From a9ff8a86478a912e25cd8e6e76786fb816e7101e Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 6 Jan 2026 09:58:11 -0800 Subject: [PATCH 1/3] Add DB Tuning Advisor suggestions --- .../SequenceAnalysis-12.329-12.330.sql | 19 +++++++++ .../SequenceAnalysis-12.329-12.330.sql | 39 +++++++++++++++++++ .../SequenceAnalysisModule.java | 2 +- 3 files changed, 59 insertions(+), 1 deletion(-) create mode 100644 SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql create mode 100644 SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql new file mode 100644 index 000000000..47273f13e --- /dev/null +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql @@ -0,0 +1,19 @@ +CREATE INDEX IDX_haplotypes_name_date ON sequenceanalysis.haplotypes +( + Name ASC, + datedisabled ASC +); + +CREATE INDEX IDX_haplotype_sequences_name_haplotype_type ON sequenceanalysis.haplotype_sequences +( + haplotype ASC, + name ASC, + type ASC +); + +CREATE INDEX IDX_alignment_summary_analysis_id_rowid_container ON sequenceanalysis.alignment_summary +( + analysis_id ASC, + rowid ASC, + container ASC +) \ No newline at end of file diff --git a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql new file mode 100644 index 000000000..89f0a1285 --- /dev/null +++ b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql @@ -0,0 +1,39 @@ +CREATE NONCLUSTERED INDEX IDX_haplotypes_name_date ON sequenceanalysis.haplotypes +( + Name ASC, + datedisabled ASC +); + +CREATE NONCLUSTERED INDEX IDX_haplotype_sequences_name_haplotype_type ON sequenceanalysis.haplotype_sequences +( + haplotype ASC, + name ASC, + type ASC +); + +CREATE NONCLUSTERED INDEX IDX_alignment_summary_analysis_id_rowid_container ON sequenceanalysis.alignment_summary +( + analysis_id ASC, + rowid ASC, + container ASC +) +INCLUDE(total) + +CREATE STATISTICS STAT_ref_nt_sequence_rowid_locus_container ON sequenceanalysis.ref_nt_sequences (RowId, locus, container) +WITH AUTO_DROP = OFF + +CREATE STATISTICS STAT_ref_nt_sequence_locus_container ON sequenceanalysis.ref_nt_sequences (locus, container) +WITH AUTO_DROP = OFF + +CREATE STATISTICS STAT_sequence_analyses_container_readset ON sequenceanalysis.sequence_analyses (Container, readset) +WITH AUTO_DROP = OFF + +CREATE STATISTICS STAT_sequence_readsets_rowid_container ON sequenceanalysis.sequence_readsets (RowId, Container) +WITH AUTO_DROP = OFF + +CREATE STATISTICS STAT_asj_alignmentid_container_ref_nt_id ON sequenceanalysis.alignment_summary_junction(alignment_id, container, ref_nt_id) +WITH AUTO_DROP = OFF + +CREATE STATISTICS STAT_asj_alignmentid_ref_nt_id_status_alignment_id ON sequenceanalysis.alignment_summary_junction(ref_nt_id, status, alignment_id) +WITH AUTO_DROP = OFF + diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java index 466c12ac7..3fc642130 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java @@ -211,7 +211,7 @@ public String getName() @Override public Double getSchemaVersion() { - return 12.329; + return 12.330; } @Override From c0fbc5cd1e0f8c2b5f0dfe69486377dcac98d2c9 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 6 Jan 2026 12:27:02 -0800 Subject: [PATCH 2/3] Sql fix --- .../postgresql/SequenceAnalysis-12.329-12.330.sql | 9 +-------- .../sqlserver/SequenceAnalysis-12.329-12.330.sql | 2 +- 2 files changed, 2 insertions(+), 9 deletions(-) diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql index 47273f13e..b46a9866d 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/SequenceAnalysis-12.329-12.330.sql @@ -9,11 +9,4 @@ CREATE INDEX IDX_haplotype_sequences_name_haplotype_type ON sequenceanalysis.hap haplotype ASC, name ASC, type ASC -); - -CREATE INDEX IDX_alignment_summary_analysis_id_rowid_container ON sequenceanalysis.alignment_summary -( - analysis_id ASC, - rowid ASC, - container ASC -) \ No newline at end of file +); \ No newline at end of file diff --git a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql index 89f0a1285..fb5ceb96e 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql @@ -11,7 +11,7 @@ CREATE NONCLUSTERED INDEX IDX_haplotype_sequences_name_haplotype_type ON sequenc type ASC ); -CREATE NONCLUSTERED INDEX IDX_alignment_summary_analysis_id_rowid_container ON sequenceanalysis.alignment_summary +CREATE NONCLUSTERED INDEX IDX_alignment_summary_analysis_id_rowid_container_total ON sequenceanalysis.alignment_summary ( analysis_id ASC, rowid ASC, From 4de021d81ec51f5aeea22cf707a782c0e7cab552 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 6 Jan 2026 13:40:19 -0800 Subject: [PATCH 3/3] Sql fix --- .../dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql index fb5ceb96e..73397ec1d 100644 --- a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql +++ b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/SequenceAnalysis-12.329-12.330.sql @@ -31,9 +31,9 @@ WITH AUTO_DROP = OFF CREATE STATISTICS STAT_sequence_readsets_rowid_container ON sequenceanalysis.sequence_readsets (RowId, Container) WITH AUTO_DROP = OFF -CREATE STATISTICS STAT_asj_alignmentid_container_ref_nt_id ON sequenceanalysis.alignment_summary_junction(alignment_id, container, ref_nt_id) +CREATE STATISTICS STAT_asj_alignmentid_container_ref_nt_id ON sequenceanalysis.alignment_summary_junction (alignment_id, container, ref_nt_id) WITH AUTO_DROP = OFF -CREATE STATISTICS STAT_asj_alignmentid_ref_nt_id_status_alignment_id ON sequenceanalysis.alignment_summary_junction(ref_nt_id, status, alignment_id) +CREATE STATISTICS STAT_asj_alignmentid_ref_nt_id_status_alignment_id ON sequenceanalysis.alignment_summary_junction (ref_nt_id, status, alignment_id) WITH AUTO_DROP = OFF