTER TABLE `Container` DISABLE KEYS */; -INSERT INTO `Container` (`containerId`, `dewarId`, `code`, `containerType`, `capacity`, `sampleChangerLocation`, `containerStatus`, `bltimeStamp`, `beamlineLocation`, `screenId`, `scheduleId`, `barcode`, `imagerId`, `sessionId`, `ownerId`, `requestedImagerId`, `requestedReturn`, `comments`, `experimentType`, `storageTemperature`, `containerRegistryId`, `scLocationUpdated`, `priorityPipelineId`, `experimentTypeId`, `containerTypeId`, `currentDewarId`, `parentContainerId`, `source`, `parentContainerLocation`) VALUES (1326,573,'Container-1-cm0001-1','Puck-16',16,'3','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000001',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,4,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(1329,573,'Container-2-cm0001-1','Puck-16',16,'4','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000002',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(1332,576,'Container-3-cm0001-1','Puck-16',16,'5','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000003',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(1335,579,'Container-4-cm0001-2','Puck-16',16,'6','processing',NULL,'i03',NULL,NULL,'container-cm0001-2-0001335',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(1338,582,'Container-5-cm0001-3','Puck-16',16,'7','processing',NULL,'i03',NULL,NULL,'container-cm0001-3-0001338',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(1341,573,'Manual',NULL,NULL,'9',NULL,NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(33049,8287,'cm14451-1_i03r-002','Puck',16,NULL,'at DLS',NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(34864,8572,'I03R-001','Puck',16,'29','processing','2016-02-24 12:13:05','i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(34874,8572,'test_plate2','CrystalQuickX',192,'3','in_storage','2016-02-12 09:20:44','i03',NULL,2,'test_plate2',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(34877,8572,'test_plate3','CrystalQuickX',192,'3','in_storage','2016-10-04 10:50:05','i03',NULL,2,'test_plate3',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(34879,8572,'test_plate4','CrystalQuickX',192,'4','processing',NULL,'i02-2',NULL,2,'test_plate4',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(34883,NULL,'XPDF-container-1','XPDF container',NULL,NULL,'processing',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL), -(34888,8578,'TestSim01','CrystalQuickX',192,'1','in_storage',NULL,'i02-2',NULL,2,'VMXiSim-001',7,339535,1,7,0,NULL,NULL,NULL,5,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL); +INSERT INTO `Container` (`containerId`, `dewarId`, `code`, `containerType`, `capacity`, `sampleChangerLocation`, `containerStatus`, `bltimeStamp`, `beamlineLocation`, `screenId`, `scheduleId`, `barcode`, `imagerId`, `sessionId`, `ownerId`, `requestedImagerId`, `requestedReturn`, `comments`, `experimentType`, `storageTemperature`, `containerRegistryId`, `scLocationUpdated`, `priorityPipelineId`, `experimentTypeId`, `containerTypeId`, `currentDewarId`, `parentContainerId`, `source`, `parentContainerLocation`) VALUES (1326,573,'Container-1-cm0001-1','Puck-16',16,'3','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000001',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,4,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(1329,573,'Container-2-cm0001-1','Puck-16',16,'4','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000002',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(1332,576,'Container-3-cm0001-1','Puck-16',16,'5','processing',NULL,'i03',NULL,NULL,'container-cm0001-1-0000003',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(1335,579,'Container-4-cm0001-2','Puck-16',16,'6','processing',NULL,'i03',NULL,NULL,'container-cm0001-2-0001335',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(1338,582,'Container-5-cm0001-3','Puck-16',16,'7','processing',NULL,'i03',NULL,NULL,'container-cm0001-3-0001338',NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(1341,573,'Manual',NULL,NULL,'9',NULL,NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(33049,8287,'cm14451-1_i03r-002','Puck',16,NULL,'at DLS',NULL,'i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(34864,8572,'I03R-001','Puck',16,'29','processing','2016-02-24 12:13:05','i03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(34874,8572,'test_plate2','CrystalQuickX',192,'3','in_storage','2016-02-12 09:20:44','i03',NULL,2,'test_plate2',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(34877,8572,'test_plate3','CrystalQuickX',192,'3','in_storage','2016-10-04 10:50:05','i03',NULL,2,'test_plate3',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(34879,8572,'test_plate4','CrystalQuickX',192,'4','processing',NULL,'i02-2',NULL,2,'test_plate4',2,NULL,NULL,2,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(34883,NULL,'XPDF-container-1','XPDF container',NULL,NULL,'processing',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL),(34888,8578,'TestSim01','CrystalQuickX',192,'1','in_storage',NULL,'i02-2',NULL,2,'VMXiSim-001',7,339535,1,7,0,NULL,NULL,NULL,5,NULL,NULL,NULL,NULL,NULL,NULL,'root@%',NULL); /*!40000 ALTER TABLE `Container` ENABLE KEYS */; /*!40000 ALTER TABLE `ContainerHistory` DISABLE KEYS */; -INSERT INTO `ContainerHistory` (`containerHistoryId`, `containerId`, `location`, `blTimeStamp`, `status`, `beamlineName`, `currentDewarId`) VALUES (6,34874,'3','2016-09-30 12:56:21','in_localstorage','i03',NULL), -(7,34874,'3','2017-10-19 13:35:34','in_storage','i02-2',NULL); +INSERT INTO `ContainerHistory` (`containerHistoryId`, `containerId`, `location`, `blTimeStamp`, `status`, `beamlineName`, `currentDewarId`) VALUES (6,34874,'3','2016-09-30 12:56:21','in_localstorage','i03',NULL),(7,34874,'3','2017-10-19 13:35:34','in_storage','i02-2',NULL); /*!40000 ALTER TABLE `ContainerHistory` ENABLE KEYS */; /*!40000 ALTER TABLE `ContainerInspection` DISABLE KEYS */; @@ -357,8 +188,7 @@ INSERT INTO `ContainerInspection` (`containerInspectionId`, `containerId`, `insp /*!40000 ALTER TABLE `ContainerInspection` ENABLE KEYS */; /*!40000 ALTER TABLE `ContainerQueue` DISABLE KEYS */; -INSERT INTO `ContainerQueue` (`containerQueueId`, `containerId`, `personId`, `createdTimeStamp`, `completedTimeStamp`) VALUES (2,34874,NULL,'2016-09-30 12:56:21',NULL), -(8,34877,NULL,'2016-10-05 09:09:59',NULL); +INSERT INTO `ContainerQueue` (`containerQueueId`, `containerId`, `personId`, `createdTimeStamp`, `completedTimeStamp`) VALUES (2,34874,NULL,'2016-09-30 12:56:21',NULL),(8,34877,NULL,'2016-10-05 09:09:59',NULL); /*!40000 ALTER TABLE `ContainerQueue` ENABLE KEYS */; /*!40000 ALTER TABLE `ContainerQueueSample` DISABLE KEYS */; @@ -366,8 +196,7 @@ INSERT INTO `ContainerQueueSample` (`containerQueueSampleId`, `containerQueueId` /*!40000 ALTER TABLE `ContainerQueueSample` ENABLE KEYS */; /*!40000 ALTER TABLE `ContainerRegistry` DISABLE KEYS */; -INSERT INTO `ContainerRegistry` (`containerRegistryId`, `barcode`, `comments`, `recordTimestamp`) VALUES (4,'DLS-0001',NULL,'2017-09-21 10:01:07'), -(5,'VMXiSim-001',NULL,'2019-03-22 11:48:43'); +INSERT INTO `ContainerRegistry` (`containerRegistryId`, `barcode`, `comments`, `recordTimestamp`) VALUES (4,'DLS-0001',NULL,'2017-09-21 10:01:07'),(5,'VMXiSim-001',NULL,'2019-03-22 11:48:43'); /*!40000 ALTER TABLE `ContainerRegistry` ENABLE KEYS */; /*!40000 ALTER TABLE `ContainerRegistry_has_Proposal` DISABLE KEYS */; @@ -383,24 +212,7 @@ INSERT INTO `ContainerRegistry` (`containerRegistryId`, `barcode`, `comments`, ` /*!40000 ALTER TABLE `CryoemInitialModel` ENABLE KEYS */; /*!40000 ALTER TABLE `Crystal` DISABLE KEYS */; -INSERT INTO `Crystal` (`crystalId`, `diffractionPlanId`, `proteinId`, `crystalUUID`, `name`, `spaceGroup`, `morphology`, `color`, `size_X`, `size_Y`, `size_Z`, `cell_a`, `cell_b`, `cell_c`, `cell_alpha`, `cell_beta`, `cell_gamma`, `comments`, `pdbFileName`, `pdbFilePath`, `recordTimeStamp`, `abundance`, `theoreticalDensity`) VALUES (3918,NULL,4380,NULL,'Crystal 01',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3921,NULL,4383,NULL,'Crystal 02',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3924,NULL,4386,NULL,'Crystal 03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3927,NULL,4389,NULL,'Crystal 04',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3930,NULL,4392,NULL,'Crystal 05',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3933,NULL,4395,NULL,'Crystal 06',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3936,NULL,4398,NULL,'Crystal 07',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3939,NULL,4401,NULL,'Crystal 08',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3942,NULL,4404,NULL,'Crystal 09',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3945,NULL,4407,NULL,'Crystal 10',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3948,NULL,4407,NULL,'Crystal 11',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3951,NULL,4410,NULL,'Crystal 12',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3954,NULL,4410,NULL,'Crystal 13',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3957,NULL,4413,NULL,'Crystal 14',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(3960,NULL,4413,NULL,'Crystal 15',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL), -(310037,NULL,121393,NULL,'crystal-4-cm14451-1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:58:00',NULL,NULL), -(333301,NULL,123491,NULL,NULL,'P41212',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:58:00',NULL,NULL), -(333308,NULL,123497,NULL,'SampleType01','P12121',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'sample type comments ...',NULL,NULL,'2017-03-23 22:06:42',NULL,NULL); +INSERT INTO `Crystal` (`crystalId`, `diffractionPlanId`, `proteinId`, `crystalUUID`, `name`, `spaceGroup`, `morphology`, `color`, `size_X`, `size_Y`, `size_Z`, `cell_a`, `cell_b`, `cell_c`, `cell_alpha`, `cell_beta`, `cell_gamma`, `comments`, `pdbFileName`, `pdbFilePath`, `recordTimeStamp`, `abundance`, `theoreticalDensity`) VALUES (3918,NULL,4380,NULL,'Crystal 01',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3921,NULL,4383,NULL,'Crystal 02',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3924,NULL,4386,NULL,'Crystal 03',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3927,NULL,4389,NULL,'Crystal 04',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3930,NULL,4392,NULL,'Crystal 05',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3933,NULL,4395,NULL,'Crystal 06',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3936,NULL,4398,NULL,'Crystal 07',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3939,NULL,4401,NULL,'Crystal 08',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3942,NULL,4404,NULL,'Crystal 09',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3945,NULL,4407,NULL,'Crystal 10',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3948,NULL,4407,NULL,'Crystal 11',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3951,NULL,4410,NULL,'Crystal 12',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3954,NULL,4410,NULL,'Crystal 13',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3957,NULL,4413,NULL,'Crystal 14',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(3960,NULL,4413,NULL,'Crystal 15',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-17 16:11:19',NULL,NULL),(310037,NULL,121393,NULL,'crystal-4-cm14451-1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:58:00',NULL,NULL),(333301,NULL,123491,NULL,NULL,'P41212',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-19 22:58:00',NULL,NULL),(333308,NULL,123497,NULL,'SampleType01','P12121',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'sample type comments ...',NULL,NULL,'2017-03-23 22:06:42',NULL,NULL); /*!40000 ALTER TABLE `Crystal` ENABLE KEYS */; /*!40000 ALTER TABLE `CrystalComposition` DISABLE KEYS */; @@ -413,12 +225,7 @@ INSERT INTO `Crystal` (`crystalId`, `diffractionPlanId`, `proteinId`, `crystalUU /*!40000 ALTER TABLE `DataAcquisition` ENABLE KEYS */; /*!40000 ALTER TABLE `DataCollection` DISABLE KEYS */; -INSERT INTO `DataCollection` (`dataCollectionId`, `BLSAMPLEID`, `SESSIONID`, `experimenttype`, `dataCollectionNumber`, `startTime`, `endTime`, `runStatus`, `axisStart`, `axisEnd`, `axisRange`, `overlap`, `numberOfImages`, `startImageNumber`, `numberOfPasses`, `exposureTime`, `imageDirectory`, `imagePrefix`, `imageSuffix`, `imageContainerSubPath`, `fileTemplate`, `wavelength`, `resolution`, `detectorDistance`, `xBeam`, `yBeam`, `comments`, `printableForReport`, `CRYSTALCLASS`, `slitGapVertical`, `slitGapHorizontal`, `transmission`, `synchrotronMode`, `xtalSnapshotFullPath1`, `xtalSnapshotFullPath2`, `xtalSnapshotFullPath3`, `xtalSnapshotFullPath4`, `rotationAxis`, `phiStart`, `kappaStart`, `omegaStart`, `chiStart`, `resolutionAtCorner`, `detector2Theta`, `DETECTORMODE`, `undulatorGap1`, `undulatorGap2`, `undulatorGap3`, `beamSizeAtSampleX`, `beamSizeAtSampleY`, `centeringMethod`, `averageTemperature`, `ACTUALSAMPLEBARCODE`, `ACTUALSAMPLESLOTINCONTAINER`, `ACTUALCONTAINERBARCODE`, `ACTUALCONTAINERSLOTINSC`, `actualCenteringPosition`, `beamShape`, `dataCollectionGroupId`, `POSITIONID`, `detectorId`, `FOCALSPOTSIZEATSAMPLEX`, `POLARISATION`, `FOCALSPOTSIZEATSAMPLEY`, `APERTUREID`, `screeningOrigId`, `startPositionId`, `endPositionId`, `flux`, `strategySubWedgeOrigId`, `blSubSampleId`, `flux_end`, `bestWilsonPlotPath`, `processedDataFile`, `datFullPath`, `magnification`, `totalAbsorbedDose`, `binning`, `particleDiameter`, `boxSize_CTF`, `minResolution`, `minDefocus`, `maxDefocus`, `defocusStepSize`, `amountAstigmatism`, `extractSize`, `bgRadius`, `voltage`, `objAperture`, `c1aperture`, `c2aperture`, `c3aperture`, `c1lens`, `c2lens`, `c3lens`, `totalExposedDose`, `nominalMagnification`, `nominalDefocus`, `imageSizeX`, `imageSizeY`, `pixelSizeOnImage`, `phasePlate`, `dataCollectionPlanId`) VALUES (993677,374695,55167,NULL,1,'2016-01-14 12:40:34','2016-01-14 12:41:54','DataCollection Successful',45,0.1,0.1,0,3600,1,1,0.02,'/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/','tlys_jan_4','cbf',NULL,'tlys_jan_4_1_####.cbf',1.28255,1.6,193.087,215.62,208.978,'(-402,345,142) EDNAStrategy4: subWedge:1Aperture: Medium',1,NULL,0.059918,0.099937,40.1936,'User','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_315.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_225.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_135.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_45.0.png','Omega',NULL,NULL,45,NULL,NULL,NULL,NULL,5.685,NULL,NULL,0.05,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,988855,595236,NULL,80,NULL,20,6,NULL,NULL,NULL,833107367454.3083,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(1002287,NULL,55167,NULL,2,'2016-01-22 11:25:18','2016-01-22 11:28:23','DataCollection Successful',0,0.1,0.1,0,7200,1,1,0.025,'/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/','ins2','cbf',NULL,'ins2_2_####.cbf',1.2,1.41777,175,215.618,209.102,'(-307,322,-184) Aperture: Large',1,NULL,0.059918,0.099937,0.999423,'User','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_270.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_180.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_90.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_0.0.png','Omega',NULL,NULL,0,NULL,NULL,NULL,NULL,6.1213,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,996311,602072,NULL,80,NULL,20,3752,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(1052494,NULL,55168,NULL,1,'2016-04-13 12:18:12','2016-04-13 12:18:50','DataCollection Successful',0,0.4,0.4,-89.6,2,1,1,0.01,'/dls/i03/data/2016/cm14451-2/20160413/test_xtal/','xtal1','cbf',NULL,'xtal1_1_####.cbf',0.976254,1.24362,200,214.33,208.71,'(-703,-47,-74) Aperture: Large',1,NULL,0.059918,0.099937,100,'User','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_90.0.png','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_0.0.png',NULL,NULL,'Omega',NULL,NULL,0,NULL,NULL,NULL,NULL,5.30095,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1040398,647536,NULL,80,NULL,20,3752,NULL,NULL,NULL,1959830505829.428,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(1052503,NULL,55168,NULL,3,'2016-04-13 12:21:26','2016-04-13 12:21:54','DataCollection Successful',93,0.3,0.3,-44.7,3,1,1,0.01,'/dls/i03/data/2016/cm14451-2/20160413/test_xtal/','xtal1','cbf',NULL,'xtal1_3_####.cbf',0.976253,1.5,266.693,214.372,208.299,'(-703,-47,-74) Aperture: Large',1,NULL,0.059918,0.099937,100,'User','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_183.0.png','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_93.0.png',NULL,NULL,'Omega',NULL,NULL,93,NULL,NULL,NULL,NULL,5.30095,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1040407,647545,NULL,80,NULL,20,3752,NULL,NULL,NULL,1972385107622.2878,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(1066786,398810,55168,NULL,2,'2016-04-18 11:04:44','2016-04-18 11:04:57','DataCollection Successful',0,0.5,0.5,-44.5,3,1,1,0.1,'/dls/i03/data/2016/cm14451-2/gw/20160418/thau/edna_test/','thau','cbf',NULL,'thau_2_####.cbf',0.976253,1.5,266.693,214.372,208.299,'(-345,-241,-185) Aperture: Large',1,NULL,0.059918,0.099937,5.00016,'User','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_1_90.0.png','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_1_0.0.png',NULL,NULL,'Omega',NULL,NULL,0,NULL,NULL,NULL,NULL,5.301,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1054243,661459,NULL,80,NULL,20,3752,NULL,NULL,NULL,57087013071.909134,NULL,2,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(6017405,374695,55167,NULL,1,'2021-02-25 10:15:06','2021-02-25 10:15:47','DataCollection Successful',210,0,0,0,480,1,1,0.004,'/dls/i03/data/2021/cm28170-1/xraycentring/screening/TestLysozyme/Lys_6/','Lys_6','h5',NULL,'Lys_6_1_master.h5',0.976254,4.2989,337,78.0483,83.9258,'Xray centring - Diffraction grid scan of 30 by 16 images, Top left [304,229], Bottom right [1024,599]',1,NULL,0.499922,0.49994,100,'User','/dls/i03/data/2021/cm28170-1/jpegs/xraycentring/screening/TestLysozyme/Lys_6/Lys_6_1_210.0.png','/dls/i03/data/2021/cm28170-1/jpegs/xraycentring/screening/TestLysozyme/Lys_6/Lys_6_1_210.0.png','/dls/i03/data/2021/cm28170-1/jpegs/xraycentring/screening/TestLysozyme/Lys_6/Lys_6_1_210.0.png',NULL,NULL,0,NULL,210,-0.000047,NULL,NULL,NULL,5.28695,NULL,NULL,0.02,0.02,'UNSPECIFIED',NULL,NULL,NULL,NULL,NULL,NULL,NULL,5440739,4642226,78,80,NULL,20,NULL,NULL,NULL,NULL,731694586254.7522,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `DataCollection` (`dataCollectionId`, `BLSAMPLEID`, `SESSIONID`, `experimenttype`, `dataCollectionNumber`, `startTime`, `endTime`, `runStatus`, `axisStart`, `axisEnd`, `axisRange`, `overlap`, `numberOfImages`, `startImageNumber`, `numberOfPasses`, `exposureTime`, `imageDirectory`, `imagePrefix`, `imageSuffix`, `imageContainerSubPath`, `fileTemplate`, `wavelength`, `resolution`, `detectorDistance`, `xBeam`, `yBeam`, `comments`, `printableForReport`, `CRYSTALCLASS`, `slitGapVertical`, `slitGapHorizontal`, `transmission`, `synchrotronMode`, `xtalSnapshotFullPath1`, `xtalSnapshotFullPath2`, `xtalSnapshotFullPath3`, `xtalSnapshotFullPath4`, `rotationAxis`, `phiStart`, `kappaStart`, `omegaStart`, `chiStart`, `resolutionAtCorner`, `detector2Theta`, `DETECTORMODE`, `undulatorGap1`, `undulatorGap2`, `undulatorGap3`, `beamSizeAtSampleX`, `beamSizeAtSampleY`, `centeringMethod`, `averageTemperature`, `ACTUALSAMPLEBARCODE`, `ACTUALSAMPLESLOTINCONTAINER`, `ACTUALCONTAINERBARCODE`, `ACTUALCONTAINERSLOTINSC`, `actualCenteringPosition`, `beamShape`, `dataCollectionGroupId`, `POSITIONID`, `detectorId`, `FOCALSPOTSIZEATSAMPLEX`, `POLARISATION`, `FOCALSPOTSIZEATSAMPLEY`, `APERTUREID`, `screeningOrigId`, `startPositionId`, `endPositionId`, `flux`, `strategySubWedgeOrigId`, `blSubSampleId`, `flux_end`, `bestWilsonPlotPath`, `processedDataFile`, `datFullPath`, `magnification`, `totalAbsorbedDose`, `binning`, `particleDiameter`, `boxSize_CTF`, `minResolution`, `minDefocus`, `maxDefocus`, `defocusStepSize`, `amountAstigmatism`, `extractSize`, `bgRadius`, `voltage`, `objAperture`, `c1aperture`, `c2aperture`, `c3aperture`, `c1lens`, `c2lens`, `c3lens`, `totalExposedDose`, `nominalMagnification`, `nominalDefocus`, `imageSizeX`, `imageSizeY`, `pixelSizeOnImage`, `phasePlate`, `dataCollectionPlanId`) VALUES (993677,374695,55167,NULL,1,'2016-01-14 12:40:34','2016-01-14 12:41:54','DataCollection Successful',45,0.1,0.1,0,3600,1,1,0.02,'/dls/i03/data/2016/cm14451-1/20160114/tlys_jan_4/','tlys_jan_4','cbf',NULL,'tlys_jan_4_1_####.cbf',1.28255,1.6,193.087,215.62,208.978,'(-402,345,142) EDNAStrategy4: subWedge:1Aperture: Medium',1,NULL,0.059918,0.099937,40.1936,'User','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_315.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_225.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_135.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160114/tlys_jan_4/tlys_jan_4_1_1_45.0.png','Omega',NULL,NULL,45,NULL,NULL,NULL,NULL,5.685,NULL,NULL,0.05,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,988855,595236,NULL,80,NULL,20,6,NULL,NULL,NULL,833107367454.3083,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1002287,NULL,55167,NULL,2,'2016-01-22 11:25:18','2016-01-22 11:28:23','DataCollection Successful',0,0.1,0.1,0,7200,1,1,0.025,'/dls/i03/data/2016/cm14451-1/20160122/gw/ins2/001/','ins2','cbf',NULL,'ins2_2_####.cbf',1.2,1.41777,175,215.618,209.102,'(-307,322,-184) Aperture: Large',1,NULL,0.059918,0.099937,0.999423,'User','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_270.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_180.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_90.0.png','/dls/i03/data/2016/cm14451-1/jpegs/20160122/gw/ins2/001/ins2_2_1_0.0.png','Omega',NULL,NULL,0,NULL,NULL,NULL,NULL,6.1213,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,996311,602072,NULL,80,NULL,20,3752,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1052494,NULL,55168,NULL,1,'2016-04-13 12:18:12','2016-04-13 12:18:50','DataCollection Successful',0,0.4,0.4,-89.6,2,1,1,0.01,'/dls/i03/data/2016/cm14451-2/20160413/test_xtal/','xtal1','cbf',NULL,'xtal1_1_####.cbf',0.976254,1.24362,200,214.33,208.71,'(-703,-47,-74) Aperture: Large',1,NULL,0.059918,0.099937,100,'User','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_90.0.png','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_1_0.0.png',NULL,NULL,'Omega',NULL,NULL,0,NULL,NULL,NULL,NULL,5.30095,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1040398,647536,NULL,80,NULL,20,3752,NULL,NULL,NULL,1959830505829.428,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1052503,NULL,55168,NULL,3,'2016-04-13 12:21:26','2016-04-13 12:21:54','DataCollection Successful',93,0.3,0.3,-44.7,3,1,1,0.01,'/dls/i03/data/2016/cm14451-2/20160413/test_xtal/','xtal1','cbf',NULL,'xtal1_3_####.cbf',0.976253,1.5,266.693,214.372,208.299,'(-703,-47,-74) Aperture: Large',1,NULL,0.059918,0.099937,100,'User','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_183.0.png','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_1_93.0.png',NULL,NULL,'Omega',NULL,NULL,93,NULL,NULL,NULL,NULL,5.30095,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1040407,647545,NULL,80,NULL,20,3752,NULL,NULL,NULL,1972385107622.2878,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1066786,398810,55168,NULL,2,'2016-04-18 11:04:44','2016-04-18 11:04:57','DataCollection Successful',0,0.5,0.5,-44.5,3,1,1,0.1,'/dls/i03/data/2016/cm14451-2/gw/20160418/thau/edna_test/','thau','cbf',NULL,'thau_2_####.cbf',0.976253,1.5,266.693,214.372,208.299,'(-345,-241,-185) Aperture: Large',1,NULL,0.059918,0.099937,5.00016,'User','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_1_90.0.png','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_1_0.0.png',NULL,NULL,'Omega',NULL,NULL,0,NULL,NULL,NULL,NULL,5.301,NULL,NULL,0.08,0.02,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1054243,661459,NULL,80,NULL,20,3752,NULL,NULL,NULL,57087013071.909134,NULL,2,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(6017405,374695,55167,NULL,1,'2021-02-25 10:15:06','2021-02-25 10:15:47','DataCollection Successful',210,0,0,0,480,1,1,0.004,'/dls/i03/data/2021/cm28170-1/xraycentring/screening/TestLysozyme/Lys_6/','Lys_6','h5',NULL,'Lys_6_1_master.h5',0.976254,4.2989,337,78.0483,83.9258,'Xray centring - Diffraction grid scan of 30 by 16 images, Top left [304,229], Bottom right [1024,599]',1,NULL,0.499922,0.49994,100,'User','/dls/i03/data/2021/cm28170-1/jpegs/xraycentring/screening/TestLysozyme/Lys_6/Lys_6_1_210.0.png','/dls/i03/data/2021/cm28170-1/jpegs/xraycentring/screening/TestLysozyme/Lys_6/Lys_6_1_210.0.png','/dls/i03/data/2021/cm28170-1/jpegs/xraycentring/screening/TestLysozyme/Lys_6/Lys_6_1_210.0.png',NULL,NULL,0,NULL,210,-0.000047,NULL,NULL,NULL,5.28695,NULL,NULL,0.02,0.02,'UNSPECIFIED',NULL,NULL,NULL,NULL,NULL,NULL,NULL,5440739,4642226,78,80,NULL,20,NULL,NULL,NULL,NULL,731694586254.7522,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `DataCollection` ENABLE KEYS */; /*!40000 ALTER TABLE `DataCollectionComment` DISABLE KEYS */; @@ -428,12 +235,7 @@ INSERT INTO `DataCollection` (`dataCollectionId`, `BLSAMPLEID`, `SESSIONID`, `ex /*!40000 ALTER TABLE `DataCollectionFileAttachment` ENABLE KEYS */; /*!40000 ALTER TABLE `DataCollectionGroup` DISABLE KEYS */; -INSERT INTO `DataCollectionGroup` (`dataCollectionGroupId`, `sessionId`, `comments`, `blSampleId`, `experimentType`, `startTime`, `endTime`, `crystalClass`, `detectorMode`, `actualSampleBarcode`, `actualSampleSlotInContainer`, `actualContainerBarcode`, `actualContainerSlotInSC`, `xtalSnapshotFullPath`, `scanParameters`, `experimentTypeId`) VALUES (988855,55167,NULL,374695,'SAD',NULL,NULL,NULL,'Ext. Trigger','HA00AU3712',NULL,NULL,NULL,NULL,NULL,NULL), -(996311,55167,NULL,NULL,'SAD',NULL,NULL,NULL,'Ext. Trigger',NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(1040398,55168,NULL,NULL,'SAD',NULL,NULL,NULL,'Ext. Trigger',NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(1040407,55168,NULL,NULL,'SAD',NULL,NULL,NULL,'Ext. Trigger',NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(1054243,55168,NULL,398810,'SAD',NULL,NULL,NULL,'Ext. Trigger','CA00AG9993',NULL,NULL,NULL,NULL,NULL,NULL), -(5440739,55167,NULL,374695,'Mesh',NULL,NULL,NULL,NULL,'NR',NULL,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `DataCollectionGroup` (`dataCollectionGroupId`, `sessionId`, `comments`, `blSampleId`, `experimentType`, `startTime`, `endTime`, `crystalClass`, `detectorMode`, `actualSampleBarcode`, `actualSampleSlotInContainer`, `actualContainerBarcode`, `actualContainerSlotInSC`, `xtalSnapshotFullPath`, `scanParameters`, `experimentTypeId`) VALUES (988855,55167,NULL,374695,'SAD',NULL,NULL,NULL,'Ext. Trigger','HA00AU3712',NULL,NULL,NULL,NULL,NULL,NULL),(996311,55167,NULL,NULL,'SAD',NULL,NULL,NULL,'Ext. Trigger',NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1040398,55168,NULL,NULL,'SAD',NULL,NULL,NULL,'Ext. Trigger',NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1040407,55168,NULL,NULL,'SAD',NULL,NULL,NULL,'Ext. Trigger',NULL,NULL,NULL,NULL,NULL,NULL,NULL),(1054243,55168,NULL,398810,'SAD',NULL,NULL,NULL,'Ext. Trigger','CA00AG9993',NULL,NULL,NULL,NULL,NULL,NULL),(5440739,55167,NULL,374695,'Mesh',NULL,NULL,NULL,NULL,'NR',NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `DataCollectionGroup` ENABLE KEYS */; /*!40000 ALTER TABLE `DataCollectionPlan_has_Detector` DISABLE KEYS */; @@ -441,13 +243,7 @@ INSERT INTO `DataCollectionPlan_has_Detector` (`dataCollectionPlanHasDetectorId` /*!40000 ALTER TABLE `DataCollectionPlan_has_Detector` ENABLE KEYS */; /*!40000 ALTER TABLE `Dewar` DISABLE KEYS */; -INSERT INTO `Dewar` (`dewarId`, `shippingId`, `code`, `comments`, `storageLocation`, `dewarStatus`, `bltimeStamp`, `isStorageDewar`, `barCode`, `firstExperimentId`, `customsValue`, `transportValue`, `trackingNumberToSynchrotron`, `trackingNumberFromSynchrotron`, `type`, `facilityCode`, `weight`, `deliveryAgent_barcode`, `extra`, `source`, `externalShippingIdFromSynchrotron`, `dewarRegistryId`) VALUES (573,474,'Dewar-1-cm0001-1',NULL,NULL,'processing',NULL,0,'dewar-cm0001-1-0000001',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), -(576,474,'Dewar-2-cm0001-1',NULL,NULL,'at DLS',NULL,0,'dewar-cm0001-1-0000002',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), -(579,477,'Dewar-3-cm0001-2',NULL,NULL,'processing',NULL,0,'dewar-cm0001-2-0000477',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), -(582,480,'Dewar-4-cm0001-3',NULL,NULL,'processing',NULL,0,'dewar-cm0001-3-0000480',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), -(8287,6988,'Default Dewar:cm14451-1',NULL,NULL,'processing',NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), -(8572,7227,'cm14451-2_Dewar1',NULL,NULL,'processing','2016-02-10 13:03:07',0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL), -(8578,7231,'Dewar_1',NULL,NULL,'opened',NULL,0,'cm14451-12345',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL); +INSERT INTO `Dewar` (`dewarId`, `shippingId`, `code`, `comments`, `storageLocation`, `dewarStatus`, `bltimeStamp`, `isStorageDewar`, `barCode`, `firstExperimentId`, `customsValue`, `transportValue`, `trackingNumberToSynchrotron`, `trackingNumberFromSynchrotron`, `type`, `facilityCode`, `weight`, `deliveryAgent_barcode`, `extra`, `source`, `externalShippingIdFromSynchrotron`, `dewarRegistryId`) VALUES (573,474,'Dewar-1-cm0001-1',NULL,NULL,'processing',NULL,0,'dewar-cm0001-1-0000001',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL),(576,474,'Dewar-2-cm0001-1',NULL,NULL,'at DLS',NULL,0,'dewar-cm0001-1-0000002',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL),(579,477,'Dewar-3-cm0001-2',NULL,NULL,'processing',NULL,0,'dewar-cm0001-2-0000477',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL),(582,480,'Dewar-4-cm0001-3',NULL,NULL,'processing',NULL,0,'dewar-cm0001-3-0000480',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL),(8287,6988,'Default Dewar:cm14451-1',NULL,NULL,'processing',NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL),(8572,7227,'cm14451-2_Dewar1',NULL,NULL,'processing','2016-02-10 13:03:07',0,NULL,NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL),(8578,7231,'Dewar_1',NULL,NULL,'opened',NULL,0,'cm14451-12345',NULL,NULL,NULL,NULL,NULL,'Dewar',NULL,NULL,NULL,NULL,'root@%',NULL,NULL); /*!40000 ALTER TABLE `Dewar` ENABLE KEYS */; /*!40000 ALTER TABLE `DewarLocation` DISABLE KEYS */; @@ -466,39 +262,11 @@ INSERT INTO `Dewar` (`dewarId`, `shippingId`, `code`, `comments`, `storageLocati /*!40000 ALTER TABLE `DewarTransportHistory` ENABLE KEYS */; /*!40000 ALTER TABLE `DiffractionPlan` DISABLE KEYS */; -INSERT INTO `DiffractionPlan` (`diffractionPlanId`, `name`, `experimentKind`, `observedResolution`, `minimalResolution`, `exposureTime`, `oscillationRange`, `maximalResolution`, `screeningResolution`, `radiationSensitivity`, `anomalousScatterer`, `preferredBeamSizeX`, `preferredBeamSizeY`, `preferredBeamDiameter`, `comments`, `DIFFRACTIONPLANUUID`, `aimedCompleteness`, `aimedIOverSigmaAtHighestRes`, `aimedMultiplicity`, `aimedResolution`, `anomalousData`, `complexity`, `estimateRadiationDamage`, `forcedSpaceGroup`, `requiredCompleteness`, `requiredMultiplicity`, `requiredResolution`, `strategyOption`, `kappaStrategyOption`, `numberOfPositions`, `minDimAccrossSpindleAxis`, `maxDimAccrossSpindleAxis`, `radiationSensitivityBeta`, `radiationSensitivityGamma`, `minOscWidth`, `recordTimeStamp`, `monochromator`, `energy`, `transmission`, `boxSizeX`, `boxSizeY`, `kappaStart`, `axisStart`, `axisRange`, `numberOfImages`, `presetForProposalId`, `beamLineName`, `detectorId`, `distance`, `orientation`, `monoBandwidth`, `centringMethod`, `userPath`, `robotPlateTemperature`, `exposureTemperature`, `experimentTypeId`, `purificationColumnId`, `collectionMode`, `priority`, `qMin`, `qMax`, `reductionParametersAveraging`, `scanParameters`) VALUES (197784,NULL,'OSC',NULL,NULL,0.2,NULL,NULL,NULL,NULL,NULL,10.5,10.5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,1.1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-20 23:50:27',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(197788,NULL,NULL,NULL,NULL,10,NULL,NULL,NULL,NULL,NULL,160,100,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-26 15:28:12',NULL,150,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,4,162.5,45,330.6,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(197792,'XPDF-1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2017-03-22 10:56:32',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `DiffractionPlan` (`diffractionPlanId`, `name`, `experimentKind`, `observedResolution`, `minimalResolution`, `exposureTime`, `oscillationRange`, `maximalResolution`, `screeningResolution`, `radiationSensitivity`, `anomalousScatterer`, `preferredBeamSizeX`, `preferredBeamSizeY`, `preferredBeamDiameter`, `comments`, `DIFFRACTIONPLANUUID`, `aimedCompleteness`, `aimedIOverSigmaAtHighestRes`, `aimedMultiplicity`, `aimedResolution`, `anomalousData`, `complexity`, `estimateRadiationDamage`, `forcedSpaceGroup`, `requiredCompleteness`, `requiredMultiplicity`, `requiredResolution`, `strategyOption`, `kappaStrategyOption`, `numberOfPositions`, `minDimAccrossSpindleAxis`, `maxDimAccrossSpindleAxis`, `radiationSensitivityBeta`, `radiationSensitivityGamma`, `minOscWidth`, `recordTimeStamp`, `monochromator`, `energy`, `transmission`, `boxSizeX`, `boxSizeY`, `kappaStart`, `axisStart`, `axisRange`, `numberOfImages`, `presetForProposalId`, `beamLineName`, `detectorId`, `distance`, `orientation`, `monoBandwidth`, `centringMethod`, `userPath`, `robotPlateTemperature`, `exposureTemperature`, `experimentTypeId`, `purificationColumnId`, `collectionMode`, `priority`, `qMin`, `qMax`, `reductionParametersAveraging`, `scanParameters`) VALUES (197784,NULL,'OSC',NULL,NULL,0.2,NULL,NULL,NULL,NULL,NULL,10.5,10.5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,1.1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-03-20 23:50:27',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(197788,NULL,NULL,NULL,NULL,10,NULL,NULL,NULL,NULL,NULL,160,100,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2016-10-26 15:28:12',NULL,150,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,4,162.5,45,330.6,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(197792,'XPDF-1',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,NULL,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,'2017-03-22 10:56:32',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `DiffractionPlan` ENABLE KEYS */; /*!40000 ALTER TABLE `EnergyScan` DISABLE KEYS */; -INSERT INTO `EnergyScan` (`energyScanId`, `sessionId`, `blSampleId`, `fluorescenceDetector`, `scanFileFullPath`, `jpegChoochFileFullPath`, `element`, `startEnergy`, `endEnergy`, `transmissionFactor`, `exposureTime`, `axisPosition`, `synchrotronCurrent`, `temperature`, `peakEnergy`, `peakFPrime`, `peakFDoublePrime`, `inflectionEnergy`, `inflectionFPrime`, `inflectionFDoublePrime`, `xrayDose`, `startTime`, `endTime`, `edgeEnergy`, `filename`, `beamSizeVertical`, `beamSizeHorizontal`, `choochFileFullPath`, `crystalClass`, `comments`, `flux`, `flux_end`, `workingDirectory`, `blSubSampleId`) VALUES (49661,55167,NULL,'Vortex1_MCAScaler','/dls/i03/data/2016/cm14451-1/fe1.fluo','/dls/i03/data/2016/cm14451-1/fluorescence_scans/fe1_chooch.png','Fe',7062.75,7170.88,0.016,1,NULL,298.569,100,7115.73,-4.79,4.66,7095.13,-7.26,1.66,0,'2016-01-12 14:51:20','2016-01-12 14:58:33','K',NULL,20,50,NULL,NULL,NULL,NULL,NULL,NULL,NULL), 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`recordTimeStamp`) VALUES (274837165,1052494,1,'xtal1_1_0001.cbf','/dls/i03/data/2016/cm14451-2/20160413/test_xtal',0,'/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0001.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0001.thumb.jpeg',294,0,298.847,NULL,NULL,'2016-04-13 11:18:39',NULL,'2016-04-13 11:18:39'), -(274837168,1052494,2,'xtal1_1_0002.cbf','/dls/i03/data/2016/cm14451-2/20160413/test_xtal',0,'/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0002.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0002.thumb.jpeg',294,0,298.74,NULL,NULL,'2016-04-13 11:18:50',NULL,'2016-04-13 11:18:50'), -(274837177,1052503,1,'xtal1_3_0001.cbf','/dls/i03/data/2016/cm14451-2/20160413/test_xtal',0,'/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_0001.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_0001.thumb.jpeg',294,0,302.004,NULL,NULL,'2016-04-13 11:21:36',NULL,'2016-04-13 11:21:36'), 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-(284718055,1066786,2,'thau_2_0002.cbf','/dls/i03/data/2016/cm14451-2/gw/20160418/thau/edna_test',0,'/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0002.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0002.thumb.jpeg',294,0,299.933,NULL,NULL,'2016-04-14 02:19:04',NULL,'2016-04-14 02:19:04'), -(284718118,1066786,3,'thau_2_0003.cbf','/dls/i03/data/2016/cm14451-2/gw/20160418/thau/edna_test',0,'/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0003.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0003.thumb.jpeg',294,0,299.908,NULL,NULL,'2016-04-14 02:19:04',NULL,'2016-04-14 02:19:04'); +INSERT INTO `Image` (`imageId`, `dataCollectionId`, `imageNumber`, `fileName`, `fileLocation`, `measuredIntensity`, `jpegFileFullPath`, `jpegThumbnailFileFullPath`, `temperature`, `cumulativeIntensity`, `synchrotronCurrent`, `comments`, `machineMessage`, `BLTIMESTAMP`, `motorPositionId`, `recordTimeStamp`) VALUES (274837165,1052494,1,'xtal1_1_0001.cbf','/dls/i03/data/2016/cm14451-2/20160413/test_xtal',0,'/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0001.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0001.thumb.jpeg',294,0,298.847,NULL,NULL,'2016-04-13 11:18:39',NULL,'2016-04-13 11:18:39'),(274837168,1052494,2,'xtal1_1_0002.cbf','/dls/i03/data/2016/cm14451-2/20160413/test_xtal',0,'/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0002.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_1_0002.thumb.jpeg',294,0,298.74,NULL,NULL,'2016-04-13 11:18:50',NULL,'2016-04-13 11:18:50'),(274837177,1052503,1,'xtal1_3_0001.cbf','/dls/i03/data/2016/cm14451-2/20160413/test_xtal',0,'/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_0001.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/20160413/test_xtal/xtal1_3_0001.thumb.jpeg',294,0,302.004,NULL,NULL,'2016-04-13 11:21:36',NULL,'2016-04-13 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02:19:04'),(284718055,1066786,2,'thau_2_0002.cbf','/dls/i03/data/2016/cm14451-2/gw/20160418/thau/edna_test',0,'/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0002.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0002.thumb.jpeg',294,0,299.933,NULL,NULL,'2016-04-14 02:19:04',NULL,'2016-04-14 02:19:04'),(284718118,1066786,3,'thau_2_0003.cbf','/dls/i03/data/2016/cm14451-2/gw/20160418/thau/edna_test',0,'/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0003.jpeg','/dls/i03/data/2016/cm14451-2/jpegs/gw/20160418/thau/edna_test/thau_2_0003.thumb.jpeg',294,0,299.908,NULL,NULL,'2016-04-14 02:19:04',NULL,'2016-04-14 02:19:04'); /*!40000 ALTER TABLE `Image` ENABLE KEYS */; /*!40000 ALTER TABLE `ImageQualityIndicators` DISABLE KEYS */; -INSERT INTO `ImageQualityIndicators` (`dataCollectionId`, `imageNumber`, `imageId`, `autoProcProgramId`, `spotTotal`, `inResTotal`, `goodBraggCandidates`, `iceRings`, `method1Res`, `method2Res`, `maxUnitCell`, `pctSaturationTop50Peaks`, `inResolutionOvrlSpots`, `binPopCutOffMethod2Res`, `recordTimeStamp`, `totalIntegratedSignal`, `dozor_score`, `driftFactor`) VALUES (1052494,1,NULL,NULL,296,296,259,0,2.03,2.03,0,0,0,0,NULL,2.61,NULL,NULL), -(1052494,2,NULL,NULL,239,239,224,0,2.12,2.12,0,0,0,0,NULL,2.95,NULL,NULL), -(1052503,1,274837177,NULL,217,217,202,0,2.07,2.07,0,0,0,0,NULL,2.99,NULL,NULL), -(1052503,2,NULL,NULL,257,257,236,0,2.06,2.06,0,0,0,0,NULL,3.02,NULL,NULL), -(1052503,3,NULL,NULL,306,306,278,0,2.04,2.04,0,0,0,0,NULL,2.75,NULL,NULL), -(1066786,1,284717989,NULL,1132,1132,872,0,1.63,1.63,0,0,0,0,NULL,2.09,NULL,NULL), -(1066786,2,284718055,NULL,848,848,652,0,1.56,1.56,0,0,0,0,NULL,2.03,NULL,NULL), -(1066786,3,284718118,NULL,922,922,735,0,1.57,1.57,0,0,0,0,NULL,2.13,NULL,NULL); +INSERT INTO `ImageQualityIndicators` (`dataCollectionId`, `imageNumber`, `imageId`, `autoProcProgramId`, `spotTotal`, `inResTotal`, `goodBraggCandidates`, `iceRings`, `method1Res`, `method2Res`, `maxUnitCell`, `pctSaturationTop50Peaks`, `inResolutionOvrlSpots`, `binPopCutOffMethod2Res`, `recordTimeStamp`, `totalIntegratedSignal`, `dozor_score`, `driftFactor`) VALUES (1052494,1,NULL,NULL,296,296,259,0,2.03,2.03,0,0,0,0,NULL,2.61,NULL,NULL),(1052494,2,NULL,NULL,239,239,224,0,2.12,2.12,0,0,0,0,NULL,2.95,NULL,NULL),(1052503,1,274837177,NULL,217,217,202,0,2.07,2.07,0,0,0,0,NULL,2.99,NULL,NULL),(1052503,2,NULL,NULL,257,257,236,0,2.06,2.06,0,0,0,0,NULL,3.02,NULL,NULL),(1052503,3,NULL,NULL,306,306,278,0,2.04,2.04,0,0,0,0,NULL,2.75,NULL,NULL),(1066786,1,284717989,NULL,1132,1132,872,0,1.63,1.63,0,0,0,0,NULL,2.09,NULL,NULL),(1066786,2,284718055,NULL,848,848,652,0,1.56,1.56,0,0,0,0,NULL,2.03,NULL,NULL),(1066786,3,284718118,NULL,922,922,735,0,1.57,1.57,0,0,0,0,NULL,2.13,NULL,NULL); /*!40000 ALTER TABLE `ImageQualityIndicators` ENABLE KEYS */; /*!40000 ALTER TABLE `IspybCrystalClass` DISABLE KEYS */; @@ -573,8 +327,7 @@ INSERT INTO `ImageQualityIndicators` (`dataCollectionId`, `imageNumber`, `imageI /*!40000 ALTER TABLE `Ligand_has_PDB` ENABLE KEYS */; /*!40000 ALTER TABLE `MXMRRun` DISABLE KEYS */; -INSERT INTO `MXMRRun` (`mxMRRunId`, `autoProcScalingId`, `rValueStart`, `rValueEnd`, `rFreeValueStart`, `rFreeValueEnd`, `LLG`, `TFZ`, `spaceGroup`, `autoProcProgramId`) VALUES (672897,603470,0.1812,0.1682,0.1896,0.1888,NULL,NULL,NULL,56986674), -(672900,603470,NULL,NULL,NULL,NULL,NULL,NULL,NULL,56986675); +INSERT INTO `MXMRRun` (`mxMRRunId`, `autoProcScalingId`, `rValueStart`, `rValueEnd`, `rFreeValueStart`, `rFreeValueEnd`, `LLG`, `TFZ`, `spaceGroup`, `autoProcProgramId`) VALUES (672897,603470,0.1812,0.1682,0.1896,0.1888,NULL,NULL,NULL,56986674),(672900,603470,NULL,NULL,NULL,NULL,NULL,NULL,NULL,56986675); /*!40000 ALTER TABLE `MXMRRun` ENABLE KEYS */; /*!40000 ALTER TABLE `MXMRRunBlob` DISABLE KEYS */; @@ -615,9 +368,7 @@ INSERT INTO `PDB` (`pdbId`, `name`, `contents`, `code`, `source`) VALUES (6,'ceo /*!40000 ALTER TABLE `ParticlePicker` ENABLE KEYS */; /*!40000 ALTER TABLE `Person` DISABLE KEYS */; -INSERT INTO `Person` (`personId`, `laboratoryId`, `siteId`, `personUUID`, `familyName`, `givenName`, `title`, `emailAddress`, `phoneNumber`, `login`, `faxNumber`, `recordTimeStamp`, `cache`, `externalId`) VALUES (1,NULL,NULL,NULL,'McBoatface','Boaty','Mr',NULL,NULL,'boaty',NULL,'2016-03-20 13:56:45','a:1:{s:9:\"container\";N;}',NULL), -(46266,NULL,NULL,NULL,NULL,NULL,'User',NULL,NULL,NULL,NULL,'2016-03-16 15:53:55',NULL,NULL), -(46269,NULL,NULL,NULL,NULL,NULL,'User',NULL,NULL,NULL,NULL,'2016-03-16 15:59:22',NULL,NULL); +INSERT INTO `Person` (`personId`, `laboratoryId`, `siteId`, `personUUID`, `familyName`, `givenName`, `title`, `emailAddress`, `phoneNumber`, `login`, `faxNumber`, `recordTimeStamp`, `cache`, `externalId`) VALUES (1,NULL,NULL,NULL,'McBoatface','Boaty','Mr',NULL,NULL,'boaty',NULL,'2016-03-20 13:56:45','a:1:{s:9:\"container\";N;}',NULL),(46266,NULL,NULL,NULL,NULL,NULL,'User',NULL,NULL,NULL,NULL,'2016-03-16 15:53:55',NULL,NULL),(46269,NULL,NULL,NULL,NULL,NULL,'User',NULL,NULL,NULL,NULL,'2016-03-16 15:59:22',NULL,NULL); /*!40000 ALTER TABLE `Person` ENABLE KEYS */; /*!40000 ALTER TABLE `Phasing` DISABLE KEYS */; @@ -642,8 +393,7 @@ INSERT INTO `Person` (`personId`, `laboratoryId`, `siteId`, `personUUID`, `famil /*!40000 ALTER TABLE `Phasing_has_Scaling` ENABLE KEYS */; /*!40000 ALTER TABLE `Position` DISABLE KEYS */; -INSERT INTO `Position` (`positionId`, `relativePositionId`, `posX`, `posY`, `posZ`, `scale`, `recordTimeStamp`, `X`, `Y`, `Z`) VALUES (2,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `Position` (`positionId`, `relativePositionId`, `posX`, `posY`, `posZ`, `scale`, `recordTimeStamp`, `X`, `Y`, `Z`) VALUES (2,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(5,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `Position` ENABLE KEYS */; /*!40000 ALTER TABLE `Positioner` DISABLE KEYS */; @@ -660,13 +410,11 @@ INSERT INTO `ProcessingJob` (`processingJobId`, `dataCollectionId`, `displayName /*!40000 ALTER TABLE `ProcessingJob` ENABLE KEYS */; /*!40000 ALTER TABLE `ProcessingJobImageSweep` DISABLE KEYS */; -INSERT INTO `ProcessingJobImageSweep` (`processingJobImageSweepId`, `processingJobId`, `dataCollectionId`, `startImage`, `endImage`) VALUES (5,5,1002287,1,270), -(8,5,1002287,271,360); +INSERT INTO `ProcessingJobImageSweep` (`processingJobImageSweepId`, `processingJobId`, `dataCollectionId`, `startImage`, `endImage`) VALUES (5,5,1002287,1,270),(8,5,1002287,271,360); /*!40000 ALTER TABLE `ProcessingJobImageSweep` ENABLE KEYS */; /*!40000 ALTER TABLE `ProcessingJobParameter` DISABLE KEYS */; -INSERT INTO `ProcessingJobParameter` (`processingJobParameterId`, `processingJobId`, `parameterKey`, `parameterValue`) VALUES (5,5,'vortex factor','1.8*10^102'), -(8,5,'80s factor','0.87*10^-93'); +INSERT INTO `ProcessingJobParameter` (`processingJobParameterId`, `processingJobId`, `parameterKey`, `parameterValue`) VALUES (5,5,'vortex factor','1.8*10^102'),(8,5,'80s factor','0.87*10^-93'); /*!40000 ALTER TABLE `ProcessingJobParameter` ENABLE KEYS */; /*!40000 ALTER TABLE `Project` DISABLE KEYS */; @@ -700,8 +448,7 @@ INSERT INTO `ProcessingJobParameter` (`processingJobParameterId`, `processingJob /*!40000 ALTER TABLE `Project_has_XFEFSpectrum` ENABLE KEYS */; /*!40000 ALTER TABLE `Proposal` DISABLE KEYS */; -INSERT INTO `Proposal` (`proposalId`, `personId`, `title`, `proposalCode`, `proposalNumber`, `bltimeStamp`, `proposalType`, `externalId`, `state`, `startDate`, `endDate`) VALUES (37027,1,'I03 Commissioning Directory 2016','cm','14451','2015-12-21 15:20:43',NULL,NULL,'Open',NULL,NULL), -(141666,46266,'Test Proposal cm-0001','cm','1','2016-03-16 16:01:34',NULL,NULL,'Open',NULL,NULL); +INSERT INTO `Proposal` (`proposalId`, `personId`, `title`, `proposalCode`, `proposalNumber`, `bltimeStamp`, `proposalType`, `externalId`, `state`, `startDate`, `endDate`) VALUES (37027,1,'I03 Commissioning Directory 2016','cm','14451','2015-12-21 15:20:43',NULL,NULL,'Open',NULL,NULL),(141666,46266,'Test Proposal cm-0001','cm','1','2016-03-16 16:01:34',NULL,NULL,'Open',NULL,NULL); /*!40000 ALTER TABLE `Proposal` ENABLE KEYS */; /*!40000 ALTER TABLE `ProposalHasPerson` DISABLE KEYS */; @@ -709,21 +456,7 @@ INSERT INTO `ProposalHasPerson` (`proposalHasPersonId`, `proposalId`, `personId` /*!40000 ALTER TABLE `ProposalHasPerson` ENABLE KEYS */; /*!40000 ALTER TABLE `Protein` DISABLE KEYS */; -INSERT INTO `Protein` (`proteinId`, `proposalId`, `name`, `acronym`, `description`, `hazardGroup`, `containmentLevel`, `safetyLevel`, `molecularMass`, `proteinType`, `personId`, `bltimeStamp`, `isCreatedBySampleSheet`, `sequence`, `MOD_ID`, `componentTypeId`, `concentrationTypeId`, `global`, `externalId`, `density`, `abundance`, `isotropy`) VALUES (4380,141666,'Protein 01','PRT-01',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 15:57:52',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4383,141666,'Protein 02','PRT-02',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4386,141666,'Protein 03','PRT-03',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4389,141666,'Protein 04','PRT-04',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4392,141666,'Protein 05','PRT-05',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4395,141666,'Protein 06','PRT-06',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4398,141666,'Protein 07','PRT-07',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4401,141666,'Protein 08','PRT-08',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4404,141666,'Protein 09','PRT-09',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4407,141666,'Protein 10','PRT-10',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4410,141666,'Protein 11','PRT-11',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(4413,141666,'Protein 12','PRT-12',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(121393,37027,'therm','therm',NULL,1,1,NULL,NULL,NULL,NULL,'2016-01-13 13:50:20',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL), -(123491,37027,NULL,'thau',NULL,1,1,NULL,NULL,NULL,NULL,'2016-02-24 12:12:16',0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(123497,37027,'XPDF comp1','xpdf-comp-01',NULL,1,1,NULL,NULL,NULL,NULL,'2017-03-23 22:03:40',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL); +INSERT INTO `Protein` (`proteinId`, `proposalId`, `name`, `acronym`, `description`, `hazardGroup`, `containmentLevel`, `safetyLevel`, `molecularMass`, `proteinType`, `personId`, `bltimeStamp`, `isCreatedBySampleSheet`, `sequence`, `MOD_ID`, `componentTypeId`, `concentrationTypeId`, `global`, `externalId`, `density`, `abundance`, `isotropy`) VALUES (4380,141666,'Protein 01','PRT-01',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 15:57:52',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4383,141666,'Protein 02','PRT-02',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4386,141666,'Protein 03','PRT-03',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4389,141666,'Protein 04','PRT-04',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4392,141666,'Protein 05','PRT-05',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4395,141666,'Protein 06','PRT-06',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4398,141666,'Protein 07','PRT-07',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4401,141666,'Protein 08','PRT-08',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4404,141666,'Protein 09','PRT-09',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4407,141666,'Protein 10','PRT-10',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4410,141666,'Protein 11','PRT-11',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(4413,141666,'Protein 12','PRT-12',NULL,1,1,NULL,NULL,NULL,NULL,'2016-03-17 16:02:07',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(121393,37027,'therm','therm',NULL,1,1,NULL,NULL,NULL,NULL,'2016-01-13 13:50:20',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL),(123491,37027,NULL,'thau',NULL,1,1,NULL,NULL,NULL,NULL,'2016-02-24 12:12:16',0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL),(123497,37027,'XPDF comp1','xpdf-comp-01',NULL,1,1,NULL,NULL,NULL,NULL,'2017-03-23 22:03:40',0,NULL,NULL,NULL,NULL,0,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `Protein` ENABLE KEYS */; /*!40000 ALTER TABLE `Protein_has_PDB` DISABLE KEYS */; @@ -746,13 +479,7 @@ INSERT INTO `Protein_has_PDB` (`proteinhaspdbid`, `proteinid`, `pdbid`) VALUES ( /*!40000 ALTER TABLE `SampleComposition` ENABLE KEYS */; /*!40000 ALTER TABLE `ScanParametersModel` DISABLE KEYS */; -INSERT INTO `ScanParametersModel` (`scanParametersModelId`, `scanParametersServiceId`, `dataCollectionPlanId`, `sequenceNumber`, `start`, `stop`, `step`, `array`, `duration`) VALUES (4,4,197788,1,0,90,10,NULL,NULL), -(7,4,197788,2,90,180,5,NULL,NULL), -(10,4,197788,3,180,270,1,NULL,NULL), -(13,4,197788,3,270,360,0.5,NULL,NULL), -(16,7,197788,4,20,120,10,NULL,NULL), -(20,7,197792,1,0,90,5,NULL,NULL), -(23,7,197792,2,90,120,1,NULL,NULL); +INSERT INTO `ScanParametersModel` (`scanParametersModelId`, `scanParametersServiceId`, `dataCollectionPlanId`, `sequenceNumber`, `start`, `stop`, `step`, `array`, `duration`) VALUES (4,4,197788,1,0,90,10,NULL,NULL),(7,4,197788,2,90,180,5,NULL,NULL),(10,4,197788,3,180,270,1,NULL,NULL),(13,4,197788,3,270,360,0.5,NULL,NULL),(16,7,197788,4,20,120,10,NULL,NULL),(20,7,197792,1,0,90,5,NULL,NULL),(23,7,197792,2,90,120,1,NULL,NULL); /*!40000 ALTER TABLE `ScanParametersModel` ENABLE KEYS */; /*!40000 ALTER TABLE `Screen` DISABLE KEYS */; @@ -765,93 +492,19 @@ INSERT INTO `ScanParametersModel` (`scanParametersModelId`, `scanParametersServi /*!40000 ALTER TABLE `ScreenComponentGroup` ENABLE KEYS */; /*!40000 ALTER TABLE `Screening` DISABLE KEYS */; -INSERT INTO `Screening` (`screeningId`, `dataCollectionId`, `bltimeStamp`, `programVersion`, `comments`, `shortComments`, `diffractionPlanId`, `dataCollectionGroupId`, `xmlSampleInformation`, `autoProcProgramId`) VALUES (1894770,1052494,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm native',NULL,1040398,NULL,NULL), -(1894773,1052494,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm anomalous',NULL,1040398,NULL,NULL), -(1894774,1052494,'2016-10-26 08:50:31','EDNA MXv1','Standard Native Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy1',NULL,1040398,NULL,NULL), -(1894777,1052494,'2016-10-26 08:50:31','EDNA MXv1','strategy with target multiplicity=16, target I/sig=2 Maxlifespan=202 s','EDNAStrategy3',NULL,1040398,NULL,NULL), -(1894780,1052494,'2016-10-26 08:50:31','EDNA MXv1','Gentle: Target Multiplicity=2 and target I/Sig 2 and Maxlifespan=20 s','EDNAStrategy4',NULL,1040398,NULL,NULL), -(1894783,1052494,'2016-10-26 08:50:31','EDNA MXv1','Standard Anomalous Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy2',NULL,1040398,NULL,NULL), -(1894786,1052494,'2016-10-26 08:50:31','EDNA MXv1','UnderDEV Anomalous Dataset, RadDamage of standard protein','EDNAStrategy5',NULL,1040398,NULL,NULL), -(1894807,1052503,'2016-10-26 08:50:31','EDNA MXv1','strategy with target multiplicity=16, target I/sig=2 Maxlifespan=202 s','EDNAStrategy3',NULL,1040407,NULL,NULL), -(1894810,1052503,'2016-10-26 08:50:31','EDNA MXv1','Standard Anomalous Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy2',NULL,1040407,NULL,NULL), -(1894812,1052503,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm native',NULL,1040407,NULL,NULL), -(1894815,1052503,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm anomalous',NULL,1040407,NULL,NULL), -(1894816,1052503,'2016-10-26 08:50:31','EDNA MXv1','Gentle: Target Multiplicity=2 and target I/Sig 2 and Maxlifespan=20 s','EDNAStrategy4',NULL,1040407,NULL,NULL), -(1894819,1052503,'2016-10-26 08:50:31','EDNA MXv1','UnderDEV Anomalous Dataset, RadDamage of standard protein','EDNAStrategy5',NULL,1040407,NULL,NULL), -(1894822,1052503,'2016-10-26 08:50:31','EDNA MXv1','Standard Native Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy1',NULL,1040407,NULL,NULL), -(1927968,1066786,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm native',NULL,1054243,NULL,NULL), -(1927971,1066786,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm anomalous',NULL,1054243,NULL,NULL), -(1927972,1066786,'2016-10-26 08:50:31','EDNA MXv1','Standard Native Dataset Multiplicity=3 I/sig=2 Maxlifespan=4034 s','EDNAStrategy1',NULL,1054243,NULL,NULL), -(1927981,1066786,'2016-10-26 08:50:31','EDNA MXv1','Gentle: Target Multiplicity=2 and target I/Sig 2 and Maxlifespan=403 s','EDNAStrategy4',NULL,1054243,NULL,NULL), -(1927984,1066786,'2016-10-26 08:50:31','EDNA MXv1','strategy with target multiplicity=16, target I/sig=2 Maxlifespan=4034 s','EDNAStrategy3',NULL,1054243,NULL,NULL), -(1927987,1066786,'2016-10-26 08:50:31','EDNA MXv1','Standard Anomalous Dataset Multiplicity=3 I/sig=2 Maxlifespan=4034 s','EDNAStrategy2',NULL,1054243,NULL,NULL), -(1927990,1066786,'2016-10-26 08:50:31','EDNA MXv1','UnderDEV Anomalous Dataset, RadDamage of standard protein','EDNAStrategy5',NULL,1054243,NULL,NULL); +INSERT INTO `Screening` (`screeningId`, `dataCollectionId`, `bltimeStamp`, `programVersion`, `comments`, `shortComments`, `diffractionPlanId`, `dataCollectionGroupId`, `xmlSampleInformation`, `autoProcProgramId`) VALUES (1894770,1052494,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm native',NULL,1040398,NULL,NULL),(1894773,1052494,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm anomalous',NULL,1040398,NULL,NULL),(1894774,1052494,'2016-10-26 08:50:31','EDNA MXv1','Standard Native Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy1',NULL,1040398,NULL,NULL),(1894777,1052494,'2016-10-26 08:50:31','EDNA MXv1','strategy with target multiplicity=16, target I/sig=2 Maxlifespan=202 s','EDNAStrategy3',NULL,1040398,NULL,NULL),(1894780,1052494,'2016-10-26 08:50:31','EDNA MXv1','Gentle: Target Multiplicity=2 and target I/Sig 2 and Maxlifespan=20 s','EDNAStrategy4',NULL,1040398,NULL,NULL),(1894783,1052494,'2016-10-26 08:50:31','EDNA MXv1','Standard Anomalous Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy2',NULL,1040398,NULL,NULL),(1894786,1052494,'2016-10-26 08:50:31','EDNA MXv1','UnderDEV Anomalous Dataset, RadDamage of standard protein','EDNAStrategy5',NULL,1040398,NULL,NULL),(1894807,1052503,'2016-10-26 08:50:31','EDNA MXv1','strategy with target multiplicity=16, target I/sig=2 Maxlifespan=202 s','EDNAStrategy3',NULL,1040407,NULL,NULL),(1894810,1052503,'2016-10-26 08:50:31','EDNA MXv1','Standard Anomalous Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy2',NULL,1040407,NULL,NULL),(1894812,1052503,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm native',NULL,1040407,NULL,NULL),(1894815,1052503,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm anomalous',NULL,1040407,NULL,NULL),(1894816,1052503,'2016-10-26 08:50:31','EDNA MXv1','Gentle: Target Multiplicity=2 and target I/Sig 2 and Maxlifespan=20 s','EDNAStrategy4',NULL,1040407,NULL,NULL),(1894819,1052503,'2016-10-26 08:50:31','EDNA MXv1','UnderDEV Anomalous Dataset, RadDamage of standard protein','EDNAStrategy5',NULL,1040407,NULL,NULL),(1894822,1052503,'2016-10-26 08:50:31','EDNA MXv1','Standard Native Dataset Multiplicity=3 I/sig=2 Maxlifespan=202 s','EDNAStrategy1',NULL,1040407,NULL,NULL),(1927968,1066786,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm native',NULL,1054243,NULL,NULL),(1927971,1066786,'2016-10-26 08:50:31','mosflm',NULL,'Mosflm anomalous',NULL,1054243,NULL,NULL),(1927972,1066786,'2016-10-26 08:50:31','EDNA MXv1','Standard Native Dataset Multiplicity=3 I/sig=2 Maxlifespan=4034 s','EDNAStrategy1',NULL,1054243,NULL,NULL),(1927981,1066786,'2016-10-26 08:50:31','EDNA MXv1','Gentle: Target Multiplicity=2 and target I/Sig 2 and Maxlifespan=403 s','EDNAStrategy4',NULL,1054243,NULL,NULL),(1927984,1066786,'2016-10-26 08:50:31','EDNA MXv1','strategy with target multiplicity=16, target I/sig=2 Maxlifespan=4034 s','EDNAStrategy3',NULL,1054243,NULL,NULL),(1927987,1066786,'2016-10-26 08:50:31','EDNA MXv1','Standard Anomalous Dataset Multiplicity=3 I/sig=2 Maxlifespan=4034 s','EDNAStrategy2',NULL,1054243,NULL,NULL),(1927990,1066786,'2016-10-26 08:50:31','EDNA MXv1','UnderDEV Anomalous Dataset, RadDamage of standard protein','EDNAStrategy5',NULL,1054243,NULL,NULL); /*!40000 ALTER TABLE `Screening` ENABLE KEYS */; /*!40000 ALTER TABLE `ScreeningInput` DISABLE KEYS */; -INSERT INTO `ScreeningInput` (`screeningInputId`, `screeningId`, `beamX`, `beamY`, `rmsErrorLimits`, `minimumFractionIndexed`, `maximumFractionRejected`, `minimumSignalToNoise`, `diffractionPlanId`, `xmlSampleInformation`) VALUES (983791,1894774,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL), -(983794,1894777,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL), -(983797,1894780,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL), -(983800,1894783,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL), -(983803,1894786,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL), -(983821,1894807,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(983824,1894810,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(983827,1894816,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(983830,1894819,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(983833,1894822,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(1013146,1927972,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(1013155,1927981,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(1013158,1927984,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(1013161,1927987,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL), -(1013164,1927990,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `ScreeningInput` (`screeningInputId`, `screeningId`, `beamX`, `beamY`, `rmsErrorLimits`, `minimumFractionIndexed`, `maximumFractionRejected`, `minimumSignalToNoise`, `diffractionPlanId`, `xmlSampleInformation`) VALUES (983791,1894774,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL),(983794,1894777,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL),(983797,1894780,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL),(983800,1894783,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL),(983803,1894786,208.731,214.298,NULL,NULL,NULL,NULL,NULL,NULL),(983821,1894807,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(983824,1894810,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(983827,1894816,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(983830,1894819,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(983833,1894822,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(1013146,1927972,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(1013155,1927981,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(1013158,1927984,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(1013161,1927987,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL),(1013164,1927990,208.32,214.339,NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `ScreeningInput` ENABLE KEYS */; /*!40000 ALTER TABLE `ScreeningOutput` DISABLE KEYS */; -INSERT INTO `ScreeningOutput` (`screeningOutputId`, `screeningId`, `statusDescription`, `rejectedReflections`, `resolutionObtained`, `spotDeviationR`, `spotDeviationTheta`, `beamShiftX`, `beamShiftY`, `numSpotsFound`, `numSpotsUsed`, `numSpotsRejected`, `mosaicity`, `iOverSigma`, `diffractionRings`, `SCREENINGSUCCESS`, `mosaicityEstimated`, `rankingResolution`, `program`, `doseTotal`, `totalExposureTime`, `totalRotationRange`, `totalNumberOfImages`, `rFriedel`, `indexingSuccess`, `strategySuccess`, `alignmentSuccess`) VALUES (1489401,1894770,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489404,1894773,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489405,1894774,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489408,1894777,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489411,1894780,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489414,1894783,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489417,1894786,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489438,1894807,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489441,1894810,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489443,1894812,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1.6,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489446,1894815,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1.6,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489447,1894816,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489450,1894819,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1489453,1894822,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1522596,1927968,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0.8,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1522599,1927971,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0.8,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1522600,1927972,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1522609,1927981,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1522612,1927984,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1522615,1927987,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0), -(1522618,1927990,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0); +INSERT INTO `ScreeningOutput` (`screeningOutputId`, `screeningId`, `statusDescription`, `rejectedReflections`, `resolutionObtained`, `spotDeviationR`, `spotDeviationTheta`, `beamShiftX`, `beamShiftY`, `numSpotsFound`, `numSpotsUsed`, `numSpotsRejected`, `mosaicity`, `iOverSigma`, `diffractionRings`, `SCREENINGSUCCESS`, `mosaicityEstimated`, `rankingResolution`, `program`, `doseTotal`, `totalExposureTime`, `totalRotationRange`, `totalNumberOfImages`, `rFriedel`, `indexingSuccess`, `strategySuccess`, `alignmentSuccess`) VALUES (1489401,1894770,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489404,1894773,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489405,1894774,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489408,1894777,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489411,1894780,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489414,1894783,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489417,1894786,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.197,NULL,-0.0094,-0.0618,303,303,0,1.2,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489438,1894807,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489441,1894810,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489443,1894812,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1.6,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489446,1894815,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,1.6,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489447,1894816,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489450,1894819,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1489453,1894822,'Labelit: Indexing successful (I23). Integration successful. Strategy calculation successful.',NULL,NULL,0.184,NULL,0.0495,-0.0405,294,294,0,1.35,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1522596,1927968,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0.8,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1522599,1927971,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0.8,NULL,NULL,0,0,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1522600,1927972,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1522609,1927981,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1522612,1927984,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1522615,1927987,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0),(1522618,1927990,'Labelit: Indexing successful (P4). Integration successful. Strategy calculation successful.',NULL,NULL,0.166,NULL,0.0195,-0.0105,434,434,0,0.7,NULL,NULL,1,1,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,0,0); /*!40000 ALTER TABLE `ScreeningOutput` ENABLE KEYS */; /*!40000 ALTER TABLE `ScreeningOutputLattice` DISABLE KEYS */; -INSERT INTO `ScreeningOutputLattice` (`screeningOutputLatticeId`, `screeningOutputId`, `spaceGroup`, `pointGroup`, `bravaisLattice`, `rawOrientationMatrix_a_x`, `rawOrientationMatrix_a_y`, `rawOrientationMatrix_a_z`, `rawOrientationMatrix_b_x`, `rawOrientationMatrix_b_y`, `rawOrientationMatrix_b_z`, `rawOrientationMatrix_c_x`, `rawOrientationMatrix_c_y`, `rawOrientationMatrix_c_z`, `unitCell_a`, `unitCell_b`, `unitCell_c`, `unitCell_alpha`, `unitCell_beta`, `unitCell_gamma`, `bltimeStamp`, `labelitIndexing`) VALUES (1309566,1489401,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.339,76.339,76.339,90,90,90,'2016-04-13 11:19:21',0), -(1309569,1489404,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.339,76.339,76.339,90,90,90,'2016-04-13 11:19:21',0), -(1309570,1489405,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:24',0), -(1309573,1489408,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:27',0), -(1309576,1489411,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:29',0), -(1309579,1489414,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:34',0), -(1309582,1489417,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:34',0), -(1309603,1489438,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:30',0), -(1309606,1489441,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:35',0), -(1309608,1489443,'C2221',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.645,108.218,108.03,90,90,90,'2016-04-13 11:22:36',0), -(1309611,1489446,'C2221',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.645,108.218,108.03,90,90,90,'2016-04-13 11:22:36',0), -(1309612,1489447,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:39',0), -(1309615,1489450,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:40',0), -(1309618,1489453,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:44',0), -(1323825,1522596,'P41212',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.334,57.334,148.969,90,90,90,'2016-04-18 10:05:24',0), -(1323828,1522599,'P41212',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.334,57.334,148.969,90,90,90,'2016-04-18 10:05:24',0), -(1323829,1522600,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0), -(1323838,1522609,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0), -(1323841,1522612,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0), -(1323844,1522615,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0), -(1323847,1522618,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0); +INSERT INTO `ScreeningOutputLattice` (`screeningOutputLatticeId`, `screeningOutputId`, `spaceGroup`, `pointGroup`, `bravaisLattice`, `rawOrientationMatrix_a_x`, `rawOrientationMatrix_a_y`, `rawOrientationMatrix_a_z`, `rawOrientationMatrix_b_x`, `rawOrientationMatrix_b_y`, `rawOrientationMatrix_b_z`, `rawOrientationMatrix_c_x`, `rawOrientationMatrix_c_y`, `rawOrientationMatrix_c_z`, `unitCell_a`, `unitCell_b`, `unitCell_c`, `unitCell_alpha`, `unitCell_beta`, `unitCell_gamma`, `bltimeStamp`, `labelitIndexing`) VALUES (1309566,1489401,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.339,76.339,76.339,90,90,90,'2016-04-13 11:19:21',0),(1309569,1489404,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.339,76.339,76.339,90,90,90,'2016-04-13 11:19:21',0),(1309570,1489405,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:24',0),(1309573,1489408,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:27',0),(1309576,1489411,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:29',0),(1309579,1489414,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:34',0),(1309582,1489417,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.3,76.3,76.3,90,90,90,'2016-04-13 11:19:34',0),(1309603,1489438,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:30',0),(1309606,1489441,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:35',0),(1309608,1489443,'C2221',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.645,108.218,108.03,90,90,90,'2016-04-13 11:22:36',0),(1309611,1489446,'C2221',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.645,108.218,108.03,90,90,90,'2016-04-13 11:22:36',0),(1309612,1489447,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:39',0),(1309615,1489450,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:40',0),(1309618,1489453,'I23',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,76.52,76.52,76.52,90,90,90,'2016-04-13 11:22:44',0),(1323825,1522596,'P41212',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.334,57.334,148.969,90,90,90,'2016-04-18 10:05:24',0),(1323828,1522599,'P41212',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.334,57.334,148.969,90,90,90,'2016-04-18 10:05:24',0),(1323829,1522600,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0),(1323838,1522609,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0),(1323841,1522612,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0),(1323844,1522615,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0),(1323847,1522618,'P4',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,57.29,57.29,149.07,90,90,90,'2016-04-14 02:19:04',0); /*!40000 ALTER TABLE `ScreeningOutputLattice` ENABLE KEYS */; /*!40000 ALTER TABLE `ScreeningRank` DISABLE KEYS */; @@ -861,100 +514,30 @@ INSERT INTO `ScreeningOutputLattice` (`screeningOutputLatticeId`, `screeningOutp /*!40000 ALTER TABLE `ScreeningRankSet` ENABLE KEYS */; /*!40000 ALTER TABLE `ScreeningStrategy` DISABLE KEYS */; -INSERT INTO `ScreeningStrategy` (`screeningStrategyId`, `screeningOutputId`, `phiStart`, `phiEnd`, `rotation`, `exposureTime`, `resolution`, `completeness`, `multiplicity`, `anomalous`, `program`, `rankingResolution`, `transmission`) VALUES (1473909,1489401,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - native',NULL,NULL), -(1473912,1489404,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - anomalous',NULL,NULL), -(1473913,1489405,NULL,NULL,NULL,0.428,NULL,NULL,NULL,0,'BEST',1.41,NULL), -(1473916,1489408,NULL,NULL,NULL,0.112,NULL,NULL,NULL,0,'BEST',1.41,NULL), -(1473919,1489411,NULL,NULL,NULL,0.049,NULL,NULL,NULL,0,'BEST',1.49,NULL), -(1473922,1489414,NULL,NULL,NULL,0.365,NULL,NULL,NULL,1,'BEST',1.41,NULL), -(1473925,1489417,NULL,NULL,NULL,0.365,NULL,NULL,NULL,1,'BEST',1.41,NULL), -(1473946,1489438,NULL,NULL,NULL,0.073,NULL,NULL,NULL,0,'BEST',1.44,NULL), -(1473949,1489441,NULL,NULL,NULL,0.333,NULL,NULL,NULL,1,'BEST',1.47,NULL), -(1473951,1489443,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - native',NULL,NULL), -(1473954,1489446,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - anomalous',NULL,NULL), -(1473955,1489447,NULL,NULL,NULL,0.086,NULL,NULL,NULL,0,'BEST',1.57,NULL), -(1473958,1489450,NULL,NULL,NULL,0.333,NULL,NULL,NULL,1,'BEST',1.47,NULL), -(1473961,1489453,NULL,NULL,NULL,0.296,NULL,NULL,NULL,0,'BEST',1.44,NULL), -(1507101,1522596,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - native',NULL,NULL), -(1507104,1522599,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - anomalous',NULL,NULL), -(1507105,1522600,NULL,NULL,NULL,0.01,NULL,NULL,NULL,0,'BEST',1.13,NULL), -(1507114,1522609,NULL,NULL,NULL,0.01,NULL,NULL,NULL,0,'BEST',1.23,NULL), -(1507117,1522612,NULL,NULL,NULL,0.01,NULL,NULL,NULL,0,'BEST',1.14,NULL), -(1507120,1522615,NULL,NULL,NULL,0.01,NULL,NULL,NULL,1,'BEST',1.16,NULL), -(1507123,1522618,NULL,NULL,NULL,0.01,NULL,NULL,NULL,1,'BEST',1.16,NULL); +INSERT INTO `ScreeningStrategy` (`screeningStrategyId`, `screeningOutputId`, `phiStart`, `phiEnd`, `rotation`, `exposureTime`, `resolution`, `completeness`, `multiplicity`, `anomalous`, `program`, `rankingResolution`, `transmission`) VALUES (1473909,1489401,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - native',NULL,NULL),(1473912,1489404,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - anomalous',NULL,NULL),(1473913,1489405,NULL,NULL,NULL,0.428,NULL,NULL,NULL,0,'BEST',1.41,NULL),(1473916,1489408,NULL,NULL,NULL,0.112,NULL,NULL,NULL,0,'BEST',1.41,NULL),(1473919,1489411,NULL,NULL,NULL,0.049,NULL,NULL,NULL,0,'BEST',1.49,NULL),(1473922,1489414,NULL,NULL,NULL,0.365,NULL,NULL,NULL,1,'BEST',1.41,NULL),(1473925,1489417,NULL,NULL,NULL,0.365,NULL,NULL,NULL,1,'BEST',1.41,NULL),(1473946,1489438,NULL,NULL,NULL,0.073,NULL,NULL,NULL,0,'BEST',1.44,NULL),(1473949,1489441,NULL,NULL,NULL,0.333,NULL,NULL,NULL,1,'BEST',1.47,NULL),(1473951,1489443,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - native',NULL,NULL),(1473954,1489446,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - anomalous',NULL,NULL),(1473955,1489447,NULL,NULL,NULL,0.086,NULL,NULL,NULL,0,'BEST',1.57,NULL),(1473958,1489450,NULL,NULL,NULL,0.333,NULL,NULL,NULL,1,'BEST',1.47,NULL),(1473961,1489453,NULL,NULL,NULL,0.296,NULL,NULL,NULL,0,'BEST',1.44,NULL),(1507101,1522596,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - native',NULL,NULL),(1507104,1522599,NULL,NULL,NULL,NULL,NULL,NULL,NULL,0,'mosflm - anomalous',NULL,NULL),(1507105,1522600,NULL,NULL,NULL,0.01,NULL,NULL,NULL,0,'BEST',1.13,NULL),(1507114,1522609,NULL,NULL,NULL,0.01,NULL,NULL,NULL,0,'BEST',1.23,NULL),(1507117,1522612,NULL,NULL,NULL,0.01,NULL,NULL,NULL,0,'BEST',1.14,NULL),(1507120,1522615,NULL,NULL,NULL,0.01,NULL,NULL,NULL,1,'BEST',1.16,NULL),(1507123,1522618,NULL,NULL,NULL,0.01,NULL,NULL,NULL,1,'BEST',1.16,NULL); /*!40000 ALTER TABLE `ScreeningStrategy` ENABLE KEYS */; /*!40000 ALTER TABLE `ScreeningStrategySubWedge` DISABLE KEYS */; -INSERT INTO `ScreeningStrategySubWedge` (`screeningStrategySubWedgeId`, `screeningStrategyWedgeId`, `subWedgeNumber`, `rotationAxis`, `axisStart`, `axisEnd`, `exposureTime`, `transmission`, `oscillationRange`, `completeness`, `multiplicity`, `RESOLUTION`, `doseTotal`, `numberOfImages`, `comments`) VALUES (1111566,1143792,NULL,'Omega',64,109,0,NULL,1.4,1,NULL,1.22,NULL,33,NULL), 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DISABLE KEYS */; -INSERT INTO `ExperimentType` (`experimentTypeId`, `name`, `proposalType`, `active`) VALUES (1,'Default',NULL,1), -(2,'MXPressE','mx',1), -(3,'MXPressO','mx',1), -(4,'MXPressE_SAD','mx',1), -(5,'MXScore','mx',1), -(6,'MXPressM','mx',1), -(7,'MAD','mx',1), -(8,'SAD','mx',1), -(9,'Fixed','mx',1), -(10,'Ligand binding','mx',1), -(11,'Refinement','mx',1), -(12,'OSC','mx',1), -(13,'MAD - Inverse Beam','mx',1), -(14,'SAD - Inverse Beam','mx',1), -(15,'MESH','mx',1), -(16,'XFE','mx',1), -(17,'Stepped transmission','mx',1), -(18,'XChem High Symmetry','mx',1), -(19,'XChem Low Symmetry','mx',1), -(20,'Commissioning','mx',1), -(21,'HPLC','saxs',1), -(22,'Robot','saxs',1), -(23,'Rack','saxs',1), -(24,'Grid','saxs',1), -(25,'Solids','saxs',1), -(26,'Powder','saxs',1), -(27,'Peltier','saxs',1), -(28,'Spectroscopy','saxs',1), -(29,'CD Spectroscopy','saxs',1), -(30,'Microscopy','saxs',1), -(31,'Imaging','saxs',1), -(32,'CD Thermal Melt','saxs',1), -(33,'Fixed Energy At Ambient With 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Symmetry','mx',1),(20,'Commissioning','mx',1),(21,'HPLC','saxs',1),(22,'Robot','saxs',1),(23,'Rack','saxs',1),(24,'Grid','saxs',1),(25,'Solids','saxs',1),(26,'Powder','saxs',1),(27,'Peltier','saxs',1),(28,'Spectroscopy','saxs',1),(29,'CD Spectroscopy','saxs',1),(30,'Microscopy','saxs',1),(31,'Imaging','saxs',1),(32,'CD Thermal Melt','saxs',1),(33,'Fixed Energy At Ambient With Robot','saxs',1),(34,'Mesh3D','mx',1),(35,'Screening','sm',1),(36,'Tomography','em',1),(37,'Single Particle','em',1),(38,'Serial Fixed','mx',1),(39,'Serial Jet','mx',1),(40,'Still','mx',1),(41,'SSX-Chip','mx',1),(42,'SSX-Jet','mx',1),(43,'Metal ID','mx',1),(44,'Atlas','em',1),(45,'CLEM','em',1),(46,'FIB','em',1); /*!40000 ALTER TABLE `ExperimentType` ENABLE KEYS */; /*!40000 ALTER TABLE `InspectionType` DISABLE KEYS */; -INSERT INTO `InspectionType` (`inspectionTypeId`, `name`) VALUES (1,'Visible'), -(2,'UV'); +INSERT INTO `InspectionType` (`inspectionTypeId`, `name`) VALUES (1,'Visible'),(2,'UV'); /*!40000 ALTER TABLE `InspectionType` ENABLE KEYS */; /*!40000 ALTER TABLE `Schedule` DISABLE KEYS */; -INSERT INTO `Schedule` (`scheduleId`, `name`) VALUES (1,'Daily - 1 week'), -(2,'Schedule 2'), -(11,'Fibonacci'), -(15,'3 Hour Interval'); +INSERT INTO `Schedule` (`scheduleId`, `name`) VALUES (1,'Daily - 1 week'),(2,'Schedule 2'),(11,'Fibonacci'),(15,'3 Hour Interval'); /*!40000 ALTER TABLE `Schedule` ENABLE KEYS */; /*!40000 ALTER TABLE `ScheduleComponent` DISABLE KEYS */; -INSERT INTO `ScheduleComponent` (`scheduleComponentId`, `scheduleId`, `offset_hours`, `inspectionTypeId`) VALUES (1,1,0,1), -(2,1,12,1), -(3,1,24,1), -(4,1,96,1), -(5,1,48,1), -(6,1,72,1), -(8,2,24,1), -(11,2,48,2), -(14,11,0,1), -(17,11,12,1), -(20,11,24,1), -(23,11,36,1), -(26,11,60,1), -(29,11,96,1), -(32,11,156,1), -(35,11,252,1), -(38,11,408,1), -(41,11,660,1), -(44,11,1068,1), -(47,11,1728,1), -(50,11,2796,1), -(54,15,3,1), -(57,15,6,1), -(60,15,9,1), -(63,15,12,1), -(66,15,18,1), -(69,15,24,1), -(72,15,30,1), -(75,15,36,1), -(78,15,42,1), -(81,15,48,1), -(84,1,120,1), -(87,1,144,1), -(90,1,168,1), -(93,1,336,1), -(96,1,504,1); +INSERT INTO `ScheduleComponent` (`scheduleComponentId`, `scheduleId`, `offset_hours`, `inspectionTypeId`) VALUES (1,1,0,1),(2,1,12,1),(3,1,24,1),(4,1,96,1),(5,1,48,1),(6,1,72,1),(8,2,24,1),(11,2,48,2),(14,11,0,1),(17,11,12,1),(20,11,24,1),(23,11,36,1),(26,11,60,1),(29,11,96,1),(32,11,156,1),(35,11,252,1),(38,11,408,1),(41,11,660,1),(44,11,1068,1),(47,11,1728,1),(50,11,2796,1),(54,15,3,1),(57,15,6,1),(60,15,9,1),(63,15,12,1),(66,15,18,1),(69,15,24,1),(72,15,30,1),(75,15,36,1),(78,15,42,1),(81,15,48,1),(84,1,120,1),(87,1,144,1),(90,1,168,1),(93,1,336,1),(96,1,504,1); /*!40000 ALTER TABLE `ScheduleComponent` ENABLE KEYS */; /*!40000 ALTER TABLE `Imager` DISABLE KEYS */; -INSERT INTO `Imager` (`imagerId`, `name`, `temperature`, `serial`, `capacity`) VALUES (2,'Imager1 20c',20,'Z125434',1000), -(7,'VMXi sim',20,'RI1000-0000',750); +INSERT INTO `Imager` (`imagerId`, `name`, `temperature`, `serial`, `capacity`) VALUES (2,'Imager1 20c',20,'Z125434',1000),(7,'VMXi sim',20,'RI1000-0000',750); /*!40000 ALTER TABLE `Imager` ENABLE KEYS */; /*!40000 ALTER TABLE `Detector` DISABLE KEYS */; -INSERT INTO `Detector` (`detectorId`, `detectorType`, `detectorManufacturer`, `detectorModel`, `detectorPixelSizeHorizontal`, `detectorPixelSizeVertical`, `DETECTORMAXRESOLUTION`, `DETECTORMINRESOLUTION`, `detectorSerialNumber`, `detectorDistanceMin`, `detectorDistanceMax`, `trustedPixelValueRangeLower`, `trustedPixelValueRangeUpper`, `sensorThickness`, `overload`, `XGeoCorr`, `YGeoCorr`, `detectorMode`, `density`, `composition`, `numberOfPixelsX`, `numberOfPixelsY`, `detectorRollMin`, `detectorRollMax`, `localName`, `numberOfROIPixelsX`, `numberOfROIPixelsY`) VALUES (4,'Photon counting','In-house','Excalibur',NULL,NULL,NULL,NULL,'1109-434',100,300,NULL,NULL,NULL,NULL,NULL,NULL,NULL,55,'CrO3Br5Sr10',NULL,NULL,NULL,NULL,NULL,NULL,NULL), -(8,'Diamond XPDF detector',NULL,NULL,NULL,NULL,NULL,NULL,'1109-761',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,10.4,'C+Br+He',NULL,NULL,NULL,NULL,NULL,NULL,NULL); +INSERT INTO `Detector` (`detectorId`, `detectorType`, `detectorManufacturer`, `detectorModel`, `detectorPixelSizeHorizontal`, `detectorPixelSizeVertical`, `DETECTORMAXRESOLUTION`, `DETECTORMINRESOLUTION`, `detectorSerialNumber`, `detectorDistanceMin`, `detectorDistanceMax`, `trustedPixelValueRangeLower`, `trustedPixelValueRangeUpper`, `sensorThickness`, `overload`, `XGeoCorr`, `YGeoCorr`, `detectorMode`, `density`, `composition`, `numberOfPixelsX`, `numberOfPixelsY`, `detectorRollMin`, `detectorRollMax`, `localName`, `numberOfROIPixelsX`, `numberOfROIPixelsY`) VALUES (4,'Photon counting','In-house','Excalibur',NULL,NULL,NULL,NULL,'1109-434',100,300,NULL,NULL,NULL,NULL,NULL,NULL,NULL,55,'CrO3Br5Sr10',NULL,NULL,NULL,NULL,NULL,NULL,NULL),(8,'Diamond XPDF detector',NULL,NULL,NULL,NULL,NULL,NULL,'1109-761',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,10.4,'C+Br+He',NULL,NULL,NULL,NULL,NULL,NULL,NULL); /*!40000 ALTER TABLE `Detector` ENABLE KEYS */; /*!40000 ALTER TABLE `DewarLocationList` DISABLE KEYS */; @@ -502,428 +71,51 @@ INSERT INTO `Detector` (`detectorId`, `detectorType`, `detectorManufacturer`, `d /*!40000 ALTER TABLE `BF_system` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleImageAutoScoreSchema` DISABLE KEYS */; -INSERT INTO `BLSampleImageAutoScoreSchema` (`blSampleImageAutoScoreSchemaId`, `schemaName`, `enabled`) VALUES (1,'MARCO',1), -(2,'CHIMP',1); +INSERT INTO `BLSampleImageAutoScoreSchema` (`blSampleImageAutoScoreSchemaId`, `schemaName`, `enabled`) VALUES (1,'MARCO',1),(2,'CHIMP',1); /*!40000 ALTER TABLE `BLSampleImageAutoScoreSchema` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleImageAutoScoreClass` DISABLE KEYS */; -INSERT INTO `BLSampleImageAutoScoreClass` (`blSampleImageAutoScoreClassId`, `blSampleImageAutoScoreSchemaId`, `scoreClass`) VALUES (1,1,'clear'), -(2,1,'crystal'), -(3,1,'precipitant'), -(4,1,'other'), -(5,2,'clear'), -(6,2,'crystal'), -(7,2,'precipitant'), -(8,2,'other'); +INSERT INTO `BLSampleImageAutoScoreClass` (`blSampleImageAutoScoreClassId`, `blSampleImageAutoScoreSchemaId`, `scoreClass`) VALUES (1,1,'clear'),(2,1,'crystal'),(3,1,'precipitant'),(4,1,'other'),(5,2,'clear'),(6,2,'crystal'),(7,2,'precipitant'),(8,2,'other'); /*!40000 ALTER TABLE `BLSampleImageAutoScoreClass` ENABLE KEYS */; /*!40000 ALTER TABLE `SpaceGroup` DISABLE KEYS */; -INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortName`, `spaceGroupName`, `bravaisLattice`, `bravaisLatticeName`, `pointGroup`, `geometryClassnameId`, `MX_used`) VALUES (1,1,'P1','P 1','aP',NULL,NULL,NULL,1), -(2,2,'P-1','P-1',NULL,NULL,NULL,NULL,1), -(3,3,'P2','P 12 1','mP',NULL,NULL,NULL,1), -(4,4,'P21','P 121 1','mP',NULL,NULL,NULL,1), -(5,5,'C2','C 12 1','mC,mI',NULL,NULL,NULL,1), 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-(204,204,'Im-3','Im -3',NULL,NULL,NULL,NULL,0), -(205,205,'Pa-3','Pa -31',NULL,NULL,NULL,NULL,0), -(206,206,'Ia-3','Ia -31',NULL,NULL,NULL,NULL,0), -(207,207,'P432','P4 3 2','cP',NULL,NULL,NULL,1), -(208,208,'P4232','P42 3 2','cP',NULL,NULL,NULL,1), -(209,209,'F432','F4 3 2','cF',NULL,NULL,NULL,1), -(210,210,'F4132','F41 3 2','cF',NULL,NULL,NULL,1), -(211,211,'I432','I4 3 2','cI',NULL,NULL,NULL,1), -(212,212,'P4332','P43 3 2','cP',NULL,NULL,NULL,1), -(213,213,'P4132','P41 3 2','cP',NULL,NULL,NULL,1), -(214,214,'I4132','I41 3 2','cI',NULL,NULL,NULL,1), -(215,215,'P-43m','P-4 3 m',NULL,NULL,NULL,NULL,0), -(216,216,'F-43m','F-4 3 m',NULL,NULL,NULL,NULL,0), -(217,217,'I-43m','I-4 3 m',NULL,NULL,NULL,NULL,0), -(218,218,'P-43n','P-4 3 n',NULL,NULL,NULL,NULL,0), -(219,219,'F-43c','F-4 3 c',NULL,NULL,NULL,NULL,0), -(220,220,'I-43d','I-4 3 d',NULL,NULL,NULL,NULL,0), -(221,221,'Pm-3m','Pm -3 m',NULL,NULL,NULL,NULL,0), -(222,222,'Pn-3n','Pn -3 n',NULL,NULL,NULL,NULL,0), -(223,223,'Pm-3n','Pm -3 n1',NULL,NULL,NULL,NULL,0), -(224,224,'Pn-3m','Pn -3 m1',NULL,NULL,NULL,NULL,0), -(225,225,'Fm-3m','Fm -3 m',NULL,NULL,NULL,NULL,0), -(226,226,'Fm-3c','Fm -3 c',NULL,NULL,NULL,NULL,0), -(227,227,'Fd-3m','Fd -3 m1',NULL,NULL,NULL,NULL,0), -(228,228,'Fd-3c','Fd -3 c1',NULL,NULL,NULL,NULL,0), -(229,229,'Im-3m','Im -3 m',NULL,NULL,NULL,NULL,0), -(230,230,'Ia-3d','Ia -3 d1',NULL,NULL,NULL,NULL,0); +INSERT INTO `SpaceGroup` (`spaceGroupId`, `spaceGroupNumber`, `spaceGroupShortName`, `spaceGroupName`, `bravaisLattice`, `bravaisLatticeName`, `pointGroup`, `geometryClassnameId`, `MX_used`) VALUES (1,1,'P1','P 1','aP',NULL,NULL,NULL,1),(2,2,'P-1','P-1',NULL,NULL,NULL,NULL,1),(3,3,'P2','P 12 1','mP',NULL,NULL,NULL,1),(4,4,'P21','P 121 1','mP',NULL,NULL,NULL,1),(5,5,'C2','C 12 1','mC,mI',NULL,NULL,NULL,1),(6,6,'P1m1','P 1m 1',NULL,NULL,NULL,NULL,0),(7,7,'P1c1','P 1c 1',NULL,NULL,NULL,NULL,0),(8,8,'C1m1','C 1m 1',NULL,NULL,NULL,NULL,0),(9,9,'C1c1','C 1c 1',NULL,NULL,NULL,NULL,0),(10,10,'P12/m1','P 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2',NULL,NULL,NULL,NULL,0),(189,189,'P-62m','P-6 2 m',NULL,NULL,NULL,NULL,0),(190,190,'P-62c','P-6 2 c',NULL,NULL,NULL,NULL,0),(191,191,'P6/mmm','P6/m m m',NULL,NULL,NULL,NULL,0),(192,192,'P6/mcc','P6/m c c',NULL,NULL,NULL,NULL,0),(193,193,'P63/mcm','P63/m c m',NULL,NULL,NULL,NULL,0),(194,194,'P63/mmc','P63/m m c',NULL,NULL,NULL,NULL,0),(195,195,'P23','P2 3','cP',NULL,NULL,NULL,1),(196,196,'F23','F2 3','cF',NULL,NULL,NULL,1),(197,197,'I23','I2 3','cI',NULL,NULL,NULL,1),(198,198,'P213','P21 3','cP',NULL,NULL,NULL,1),(199,199,'I213','I21 3','cI',NULL,NULL,NULL,1),(200,200,'Pm-3','Pm -3',NULL,NULL,NULL,NULL,0),(201,201,'Pn-3','Pn -3',NULL,NULL,NULL,NULL,0),(202,202,'Fm-3','Fm -3',NULL,NULL,NULL,NULL,0),(203,203,'Fd-3','Fd -3',NULL,NULL,NULL,NULL,0),(204,204,'Im-3','Im -3',NULL,NULL,NULL,NULL,0),(205,205,'Pa-3','Pa -31',NULL,NULL,NULL,NULL,0),(206,206,'Ia-3','Ia -31',NULL,NULL,NULL,NULL,0),(207,207,'P432','P4 3 2','cP',NULL,NULL,NULL,1),(208,208,'P4232','P42 3 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c1',NULL,NULL,NULL,NULL,0),(229,229,'Im-3m','Im -3 m',NULL,NULL,NULL,NULL,0),(230,230,'Ia-3d','Ia -3 d1',NULL,NULL,NULL,NULL,0); /*!40000 ALTER TABLE `SpaceGroup` ENABLE KEYS */; /*!40000 ALTER TABLE `ProcessingPipelineCategory` DISABLE KEYS */; -INSERT INTO `ProcessingPipelineCategory` (`processingPipelineCategoryId`, `name`) VALUES (1,'screening'), -(2,'processing'), -(3,'post processing'); +INSERT INTO `ProcessingPipelineCategory` (`processingPipelineCategoryId`, `name`) VALUES (1,'screening'),(2,'processing'),(3,'post processing'); /*!40000 ALTER TABLE `ProcessingPipelineCategory` ENABLE KEYS */; /*!40000 ALTER TABLE `ProcessingPipeline` DISABLE KEYS */; -INSERT INTO `ProcessingPipeline` (`processingPipelineId`, `processingPipelineCategoryId`, `name`, `discipline`, `pipelineStatus`, `reprocessing`) VALUES (1,1,'Mosflm','MX','automatic',0), -(2,1,'EDNA','MX','automatic',0), -(3,2,'Fast DP','MX','automatic',1), -(4,2,'xia2/3dii','MX','deprecated',0), -(5,2,'xia2/Multiplex','MX','automatic',1), -(6,2,'xia2/DIALS','MX','optional',1), -(7,2,'xia2/XDS','MX','optional',1), -(8,2,'autoPROC','MX','optional',1), -(9,3,'Fast EP','MX','automatic',0), -(10,3,'Dimple','MX','automatic',0), -(11,3,'MrBUMP','MX','automatic',0), -(12,3,'Big EP/XDS','MX','automatic',0), -(13,3,'Big EP/DIALS','MX','automatic',0); +INSERT INTO `ProcessingPipeline` (`processingPipelineId`, `processingPipelineCategoryId`, `name`, `discipline`, `pipelineStatus`, `reprocessing`) VALUES (1,1,'Mosflm','MX','automatic',0),(2,1,'EDNA','MX','automatic',0),(3,2,'Fast DP','MX','automatic',1),(4,2,'xia2/3dii','MX','deprecated',0),(5,2,'xia2/Multiplex','MX','automatic',1),(6,2,'xia2/DIALS','MX','optional',1),(7,2,'xia2/XDS','MX','optional',1),(8,2,'autoPROC','MX','optional',1),(9,3,'Fast EP','MX','automatic',0),(10,3,'Dimple','MX','automatic',0),(11,3,'MrBUMP','MX','automatic',0),(12,3,'Big EP/XDS','MX','automatic',0),(13,3,'Big EP/DIALS','MX','automatic',0); /*!40000 ALTER TABLE `ProcessingPipeline` ENABLE KEYS */; /*!40000 ALTER TABLE `BLSampleType` DISABLE KEYS */; -INSERT INTO `BLSampleType` (`blSampleTypeId`, `name`, `proposalType`, `active`) VALUES (1,'background','xpdf',1), -(2,'container','xpdf',1), -(3,'sample','xpdf',1), -(4,'calibrant','xpdf',1), -(5,'buffer','scm',1), -(6,'sample','scm',1), -(7,'sample','mx',1); +INSERT INTO `BLSampleType` (`blSampleTypeId`, `name`, `proposalType`, `active`) VALUES (1,'background','xpdf',1),(2,'container','xpdf',1),(3,'sample','xpdf',1),(4,'calibrant','xpdf',1),(5,'buffer','scm',1),(6,'sample','scm',1),(7,'sample','mx',1); /*!40000 ALTER TABLE `BLSampleType` ENABLE KEYS */; /*!40000 ALTER TABLE `PurificationColumn` DISABLE KEYS */; -INSERT INTO `PurificationColumn` (`purificationColumnId`, `name`, `active`) VALUES (1,'user supplied',1), -(2,'s75',1), -(3,'s200',1), -(4,'superose6',1), -(5,'kw402.5',1), -(6,'kw403',1), -(7,'kw404',1), -(8,'kw405',1); +INSERT INTO `PurificationColumn` (`purificationColumnId`, `name`, `active`) VALUES (1,'user supplied',1),(2,'s75',1),(3,'s200',1),(4,'superose6',1),(5,'kw402.5',1),(6,'kw403',1),(7,'kw404',1),(8,'kw405',1); /*!40000 ALTER TABLE `PurificationColumn` ENABLE KEYS */; /*!40000 ALTER TABLE `UserGroup` DISABLE KEYS */; -INSERT INTO `UserGroup` (`userGroupId`, `name`) VALUES (39,'autocollect'), -(17,'bag_stats'), -(20,'bl_stats'), -(45,'detector_admin'), -(8,'developers'), -(9,'ehc'), -(6,'em_admin'), -(10,'fault_admin'), -(50,'goods_handling'), -(53,'imaging_admin'), -(59,'mm_admin'), -(2,'mx_admin'), -(14,'pdb_stats'), -(4,'powder_admin'), -(47,'prop_admin'), -(3,'saxs_admin'), -(28,'ship_manage'), -(12,'sm_admin'), -(56,'spectroscopy_admin'), -(1,'super_admin'), -(24,'temp_mx_admin'), -(5,'tomo_admin'), -(11,'vmxi'), -(34,'xpdf_admin'); +INSERT INTO `UserGroup` (`userGroupId`, `name`) VALUES (39,'autocollect'),(17,'bag_stats'),(20,'bl_stats'),(45,'detector_admin'),(8,'developers'),(9,'ehc'),(6,'em_admin'),(10,'fault_admin'),(50,'goods_handling'),(53,'imaging_admin'),(59,'mm_admin'),(2,'mx_admin'),(14,'pdb_stats'),(4,'powder_admin'),(47,'prop_admin'),(3,'saxs_admin'),(28,'ship_manage'),(12,'sm_admin'),(56,'spectroscopy_admin'),(1,'super_admin'),(24,'temp_mx_admin'),(5,'tomo_admin'),(11,'vmxi'),(34,'xpdf_admin'); /*!40000 ALTER TABLE `UserGroup` ENABLE KEYS */; /*!40000 ALTER TABLE `Permission` DISABLE KEYS */; -INSERT INTO `Permission` (`permissionId`, `type`, `description`) VALUES (1,'mx_admin','MX Administrator'), -(2,'manage_groups','Manage User Groups'), -(4,'manage_perms','Manage User Group Permissions'), -(5,'global_stats','View Global Statistics'), -(6,'fault_view','View Fault Reports'), -(7,'saxs_admin','SAXS Administrator'), -(8,'em_admin','EM Administrator'), -(9,'gen_admin','Powder Admin'), -(10,'tomo_admin','Tomo Admin'), -(11,'super_admin','Site Admin'), -(12,'fault_global','Globally edit all faults'), -(13,'schedules','Manage Imaging Schedules'), -(15,'schedule_comps','Manage Imaging Schedule Components'), -(16,'imaging_dash','Imaging Dashboard'), -(17,'vmxi_queue','VMXi Data Collection Queue'), -(18,'sm_admin','Small Molecule Admin'), -(20,'pow_admin','Power Admin'), -(23,'all_dewars','View All Dewars'), -(26,'all_prop_stats','View All Proposal Stats'), -(29,'all_breakdown','View Aggregated Visit Breakdown Stats'), -(32,'disp_cont','VMXi Dispose Container'), -(37,'view_manifest','View Shipping Manifest'), -(43,'schedule_comp','typo fill in'), -(49,'xpdf_admin','XPDF Admin'), -(55,'edit_presets','Edit Beamline DC Presets'), -(58,'manage_params','Edit Beamline Parameter Limits'), -(64,'manage_detector','Manage Beamline Detector Limits'), -(69,'auto_dash','AutoCollect Dashboard'), -(77,'fault_admin','Edit Fault Categories'), -(80,'fault_add','Add New Fault Reports'); +INSERT INTO `Permission` (`permissionId`, `type`, `description`) VALUES (1,'mx_admin','MX Administrator'),(2,'manage_groups','Manage User Groups'),(4,'manage_perms','Manage User Group Permissions'),(5,'global_stats','View Global Statistics'),(6,'fault_view','View Fault Reports'),(7,'saxs_admin','SAXS Administrator'),(8,'em_admin','EM Administrator'),(9,'gen_admin','Powder Admin'),(10,'tomo_admin','Tomo Admin'),(11,'super_admin','Site Admin'),(12,'fault_global','Globally edit all faults'),(13,'schedules','Manage Imaging Schedules'),(15,'schedule_comps','Manage Imaging Schedule Components'),(16,'imaging_dash','Imaging Dashboard'),(17,'vmxi_queue','VMXi Data Collection Queue'),(18,'sm_admin','Small Molecule Admin'),(20,'pow_admin','Power Admin'),(23,'all_dewars','View All Dewars'),(26,'all_prop_stats','View All Proposal Stats'),(29,'all_breakdown','View Aggregated Visit Breakdown Stats'),(32,'disp_cont','VMXi Dispose Container'),(37,'view_manifest','View Shipping Manifest'),(43,'schedule_comp','typo fill in'),(49,'xpdf_admin','XPDF Admin'),(55,'edit_presets','Edit Beamline DC Presets'),(58,'manage_params','Edit Beamline Parameter Limits'),(64,'manage_detector','Manage Beamline Detector Limits'),(69,'auto_dash','AutoCollect Dashboard'),(77,'fault_admin','Edit Fault Categories'),(80,'fault_add','Add New Fault Reports'); /*!40000 ALTER TABLE `Permission` ENABLE KEYS */; /*!40000 ALTER TABLE `UserGroup_has_Permission` DISABLE KEYS */; -INSERT INTO `UserGroup_has_Permission` (`userGroupId`, `permissionId`) VALUES (1,1), -(2,1), -(8,1), -(9,1), -(14,1), -(24,1), -(8,2), -(8,4), -(2,6), -(8,6), -(9,6), -(1,7), -(3,7), -(8,7), -(1,8), -(6,8), -(8,8), -(1,9), -(8,9), -(1,10), -(5,10), -(8,10), -(1,11), -(8,11), -(10,12), -(11,13), -(11,15), -(11,16), -(11,17), -(1,18), -(8,18), -(12,18), -(1,20), -(4,20), -(8,20), -(1,23), -(2,23), -(3,23), -(6,23), -(8,23), -(28,23), -(8,26), -(17,26), -(8,29), -(20,29), -(11,32), -(8,37), -(28,37), -(11,43), -(1,49), -(8,49), -(34,49), -(11,55), -(11,58), -(11,64), -(39,69), -(10,77), -(2,80); +INSERT INTO `UserGroup_has_Permission` (`userGroupId`, `permissionId`) VALUES (1,1),(1,7),(1,8),(1,9),(1,10),(1,11),(1,18),(1,20),(1,23),(1,49),(2,1),(2,6),(2,23),(2,80),(3,7),(3,23),(4,20),(5,10),(6,8),(6,23),(8,1),(8,2),(8,4),(8,6),(8,7),(8,8),(8,9),(8,10),(8,11),(8,18),(8,20),(8,23),(8,26),(8,29),(8,37),(8,49),(9,1),(9,6),(10,12),(10,77),(11,13),(11,15),(11,16),(11,17),(11,32),(11,43),(11,55),(11,58),(11,64),(12,18),(14,1),(17,26),(20,29),(24,1),(28,23),(28,37),(34,49),(39,69); /*!40000 ALTER TABLE `UserGroup_has_Permission` ENABLE KEYS */; /*!40000 ALTER TABLE `ScanParametersService` DISABLE KEYS */; -INSERT INTO `ScanParametersService` (`scanParametersServiceId`, `name`, `description`) VALUES (4,'Temperature','Temperature in Celsius'), -(7,'Pressure','Pressure in pascal (Pa)'); +INSERT INTO `ScanParametersService` (`scanParametersServiceId`, `name`, `description`) VALUES (4,'Temperature','Temperature in Celsius'),(7,'Pressure','Pressure in pascal (Pa)'); /*!40000 ALTER TABLE `ScanParametersService` ENABLE KEYS */; /*!40000 ALTER TABLE `EventType` DISABLE KEYS */; -INSERT INTO `EventType` (`eventTypeId`, `name`) VALUES (3,'LaserExcitation'), -(4,'ReactionTrigger'), -(1,'XrayDetection'), -(2,'XrayExposure'); +INSERT INTO `EventType` (`eventTypeId`, `name`) VALUES (3,'LaserExcitation'),(4,'ReactionTrigger'),(1,'XrayDetection'),(2,'XrayExposure'); /*!40000 ALTER TABLE `EventType` ENABLE KEYS */; /*!40000 ALTER TABLE `LDAPSearchParameters` DISABLE KEYS */;