From 3be4d6df32d89bbfff196635dd5487ac1d18c079 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 28 Aug 2024 10:25:54 -0700 Subject: [PATCH 01/21] Bugfix to 10x metrics handling --- .../labkey/singlecell/run/CellRangerVDJWrapper.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java index 12fa0555a..0b1b9ba8f 100644 --- a/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java +++ b/singlecell/src/org/labkey/singlecell/run/CellRangerVDJWrapper.java @@ -776,20 +776,26 @@ public void complete(SequenceAnalysisJobSupport support, AnalysisModel model, Co throw new PipelineJobException("Expected sequence outputs to be created"); } + File folderWithMetricFile; SequenceOutputFile outputForData = outputFilesCreated.stream().filter(x -> VLOUPE_CATEGORY.equals(x.getCategory())).findFirst().orElse(null); if (outputForData == null) { outputForData = outputFilesCreated.stream().filter(x -> "10x Run Summary".equals(x.getCategory())).findFirst().orElseThrow(); + folderWithMetricFile = outputForData.getFile().getParentFile(); + } + else + { + // The metric file is one level above the vloupe, but in the same folder as HTML + folderWithMetricFile = outputForData.getFile().getParentFile().getParentFile(); } - File outsDir = outputForData.getFile().getParentFile(); Integer dataId = outputForData.getDataId(); if (dataId == null) { throw new PipelineJobException("Unable to find dataId for output file"); } - addMetrics(outsDir, model, dataId); + addMetrics(folderWithMetricFile, model, dataId); } private static final Pattern FILE_PATTERN = Pattern.compile("^(.+?)(_S[0-9]+){0,1}_L(.+?)_(R){0,1}([0-9])(_[0-9]+){0,1}(.*?)(\\.f(ast){0,1}q)(\\.gz)?$"); From 90dc3ffee34ba4e2e15c865743e99e3ef7730028 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 28 Aug 2024 10:41:56 -0700 Subject: [PATCH 02/21] Add natural sort to instrument_runs table --- .../sequenceanalysis/query/SequenceAnalysisUserSchema.java | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java index 33fbd6395..858cbcc92 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java @@ -118,6 +118,13 @@ else if (SequenceAnalysisSchema.TABLE_BARCODES.equalsIgnoreCase(name)) return ret; } + else if (SequenceAnalysisSchema.TABLE_INSTRUMENT_RUNS.equalsIgnoreCase(name)) + { + TableInfo ret = super.createWrappedTable(name, sourceTable, cf); + LDKService.get().applyNaturalSort((AbstractTableInfo)ret, "name"); + + return ret; + } else if (SequenceAnalysisSchema.TABLE_ANALYSES.equalsIgnoreCase(name)) { return createAnalysesTable(sourceTable, cf); From d5cb20ddf503ae59fa56b5d3a2606eb981cecaad Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 30 Aug 2024 09:53:11 -0700 Subject: [PATCH 03/21] Bugfix to readset import when one pair is archived to SRA --- .../labkey/sequenceanalysis/ReadDataImpl.java | 18 ++++++++++++++---- .../pipeline/ReadsetInitTask.java | 4 ++-- 2 files changed, 16 insertions(+), 6 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java index 50df2c90e..a1437071c 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java @@ -201,18 +201,28 @@ public void setModifiedBy(Integer modifiedBy) _modifiedBy = modifiedBy; } + public File getFile1(boolean allowArchived) + { + return getFile(1, _fileId1, allowArchived); + } + @Override @Transient public File getFile1() { - return getFile(1, _fileId1); + return getFile1(false); } @Override @Transient public File getFile2() { - return getFile(2, _fileId2); + return getFile2(false); + } + + public File getFile2(boolean allowArchived) + { + return getFile(2, _fileId2, false); } public void setFile(File f, int fileIdx) @@ -248,9 +258,9 @@ public Integer getTotalReads() } @Transient - private File getFile(int fileIdx, Integer fileId) + private File getFile(int fileIdx, Integer fileId, boolean allowArchived) { - if (isArchived()) + if (isArchived() && !allowArchived) { return null; } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java index 2c462ce90..8166035ad 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java @@ -505,10 +505,10 @@ private void checkForDuplicateFileNames(List readsets, List { Map existingFileNames = new HashMap<>(); preexistingReadData.forEach(rd -> { - existingFileNames.put(rd.getFile1().getName(), rd.getFile1()); + existingFileNames.put(rd.getFile1(true).getName(), rd.getFile1(true)); if (rd.getFile2() != null) { - existingFileNames.put(rd.getFile2().getName(), rd.getFile2()); + existingFileNames.put(rd.getFile2(true).getName(), rd.getFile2(true)); } }); From cf1fa97d1a7487be51defcfe10fe613fe888437b Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 30 Aug 2024 10:47:19 -0700 Subject: [PATCH 04/21] Bugfix to readset import when one pair is archived to SRA --- .../src/org/labkey/sequenceanalysis/ReadDataImpl.java | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java index a1437071c..1d8901057 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/ReadDataImpl.java @@ -284,13 +284,16 @@ private File getFile(int fileIdx, Integer fileId, boolean allowArchived) ret = d.getFile(); } - if (ret != null && !ret.exists()) + if (!isArchived() && ret != null && !ret.exists()) { throw new IllegalArgumentException("File does not exist: " + ret.getPath()); } } - _cachedFiles.put(fileIdx, ret); + if (!isArchived()) + { + _cachedFiles.put(fileIdx, ret); + } return ret; } From cb09960e2fab20ad84e25914e41d7e7317e8a979 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 30 Aug 2024 12:41:32 -0700 Subject: [PATCH 05/21] Bugfix to readset import when one pair is archived to SRA --- .../org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java | 4 +++- .../sequenceanalysis/pipeline/SequenceNormalizationTask.java | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java index 8166035ad..92ae0ec75 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReadsetInitTask.java @@ -218,7 +218,9 @@ public RecordedActionSet run() throws PipelineJobException for (SequenceReadsetImpl rs : readsets) { getJob().getLogger().debug("caching readset: " + rs.getName() + " with " + rs.getReadData().size() + " files"); - getPipelineJob().getSequenceSupport().cacheReadset(rs); + + // NOTE: allow archived data + getPipelineJob().getSequenceSupport().cacheReadset(rs, true); } } catch (IOException e) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java index 58b0d913a..1184d9c07 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceNormalizationTask.java @@ -626,7 +626,7 @@ else if (lane.isEmpty()) if (rd.isEmpty()) { - getJob().getLogger().warn("no file groups found ofr rs: " + rs.getName() + " with fileGroupId: " + rs.getFileSetName()); + getJob().getLogger().warn("no file groups found for readset: " + rs.getName() + " with fileGroupId: " + rs.getFileSetName()); } rs.setReadData(rd); From f41acdb586831b2f95f187848f7a867309129fb0 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 3 Sep 2024 13:56:53 -0700 Subject: [PATCH 06/21] Remove old query --- .../alignment_summary_grouped.query.xml | 6 +- .../singlecell/sortStatusByPlate.query.xml | 21 ----- .../queries/singlecell/sortStatusByPlate.sql | 88 ------------------- .../singlecell/sortStatusByPlate/.qview.xml | 6 -- .../sortStatusByPlateAndSample.query.xml | 21 ----- .../singlecell/sortStatusByPlateAndSample.sql | 72 --------------- .../sortStatusByPlateAndSample/.qview.xml | 7 -- .../queries/singlecell/sorts/.qview.xml | 1 - 8 files changed, 2 insertions(+), 220 deletions(-) delete mode 100644 singlecell/resources/queries/singlecell/sortStatusByPlate.query.xml delete mode 100644 singlecell/resources/queries/singlecell/sortStatusByPlate.sql delete mode 100644 singlecell/resources/queries/singlecell/sortStatusByPlate/.qview.xml delete mode 100644 singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.query.xml delete mode 100644 singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.sql delete mode 100644 singlecell/resources/queries/singlecell/sortStatusByPlateAndSample/.qview.xml diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml index 0e0137d04..4f755a30e 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/alignment_summary_grouped.query.xml @@ -7,6 +7,8 @@ rowids + RowIds + true true @@ -50,10 +52,6 @@ - - RowIds - true - # Alignments true diff --git a/singlecell/resources/queries/singlecell/sortStatusByPlate.query.xml b/singlecell/resources/queries/singlecell/sortStatusByPlate.query.xml deleted file mode 100644 index 277aa4298..000000000 --- a/singlecell/resources/queries/singlecell/sortStatusByPlate.query.xml +++ /dev/null @@ -1,21 +0,0 @@ - - - - - TCR Status By Plate - - - true - /query/executeQuery.view?schemaName=singlecell&query.queryName=sorts&query.plateId~eq=${plateId} - - - true - - - Plate Complete - - -
- - - \ No newline at end of file diff --git a/singlecell/resources/queries/singlecell/sortStatusByPlate.sql b/singlecell/resources/queries/singlecell/sortStatusByPlate.sql deleted file mode 100644 index 9e3618943..000000000 --- a/singlecell/resources/queries/singlecell/sortStatusByPlate.sql +++ /dev/null @@ -1,88 +0,0 @@ -SELECT - t3.sortPlateId, - t3.container, - t3.workbook, - t3.sortType, - t3.processingRequested, - t3.subjects, - t3.stims, - t3.sampleDates, - t3.totalSorts, - t3.totalBulkSorts, - t3.totalSingleCells, - t3.totalLibraries, - t3.totalLibrariesWithData, - t3.totalLibrariesWithBulkData, - t3.totalLibrariesWithEnrichedData, - t3.librariesComplete, - t3.sequencingComplete, - CASE - WHEN (t3.librariesComplete = TRUE AND t3.sequencingComplete = TRUE) THEN TRUE - ELSE FALSE - END as isComplete - -FROM ( -SELECT - t2.sortPlateId, - t2.container, - t2.workbook, - t2.subjects, - t2.stims, - t2.sampleDates, - t2.totalSorts, - t2.totalBulkSorts, - t2.totalSingleCells, - t2.totalLibraries, - t2.totalLibrariesWithData, - t2.totalLibrariesWithBulkData, - t2.totalLibrariesWithEnrichedData, - CASE WHEN t2.totalSorts - t2.totalLibraries <= 0 THEN true ELSE false END as librariesComplete, - CASE - WHEN (t2.processingRequested LIKE '%Whole Transcriptome%' AND t2.totalSorts - t2.totalLibrariesWithBulkData > 0) THEN FALSE - WHEN (t2.processingRequested LIKE '%Enriched%' AND t2.totalSorts - t2.totalLibrariesWithEnrichedData > 0) THEN FALSE - WHEN (t2.totalSorts - t2.totalLibrariesWithData > 0) THEN FALSE - ELSE TRUE - END as sequencingComplete, - CASE - WHEN (t2.totalBulkSorts > 0 AND t2.totalSingleCells > 0) THEN 'MIXED' - WHEN (t2.totalBulkSorts > 0) THEN 'BULK' - WHEN (t2.totalSingleCells > 0) THEN 'SINGLE' - END as sortType, - t2.processingRequested -FROM ( -SELECT - t.plateId as sortPlateId, - t.totalSorts, - t.totalBulkSorts, - t.totalSingleCells, - t.subjects, - t.stims, - t.sampleDates, - t.container, - t.workbook, - t.processingRequested, - (SELECT count(*) as expr from singlecell.cdna_libraries c1 WHERE c1.sortId.plateId = t.plateId) as totalLibraries, - (SELECT count(*) as expr from singlecell.cdna_libraries c2 WHERE c2.sortId.plateId = t.plateId AND c2.hasReadsetWithData = true) as totalLibrariesWithData, - (SELECT count(*) as expr from singlecell.cdna_libraries c3 WHERE c3.sortId.plateId = t.plateId AND c3.readsetId.totalFiles > 0) as totalLibrariesWithBulkData, - (SELECT count(*) as expr from singlecell.cdna_libraries c4 WHERE c4.sortId.plateId = t.plateId AND c4.tcrReadsetId.totalFiles > 0) as totalLibrariesWithEnrichedData, - (SELECT group_concat(distinct c3.plateId, chr(10)) as expr from singlecell.cdna_libraries c3 WHERE c3.sortId.plateId = t.plateId) as libraryPlates - -FROM ( - SELECT - s.plateId, - s.container, - s.workbook, - count(*) AS totalSorts, - SUM(CASE WHEN s.cells > 1 THEN 1 ELSE 0 END) AS totalBulkSorts, - SUM(CASE WHEN s.cells = 1 THEN 1 ELSE 0 END) AS totalSingleCells, - group_concat(distinct s.sampleId.subjectId) as subjects, - group_concat(distinct s.sampleId.stim) as stims, - group_concat(distinct ((year(s.sampleId.sampledate) || '-' || month(s.sampleId.sampledate) || '-' || dayofmonth(s.sampleId.sampledate)))) as sampleDates, - group_concat(distinct s.processingRequested) as processingRequested - - FROM singlecell.sorts s - GROUP BY s.plateId, s.container, s.workbook - -) t -) t2 -) t3 \ No newline at end of file diff --git a/singlecell/resources/queries/singlecell/sortStatusByPlate/.qview.xml b/singlecell/resources/queries/singlecell/sortStatusByPlate/.qview.xml deleted file mode 100644 index 366339a29..000000000 --- a/singlecell/resources/queries/singlecell/sortStatusByPlate/.qview.xml +++ /dev/null @@ -1,6 +0,0 @@ - - - - - - \ No newline at end of file diff --git a/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.query.xml b/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.query.xml deleted file mode 100644 index 277aa4298..000000000 --- a/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.query.xml +++ /dev/null @@ -1,21 +0,0 @@ - - - - - TCR Status By Plate - - - true - /query/executeQuery.view?schemaName=singlecell&query.queryName=sorts&query.plateId~eq=${plateId} - - - true - - - Plate Complete - - -
- - - \ No newline at end of file diff --git a/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.sql b/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.sql deleted file mode 100644 index e7bca2ffb..000000000 --- a/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample.sql +++ /dev/null @@ -1,72 +0,0 @@ -SELECT - t3.sortPlateId, - t3.container, - t3.workbook, - t3.sortType, - t3.subjectId, - t3.stim, - t3.sampledate, - t3.totalSorts, - t3.totalBulkSorts, - t3.totalSingleCells, - t3.totalLibraries, - t3.totalLibrariesWithData, - t3.totalLibrariesWithBulkData, - t3.totalLibrariesWithEnrichedData, - t3.librariesComplete - -FROM ( -SELECT - t2.sortPlateId, - t2.container, - t2.workbook, - t2.subjectId, - t2.stim, - t2.sampledate, - t2.totalSorts, - t2.totalBulkSorts, - t2.totalSingleCells, - t2.totalLibraries, - t2.totalLibrariesWithData, - t2.totalLibrariesWithBulkData, - t2.totalLibrariesWithEnrichedData, - CASE WHEN t2.totalSorts - t2.totalLibraries <= 0 THEN true ELSE false END as librariesComplete, - CASE - WHEN (t2.totalBulkSorts > 0 AND t2.totalSingleCells > 0) THEN 'MIXED' - WHEN (t2.totalBulkSorts > 0) THEN 'BULK' - WHEN (t2.totalSingleCells > 0) THEN 'SINGLE' - END as sortType -FROM ( -SELECT - t.plateId as sortPlateId, - t.totalSorts, - t.totalBulkSorts, - t.totalSingleCells, - t.subjectId, - t.stim, - t.sampledate, - t.container, - t.workbook, - (SELECT count(*) as expr from singlecell.cdna_libraries c1 WHERE c1.sortId.plateId = t.plateId) as totalLibraries, - (SELECT count(*) as expr from singlecell.cdna_libraries c2 WHERE c2.sortId.plateId = t.plateId AND c2.hasReadsetWithData = true) as totalLibrariesWithData, - (SELECT count(*) as expr from singlecell.cdna_libraries c3 WHERE c3.sortId.plateId = t.plateId AND c3.readsetId.totalFiles > 0) as totalLibrariesWithBulkData, - (SELECT count(*) as expr from singlecell.cdna_libraries c4 WHERE c4.sortId.plateId = t.plateId AND c4.tcrReadsetId.totalFiles > 0) as totalLibrariesWithEnrichedData, - (SELECT group_concat(distinct c3.plateId, chr(10)) as expr from singlecell.cdna_libraries c3 WHERE c3.sortId.plateId = t.plateId) as libraryPlates - -FROM ( - SELECT - s.plateId, - s.container, - s.workbook, - s.sampleId.subjectId, - s.sampleId.stim, - s.sampleId.sampledate, - count(*) AS totalSorts, - SUM(CASE WHEN s.cells > 1 THEN 1 ELSE 0 END) AS totalBulkSorts, - SUM(CASE WHEN s.cells = 1 THEN 1 ELSE 0 END) AS totalSingleCells - FROM singlecell.sorts s - GROUP BY s.plateId, s.container, s.workbook, s.sampleId.subjectId, s.sampleId.stim, s.sampleId.sampledate - -) t -) t2 -) t3 \ No newline at end of file diff --git a/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample/.qview.xml b/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample/.qview.xml deleted file mode 100644 index 094827e09..000000000 --- a/singlecell/resources/queries/singlecell/sortStatusByPlateAndSample/.qview.xml +++ /dev/null @@ -1,7 +0,0 @@ - - - - - - - \ No newline at end of file diff --git a/singlecell/resources/queries/singlecell/sorts/.qview.xml b/singlecell/resources/queries/singlecell/sorts/.qview.xml index 717769530..862b448bf 100644 --- a/singlecell/resources/queries/singlecell/sorts/.qview.xml +++ b/singlecell/resources/queries/singlecell/sorts/.qview.xml @@ -17,7 +17,6 @@ - From bef32e48a46679c7cf04da002e4f9d3eaacfe90b Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 3 Sep 2024 14:07:01 -0700 Subject: [PATCH 07/21] Query syntax --- .../queries/sequenceanalysis/outputfile_categories.sql | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/SequenceAnalysis/resources/queries/sequenceanalysis/outputfile_categories.sql b/SequenceAnalysis/resources/queries/sequenceanalysis/outputfile_categories.sql index 7d3a92354..fc0ae1118 100644 --- a/SequenceAnalysis/resources/queries/sequenceanalysis/outputfile_categories.sql +++ b/SequenceAnalysis/resources/queries/sequenceanalysis/outputfile_categories.sql @@ -9,19 +9,19 @@ FROM sequenceanalysis.outputfiles UNION ALL -SELECT 'VCF File' +SELECT 'VCF File' as category UNION ALL -SELECT 'BAM File' +SELECT 'BAM File' as category UNION ALL -SELECT 'BED File' +SELECT 'BED File' as category UNION ALL -SELECT 'gVCF File' +SELECT 'gVCF File' as category ) t From 9d7c18c3870492ec86f051f189689831e7f0f9fd Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 3 Sep 2024 17:02:28 -0700 Subject: [PATCH 08/21] Support native-pair-hmm-threads for HaplotypeCaller --- .../sequenceanalysis/run/util/HaplotypeCallerWrapper.java | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/HaplotypeCallerWrapper.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/HaplotypeCallerWrapper.java index 3f011aa14..56188bf18 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/HaplotypeCallerWrapper.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/util/HaplotypeCallerWrapper.java @@ -4,6 +4,7 @@ import org.apache.logging.log4j.Logger; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.pipeline.SamtoolsIndexer; +import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; import org.labkey.api.sequenceanalysis.run.AbstractGatk4Wrapper; import org.labkey.sequenceanalysis.pipeline.ReblockGvcfHandler; import org.labkey.sequenceanalysis.util.SequenceUtil; @@ -58,6 +59,13 @@ public void execute(File inputBamOrCram, File referenceFasta, File outputFile, L args.addAll(options); } + Integer maxThreads = SequencePipelineService.get().getMaxThreads(getLogger()); + if (maxThreads != null) + { + args.add("--native-pair-hmm-threads"); + args.add(maxThreads.toString()); + } + args.add("-ERC"); args.add("GVCF"); From 8377f37d8794eb00f3c283a17a7e45cf45cfc3b2 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 6 Sep 2024 16:51:43 -0700 Subject: [PATCH 09/21] Increase logging --- .../labkey/sequenceanalysis/run/RestoreSraDataHandler.java | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java index 4fd234370..d25ca0c82 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/RestoreSraDataHandler.java @@ -26,6 +26,7 @@ import org.labkey.api.query.InvalidKeyException; import org.labkey.api.query.QueryService; import org.labkey.api.query.QueryUpdateServiceException; +import org.labkey.api.sequenceanalysis.SequenceAnalysisService; import org.labkey.api.sequenceanalysis.SequenceOutputFile; import org.labkey.api.sequenceanalysis.model.ReadData; import org.labkey.api.sequenceanalysis.model.Readset; @@ -271,7 +272,7 @@ private Map getCachedReadCounts(SequenceAnalysisJobSupport supp @Override public void complete(PipelineJob job, List readsets, List outputsCreated) throws PipelineJobException { - Readset rs = readsets.get(0); + Readset rs = SequenceAnalysisService.get().getReadset(readsets.get(0).getRowId(), job.getUser()); List> rows = new ArrayList<>(); for (ReadData rd : rs.getReadData()) @@ -341,6 +342,7 @@ public void complete(PipelineJob job, List readsets, List Date: Sat, 7 Sep 2024 16:35:20 -0700 Subject: [PATCH 10/21] Update samtools version --- .../pipeline_code/sequence_tools_install.sh | 22 +++++++++---------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/SequenceAnalysis/pipeline_code/sequence_tools_install.sh b/SequenceAnalysis/pipeline_code/sequence_tools_install.sh index 9333860c7..be6ba226c 100755 --- a/SequenceAnalysis/pipeline_code/sequence_tools_install.sh +++ b/SequenceAnalysis/pipeline_code/sequence_tools_install.sh @@ -457,12 +457,12 @@ then rm -Rf $LKTOOLS_DIR/samtools rm -Rf $LKTOOLS_DIR/bcftools - wget $WGET_OPTS https://github.com/samtools/samtools/releases/download/1.16.1/samtools-1.16.1.tar.bz2 - bunzip2 samtools-1.16.1.tar.bz2 - tar -xf samtools-1.16.1.tar + wget $WGET_OPTS https://github.com/samtools/samtools/releases/download/1.20/samtools-1.20.tar.bz2 + bunzip2 samtools-1.20.tar.bz2 + tar -xf samtools-1.20.tar echo "Compressing TAR" - bzip2 samtools-1.16.1.tar - cd samtools-1.16.1 + bzip2 samtools-1.20.tar + cd samtools-1.20 ./configure make install ./samtools ${LKTOOLS_DIR}/samtools @@ -519,13 +519,13 @@ then rm -Rf $LKTOOLS_DIR/tabix rm -Rf $LKTOOLS_DIR/bgzip - wget $WGET_OPTS https://github.com/samtools/htslib/releases/download/1.16/htslib-1.16.tar.bz2 - bunzip2 htslib-1.16.tar.bz2 - tar -xf htslib-1.16.tar + wget $WGET_OPTS https://github.com/samtools/htslib/releases/download/1.20/htslib-1.20.tar.bz2 + bunzip2 htslib-1.20.tar.bz2 + tar -xf htslib-1.20.tar echo "Compressing TAR" - bzip2 htslib-1.16.tar - chmod 755 htslib-1.16 - cd htslib-1.16 + bzip2 htslib-1.20.tar + chmod 755 htslib-1.20 + cd htslib-1.20 ./configure make From 74cc872039f3bd58a0909218534f89756ec0c448 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 8 Sep 2024 11:01:38 -0700 Subject: [PATCH 11/21] Update JBrowse version --- jbrowse/package-lock.json | 7238 +++++++++++++++++++++---------------- jbrowse/package.json | 12 +- 2 files changed, 4113 insertions(+), 3137 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 026db4de0..813a8e263 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -9,14 +9,14 @@ "version": "1.0.0", "dependencies": { "@gmod/vcf": "^5.0.10", - "@jbrowse/core": "^2.10.3", - "@jbrowse/plugin-linear-genome-view": "^2.10.3", - "@jbrowse/plugin-svg": "^2.10.3", - "@jbrowse/plugin-variants": "^2.10.3", - "@jbrowse/react-linear-genome-view": "^2.10.3", + "@jbrowse/core": "^2.14.0", + "@jbrowse/plugin-linear-genome-view": "^2.14.0", + "@jbrowse/plugin-svg": "^2.14.0", + "@jbrowse/plugin-variants": "^2.14.0", + 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"node_modules/webpack-bundle-analyzer/node_modules/ws": { "version": "7.5.10", "resolved": "https://registry.npmjs.org/ws/-/ws-7.5.10.tgz", @@ -18339,9 +19305,9 @@ } }, "node_modules/webpack-dev-server": { - "version": "4.15.1", - "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-4.15.1.tgz", - "integrity": "sha512-5hbAst3h3C3L8w6W4P96L5vaV0PxSmJhxZvWKYIdgxOQm8pNZ5dEOmmSLBVpP85ReeyRt6AS1QJNyo/oFFPeVA==", + "version": "4.15.2", + "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-4.15.2.tgz", + "integrity": "sha512-0XavAZbNJ5sDrCbkpWL8mia0o5WPOd2YGtxrEiZkBK9FjLppIUK2TgxK6qGD2P3hUXTJNNPVibrerKcx5WkR1g==", "dev": true, "dependencies": { "@types/bonjour": "^3.5.9", @@ -18372,7 +19338,7 @@ "serve-index": "^1.9.1", "sockjs": "^0.3.24", "spdy": "^4.0.2", - "webpack-dev-middleware": "^5.3.1", + "webpack-dev-middleware": "^5.3.4", "ws": "^8.13.0" }, "bin": { @@ -18568,29 +19534,32 @@ } }, "node_modules/which-collection": { - "version": 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+19789,14 @@ "node": ">=12" } }, + "node_modules/yargs/node_modules/yargs-parser": { + "version": "20.2.9", + "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz", + "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==", + "engines": { + "node": ">=10" + } + }, "node_modules/yocto-queue": { "version": "0.1.0", "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", diff --git a/jbrowse/package.json b/jbrowse/package.json index 7d4edd869..92ed737c4 100644 --- a/jbrowse/package.json +++ b/jbrowse/package.json @@ -16,14 +16,14 @@ }, "dependencies": { "@gmod/vcf": "^5.0.10", - "@jbrowse/core": "^2.10.3", - "@jbrowse/plugin-linear-genome-view": "^2.10.3", - "@jbrowse/plugin-svg": "^2.10.3", - "@jbrowse/plugin-variants": "^2.10.3", - "@jbrowse/react-linear-genome-view": "^2.10.3", + "@jbrowse/core": "^2.14.0", + "@jbrowse/plugin-linear-genome-view": "^2.14.0", + "@jbrowse/plugin-svg": "^2.14.0", + "@jbrowse/plugin-variants": "^2.14.0", + "@jbrowse/react-linear-genome-view": "^2.14.0", "@labkey/api": "^1.25.0", "@labkey/components": "^2.0.0", - "@mui/x-data-grid": "^6.0.1", + "@mui/x-data-grid": "^7.0.0", "assert": "^2.0.0", "browserify-zlib": "^0.2.0", "buffer": "^6.0.3", From 65ad49d529bffb6b7cb8261e6d3d6418582b8632 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 8 Sep 2024 12:50:41 -0700 Subject: [PATCH 12/21] Update JBrowse version and React --- jbrowse/package-lock.json | 16922 +++++----------- jbrowse/package.json | 42 +- jbrowse/src/client/JBrowse/Browser/dev.tsx | 14 +- .../ExtendedVariantAdapter/VcfTabixAdapter.ts | 5 +- .../src/client/JBrowse/Search/webpart/dev.tsx | 14 +- .../components/ErrorBoundary.tsx | 11 +- .../src/client/JBrowse/VariantSearch/dev.tsx | 14 +- .../JBrowse/VariantTable/VariantTable.tsx | 3 +- .../src/client/JBrowse/VariantTable/dev.tsx | 14 +- jbrowse/src/client/JBrowse/utils.ts | 3 +- jbrowse/src/client/test/jest.setup.ts | 5 - jbrowse/src/client/test/styleMock.ts | 1 - 12 files changed, 5392 insertions(+), 11656 deletions(-) delete mode 100644 jbrowse/src/client/test/jest.setup.ts delete mode 100644 jbrowse/src/client/test/styleMock.ts diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 813a8e263..2a58e8290 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -9,14 +9,15 @@ "version": "1.0.0", "dependencies": { "@gmod/vcf": "^5.0.10", - "@jbrowse/core": "^2.14.0", - "@jbrowse/plugin-linear-genome-view": "^2.14.0", - "@jbrowse/plugin-svg": "^2.14.0", - "@jbrowse/plugin-variants": "^2.14.0", - "@jbrowse/react-linear-genome-view": "^2.14.0", - "@labkey/api": "^1.25.0", - "@labkey/components": "^2.0.0", + "@jbrowse/core": "2.15.0", + "@jbrowse/plugin-linear-genome-view": "2.15.0", + "@jbrowse/plugin-svg": "2.15.0", + "@jbrowse/plugin-variants": "2.15.0", + "@jbrowse/react-linear-genome-view": "2.15.0", + "@labkey/api": "^1.35.0", + "@labkey/components": "^5.0.0", "@mui/x-data-grid": "^7.0.0", + "@yao-pkg/pkg": "^5.12.0", "assert": "^2.0.0", "browserify-zlib": "^0.2.0", "buffer": "^6.0.3", @@ -27,32 +28,26 @@ "jspdf-autotable": "^3.5.31", "node-polyfill-webpack-plugin": "2.0.1", "path-browserify": "^1.0.1", - "pkg": "^5.8.1", - "react-data-grid": "7.0.0-beta.10", + "react": "^18.0.0", + "react-data-grid": "7.0.0-beta.46", + "react-dom": "^18.0.0", "react-google-charts": "^4.0.1", - "react-hot-loader": "^4.13.1", - "react-select": "^5.7.4", + "react-select": "^5.8.0", "regenerator-runtime": "^0.13.11", "stream-browserify": "^3.0.0", - "typescript": "^5.1.6", "util": "^0.12.5", "uuid": "^9.0.0", "vm-browserify": "^1.1.2" }, "devDependencies": { - "@labkey/build": "6.16.0", - "@types/jest": "^29.0.0", + "@labkey/build": "7.6.0", "@types/jexl": "^2.3.1", "@types/jquery": "^3.0.0", "@types/node": "^18.17.1", - "@wojtekmaj/enzyme-adapter-react-17": "^0.8.0", - "enzyme": "^3.11.0", - "jest": "^29.0.0", - "jest-cli": "^29.0.0", - 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"dev": true, - "dependencies": { - "imurmurhash": "^0.1.4", - "signal-exit": "^3.0.7" - }, - "engines": { - "node": "^12.13.0 || ^14.15.0 || >=16.0.0" - } + "license": "ISC" }, "node_modules/ws": { "version": "8.18.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.0.tgz", - "integrity": "sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw==", "dev": true, + "license": "MIT", "engines": { "node": ">=10.0.0" }, @@ -19710,25 +13540,9 @@ } } }, - "node_modules/xml-name-validator": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/xml-name-validator/-/xml-name-validator-4.0.0.tgz", - "integrity": "sha512-ICP2e+jsHvAj2E2lIHxa5tjXRlKDJo4IdvPvCXbXQGdzSfmSpNVyIKMvoZHjDY9DP0zV17iI85o90vRFXNccRw==", - "dev": true, - "engines": { - "node": ">=12" - } - }, - "node_modules/xmlchars": { - "version": "2.2.0", - "resolved": "https://registry.npmjs.org/xmlchars/-/xmlchars-2.2.0.tgz", - "integrity": "sha512-JZnDKK8B0RCDw84FNdDAIpZK+JuJw+s7Lz8nksI7SIuU3UXJJslUthsi+uWBUYOwPFwW7W7PRLRfUKpxjtjFCw==", - "dev": true - }, "node_modules/xtend": { "version": "4.0.2", - "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz", - "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ==", + "license": "MIT", "engines": { "node": ">=0.4" } @@ -19743,30 +13557,26 @@ }, "node_modules/y18n": { "version": "5.0.8", - "resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", - "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", + "license": "ISC", "engines": { "node": ">=10" } }, "node_modules/yallist": { "version": "3.1.1", - "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", - "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", - "dev": true + "dev": true, + "license": "ISC" }, "node_modules/yaml": { "version": "1.10.2", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.2.tgz", - "integrity": "sha512-r3vXyErRCYJ7wg28yvBY5VSoAF8ZvlcW9/BwUzEtUsjvX/DKs24dIkuwjtuprwJJHsbyUbLApepYTR1BN4uHrg==", + "license": "ISC", "engines": { "node": ">= 6" } }, "node_modules/yargs": { "version": "16.2.0", - "resolved": "https://registry.npmjs.org/yargs/-/yargs-16.2.0.tgz", - "integrity": "sha512-D1mvvtDG0L5ft/jGWkLpG1+m0eQxOfaBvTNELraWj22wSVUMWxZUvYgJYcKh6jGGIkJFhH4IZPQhR4TKpc8mBw==", + "license": "MIT", "dependencies": { "cliui": "^7.0.2", "escalade": "^3.1.1", @@ -19780,33 +13590,11 @@ "node": ">=10" } }, - "node_modules/yargs-parser": { - "version": "21.1.1", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", - "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", - "dev": true, - "engines": { - "node": ">=12" - } - }, "node_modules/yargs/node_modules/yargs-parser": { "version": "20.2.9", - "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-20.2.9.tgz", - "integrity": "sha512-y11nGElTIV+CT3Zv9t7VKl+Q3hTQoT9a1Qzezhhl6Rp21gJ/IVTW7Z3y9EWXhuUBC2Shnf+DX0antecpAwSP8w==", - "engines": { - "node": ">=10" - } - }, - "node_modules/yocto-queue": { - "version": "0.1.0", - "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", - "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", - "dev": true, + "license": "ISC", "engines": { "node": ">=10" - }, - "funding": { - "url": "https://github.com/sponsors/sindresorhus" } } } diff --git a/jbrowse/package.json b/jbrowse/package.json index 92ed737c4..4a0e49717 100644 --- a/jbrowse/package.json +++ b/jbrowse/package.json @@ -5,25 +5,25 @@ "scripts": { "setup": "npm ci", "build": "npm run build-dev", - "start": "cross-env NODE_ENV=development webpack-dev-server --config ./config/watch.config.js", + "start": "cross-env NODE_ENV=development webpack serve --config ./config/watch.config.js", "build-no-pkg": "npm run clean && cross-env NODE_ENV=development webpack --config ./config/dev.config.js --progress --profile", "build-dev": "npm run build-no-pkg", "build-prod": "npm run clean && cross-env NODE_ENV=production PROD_SOURCE_MAP=source-map webpack --config ./config/prod.config.js --progress --profile", - "clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen && rimraf resources/views/browser*", - "test": "cross-env NODE_ENV=test jest", + "clean": "rimraf resources/web/gen && rimraf resources/web/jbrowse/gen && rimraf resources/views/gen", "prepareCli": "rimraf ./buildCli && rimraf ./resources/external/jb-cli && npm install @jbrowse/cli@1.7.4 --prefix ./buildCli", "jb-pkg": "npm run prepareCli && npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli && rimraf ./buildCli" }, "dependencies": { "@gmod/vcf": "^5.0.10", - "@jbrowse/core": "^2.14.0", - "@jbrowse/plugin-linear-genome-view": "^2.14.0", - "@jbrowse/plugin-svg": "^2.14.0", - "@jbrowse/plugin-variants": "^2.14.0", - "@jbrowse/react-linear-genome-view": "^2.14.0", - "@labkey/api": "^1.25.0", - "@labkey/components": "^2.0.0", + "@jbrowse/core": "2.15.0", + "@jbrowse/plugin-linear-genome-view": "2.15.0", + "@jbrowse/plugin-svg": "2.15.0", + "@jbrowse/plugin-variants": "2.15.0", + "@jbrowse/react-linear-genome-view": "2.15.0", + "@labkey/api": "^1.35.0", + "@labkey/components": "^5.0.0", "@mui/x-data-grid": "^7.0.0", + "@yao-pkg/pkg": "^5.12.0", "assert": "^2.0.0", "browserify-zlib": "^0.2.0", "buffer": "^6.0.3", @@ -34,31 +34,25 @@ "jspdf-autotable": "^3.5.31", "node-polyfill-webpack-plugin": "2.0.1", "path-browserify": "^1.0.1", - "pkg": "^5.8.1", - "react-data-grid": "7.0.0-beta.10", + "react": "^18.0.0", + "react-data-grid": "7.0.0-beta.46", + "react-dom": "^18.0.0", "react-google-charts": "^4.0.1", - "react-hot-loader": "^4.13.1", - "react-select": "^5.7.4", + "react-select": "^5.8.0", "regenerator-runtime": "^0.13.11", "stream-browserify": "^3.0.0", - "typescript": "^5.1.6", "util": "^0.12.5", "uuid": "^9.0.0", "vm-browserify": "^1.1.2" }, "devDependencies": { - "@labkey/build": "6.16.0", - "@types/jest": "^29.0.0", + "@labkey/build": "7.6.0", "@types/jexl": "^2.3.1", "@types/jquery": "^3.0.0", "@types/node": "^18.17.1", - "@wojtekmaj/enzyme-adapter-react-17": "^0.8.0", - "enzyme": "^3.11.0", - "jest": "^29.0.0", - "jest-cli": "^29.0.0", - "jest-environment-jsdom": "^29.7.0", - "jest-mock": "^29.0.0", + "@types/react": "^18.0.0", + "@types/react-dom": "^18.0.0", "rimraf": "^3.0.2", - "ts-jest": "^29.0.0" + "typescript": "^5.0.0" } } diff --git a/jbrowse/src/client/JBrowse/Browser/dev.tsx b/jbrowse/src/client/JBrowse/Browser/dev.tsx index 9b0910c8c..c622a6c88 100644 --- a/jbrowse/src/client/JBrowse/Browser/dev.tsx +++ b/jbrowse/src/client/JBrowse/Browser/dev.tsx @@ -1,22 +1,10 @@ import React from 'react'; import ReactDOM from 'react-dom'; -import { AppContainer } from 'react-hot-loader'; import View from './Browser'; const render = () => { - ReactDOM.render( - - - , - document.getElementById('app') - ) + ReactDOM.render(, document.getElementById('app')); }; -declare const module: any; - -if (module.hot) { - module.hot.accept(); -} - render(); \ No newline at end of file diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts index 42ad2aefb..31d3d9e84 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/ExtendedVariantAdapter/VcfTabixAdapter.ts @@ -10,7 +10,7 @@ import { TabixIndexedFile } from '@gmod/tabix' import VcfParser from '@gmod/vcf' import { VcfFeature } from '@jbrowse/plugin-variants'; -export default class extends BaseFeatureDataAdapter { +export default class VcfTabixAdapter extends BaseFeatureDataAdapter { private configured?: Promise<{ vcf: TabixIndexedFile parser: VcfParser @@ -28,8 +28,7 @@ export default class extends BaseFeatureDataAdapter { filehandle, csiFilehandle: isCSI ? openLocation(location, pm) : undefined, tbiFilehandle: !isCSI ? openLocation(location, pm) : undefined, - chunkCacheSize: 50 * 2 ** 20, - chunkSizeLimit: 1000000000, + chunkCacheSize: 50 * 2 ** 20 }) const header = await vcf.getHeader() diff --git a/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx b/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx index 294d559f6..5ce2a10cb 100644 --- a/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx +++ b/jbrowse/src/client/JBrowse/Search/webpart/dev.tsx @@ -1,17 +1,11 @@ import React from 'react'; import ReactDOM from 'react-dom'; -import { AppContainer } from 'react-hot-loader'; import { App } from '@labkey/api'; import StandaloneSearch from '../StandaloneSearch'; -App.registerApp('jbrowseSearchWebpart', (target: string, sessionId: string) => { - ReactDOM.render( - - - , - document.getElementById(target) - ); -}, true /* hot */); +const render = (target: string, sessionId: string) => { + ReactDOM.render(, document.getElementById(target)); +}; -declare const module: any; +App.registerApp('jbrowseSearchWebpart', render, true /* hot */); \ No newline at end of file diff --git a/jbrowse/src/client/JBrowse/VariantSearch/components/ErrorBoundary.tsx b/jbrowse/src/client/JBrowse/VariantSearch/components/ErrorBoundary.tsx index 188b01863..11f4bed1b 100644 --- a/jbrowse/src/client/JBrowse/VariantSearch/components/ErrorBoundary.tsx +++ b/jbrowse/src/client/JBrowse/VariantSearch/components/ErrorBoundary.tsx @@ -5,12 +5,12 @@ import ErrorPage from './ErrorPage'; interface ErrorBoundaryState { error: Error | undefined; - errorInfo: ErrorInfo | undefined; + errorInfo?: ErrorInfo | undefined; stackTrace: string | undefined; - devMode: boolean | undefined, + devMode?: boolean | undefined, } -export class ErrorBoundary extends React.PureComponent<{}, ErrorBoundaryState> { +export class ErrorBoundary extends React.Component { constructor(props) { super(props); @@ -30,14 +30,15 @@ export class ErrorBoundary extends React.PureComponent<{}, ErrorBoundaryState> { this.setState(() => ({ error, errorInfo, - stackTrace: error?.stack ? error.stack : undefined, + stackTrace: error?.stack ? error.stack : undefined })); if (Mothership) { // process stack trace against available source maps Mothership.processStackTrace(error, stackTrace => { this.setState(state => ({ - stackTrace: stackTrace || state.stackTrace, + error: error, + stackTrace: stackTrace || state.stackTrace })); }); diff --git a/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx b/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx index 2cf42ec89..daaefc0e5 100644 --- a/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx +++ b/jbrowse/src/client/JBrowse/VariantSearch/dev.tsx @@ -1,22 +1,10 @@ import React from 'react'; import ReactDOM from 'react-dom'; -import { AppContainer } from 'react-hot-loader'; import VariantTable from './VariantTable'; const render = () => { - ReactDOM.render( - - - , - document.getElementById('app') - ) + ReactDOM.render(, document.getElementById('app')); }; -declare const module: any; - -if (module.hot) { - module.hot.accept(); -} - render(); \ No newline at end of file diff --git a/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx b/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx index 102194a37..f9f9b0b4d 100644 --- a/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx +++ b/jbrowse/src/client/JBrowse/VariantTable/VariantTable.tsx @@ -14,6 +14,7 @@ import LoadingIndicator from './components/LoadingIndicator'; import JBrowseFilterPanel from '../Browser/components/JBrowseFilterPanel'; import { ErrorBoundary } from '../VariantSearch/components/ErrorBoundary'; import { Assembly } from '@jbrowse/core/assemblyManager/assembly'; +import { Theme } from 'react-select'; const nativePlugins = [ExtendedVariantPlugin, LogSession]; @@ -34,7 +35,7 @@ function VariantTable() { const [session, setSession] = useState(null); const [state, setState] = useState(null); - const [theme, setTheme] = useState(null); + const [theme, setTheme] = useState>(null); const [view, setView] = useState(null); const [parsedLocString, setParsedLocString] = useState(null) const [pluginManager, setPluginManager] = useState(null); diff --git a/jbrowse/src/client/JBrowse/VariantTable/dev.tsx b/jbrowse/src/client/JBrowse/VariantTable/dev.tsx index 2cf42ec89..daaefc0e5 100644 --- a/jbrowse/src/client/JBrowse/VariantTable/dev.tsx +++ b/jbrowse/src/client/JBrowse/VariantTable/dev.tsx @@ -1,22 +1,10 @@ import React from 'react'; import ReactDOM from 'react-dom'; -import { AppContainer } from 'react-hot-loader'; import VariantTable from './VariantTable'; const render = () => { - ReactDOM.render( - - - , - document.getElementById('app') - ) + ReactDOM.render(, document.getElementById('app')); }; -declare const module: any; - -if (module.hot) { - module.hot.accept(); -} - render(); \ No newline at end of file diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts index 32d514cab..39c522df8 100644 --- a/jbrowse/src/client/JBrowse/utils.ts +++ b/jbrowse/src/client/JBrowse/utils.ts @@ -6,6 +6,7 @@ import { getGridNumericOperators, GridCellParams, GridColDef, + GridColType, GridComparatorFn, GridFilterItem, GridFilterOperator @@ -506,7 +507,7 @@ export class FieldModel { return this.label ?? this.name } - getMuiType(): string { + getMuiType(): GridColType { let muiFieldType; switch (this.type) { diff --git a/jbrowse/src/client/test/jest.setup.ts b/jbrowse/src/client/test/jest.setup.ts deleted file mode 100644 index 4e411593c..000000000 --- a/jbrowse/src/client/test/jest.setup.ts +++ /dev/null @@ -1,5 +0,0 @@ -import 'regenerator-runtime/runtime'; -import { configure } from 'enzyme'; -import Adapter from '@wojtekmaj/enzyme-adapter-react-17'; - -configure({ adapter: new Adapter() }); \ No newline at end of file diff --git a/jbrowse/src/client/test/styleMock.ts b/jbrowse/src/client/test/styleMock.ts deleted file mode 100644 index 7c6d6c73d..000000000 --- a/jbrowse/src/client/test/styleMock.ts +++ /dev/null @@ -1 +0,0 @@ -module.exports = {} \ No newline at end of file From 0cf0b52eea22575a2519c0102ee7fe69d5e41837 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 8 Sep 2024 15:01:39 -0700 Subject: [PATCH 13/21] JBrowseTest fix --- .../test/tests/external/labModules/JBrowseTestHelper.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java index 5e539f064..596d64e9d 100644 --- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java +++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTestHelper.java @@ -156,7 +156,7 @@ public static By getVariantWithinTrack(BaseWebDriverTest test, String trackId, S public static void waitForJBrowseToLoad(BaseWebDriverTest test) { test.waitForElementToDisappear(Locator.tagWithText("p", "Loading...")); //the initial message before getSession - test.waitForElement(Locator.tagWithClass("span", "MuiTouchRipple-root").notHidden()); //this is the top-left icon + test.waitForElement(Locator.tagWithAttribute("svg", "data-testid", "MenuIcon")); //this is the top-left icon test.waitForElement(Locator.tagWithAttribute("button", "title", "close this track").notHidden()); test.waitForElement(Locator.tagWithClassContaining("button", "MuiButtonBase-root").notHidden(), WebDriverWrapper.WAIT_FOR_PAGE); //this is the icon from the track label From 2efd673374cafc5004c4f24169e3d846753eb1db Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 8 Sep 2024 16:03:17 -0700 Subject: [PATCH 14/21] JBrowseTest fix --- jbrowse/src/client/JBrowse/utils.ts | 4 ++-- .../test/tests/external/labModules/JBrowseTest.java | 8 ++++---- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/jbrowse/src/client/JBrowse/utils.ts b/jbrowse/src/client/JBrowse/utils.ts index 39c522df8..de51e775e 100644 --- a/jbrowse/src/client/JBrowse/utils.ts +++ b/jbrowse/src/client/JBrowse/utils.ts @@ -710,8 +710,8 @@ export const multiModalOperator = (operator: GridFilterOperator) => { return innerFilterFn; } - return (params: GridCellParams) => { - let cellValue = parseCellValue(params.value) + return (value) => { + let cellValue = parseCellValue(value) switch(filterItem.operator) { case "!=": diff --git a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java index 948810736..b3f7219bb 100644 --- a/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java +++ b/jbrowse/test/src/org/labkey/test/tests/external/labModules/JBrowseTest.java @@ -1431,8 +1431,8 @@ private void testVariantDataGrid() throws Exception // Test filtering waitAndClick(Locator.tagWithAttributeContaining("button", "aria-label", "Show filters")); - waitAndClick(Locator.tagWithClass("select", "MuiNativeSelect-select").notHidden().withChild(Locator.tagWithText("option", "Chromosome"))); - waitAndClick(Locator.tagWithAttributeContaining("option", "value", "ref")); + waitAndClick(Locator.tagWithClass("div", "MuiSelect-select").notHidden().withText("Chromosome")); + waitAndClick(Locator.tagWithAttributeContaining("li", "data-value", "ref")); Locator valueSelector = Locator.tagWithAttributeContaining("input", "placeholder", "Filter value"); waitAndClick(valueSelector); @@ -1570,8 +1570,8 @@ private void testVariantTableComparators() throws Exception { // Test filtering AF with wrapped comparators waitAndClick(Locator.tagWithAttributeContaining("button", "aria-label", "Show filters")); - waitAndClick(Locator.tagWithClass("select", "MuiNativeSelect-select").notHidden().withChild(Locator.tagWithText("option", "Chromosome"))); - waitAndClick(Locator.tagWithAttributeContaining("option", "value", "AF")); + waitAndClick(Locator.tagWithClass("div", "MuiSelect-select").notHidden().withText("Chromosome")); + waitAndClick(Locator.tagWithAttributeContaining("li", "data-value", "AF")); Locator valueSelector = Locator.tagWithAttributeContaining("input", "placeholder", "Filter value"); waitAndClick(valueSelector); From 0079ab99db37287230e69289bb73abb17937b128 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 9 Sep 2024 09:22:48 -0700 Subject: [PATCH 15/21] Adjust nimble defaults --- singlecell/src/org/labkey/singlecell/run/NimbleHelper.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java index 9850e99ed..f0e2f7fb3 100644 --- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java +++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java @@ -341,8 +341,9 @@ private void updateNimbleConfigFile(File configFile, NimbleGenome genome) throws { config.put("num_mismatches", 5); config.put("intersect_level", 0); + // NOTE: score_percent should almost always supersede this value config.put("score_threshold", 45); - config.put("score_percent", 0.45); + config.put("score_percent", 0.75); config.put("score_filter", 25); //discard_multiple_matches: false //discard_multi_hits: ? From ca6f47ced068b00e35553f0e45735705be532fb2 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 9 Sep 2024 14:07:42 -0700 Subject: [PATCH 16/21] Store nimble version --- .../labkey/singlecell/run/NimbleHelper.java | 39 ++++++++++++++++++- 1 file changed, 38 insertions(+), 1 deletion(-) diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java index f0e2f7fb3..891748ca0 100644 --- a/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java +++ b/singlecell/src/org/labkey/singlecell/run/NimbleHelper.java @@ -245,6 +245,8 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin List genomes = getGenomes(); List jsons = new ArrayList<>(); + String nimbleVersion = getVersion(output); + for (NimbleGenome genome : genomes) { File genomeCsv = getGenomeCsv(genome.getGenomeId()); @@ -280,7 +282,12 @@ public void doNimbleAlign(File bam, PipelineStepOutput output, Readset rs, Strin throw new PipelineJobException("Unable to find file: " + results.getPath()); } - String description = genome.getScorePercent() > 0 ? "score_percent: " + genome.getScorePercent() : null; + String description = "Nimble version: " + nimbleVersion; + if (genome.getScorePercent() > 0) + { + description += "\nscore_percent: " + genome.getScorePercent(); + } + output.addSequenceOutput(results, basename + ": nimble align", "Nimble Alignment", rs.getRowId(), null, genome.getGenomeId(), description); File outputBam = new File(results.getPath().replaceAll("results." + genome.genomeId + ".txt.gz", "nimbleAlignment." + genome.genomeId + ".bam")); @@ -688,4 +695,34 @@ public Integer getNumMismatches() return numMismatches; } } + + private String getVersion(PipelineStepOutput output) throws PipelineJobException + { + List nimbleArgs = new ArrayList<>(); + nimbleArgs.add("/bin/bash"); + nimbleArgs.add("-c"); + nimbleArgs.add("python3 -m nimble -v > /work/nimbleVersion.txt"); + + runUsingDocker(nimbleArgs, output, null); + + File outFile = new File(getPipelineCtx().getWorkingDirectory(), "nimbleVersion.txt"); + if (!outFile.exists()) + { + throw new PipelineJobException("Unable to find file: " + outFile.getPath()); + } + + String ret; + try (BufferedReader reader = Readers.getReader(outFile)) + { + ret = reader.readLine(); + } + catch (IOException e) + { + throw new PipelineJobException(e); + } + + outFile.delete(); + + return ret; + } } From c5a457878b23ac79f63140bc51024fb370ea85a5 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 10 Sep 2024 12:28:42 -0700 Subject: [PATCH 17/21] Skip cellranger-specific complete steps --- .../run/AbstractCellRangerDependentStep.java | 10 ++++++++++ .../org/labkey/singlecell/run/NimbleAlignmentStep.java | 2 +- 2 files changed, 11 insertions(+), 1 deletion(-) diff --git a/singlecell/src/org/labkey/singlecell/run/AbstractCellRangerDependentStep.java b/singlecell/src/org/labkey/singlecell/run/AbstractCellRangerDependentStep.java index 654fb1238..a17351fef 100644 --- a/singlecell/src/org/labkey/singlecell/run/AbstractCellRangerDependentStep.java +++ b/singlecell/src/org/labkey/singlecell/run/AbstractCellRangerDependentStep.java @@ -6,14 +6,18 @@ import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.sequenceanalysis.SequenceAnalysisService; +import org.labkey.api.sequenceanalysis.SequenceOutputFile; +import org.labkey.api.sequenceanalysis.model.AnalysisModel; import org.labkey.api.sequenceanalysis.model.Readset; import org.labkey.api.sequenceanalysis.pipeline.AlignmentOutputImpl; import org.labkey.api.sequenceanalysis.pipeline.AlignmentStepProvider; import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; import org.labkey.api.sequenceanalysis.pipeline.ReferenceGenome; +import org.labkey.api.sequenceanalysis.pipeline.SequenceAnalysisJobSupport; import java.io.File; import java.io.IOException; +import java.util.Collection; import java.util.List; public class AbstractCellRangerDependentStep extends CellRangerGexCountStep @@ -87,6 +91,12 @@ protected File runCellRanger(AlignmentOutputImpl output, Readset rs, List return localBam; } + @Override + public void complete(SequenceAnalysisJobSupport support, AnalysisModel model, Collection outputFilesCreated) throws PipelineJobException + { + // Skip GEX-specific complete steps. + } + @Override public boolean alwaysCopyIndexToWorkingDir() { diff --git a/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java b/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java index 04d65c79b..22985791e 100644 --- a/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java +++ b/singlecell/src/org/labkey/singlecell/run/NimbleAlignmentStep.java @@ -28,7 +28,7 @@ public class NimbleAlignmentStep extends AbstractCellRangerDependentStep public static final String ALIGN_OUTPUT = "alignmentOutput"; public static final String STRANDEDNESS = "strandedness"; - public NimbleAlignmentStep(AlignmentStepProvider provider, PipelineContext ctx, CellRangerWrapper wrapper) + public NimbleAlignmentStep(AlignmentStepProvider provider, PipelineContext ctx, CellRangerWrapper wrapper) { super(provider, ctx, wrapper); } From de92181baab96d9e0ddb1d8d6aacb5f5896e254a Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 13 Sep 2024 06:34:58 -0700 Subject: [PATCH 18/21] UpdateSeuratPrototype now updates DB record --- .../pipeline/SequenceOutputHandler.java | 2 +- .../PicardAlignmentMetricsHandler.java | 30 ++++++------- .../pipeline/ConvertToCramHandler.java | 10 ++--- .../pipeline/ProcessVariantsHandler.java | 8 ++-- .../pipeline/ReblockGvcfHandler.java | 10 ++--- .../SequenceOutputHandlerFinalTask.java | 4 +- .../run/analysis/NextCladeHandler.java | 6 +-- .../pipeline/AbstractSingleCellStep.java | 5 +++ .../analysis/AbstractSingleCellHandler.java | 19 +++++--- .../singlecell/UpdateSeuratPrototype.java | 44 ++++++++++++++++--- 10 files changed, 93 insertions(+), 45 deletions(-) diff --git a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java index 38768f2cc..1f9645621 100644 --- a/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java +++ b/SequenceAnalysis/api-src/org/labkey/api/sequenceanalysis/pipeline/SequenceOutputHandler.java @@ -198,7 +198,7 @@ default void init(JobContext ctx, List inputFiles, List inputFiles, JobContext ctx) throws UnsupportedOperationException, PipelineJobException; - default void complete(PipelineJob job, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + default void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java index bb902063e..bb5c61c56 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/analysis/PicardAlignmentMetricsHandler.java @@ -126,9 +126,9 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport } @Override - public void complete(PipelineJob job, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { - if (!(job instanceof SequenceOutputHandlerJob shj)) + if (!(ctx.getJob() instanceof SequenceOutputHandlerJob shj)) { throw new IllegalStateException("Expected job to be a SequenceOutputHandlerJob"); } @@ -144,10 +144,10 @@ public void complete(PipelineJob job, List inputs, List inputs, List metricsFiles = new ArrayList<>(); File mf = new File(outputDir, FileUtil.getBaseName(o.getFile()) + ".summary.metrics"); @@ -191,7 +191,7 @@ else if (collectInsertSize) // This output is only created for paired data: if (o.getReadset() != null) { - Readset rs = SequenceAnalysisService.get().getReadset(o.getReadset(), job.getUser()); + Readset rs = SequenceAnalysisService.get().getReadset(o.getReadset(), ctx.getJob().getUser()); if (rs.getReadData().stream().filter(rd -> rd.getFileId2() != null).count() > 0) { throw new PipelineJobException("Missing file: " + mf2.getPath()); @@ -219,7 +219,7 @@ else if (collectWgsNonZero) throw new PipelineJobException("Missing file: " + mf4.getPath()); } - File mf5 = new MarkDuplicatesWrapper(job.getLogger()).getMetricsFile(o.getFile()); + File mf5 = new MarkDuplicatesWrapper(ctx.getJob().getLogger()).getMetricsFile(o.getFile()); if (mf5.exists()) { metricsFiles.add(mf5); @@ -232,23 +232,23 @@ else if (runMarkDuplicates) TableInfo ti = SequenceAnalysisManager.get().getTable(SequenceAnalysisSchema.TABLE_QUALITY_METRICS); for (File f : metricsFiles) { - List> lines = PicardMetricsUtil.processFile(f, job.getLogger()); + List> lines = PicardMetricsUtil.processFile(f, ctx.getJob().getLogger()); for (Map row : lines) { row.put("container", o.getContainer()); - row.put("createdby", job.getUser().getUserId()); + row.put("createdby", ctx.getJob().getUser().getUserId()); row.put("created", new Date()); row.put("readset", m.getReadset()); row.put("analysis_id", m.getRowId()); row.put("dataid", m.getAlignmentFile()); - Table.insert(job.getUser(), ti, row); + Table.insert(ctx.getJob().getUser(), ti, row); } } } else { - job.getLogger().warn("Analysis Id " + o.getAnalysis_id() + " not found for file: " + o.getName()); + ctx.getJob().getLogger().warn("Analysis Id " + o.getAnalysis_id() + " not found for file: " + o.getName()); } } } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java index 56b7327e9..1d3a08c56 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ConvertToCramHandler.java @@ -161,7 +161,7 @@ private void checkCramAndIndex(SequenceOutputFile so) throws PipelineJobExceptio } @Override - public void complete(PipelineJob job, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { List> toUpdate = new ArrayList<>(); List> oldKeys = inputs.stream().map(x -> { @@ -175,11 +175,11 @@ public void complete(PipelineJob job, List inputs, List inputs, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { - SequenceTaskHelper taskHelper = new SequenceTaskHelper(getPipelineJob(job), getPipelineJob(job).getDataDirectory()); - List> providers = SequencePipelineService.get().getSteps(job, VariantProcessingStep.class); + SequenceTaskHelper taskHelper = new SequenceTaskHelper(getPipelineJob(ctx.getJob()), getPipelineJob(ctx.getJob()).getDataDirectory()); + List> providers = SequencePipelineService.get().getSteps(ctx.getJob(), VariantProcessingStep.class); for (PipelineStepCtx stepCtx : providers) { VariantProcessingStep step = stepCtx.getProvider().create(taskHelper); - step.complete(job, inputs, outputsCreated, support); + step.complete(ctx.getJob(), inputs, outputsCreated, ctx.getSequenceSupport()); } } } diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java index 8e2b99115..aa3abdd30 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ReblockGvcfHandler.java @@ -129,7 +129,7 @@ private File getReblockedName(File gvcf) } @Override - public void complete(PipelineJob job, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { List> toUpdate = new ArrayList<>(); List> oldKeys = inputs.stream().map(x -> { @@ -146,11 +146,11 @@ public void complete(PipelineJob job, List inputs, List inputs, List inputFiles, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputFiles, List outputsCreated) throws PipelineJobException { Map readsetToInput = inputFiles.stream().collect(Collectors.toMap(SequenceOutputFile::getReadset, x -> x)); - job.getLogger().info("Parsing NextClade JSON:"); + ctx.getJob().getLogger().info("Parsing NextClade JSON:"); for (SequenceOutputFile so : outputsCreated) { if (!NEXTCLADE_JSON.equals(so.getCategory())) @@ -118,7 +118,7 @@ public void complete(PipelineJob job, List inputFiles, List< throw new PipelineJobException("Unable to find parent for output: " + so.getRowid()); } - processAndImportNextCladeAa(job, so.getFile(), parent.getAnalysis_id(), so.getLibrary_id(), so.getDataId(), so.getReadset(), parent.getFile(), true); + processAndImportNextCladeAa(ctx.getJob(), so.getFile(), parent.getAnalysis_id(), so.getLibrary_id(), so.getDataId(), so.getReadset(), parent.getFile(), true); } } diff --git a/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellStep.java b/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellStep.java index f9ee71d5f..0cf0a73bf 100644 --- a/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellStep.java +++ b/singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellStep.java @@ -24,6 +24,11 @@ default void init(SequenceOutputHandler.JobContext ctx, List } + default void complete(SequenceOutputHandler.JobContext ctx, List inputFiles, List outputsCreated) throws PipelineJobException + { + + } + default boolean createsSeuratObjects() { return true; diff --git a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java index 359cc292b..628967c06 100644 --- a/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java +++ b/singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java @@ -271,30 +271,37 @@ public void processFilesOnWebserver(PipelineJob job, SequenceAnalysisJobSupport } @Override - public void complete(PipelineJob job, List inputs, List outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException + public void complete(JobContext ctx, List inputs, List outputsCreated) throws PipelineJobException { for (SequenceOutputFile so : outputsCreated) { if ("Seurat Cell Hashing Calls".equals(so.getCategory())) { - job.getLogger().info("Adding metrics for output: " + so.getName()); - CellHashingService.get().processMetrics(so, job, true); + ctx.getJob().getLogger().info("Adding metrics for output: " + so.getName()); + CellHashingService.get().processMetrics(so, ctx.getJob(), true); } if (SEURAT_PROTOTYPE.equals(so.getCategory())) { //NOTE: upstream we enforce one dataset per job, so we can safely assume this is the only dataset here: - File metricFile = new File(job.getLogFile().getParentFile(), "seurat.metrics.txt"); + File metricFile = new File(ctx.getJob().getLogFile().getParentFile(), "seurat.metrics.txt"); if (metricFile.exists()) { - processMetrics(so, job, metricFile); + processMetrics(so, ctx.getJob(), metricFile); } else { - job.getLogger().info("Metrics file not found, skipping"); + ctx.getJob().getLogger().info("Metrics file not found, skipping"); } } } + + List> steps = SequencePipelineService.get().getSteps(ctx.getJob(), SingleCellStep.class); + for (PipelineStepCtx stepCtx : steps) + { + SingleCellStep step = stepCtx.getProvider().create(ctx); + step.complete(ctx, inputs, outputsCreated); + } } private void processMetrics(SequenceOutputFile so, PipelineJob job, File metricsFile) throws PipelineJobException diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java index accf676c7..d44f48a40 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java @@ -3,6 +3,11 @@ import org.apache.commons.io.FileUtils; import org.json.JSONObject; import org.labkey.api.pipeline.PipelineJobException; +import org.labkey.api.query.BatchValidationException; +import org.labkey.api.query.InvalidKeyException; +import org.labkey.api.query.QueryService; +import org.labkey.api.query.QueryUpdateService; +import org.labkey.api.query.QueryUpdateServiceException; import org.labkey.api.sequenceanalysis.SequenceOutputFile; import org.labkey.api.sequenceanalysis.model.Readset; import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; @@ -10,16 +15,16 @@ import org.labkey.api.sequenceanalysis.pipeline.SequenceOutputHandler; import org.labkey.api.singlecell.pipeline.SeuratToolParameter; import org.labkey.api.singlecell.pipeline.SingleCellStep; -import org.labkey.api.util.FileUtil; -import org.labkey.api.writer.PrintWriters; -import org.labkey.singlecell.analysis.AbstractSingleCellHandler; +import org.labkey.singlecell.SingleCellSchema; import java.io.File; import java.io.IOException; -import java.io.PrintWriter; -import java.nio.file.Files; +import java.sql.SQLException; import java.util.Arrays; +import java.util.Collections; import java.util.List; +import java.util.Map; +import java.util.Queue; import static org.labkey.singlecell.analysis.AbstractSingleCellHandler.SEURAT_PROTOTYPE; @@ -143,4 +148,33 @@ public Output execute(SequenceOutputHandler.JobContext ctx, List inputFiles, List outputsCreated) throws PipelineJobException + { + if (inputFiles.size() != 1) + { + throw new PipelineJobException("Expected a single input file"); + } + + SequenceOutputFile so = inputFiles.get(0); + if (so.getDescription() == null) + { + so.setDescription("Prototype Updated"); + } + else + { + so.setDescription(so.getDescription() + "\nPrototype Updated"); + } + + try + { + QueryUpdateService us = QueryService.get().getUserSchema(ctx.getJob().getUser(), so.getContainerObj(), SingleCellSchema.SEQUENCE_SCHEMA_NAME).getTable("outputfiles").getUpdateService(); + us.updateRows(ctx.getJob().getUser(), so.getContainerObj(), Collections.singletonList(Map.of("rowid", so.getRowid(), "description", so.getDescription())), Collections.singletonList(Map.of("rowid", so.getRowid())), new BatchValidationException(), null, null); + } + catch (SQLException | BatchValidationException | QueryUpdateServiceException | InvalidKeyException e) + { + throw new PipelineJobException(e); + } + } } From 003dfaef74c58bda7da1837a90615f03a33b95dc Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 17 Sep 2024 16:54:17 -0700 Subject: [PATCH 19/21] Add param to force re-processing of cell hashing --- .../org/labkey/api/singlecell/CellHashingService.java | 3 +++ .../src/org/labkey/singlecell/CellHashingServiceImpl.java | 6 ++++++ 2 files changed, 9 insertions(+) diff --git a/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java b/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java index 97b12c45f..cfd24d865 100644 --- a/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java +++ b/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java @@ -112,6 +112,7 @@ public static class CellHashingParameters public boolean keepMarkdown = false; public File h5File = null; public boolean doTSNE = false; + public boolean doNotAllowResume = false; private CellHashingParameters() { @@ -128,6 +129,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu ret.minAllowableDoubletRateFilter = step.getProvider().getParameterByName("minAllowableDoubletRateFilter").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null); ret.callerDisagreementThreshold = step.getProvider().getParameterByName("callerDisagreementThreshold").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null); ret.doTSNE = step.getProvider().getParameterByName("doTSNE").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false); + ret.doNotAllowResume = step.getProvider().getParameterByName("doNotAllowResume").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false); ret.retainRawCountFile = step.getProvider().getParameterByName("retainRawCountFile").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true); ret.failIfUnexpectedHtosFound = step.getProvider().getParameterByName("failIfUnexpectedHtosFound").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true); ret.htoReadset = htoReadset; @@ -171,6 +173,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse ret.minAllowableDoubletRateFilter = params.get("minAllowableDoubletRateFilter") == null ? null : params.getDouble("minAllowableDoubletRateFilter"); ret.callerDisagreementThreshold = params.get("callerDisagreementThreshold") == null ? null : params.getDouble("callerDisagreementThreshold"); ret.doTSNE = params.optBoolean("doTSNE", false); + ret.doNotAllowResume = params.optBoolean("doNotAllowResume", false); ret.retainRawCountFile = params.optBoolean("retainRawCountFile", true); ret.failIfUnexpectedHtosFound = params.optBoolean("failIfUnexpectedHtosFound", true); ret.htoReadset = htoReadset; diff --git a/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java b/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java index 4e2a03321..41cd22bdd 100644 --- a/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java +++ b/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java @@ -627,6 +627,12 @@ public File generateHashingCallsForRawMatrix(Readset parentReadset, PipelineOutp String outputBasename = parameters.getBasename() + "." + parameters.type.name(); File callsFile = getExpectedCallsFile(ctx.getOutputDir(), outputBasename); File doneFile = new File(callsFile.getPath() + ".done"); + if (doneFile.exists() & parameters.doNotAllowResume) + { + ctx.getLogger().debug("doneFile exists, but doNotAllowResume was selected"); + doneFile.delete(); + } + if (!doneFile.exists()) { callsFile = generateCellHashingCalls(rawCountMatrixDir, ctx.getOutputDir(), outputBasename, ctx.getLogger(), ctx.getSourceDirectory(), parameters); From aa003022c69530b2d80f593bc7b56a24ccc7ed6f Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 19 Sep 2024 14:48:06 -0700 Subject: [PATCH 20/21] Switch RIRA project location --- .../labkey/singlecell/pipeline/singlecell/AbstractRiraStep.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AbstractRiraStep.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AbstractRiraStep.java index 51383b285..39d89abc5 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AbstractRiraStep.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AbstractRiraStep.java @@ -9,7 +9,7 @@ abstract public class AbstractRiraStep extends AbstractSingleCellPipelineStep { - public static String CONTAINER_NAME = "ghcr.io/bimberlabinternal/rira:latest"; + public static String CONTAINER_NAME = "ghcr.io/bimberlab/rira:latest"; public AbstractRiraStep(PipelineStepProvider provider, PipelineContext ctx) { From bcc17030dc8bd773770ec195587e1e18bcf9336b Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 24 Sep 2024 06:24:08 -0700 Subject: [PATCH 21/21] Update jbrowse --- jbrowse/package-lock.json | 123 +++----------------------------------- jbrowse/package.json | 10 ++-- 2 files changed, 13 insertions(+), 120 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index ff17759de..c7c16ed5d 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -9,11 +9,11 @@ "version": "1.0.0", "dependencies": { "@gmod/vcf": "^5.0.10", - "@jbrowse/core": "2.15.0", - "@jbrowse/plugin-linear-genome-view": "2.15.0", - "@jbrowse/plugin-svg": "2.15.0", - "@jbrowse/plugin-variants": "2.15.0", - "@jbrowse/react-linear-genome-view": "2.15.0", + "@jbrowse/core": "^2.15.0", + "@jbrowse/plugin-linear-genome-view": "^2.15.0", + "@jbrowse/plugin-svg": "^2.15.0", + "@jbrowse/plugin-variants": "^2.15.0", + "@jbrowse/react-linear-genome-view": "^2.15.0", "@labkey/api": "^1.35.0", "@labkey/components": "^5.0.0", "@mui/x-data-grid": "^7.0.0", @@ -2642,9 +2642,9 @@ } }, "node_modules/@jbrowse/core": { - "version": "2.15.0", - "resolved": "https://registry.npmjs.org/@jbrowse/core/-/core-2.15.0.tgz", - "integrity": "sha512-A6xGeAXA5cDlTsUMtvEXpvJPBjAvS4rKStC0MfgJVpB3QOtW+vH/bnuEC8RGGO+5jGO2lPmpz3fT1gRVw68vrQ==", + "version": "2.15.4", + "resolved": "https://registry.npmjs.org/@jbrowse/core/-/core-2.15.4.tgz", + "integrity": "sha512-eSjb5cEQPla49BrgKHWJCAQR+YGY+lUKiP8Jd9W9Iorz65/vRRgyoWqtGHTwE2UtsS8wXi8HFynCdw1giptG+w==", "license": "Apache-2.0", "dependencies": { "@babel/runtime": "^7.17.9", @@ -2711,52 +2711,6 @@ "tss-react": "^4.0.0" } }, - "node_modules/@jbrowse/embedded-core/node_modules/@jbrowse/core": { - "version": "2.15.4", - "resolved": "https://registry.npmjs.org/@jbrowse/core/-/core-2.15.4.tgz", - "integrity": "sha512-eSjb5cEQPla49BrgKHWJCAQR+YGY+lUKiP8Jd9W9Iorz65/vRRgyoWqtGHTwE2UtsS8wXi8HFynCdw1giptG+w==", - "license": "Apache-2.0", - "dependencies": { - "@babel/runtime": "^7.17.9", - "@gmod/abortable-promise-cache": "^2.0.0", - "@gmod/bgzf-filehandle": "^1.4.3", - "@gmod/http-range-fetcher": "^3.0.4", - "@mui/icons-material": "^6.0.0", - "@mui/x-data-grid": "^7.0.0", - "@types/clone": "^2.0.0", - "canvas-sequencer": "^3.1.0", - "canvas2svg": "^1.0.16", - "clone": "^2.1.2", - "colord": "^2.9.3", - "copy-to-clipboard": "^3.3.1", - "deepmerge": "^4.2.2", - "detect-node": "^2.1.0", - "dompurify": "^3.0.0", - "escape-html": "^1.0.3", - "fast-deep-equal": "^3.1.3", - "generic-filehandle": "^3.0.0", - "is-object": "^1.0.1", - "jexl": "^2.3.0", - "librpc-web-mod": "^1.1.5", - "load-script": "^2.0.0", - "material-ui-popup-state": "^5.0.0", - "rbush": "^3.0.1", - "react-error-boundary": "^4.0.3", - "serialize-error": "^8.0.0", - "source-map-js": "^1.0.2", - "svg-path-generator": "^1.1.0" - }, - "peerDependencies": { - "@mui/material": "^6.0.0", - "mobx": "^6.0.0", - "mobx-react": "^9.0.0", - "mobx-state-tree": "^5.0.0", - "react": ">=16.8.0", - "react-dom": ">=16.8.0", - "rxjs": "^7.0.0", - "tss-react": "^4.0.0" - } - }, "node_modules/@jbrowse/plugin-alignments": { "version": "2.15.4", "resolved": "https://registry.npmjs.org/@jbrowse/plugin-alignments/-/plugin-alignments-2.15.4.tgz", @@ -3131,52 +3085,6 @@ "tss-react": "^4.0.0" } }, - "node_modules/@jbrowse/product-core/node_modules/@jbrowse/core": { - "version": "2.15.4", - "resolved": "https://registry.npmjs.org/@jbrowse/core/-/core-2.15.4.tgz", - "integrity": "sha512-eSjb5cEQPla49BrgKHWJCAQR+YGY+lUKiP8Jd9W9Iorz65/vRRgyoWqtGHTwE2UtsS8wXi8HFynCdw1giptG+w==", - "license": "Apache-2.0", - "dependencies": { - "@babel/runtime": "^7.17.9", - "@gmod/abortable-promise-cache": "^2.0.0", - "@gmod/bgzf-filehandle": "^1.4.3", - "@gmod/http-range-fetcher": "^3.0.4", - "@mui/icons-material": "^6.0.0", - "@mui/x-data-grid": "^7.0.0", - "@types/clone": "^2.0.0", - "canvas-sequencer": "^3.1.0", - "canvas2svg": "^1.0.16", - "clone": "^2.1.2", - "colord": "^2.9.3", - "copy-to-clipboard": "^3.3.1", - "deepmerge": "^4.2.2", - "detect-node": "^2.1.0", - "dompurify": "^3.0.0", - "escape-html": "^1.0.3", - "fast-deep-equal": "^3.1.3", - "generic-filehandle": "^3.0.0", - "is-object": "^1.0.1", - "jexl": "^2.3.0", - "librpc-web-mod": "^1.1.5", - "load-script": "^2.0.0", - "material-ui-popup-state": "^5.0.0", - "rbush": "^3.0.1", - "react-error-boundary": "^4.0.3", - "serialize-error": "^8.0.0", - "source-map-js": "^1.0.2", - "svg-path-generator": "^1.1.0" - }, - "peerDependencies": { - "@mui/material": "^6.0.0", - "mobx": "^6.0.0", - "mobx-react": "^9.0.0", - "mobx-state-tree": "^5.0.0", - "react": ">=16.8.0", - "react-dom": ">=16.8.0", - "rxjs": "^7.0.0", - "tss-react": "^4.0.0" - } - }, "node_modules/@jbrowse/react-linear-genome-view": { "version": "2.15.0", "resolved": "https://registry.npmjs.org/@jbrowse/react-linear-genome-view/-/react-linear-genome-view-2.15.0.tgz", @@ -8478,21 +8386,6 @@ "dev": true, "license": "Unlicense" }, - "node_modules/fsevents": { - "version": "2.3.3", - "resolved": "https://registry.npmjs.org/fsevents/-/fsevents-2.3.3.tgz", - "integrity": "sha512-5xoDfX+fL7faATnagmWPpbFtwh/R77WmMMqqHGS65C3vvB0YHrgF+B1YmZ3441tMj5n63k0212XNoJwzlhffQw==", - "dev": true, - "hasInstallScript": true, - "license": "MIT", - "optional": true, - "os": [ - "darwin" - ], - "engines": { - "node": "^8.16.0 || ^10.6.0 || >=11.0.0" - } - }, "node_modules/function-bind": { "version": "1.1.2", "resolved": "https://registry.npmjs.org/function-bind/-/function-bind-1.1.2.tgz", diff --git a/jbrowse/package.json b/jbrowse/package.json index f91d53196..7b59ab12f 100644 --- a/jbrowse/package.json +++ b/jbrowse/package.json @@ -15,11 +15,11 @@ }, "dependencies": { "@gmod/vcf": "^5.0.10", - "@jbrowse/core": "2.15.0", - "@jbrowse/plugin-linear-genome-view": "2.15.0", - "@jbrowse/plugin-svg": "2.15.0", - "@jbrowse/plugin-variants": "2.15.0", - "@jbrowse/react-linear-genome-view": "2.15.0", + "@jbrowse/core": "^2.15.0", + "@jbrowse/plugin-linear-genome-view": "^2.15.0", + "@jbrowse/plugin-svg": "^2.15.0", + "@jbrowse/plugin-variants": "^2.15.0", + "@jbrowse/react-linear-genome-view": "^2.15.0", "@labkey/api": "^1.35.0", "@labkey/components": "^5.0.0", "@mui/x-data-grid": "^7.0.0",