From 7de3d8983d4d6f076ddc6339090d9b0c03f0ee01 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 12 Aug 2025 10:20:42 +0200 Subject: [PATCH 1/8] add script for rendering the latest report locally --- scripts/run_benchmark/render_report_local.sh | 45 ++++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100755 scripts/run_benchmark/render_report_local.sh diff --git a/scripts/run_benchmark/render_report_local.sh b/scripts/run_benchmark/render_report_local.sh new file mode 100755 index 00000000..25b048ed --- /dev/null +++ b/scripts/run_benchmark/render_report_local.sh @@ -0,0 +1,45 @@ +#!/bin/bash + +# fail on error +set -e + +# ensure we're in the root of the repo +REPO_ROOT=$(git rev-parse --show-toplevel) +cd "$REPO_ROOT" + +# set input and output directories +TASK=task_cyto_batch_integration +BASE_DIR="s3://openproblems-data/resources/$TASK/results" +OUTPUT_DIR="output/report" + +# find subdir in bucket with latest date +DATE=$(aws s3 ls $BASE_DIR --recursive | awk '{print $4}' | grep 'task_info.yaml' | sort -r | head -n 1 | sed 's#.*/run_\(.*\)/[^/]*$#\1#') + +INPUT_DIR="$BASE_DIR/run_$DATE" +TASK_STRIP_PREFIX=$(echo $TASK | sed 's/task_//') + +echo "Processing $DATE -> $OUTPUT_DIR" + +# start the run +nextflow run openproblems-bio/openproblems \ + -r build/feature/no-ref/update-process-results \ + -main-script target/nextflow/reporting/process_task_results/main.nf \ + -profile docker \ + -resume \ + -c common/nextflow_helpers/labels_ci.config \ + --id "$TASK/run_$DATE" \ + --input_scores "$INPUT_DIR/score_uns.yaml" \ + --input_dataset_info "$INPUT_DIR/dataset_uns.yaml" \ + --input_method_configs "$INPUT_DIR/method_configs.yaml" \ + --input_metric_configs "$INPUT_DIR/metric_configs.yaml" \ + --input_trace "$INPUT_DIR/trace.txt" \ + --input_task_info "$INPUT_DIR/task_info.yaml" \ + --output_state '$id/state.yaml' \ + --output_combined '$id/combined_output.json' \ + --output_report '$id/report.html' \ + --output_dataset_info '$id/dataset_info.json' \ + --output_method_info '$id/method_info.json' \ + --output_metric_info '$id/metric_info.json' \ + --output_results '$id/results.json' \ + --output_quality_control '$id/quality_control.json' \ + --publish_dir "$OUTPUT_DIR" From 3bbdf81fbc4a540016f2315e21e66345cf03b02b Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 12 Aug 2025 14:00:56 +0200 Subject: [PATCH 2/8] update script --- scripts/run_benchmark/render_report_local.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/run_benchmark/render_report_local.sh b/scripts/run_benchmark/render_report_local.sh index 25b048ed..071a5404 100755 --- a/scripts/run_benchmark/render_report_local.sh +++ b/scripts/run_benchmark/render_report_local.sh @@ -26,6 +26,7 @@ nextflow run openproblems-bio/openproblems \ -main-script target/nextflow/reporting/process_task_results/main.nf \ -profile docker \ -resume \ + -latest \ -c common/nextflow_helpers/labels_ci.config \ --id "$TASK/run_$DATE" \ --input_scores "$INPUT_DIR/score_uns.yaml" \ From 098675e19d2286439db162e13612139db6b872ed Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 14 Aug 2025 10:02:54 +0200 Subject: [PATCH 3/8] add todo --- scripts/run_benchmark/render_report_local.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/run_benchmark/render_report_local.sh b/scripts/run_benchmark/render_report_local.sh index 071a5404..d418dbac 100755 --- a/scripts/run_benchmark/render_report_local.sh +++ b/scripts/run_benchmark/render_report_local.sh @@ -21,6 +21,7 @@ TASK_STRIP_PREFIX=$(echo $TASK | sed 's/task_//') echo "Processing $DATE -> $OUTPUT_DIR" # start the run +# TODO: switch to `-r build/main` once PR openproblems-bio/openproblems#919 is merged nextflow run openproblems-bio/openproblems \ -r build/feature/no-ref/update-process-results \ -main-script target/nextflow/reporting/process_task_results/main.nf \ From b6a44bd7877cfb080de0e2163300264221f358b6 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 2 Sep 2025 14:29:44 +0200 Subject: [PATCH 4/8] fix script --- scripts/run_benchmark/render_report_local.sh | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/scripts/run_benchmark/render_report_local.sh b/scripts/run_benchmark/render_report_local.sh index d418dbac..f8a91357 100755 --- a/scripts/run_benchmark/render_report_local.sh +++ b/scripts/run_benchmark/render_report_local.sh @@ -21,9 +21,8 @@ TASK_STRIP_PREFIX=$(echo $TASK | sed 's/task_//') echo "Processing $DATE -> $OUTPUT_DIR" # start the run -# TODO: switch to `-r build/main` once PR openproblems-bio/openproblems#919 is merged nextflow run openproblems-bio/openproblems \ - -r build/feature/no-ref/update-process-results \ + -r build/main \ -main-script target/nextflow/reporting/process_task_results/main.nf \ -profile docker \ -resume \ From c4c082a3b9a31a6aa1c419979c13fa376b01e8ff Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 2 Sep 2025 14:40:55 +0200 Subject: [PATCH 5/8] add no sign request for anonymous users --- scripts/run_benchmark/render_report_local.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/run_benchmark/render_report_local.sh b/scripts/run_benchmark/render_report_local.sh index f8a91357..4157ccb1 100755 --- a/scripts/run_benchmark/render_report_local.sh +++ b/scripts/run_benchmark/render_report_local.sh @@ -13,7 +13,7 @@ BASE_DIR="s3://openproblems-data/resources/$TASK/results" OUTPUT_DIR="output/report" # find subdir in bucket with latest date -DATE=$(aws s3 ls $BASE_DIR --recursive | awk '{print $4}' | grep 'task_info.yaml' | sort -r | head -n 1 | sed 's#.*/run_\(.*\)/[^/]*$#\1#') +DATE=$(aws s3 ls $BASE_DIR --recursive --no-sign-request | awk '{print $4}' | grep 'task_info.yaml' | sort -r | head -n 1 | sed 's#.*/run_\(.*\)/[^/]*$#\1#') INPUT_DIR="$BASE_DIR/run_$DATE" TASK_STRIP_PREFIX=$(echo $TASK | sed 's/task_//') From bac33137412ff54ab7f03501f5a0faf648931086 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 Sep 2025 10:37:55 +0200 Subject: [PATCH 6/8] use more generic results script --- common | 2 +- scripts/render_report.sh | 5 +++ scripts/run_benchmark/render_report_local.sh | 46 -------------------- 3 files changed, 6 insertions(+), 47 deletions(-) create mode 100755 scripts/render_report.sh delete mode 100755 scripts/run_benchmark/render_report_local.sh diff --git a/common b/common index 79b884b4..6dcc1688 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 79b884b4c7fed300972d83a6ca025abb6116cbdc +Subproject commit 6dcc1688929cfdb7a8ba3c448df80bb2f5cb84ca diff --git a/scripts/render_report.sh b/scripts/render_report.sh new file mode 100755 index 00000000..6e5d6da7 --- /dev/null +++ b/scripts/render_report.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +set -e + +common/scripts/render_results_report "$@" diff --git a/scripts/run_benchmark/render_report_local.sh b/scripts/run_benchmark/render_report_local.sh deleted file mode 100755 index 4157ccb1..00000000 --- a/scripts/run_benchmark/render_report_local.sh +++ /dev/null @@ -1,46 +0,0 @@ -#!/bin/bash - -# fail on error -set -e - -# ensure we're in the root of the repo -REPO_ROOT=$(git rev-parse --show-toplevel) -cd "$REPO_ROOT" - -# set input and output directories -TASK=task_cyto_batch_integration -BASE_DIR="s3://openproblems-data/resources/$TASK/results" -OUTPUT_DIR="output/report" - -# find subdir in bucket with latest date -DATE=$(aws s3 ls $BASE_DIR --recursive --no-sign-request | awk '{print $4}' | grep 'task_info.yaml' | sort -r | head -n 1 | sed 's#.*/run_\(.*\)/[^/]*$#\1#') - -INPUT_DIR="$BASE_DIR/run_$DATE" -TASK_STRIP_PREFIX=$(echo $TASK | sed 's/task_//') - -echo "Processing $DATE -> $OUTPUT_DIR" - -# start the run -nextflow run openproblems-bio/openproblems \ - -r build/main \ - -main-script target/nextflow/reporting/process_task_results/main.nf \ - -profile docker \ - -resume \ - -latest \ - -c common/nextflow_helpers/labels_ci.config \ - --id "$TASK/run_$DATE" \ - --input_scores "$INPUT_DIR/score_uns.yaml" \ - --input_dataset_info "$INPUT_DIR/dataset_uns.yaml" \ - --input_method_configs "$INPUT_DIR/method_configs.yaml" \ - --input_metric_configs "$INPUT_DIR/metric_configs.yaml" \ - --input_trace "$INPUT_DIR/trace.txt" \ - --input_task_info "$INPUT_DIR/task_info.yaml" \ - --output_state '$id/state.yaml' \ - --output_combined '$id/combined_output.json' \ - --output_report '$id/report.html' \ - --output_dataset_info '$id/dataset_info.json' \ - --output_method_info '$id/method_info.json' \ - --output_metric_info '$id/metric_info.json' \ - --output_results '$id/results.json' \ - --output_quality_control '$id/quality_control.json' \ - --publish_dir "$OUTPUT_DIR" From 0db206cef2754b7a3f9e42ab3438064afb347cf8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Thu, 25 Sep 2025 10:58:25 +0200 Subject: [PATCH 7/8] update submodule --- common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common b/common index 6dcc1688..ef66a3e2 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit 6dcc1688929cfdb7a8ba3c448df80bb2f5cb84ca +Subproject commit ef66a3e26c590d0e021591c5a67186191c1107e7 From ea8294d833f730b2356ed62b6e354729a7e0f9f8 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Tue, 30 Sep 2025 10:02:37 +0200 Subject: [PATCH 8/8] fix common submodule --- common | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/common b/common index ef66a3e2..67da19a3 160000 --- a/common +++ b/common @@ -1 +1 @@ -Subproject commit ef66a3e26c590d0e021591c5a67186191c1107e7 +Subproject commit 67da19a36ae56ea068804d15ccadec88a06da920