From 68435598b0d420268d537a161eb1bfc4849c4c62 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 27 Aug 2026 06:52:44 -0700 Subject: [PATCH 01/23] Fix HTML --- .../org/labkey/sequenceanalysis/SequenceAnalysisController.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index 6849a9c81..12d76bd0b 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java @@ -717,7 +717,7 @@ else if (SequenceAnalysisSchema.TABLE_OUTPUTFILES.equals(_table.getName())) msg.append("Folder: ").unsafeAppend("" + h(target.getPath()) + "
"); } } - msg.append("
"); + msg.unsafeAppend("
"); } } } From 49b17e8417f61afec098bc4786a21fea63084b3b Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 27 Aug 2026 18:07:36 -0700 Subject: [PATCH 02/23] Support RecoverUnassignedCells() --- .../chunks/RecoverRiraUnassignedCells.R | 14 +++++++ .../labkey/singlecell/SingleCellModule.java | 2 + .../RecoverRiraUnassignedCells.java | 42 +++++++++++++++++++ 3 files changed, 58 insertions(+) create mode 100644 singlecell/resources/chunks/RecoverRiraUnassignedCells.R create mode 100644 singlecell/src/org/labkey/singlecell/pipeline/singlecell/RecoverRiraUnassignedCells.java diff --git a/singlecell/resources/chunks/RecoverRiraUnassignedCells.R b/singlecell/resources/chunks/RecoverRiraUnassignedCells.R new file mode 100644 index 000000000..00577e249 --- /dev/null +++ b/singlecell/resources/chunks/RecoverRiraUnassignedCells.R @@ -0,0 +1,14 @@ +for (datasetId in names(seuratObjects)) { + printName(datasetId) + seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) + + if (! 'RIRA_Immune_v2.cellclass.recovered' %in% names(seuratObj@meta.data)) { + seuratObj <- RIRA::RecoverUnassignedCells(seuratObj, groupField = groupField, minClusterProp = minClusterProp) + } + + saveData(seuratObj, datasetId) + + # Cleanup + rm(seuratObj) + gc() +} \ No newline at end of file diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java index 36cbb0282..0ad914eba 100644 --- a/singlecell/src/org/labkey/singlecell/SingleCellModule.java +++ b/singlecell/src/org/labkey/singlecell/SingleCellModule.java @@ -82,6 +82,7 @@ import org.labkey.singlecell.pipeline.singlecell.PredictScTour; import org.labkey.singlecell.pipeline.singlecell.PredictTcellActivation; import org.labkey.singlecell.pipeline.singlecell.PrepareRawCounts; +import org.labkey.singlecell.pipeline.singlecell.RecoverRiraUnassignedCells; import org.labkey.singlecell.pipeline.singlecell.RemoveCellCycle; import org.labkey.singlecell.pipeline.singlecell.RunCellHashing; import org.labkey.singlecell.pipeline.singlecell.RunCelltypist; @@ -278,6 +279,7 @@ public static void registerPipelineSteps() SequencePipelineService.get().registerPipelineStep(new RunCelltypist.Provider()); SequencePipelineService.get().registerPipelineStep(new RunCelltypistCustomModel.Provider()); SequencePipelineService.get().registerPipelineStep(new RunRiraClassification.Provider()); + SequencePipelineService.get().registerPipelineStep(new RecoverRiraUnassignedCells.Provider()); SequencePipelineService.get().registerPipelineStep(new TrainCelltypist.Provider()); SequencePipelineService.get().registerPipelineStep(new CheckExpectations.Provider()); SequencePipelineService.get().registerPipelineStep(new CommonFilters.Provider()); diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RecoverRiraUnassignedCells.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RecoverRiraUnassignedCells.java new file mode 100644 index 000000000..7d43a1d61 --- /dev/null +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RecoverRiraUnassignedCells.java @@ -0,0 +1,42 @@ +package org.labkey.singlecell.pipeline.singlecell; + +import org.json.JSONObject; +import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; +import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; +import org.labkey.api.singlecell.pipeline.SeuratToolParameter; +import org.labkey.api.singlecell.pipeline.SingleCellStep; + +import java.util.Arrays; + +public class RecoverRiraUnassignedCells extends AbstractRiraStep +{ + public RecoverRiraUnassignedCells(PipelineContext ctx, RecoverRiraUnassignedCells.Provider provider) + { + super(provider, ctx); + } + + public static class Provider extends AbstractPipelineStepProvider + { + public Provider() + { + super("RecoverRiraUnassignedCells", "Recover RIRA Unassigned Cells", "RIRA/Celltypist", "This will run RIRA's Celltypist-based models for course cell type and T/NK cells.", Arrays.asList( + SeuratToolParameter.create("groupField", "Group Field", "The field on which to group", "textfield", new JSONObject() + {{ + put("allowBlank", false); + }}, "ClusterNames_0.2"), + SeuratToolParameter.create("minClusterProp", "Min Cluster Proportion", "If at least this proportion of the group is one class, unassigned cells will be assigned as this class", "ldk-numberfield", new JSONObject() + {{ + put("minValue", 0); + put("maxValue", 1); + put("decimalPrecision", 2); + }}, 0.6) + ), null, null); + } + + @Override + public RecoverRiraUnassignedCells create(PipelineContext ctx) + { + return new RecoverRiraUnassignedCells(ctx, this); + } + } +} From 968d40292360837a5c603260ce8fe12ebbcf8049 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 31 Aug 2026 11:02:16 -0700 Subject: [PATCH 03/23] Switch from waitForCompletion to Future.get() --- .../SequenceAnalysisMaintenanceTask.java | 62 +++++++++---------- .../pipeline/CreateReferenceLibraryTask.java | 10 +-- .../pipeline/ImportGenomeTrackTask.java | 10 +-- 3 files changed, 42 insertions(+), 40 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java index bd691d3d4..4a9e64df5 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java @@ -54,6 +54,8 @@ import java.util.Map; import java.util.Objects; import java.util.Set; +import java.util.concurrent.ExecutionException; +import java.util.concurrent.Future; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -131,51 +133,47 @@ public void run(Logger log) } } - private void possiblySubmitRemoteTask(Logger log) + private void possiblySubmitRemoteTask(Logger log) throws InterruptedException, ExecutionException { if (SequencePipelineService.get().isRemoteGenomeCacheUsed()) { JobRunner jr = JobRunner.getDefault(); - jr.execute(new Runnable() - { - @Override - public void run() + Future future = jr.execute(() -> { + try { - try - { - Map genomeMap = new IntHashMap<>(); - new TableSelector(SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES), PageFlowUtil.set("rowid", "fasta_file"), new SimpleFilter(FieldKey.fromString("datedisabled"), null, CompareType.ISBLANK), null).forEachResults(rs -> { - int dataId = rs.getInt(FieldKey.fromString("fasta_file")); - if (dataId > -1) - { - ExpData d = ExperimentService.get().getExpData(dataId); - if (d != null && d.getFile() != null) - { - genomeMap.put(rs.getInt(FieldKey.fromString("rowid")), d.getFile()); - } - } - }); - - if (!genomeMap.isEmpty()) + Map genomeMap = new IntHashMap<>(); + new TableSelector(SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES), PageFlowUtil.set("rowid", "fasta_file"), new SimpleFilter(FieldKey.fromString("datedisabled"), null, CompareType.ISBLANK), null).forEachResults(rs -> { + int dataId = rs.getInt(FieldKey.fromString("fasta_file")); + if (dataId > -1) { - final User adminUser = LDKService.get().getBackgroundAdminUser(); - if (adminUser == null) + ExpData d = ExperimentService.get().getExpData(dataId); + if (d != null && d.getFile() != null) { - log.error("LDK module BackgroundAdminUser property not set. If this is set, JBrowseMaintenanceTask could automatically submit repair jobs."); - return; + genomeMap.put(rs.getInt(FieldKey.fromString("rowid")), d.getFile()); } - - CacheGenomeTrigger.cacheGenomes(ContainerManager.getSharedContainer(), adminUser, genomeMap, log, true); } - } - catch (Exception e) + }); + + if (!genomeMap.isEmpty()) { - log.error(e); + final User adminUser = LDKService.get().getBackgroundAdminUser(); + if (adminUser == null) + { + log.error("LDK module BackgroundAdminUser property not set. If this is set, JBrowseMaintenanceTask could automatically submit repair jobs."); + return; + } + + CacheGenomeTrigger.cacheGenomes(ContainerManager.getSharedContainer(), adminUser, genomeMap, log, true); } } - }); + catch (Exception e) + { + log.error(e); + } + }, 0); - jr.waitForCompletion(); + // Wait for this job: + future.get(); } else { diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java index 7a6f149db..b0e84f609 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/CreateReferenceLibraryTask.java @@ -68,6 +68,7 @@ import java.util.List; import java.util.Map; import java.util.Set; +import java.util.concurrent.Future; import static org.labkey.api.util.IntegerUtils.asInteger; @@ -467,7 +468,7 @@ public RecordedActionSet run() throws PipelineJobException { getJob().getLogger().info("running genome trigger: " + t.getName()); final int libraryId = rowId; - jr.execute(new Job() + Future future = jr.execute(new Job() { @Override public void run() @@ -481,11 +482,12 @@ public void run() t.onRecreate(getJob().getContainer(), getJob().getUser(), getJob().getLogger(), libraryId); } } - }); + }, 0); + + // Wait for this job: + future.get(); } } - - jr.waitForCompletion(); } } catch (Exception e) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java index 6c13f1249..a555fe306 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/ImportGenomeTrackTask.java @@ -81,6 +81,7 @@ import java.util.List; import java.util.Map; import java.util.Set; +import java.util.concurrent.Future; import static org.labkey.api.util.IntegerUtils.asInteger; @@ -163,18 +164,19 @@ public boolean isJobComplete(PipelineJob job) if (t.isAvailable(genomeContainer)) { getJob().getLogger().info("running genome trigger: " + t.getName()); - jr.execute(new Job() + Future future = jr.execute(new Job() { @Override public void run() { t.onTrackAdd(genomeContainer, getJob().getUser(), getJob().getLogger(), libraryId, trackId); } - }); + }, 0); + + // Wait for the job: + future.get(); } } - - jr.waitForCompletion(); } } From ba788cc0f40363462453ab500f3cc7a07c541810 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 31 Aug 2026 11:03:53 -0700 Subject: [PATCH 04/23] Prefer samtools merge over picard for speed --- .../pipeline/SequenceAlignmentTask.java | 7 +-- .../sequenceanalysis/run/SamtoolsMerger.java | 50 +++++++++++++++++++ 2 files changed, 54 insertions(+), 3 deletions(-) create mode 100644 SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java index 31f6c67aa..8244e6d71 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java @@ -71,6 +71,7 @@ import org.labkey.sequenceanalysis.ReadDataImpl; import org.labkey.sequenceanalysis.SequenceReadsetImpl; import org.labkey.sequenceanalysis.run.RestoreSraDataHandler; +import org.labkey.sequenceanalysis.run.SamtoolsMerger; import org.labkey.sequenceanalysis.run.bampostprocessing.SortSamStep; import org.labkey.sequenceanalysis.run.preprocessing.TrimmomaticWrapper; import org.labkey.sequenceanalysis.run.util.AddOrReplaceReadGroupsWrapper; @@ -1306,7 +1307,7 @@ private File doAlignThenMerge(ReferenceGenome referenceGenome, Readset rs, Map bams = new ArrayList<>(); for (File o : alignOutputs) { @@ -1319,8 +1320,8 @@ private File doAlignThenMerge(ReferenceGenome referenceGenome, Readset rs, Map inputBams, File outputFile) throws PipelineJobException + { + getLogger().info("Merging SAM/BAM(s):"); + + List params = new ArrayList<>(); + params.add(getSamtoolsPath().getPath()); + params.add(COMMAND); + params.add("-o"); + params.add(outputFile.getPath()); + + Integer threads = SequencePipelineService.get().getMaxThreads(getLogger()); + if (threads != null) + { + params.add(" --threads"); + params.add(String.valueOf(threads)); + } + + inputBams.forEach(f -> params.add(f.getPath())); + + execute(params); + + File idx = SequencePipelineService.get().ensureBamIndex(outputFile, getLogger(), false); + if (!idx.exists()) + { + throw new PipelineJobException("Unable to find BAM index: " + idx.getPath()); + } + + return outputFile; + } +} From ed67eec9b4d3172bf2dd80b32ac10eeb0a4c34ed Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 31 Aug 2026 13:51:42 -0700 Subject: [PATCH 05/23] Update samtools merge argument order --- .../src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java index 5df733f0e..cbd323dc3 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java @@ -25,8 +25,6 @@ public File mergeBams(List inputBams, File outputFile) throws PipelineJobE List params = new ArrayList<>(); params.add(getSamtoolsPath().getPath()); params.add(COMMAND); - params.add("-o"); - params.add(outputFile.getPath()); Integer threads = SequencePipelineService.get().getMaxThreads(getLogger()); if (threads != null) @@ -35,6 +33,9 @@ public File mergeBams(List inputBams, File outputFile) throws PipelineJobE params.add(String.valueOf(threads)); } + params.add("-o"); + params.add(outputFile.getPath()); + inputBams.forEach(f -> params.add(f.getPath())); execute(params); From 303bc6d75904f3563f9f7967548ab3263ab5a8e6 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 1 Sep 2026 06:21:09 -0700 Subject: [PATCH 06/23] Bugfix to samtools merge --- .../src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java index cbd323dc3..da232dbfb 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/SamtoolsMerger.java @@ -29,7 +29,7 @@ public File mergeBams(List inputBams, File outputFile) throws PipelineJobE Integer threads = SequencePipelineService.get().getMaxThreads(getLogger()); if (threads != null) { - params.add(" --threads"); + params.add("--threads"); params.add(String.valueOf(threads)); } From fcec9d90e32ca465aa62e114657fcfc824beaba7 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 1 Sep 2026 06:22:56 -0700 Subject: [PATCH 07/23] Try to reduce I/O in SequenceAnalysisMaintenanceTask --- .../SequenceAnalysisMaintenanceTask.java | 457 ++++++++++-------- 1 file changed, 264 insertions(+), 193 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java index 4a9e64df5..aabb844dc 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java @@ -195,7 +195,7 @@ private void verifySequenceDataPresent(Logger log) i++; if (i % 1000 == 0) { - log.info("readdata " + i + " of " + readDatas.size() + ". Current container: " + ContainerManager.getForId(rd.getContainer()).getPath()); + log.info("readdata " + i + " of " + readDatas.size() + ". Current container: " + Objects.requireNonNull(ContainerManager.getForId(rd.getContainer())).getPath()); checkJobCancelled(log); } @@ -209,14 +209,14 @@ private void verifySequenceDataPresent(Logger log) { log.error("Unable to find file associated with ReadData: " + rd.getRowid() + ", " + rd.getFileId1() + " for container: " + (c == null ? rd.getContainer() : c.getPath())); } - else if (!d.getFile().exists()) + else if (!checkFile(d.getFile())) { log.error("Unable to find file associated with ReadData: " + rd.getRowid() + ", " + rd.getFileId1() + ", " + d.getFile().getPath() + " for container: " + (c == null ? rd.getContainer() : c.getPath())); } } else { - if (d != null && d.getFile() != null && d.getFile().exists()) + if (d != null && d.getFile() != null && checkFile(d.getFile())) { log.error("ReadData marked as archived, but file exists: " + rd.getRowid() + ", " + rd.getFileId1() + ", " + d.getFile().getPath() + " for container: " + (c == null ? rd.getContainer() : c.getPath())); } @@ -233,14 +233,14 @@ else if (!d.getFile().exists()) { log.error("Unable to find file associated with ReadData: " + rd.getRowid() + ", " + rd.getFileId2() + " for container: " + (c == null ? rd.getContainer() : c.getPath())); } - else if (!d.getFile().exists()) + else if (!checkFile(d.getFile())) { log.error("Unable to find file associated with ReadData: " + rd.getRowid() + ", " + rd.getFileId2() + ", " + d.getFile().getPath() + " for container: " + (c == null ? rd.getContainer() : c.getPath())); } } else { - if (d != null && d.getFile() != null && d.getFile().exists()) + if (d != null && d.getFile() != null && checkFile(d.getFile())) { log.error("ReadData marked as archived, but file exists: " + rd.getRowid() + ", " + rd.getFileId1() + ", " + d.getFile().getPath() + " for container: " + (c == null ? rd.getContainer() : c.getPath())); } @@ -271,7 +271,7 @@ else if (!d.getFile().exists()) { log.error("Unable to find file associated with analysis: " + m.getAnalysisId() + ", " + m.getAlignmentFile() + " for container: " + (c == null ? m.getContainer() : c.getPath())); } - else if (!d.getFile().exists()) + else if (!checkFile(d.getFile())) { log.error("Unable to find file associated with analysis: " + m.getAnalysisId() + ", " + m.getAlignmentFile() + ", " + d.getFile().getPath() + " for container: " + (c == null ? m.getContainer() : c.getPath())); } @@ -281,6 +281,32 @@ else if (!d.getFile().exists()) } } + Set _filesPresent = new HashSet<>(); + Set _filesMissing = new HashSet<>(); + + // The purpose of this is to cache filesystem interactions and speed inspection of files: + private boolean checkFile(File f) + { + if (_filesMissing.contains(f)) + { + return false; + } + else if (_filesPresent.contains(f)) + { + return true; + } + + if (f.exists()) + { + _filesPresent.add(f); + return true; + } + else + { + _filesMissing.add(f); + return false; + } + } private void inspectForCoreFiles(Long runId, Logger log) { if (runId == null) @@ -313,7 +339,7 @@ else if (sf.getFilePath() == null) } File root = new File(sf.getFilePath()).getParentFile(); - if (!root.exists()) + if (!checkFile(root)) { log.error("Run file root does not exist. runId: " + runId + " / jobId: " + sf.getRowId() + " / " + root.getPath()); return; @@ -370,13 +396,13 @@ private void processContainer(Container c, Logger log) throws IOException, Pipel // File existence will be verified below: expectedSequences.add(d.getFile()); } - else if (!d.getFile().exists()) + else if (!checkFile(d.getFile())) { log.error("Missing sequence file {}", d.getFile().getPath()); } }); - if (sequenceDir.exists()) + if (checkFile(sequenceDir)) { inspectSequenceDir(sequenceDir, expectedSequences, log); } @@ -385,7 +411,7 @@ else if (!d.getFile().exists()) { for (File missing : expectedSequences) { - if (missing.exists()) + if (checkFile(missing)) { log.error("File exists, but wasnt removed from expectedSequences for folder {}, file: {}", sequenceDir.getPath(), missing.getPath()); } @@ -399,7 +425,7 @@ else if (!d.getFile().exists()) //then libraries log.debug("Inspecting genomes"); File libraryDir = SequenceAnalysisManager.get().getReferenceLibraryDir(c); - if (libraryDir != null && libraryDir.exists()) + if (libraryDir != null && checkFile(libraryDir)) { TableInfo ti = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES); TableSelector ts = new TableSelector(ti, Collections.singleton("rowid"), new SimpleFilter(FieldKey.fromString("container"), c.getId()), null); @@ -409,165 +435,11 @@ else if (!d.getFile().exists()) expectedLibraries.add(rowId.toString()); } - for (File child : libraryDir.listFiles()) + try (Stream stream = Files.list(libraryDir.toPath())) { - if ("log".equals(FileUtil.getExtension(child)) || "xml".equals(FileUtil.getExtension(child))) - { - continue; //always ignore log files - } - - if (!expectedLibraries.contains(child.getName())) - { - deleteFile(child, log); - } - else - { - //inspect within library - List expectedChildren = new ArrayList<>(); - int libraryId = Integer.parseInt(child.getName()); - Integer fastaId = new TableSelector(SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES), PageFlowUtil.set("fasta_file")).getObject(libraryId, Integer.class); - if (fastaId == null) - { - log.error("Unable to find FASTA ExpData in DB matching jbrowse directory: " + child.getPath()); - continue; - } - - ExpData fastaData = ExperimentService.get().getExpData(fastaId); - File fasta = fastaData.getFile(); - if (!fasta.exists()) - { - log.error("expected fasta file does not exist: " + fasta.getPath()); - } - - // Use this to retroactively convert existing genomes: - File gz = new File(fasta.getPath() + ".gz"); - if (!gz.exists()) - { - ReferenceGenomeImpl genome = new ReferenceGenomeImpl(fasta, fastaData, libraryId, null); - - // NOTE: we can hit a race condition in automated testing where a genome is newly created during a test, and the maintenance task runs concurrent with that test. - // This is a check to reduce the log level, which thereby prevents the test from erroring - Date created = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES), PageFlowUtil.set("created"), new SimpleFilter(FieldKey.fromString("rowId"), libraryId), null).getObject(Date.class); - long timeSinceCreated = new Date().getTime() - created.getTime(); - // 1000*60*20 = 20 minutes - Level l = timeSinceCreated > 1200000 ? Level.ERROR : Level.WARN; - - log.log(l, "GZipped genome missing for: " + genome.getGenomeId()); - - if (SystemUtils.IS_OS_WINDOWS) - { - log.warn("Cannot create bgzipped file on windows machine"); - } - else - { - genome.createGzippedFile(log); - } - } - - File gzi = new File(fasta.getPath() + ".gz.gzi"); - if (!gzi.exists()) - { - if (SystemUtils.IS_OS_WINDOWS) - { - log.warn("Cannot index gzipped FASTA on windows: " + fasta.getPath()); - } - else - { - new FastaIndexer(log).execute(gz); - } - } - - expectedChildren.add(fasta.getName() + ".gz"); - expectedChildren.add(fasta.getName() + ".gz.gzi"); - expectedChildren.add(fasta.getName() + ".gz.fai"); - - expectedChildren.add(fasta.getName()); - expectedChildren.add(fasta.getName() + ".fai"); - expectedChildren.add(FileUtil.getBaseName(fasta.getName()) + ".idKey.txt"); - expectedChildren.add(FileUtil.getBaseName(fasta.getName()) + ".dict"); - expectedChildren.add("libraryMembers.xml"); //temp file creating during pipeline job - expectedChildren.add("alignerIndexes"); - expectedChildren.add("tracks"); - expectedChildren.add("chainFiles"); - expectedChildren.add(".lastUpdate"); - - for (String fileName : child.list()) - { - if (!expectedChildren.contains(fileName)) - { - if ("log".equals(FileUtil.getExtension(fileName)) || "xml".equals(FileUtil.getExtension(fileName))) - { - continue; - } - - deleteFile(FileUtil.appendName(child, fileName), log); - } - } - - //check/verify tracks - File trackDir = FileUtil.appendName(child, "tracks"); - if (trackDir.exists()) - { - Set expectedTracks = new HashSet<>(); - TableInfo tracksTable = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_LIBRARY_TRACKS); - TableSelector tracksTs = new TableSelector(tracksTable, Collections.singleton("fileid"), new SimpleFilter(FieldKey.fromString("library_id"), libraryId), null); - for (Integer dataId : tracksTs.getArrayList(Integer.class)) - { - ExpData trackData = ExperimentService.get().getExpData(dataId); - if (trackData != null && trackData.getFile() != null) - { - expectedTracks.add(trackData.getFile().getName()); - if (!trackData.getFile().exists()) - { - log.error("expected track file does not exist: " + trackData.getFile().getPath()); - } - - expectedTracks.addAll(getAssociatedFiles(trackData.getFile(), true)); - } - else - { - log.warn("unable to find ExpData for track with dataId: " + dataId); - } - } - - for (File f : trackDir.listFiles()) - { - if (!expectedTracks.contains(f.getName())) - { - deleteFile(f, log); - } - } - } - - //check/verify chainFiles - File chainDir = FileUtil.appendName(child, "chainFiles"); - if (chainDir.exists()) - { - Set expectedChains = new HashSet<>(); - TableInfo chainTable = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_CHAIN_FILES); - TableSelector chainTs = new TableSelector(chainTable, Collections.singleton("chainFile"), new SimpleFilter(FieldKey.fromString("genomeId1"), libraryId), null); - for (Integer dataId : chainTs.getArrayList(Integer.class)) - { - ExpData chainData = ExperimentService.get().getExpData(dataId); - if (chainData != null && chainData.getFile() != null) - { - expectedChains.add(chainData.getFile().getName()); - if (!chainData.getFile().exists()) - { - log.error("expected chain file does not exist: " + chainData.getFile().getPath()); - } - } - } - - for (File f : chainDir.listFiles()) - { - if (!expectedChains.contains(f.getName())) - { - deleteFile(f, log); - } - } - } - } + stream.forEach(x -> { + inspectLibraryDir(x.toFile(), expectedLibraries, log); + }); } } @@ -590,7 +462,7 @@ else if (!d.getFile().exists()) expectedFileNames.add(d.getFile().getName()); expectedFileNames.addAll(getAssociatedFiles(d.getFile(), true)); - if (!d.getFile().exists()) + if (!checkFile(d.getFile())) { log.error("expected output file does not exist: " + d.getFile().getPath()); continue; @@ -600,7 +472,7 @@ else if (!d.getFile().exists()) if (_vcfFileType.isType(d.getFile()) && d.getFile().getPath().endsWith(".gz")) { File idx = new File(d.getFile().getPath() + ".tbi"); - if (!idx.exists()) + if (!checkFile(idx)) { log.warn("unable to find index for file: " + d.getFile().getPath() + ", creating"); SequenceAnalysisService.get().ensureVcfIndex(d.getFile(), log); @@ -610,14 +482,17 @@ else if (!d.getFile().exists()) } File sequenceOutputsDir = FileUtil.appendName(root.getRootPath(), "sequenceOutputs"); - if (sequenceOutputsDir.exists()) + if (checkFile(sequenceOutputsDir)) { - for (File child : sequenceOutputsDir.listFiles()) + try (Stream stream = Files.list(sequenceOutputsDir.toPath())) { - if (!expectedFileNames.contains(child.getName())) - { - deleteFile(child, log); - } + stream.forEach(path -> { + File f = path.toFile(); + if (!expectedFileNames.contains(f.getName())) + { + deleteFile(f, log); + } + }); } } @@ -630,43 +505,239 @@ else if (!d.getFile().exists()) } } - private void inspectSequenceDir(File sequenceDir, Set expectedSequences, Logger log) throws IOException + private void inspectLibraryDir(File child, Set expectedLibraries, Logger log) { - for (File child : Objects.requireNonNull(sequenceDir.listFiles())) + if ("log".equals(FileUtil.getExtension(child)) || "xml".equals(FileUtil.getExtension(child))) + { + return; //always ignore log files + } + + if (!expectedLibraries.contains(child.getName())) + { + deleteFile(child, log); + return; + } + + //inspect within library + List expectedChildren = new ArrayList<>(); + int libraryId = Integer.parseInt(child.getName()); + Integer fastaId = new TableSelector(SequenceAnalysisSchema.getInstance().getSchema().getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES), PageFlowUtil.set("fasta_file")).getObject(libraryId, Integer.class); + if (fastaId == null) + { + log.error("Unable to find FASTA ExpData in DB matching jbrowse directory: " + child.getPath()); + return; + } + + ExpData fastaData = ExperimentService.get().getExpData(fastaId); + if (fastaData == null) + { + log.error("Unable to find ExpData: {}", fastaId); + return; + } + + File fasta = fastaData.getFile(); + if (!checkFile(fasta)) { - if (child.isDirectory()) + log.error("expected fasta file does not exist: " + fasta.getPath()); + } + + try + { + // Use this to retroactively convert existing genomes: + File gz = new File(fasta.getPath() + ".gz"); + if (!checkFile(gz)) + { + ReferenceGenomeImpl genome = new ReferenceGenomeImpl(fasta, fastaData, libraryId, null); + + // NOTE: we can hit a race condition in automated testing where a genome is newly created during a test, and the maintenance task runs concurrent with that test. + // This is a check to reduce the log level, which thereby prevents the test from erroring + Date created = new TableSelector(SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_REF_LIBRARIES), PageFlowUtil.set("created"), new SimpleFilter(FieldKey.fromString("rowId"), libraryId), null).getObject(Date.class); + long timeSinceCreated = new Date().getTime() - created.getTime(); + // 1000*60*20 = 20 minutes + Level l = timeSinceCreated > 1200000 ? Level.ERROR : Level.WARN; + + log.log(l, "GZipped genome missing for: " + genome.getGenomeId()); + + if (SystemUtils.IS_OS_WINDOWS) + { + log.warn("Cannot create bgzipped file on windows machine"); + } + else + { + genome.createGzippedFile(log); + } + } + + File gzi = new File(fasta.getPath() + ".gz.gzi"); + if (!checkFile(gzi)) + { + if (SystemUtils.IS_OS_WINDOWS) + { + log.warn("Cannot index gzipped FASTA on windows: " + fasta.getPath()); + } + else + { + new FastaIndexer(log).execute(gz); + } + } + + expectedChildren.add(fasta.getName() + ".gz"); + expectedChildren.add(fasta.getName() + ".gz.gzi"); + expectedChildren.add(fasta.getName() + ".gz.fai"); + + expectedChildren.add(fasta.getName()); + expectedChildren.add(fasta.getName() + ".fai"); + expectedChildren.add(FileUtil.getBaseName(fasta.getName()) + ".idKey.txt"); + expectedChildren.add(FileUtil.getBaseName(fasta.getName()) + ".dict"); + expectedChildren.add("libraryMembers.xml"); //temp file creating during pipeline job + expectedChildren.add("alignerIndexes"); + expectedChildren.add("tracks"); + expectedChildren.add("chainFiles"); + expectedChildren.add(".lastUpdate"); + + for (String fileName : Objects.requireNonNull(child.list())) { - try (DirectoryStream stream = Files.newDirectoryStream(child.toPath())) + if (!expectedChildren.contains(fileName)) { - if (!stream.iterator().hasNext()) + if ("log".equals(FileUtil.getExtension(fileName)) || "xml".equals(FileUtil.getExtension(fileName))) { - FileUtils.deleteDirectory(child); continue; } + + deleteFile(FileUtil.appendName(child, fileName), log); + } + } + + //check/verify tracks + File trackDir = FileUtil.appendName(child, "tracks"); + if (checkFile(trackDir)) + { + Set expectedTracks = new HashSet<>(); + TableInfo tracksTable = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_LIBRARY_TRACKS); + TableSelector tracksTs = new TableSelector(tracksTable, Collections.singleton("fileid"), new SimpleFilter(FieldKey.fromString("library_id"), libraryId), null); + for (Integer dataId : tracksTs.getArrayList(Integer.class)) + { + ExpData trackData = ExperimentService.get().getExpData(dataId); + if (trackData != null && trackData.getFile() != null) + { + expectedTracks.add(trackData.getFile().getName()); + if (!checkFile(trackData.getFile())) + { + log.error("expected track file does not exist: " + trackData.getFile().getPath()); + } + + expectedTracks.addAll(getAssociatedFiles(trackData.getFile(), true)); + } + else + { + log.warn("unable to find ExpData for track with dataId: " + dataId); + } } - inspectSequenceDir(child, expectedSequences, log); + try (Stream stream = Files.list(trackDir.toPath())) + { + stream.forEach(path -> { + File f = path.toFile(); + if (!expectedTracks.contains(f.getName())) + { + deleteFile(path.toFile(), log); + } + }); + } } - else + + //check/verify chainFiles + File chainDir = FileUtil.appendName(child, "chainFiles"); + if (checkFile(chainDir)) { - if (!expectedSequences.remove(child)) + Set expectedChains = new HashSet<>(); + TableInfo chainTable = SequenceAnalysisSchema.getTable(SequenceAnalysisSchema.TABLE_CHAIN_FILES); + TableSelector chainTs = new TableSelector(chainTable, Collections.singleton("chainFile"), new SimpleFilter(FieldKey.fromString("genomeId1"), libraryId), null); + for (Integer dataId : chainTs.getArrayList(Integer.class)) { - deleteFile(child, log); + ExpData chainData = ExperimentService.get().getExpData(dataId); + if (chainData != null && chainData.getFile() != null) + { + expectedChains.add(chainData.getFile().getName()); + if (!checkFile(chainData.getFile())) + { + log.error("expected chain file does not exist: " + chainData.getFile().getPath()); + } + } + } + + try (Stream stream = Files.list(trackDir.toPath())) + { + stream.forEach(path -> { + File f = path.toFile(); + if (!expectedChains.contains(f.getName())) + { + deleteFile(f, log); + } + }); } } } + catch (PipelineJobException | IOException e) + { + log.error("Error processing library directory: " + child.getPath(), e); + } + } + + private void inspectSequenceDir(File sequenceDir, Set expectedSequences, Logger log) throws IOException + { + try (Stream stream = Files.list(sequenceDir.toPath())) + { + stream.forEach(path -> { + File child = path.toFile(); + if (child.isDirectory()) + { + try + { + try (DirectoryStream stream2 = Files.newDirectoryStream(child.toPath())) + { + if (!stream2.iterator().hasNext()) + { + deleteFile(child, log); + return; + } + } + + inspectSequenceDir(child, expectedSequences, log); + } + catch (IOException e) + { + throw new RuntimeException(e); + } + } + else + { + if (!expectedSequences.remove(child)) + { + deleteFile(child, log); + } + } + }); + } } - private void deleteFile(File f, Logger log) throws IOException + private void deleteFile(File f, Logger log) { log.info("deleting sequence file: " + f.getPath()); - if (f.isDirectory()) + try { - FileUtils.deleteDirectory(f); + if (f.isDirectory()) + { + FileUtils.deleteDirectory(f); + } + else + { + Files.delete(f.toPath()); + } } - else + catch (IOException e) { - f.delete(); + log.error("Failed to delete file: " + f.getPath(), e); } } @@ -733,7 +804,7 @@ else if (new FileType("txt.gz").isType(f)) // NOTE: this allows modules to register handlers for extra ancillary files, such as seurat metadata SequenceAnalysisServiceImpl.get().getAccessoryFileProviders().forEach(fn -> { - ret.addAll(fn.apply(f).stream().map(File::getName).collect(Collectors.toList())); + ret.addAll(fn.apply(f).stream().map(File::getName).toList()); }); return ret; From 223b85104cf6dd1e57bfe3cb7e78bbdc89f7bf96 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 1 Sep 2026 11:57:45 -0700 Subject: [PATCH 08/23] Only use samtools merge when the inputs are sorted --- .../pipeline/SequenceAlignmentTask.java | 36 +++++++++++++++---- 1 file changed, 30 insertions(+), 6 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java index 8244e6d71..c9b05c323 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/pipeline/SequenceAlignmentTask.java @@ -1307,7 +1307,6 @@ private File doAlignThenMerge(ReferenceGenome referenceGenome, Readset rs, Map bams = new ArrayList<>(); for (File o : alignOutputs) { @@ -1317,20 +1316,45 @@ private File doAlignThenMerge(ReferenceGenome referenceGenome, Readset rs, Map sortOrders = alignOutputs.stream().map(x -> { + try + { + return SequenceUtil.getBamSortOrder(x); + } + catch (IOException e) + { + throw new RuntimeException(e); + } + }).collect(Collectors.toSet()); + //NOTE: merged BAMs will be deleted as intermediate files, and if we delete too early this breaks job resume - merger.mergeBams(bams, bam); - getHelper().getFileManager().addCommandsToAction(merger.getCommandsExecuted(), mergeAction); + String toolName; + if (sortOrders.size() > 1 || sortOrders.iterator().next() != SAMFileHeader.SortOrder.coordinate) + { + toolName = "MergeSamFiles"; + MergeSamFilesWrapper merger = new MergeSamFilesWrapper(getPipelineJob().getLogger()); + merger.execute(bams, bam, false); + getHelper().getFileManager().addCommandsToAction(merger.getCommandsExecuted(), mergeAction); + } + else + { + // This will be faster, but requires sorted input: + toolName = "Samtools merge"; + SamtoolsMerger merger = new SamtoolsMerger(getPipelineJob().getLogger()); + merger.mergeBams(bams, bam); + getHelper().getFileManager().addCommandsToAction(merger.getCommandsExecuted(), mergeAction); + } Date end = new Date(); mergeAction.setEndTime(end); - getJob().getLogger().info("MergeSamFiles Duration: " + DurationFormatUtils.formatDurationWords(end.getTime() - start.getTime(), true, true)); + getJob().getLogger().info(toolName + " Duration: " + DurationFormatUtils.formatDurationWords(end.getTime() - start.getTime(), true, true)); alignActions.add(mergeAction); } else { - bam = alignOutputs.get(0); + bam = alignOutputs.getFirst(); } return bam; From 11629bd45527344637abc854ca8d69211c18623f Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 2 Sep 2026 12:45:45 -0700 Subject: [PATCH 09/23] Bugfix to readset permission check --- .../org/labkey/sequenceanalysis/SequenceAnalysisController.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index 12d76bd0b..57344f7d6 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java @@ -1914,7 +1914,7 @@ else if (!d.getFile().exists()) { throw new PipelineValidationException("Missing file for data: " + o.get("dataId")); } - else if (d.getContainer().hasPermission(u, ReadPermission.class)) + else if (!d.getContainer().hasPermission(u, ReadPermission.class)) { throw new UnauthorizedException("You do not have permission to read data: " + o.get("dataId")); } From 2c48fc5f5ef318c49078f02b84c7b6f14285eb8d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 2 Sep 2026 18:45:52 -0700 Subject: [PATCH 10/23] Bump react-router-dom from 6.30.4 to 6.30.6 in /jbrowse (#420) Bumps [react-router-dom](https://github.com/remix-run/react-router/tree/HEAD/packages/react-router-dom) from 6.30.4 to 6.30.6. - [Release notes](https://github.com/remix-run/react-router/releases) - [Changelog](https://github.com/remix-run/react-router/blob/react-router-dom@6.30.6/packages/react-router-dom/CHANGELOG.md) - [Commits](https://github.com/remix-run/react-router/commits/react-router-dom@6.30.6/packages/react-router-dom) --- updated-dependencies: - dependency-name: react-router-dom dependency-version: 6.30.6 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- jbrowse/package-lock.json | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index be30363e5..7f93e1d0b 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -2682,9 +2682,9 @@ } }, "node_modules/@remix-run/router": { - "version": "1.23.3", - "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.23.3.tgz", - "integrity": "sha512-4An71tdz9X8+3sI4Qqqd2LWd9vS39J7sqd9EU4Scw7TJE/qB10Flv/UuqbPVgfQV9XoK8Np6jNquZitnZq5i+Q==", + "version": "1.23.4", + "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.23.4.tgz", + "integrity": "sha512-q7j5geK7xs3UJSdm9/iytUNclBnLmYx1EnSeCFXHPeutdqgIMeFeHtUZgS3EhlKxdBEAu8OwtJCwmLrEzpSs7Q==", "license": "MIT", "engines": { "node": ">=14.0.0" @@ -6923,12 +6923,12 @@ } }, "node_modules/react-router": { - "version": "6.30.4", - "resolved": "https://registry.npmjs.org/react-router/-/react-router-6.30.4.tgz", - "integrity": "sha512-SVUsDe+DybHM/WmYKIVYhZh1o5Dcuf16yM6WjG02Q9XVFMZIJyHYhwrr6bFBXZkVP6z69kNkMyBCujt8FaFLJA==", + "version": "6.30.6", + "resolved": "https://registry.npmjs.org/react-router/-/react-router-6.30.6.tgz", + "integrity": "sha512-5HfK7k5im7LTOB0EqCQmfvy4C13G92Ssj1VTmouTK3AJvyjKTnFuCV0vcMAD/JS+JC4DvDIBRrlAeJIFjh5VWg==", "license": "MIT", "dependencies": { - "@remix-run/router": "1.23.3" + "@remix-run/router": "1.23.4" }, "engines": { "node": ">=14.0.0" @@ -6938,13 +6938,13 @@ } }, "node_modules/react-router-dom": { - "version": "6.30.4", - "resolved": "https://registry.npmjs.org/react-router-dom/-/react-router-dom-6.30.4.tgz", - "integrity": "sha512-q4HvNl+mmDdkS0g+MqiBZNteQJCuimWoOyHMy4T/RQLAn9Z29+E91QXRaxOujeMl2HTzRSS0KFPd7lxX3PjV0Q==", + "version": "6.30.6", + "resolved": "https://registry.npmjs.org/react-router-dom/-/react-router-dom-6.30.6.tgz", + "integrity": "sha512-0RHKZz7wwffvkU+2MFVT2NnjK44ssLEV+m0CAJaS2Ksmorrwj7WxH00jO0SOCW26/tINUnJHToXblDs33I38YQ==", "license": "MIT", "dependencies": { - "@remix-run/router": "1.23.3", - "react-router": "6.30.4" + "@remix-run/router": "1.23.4", + "react-router": "6.30.6" }, "engines": { "node": ">=14.0.0" From 5bf78834921dbae0596e31acfa8b7ccf5af2baf3 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 3 Sep 2026 06:33:18 -0700 Subject: [PATCH 11/23] Bump the npm_and_yarn group across 1 directory with 3 updates (#419) Bumps the npm_and_yarn group with 1 update in the /jbrowse directory: [bootstrap](https://github.com/twbs/bootstrap). Removes `bootstrap` Updates `immutable` from 3.8.3 to 3.8.4 - [Release notes](https://github.com/immutable-js/immutable-js/releases) - [Changelog](https://github.com/immutable-js/immutable-js/blob/main/CHANGELOG.md) - [Commits](https://github.com/immutable-js/immutable-js/compare/v3.8.3...v3.8.4) Updates `react-router` from 6.30.6 to 7.18.3 - [Release notes](https://github.com/remix-run/react-router/releases) - [Changelog](https://github.com/remix-run/react-router/blob/react-router@7.18.3/packages/react-router/CHANGELOG.md) - [Commits](https://github.com/remix-run/react-router/commits/react-router@7.18.3/packages/react-router) --- updated-dependencies: - dependency-name: bootstrap dependency-version: dependency-type: indirect - dependency-name: immutable dependency-version: 3.8.4 dependency-type: indirect - dependency-name: react-router dependency-version: 7.18.3 dependency-type: indirect ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- jbrowse/package-lock.json | 128 +++++++++++++++++++------------------- jbrowse/package.json | 2 +- 2 files changed, 64 insertions(+), 66 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 7f93e1d0b..e2e92b7c0 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -16,7 +16,7 @@ "@jbrowse/plugin-variants": "^4.3.0", "@jbrowse/react-linear-genome-view2": "^4.3.0", "@labkey/api": "^1.52.2", - "@labkey/components": "^7.48.0", + "@labkey/components": "^7.62.0", "@mui/icons-material": "^7.3.9", "@mui/material": "^7.3.9", "@mui/utils": "^7.3.9", @@ -1903,9 +1903,9 @@ } }, "node_modules/@labkey/api": { - "version": "1.52.2", - "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.52.2.tgz", - "integrity": "sha512-LhzL5wwov5cXDm0pUvc5BHDq2qFeNjc9R3Xwa8aNlj1aJoBYC2yV1T9A4h/cVnPqcXgTgqKQTD04IkZ8bOgEvg==", + "version": "1.52.3", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.52.3.tgz", + "integrity": "sha512-Ac1efrlTh9/pq6ovN+L8M1Np2MXrC7IAIghRVRVbWg80gudq5Slh4NJOcnnfWmes+1D5Q+IJjI9xZ0BOZjWykw==", "license": "Apache-2.0" }, "node_modules/@labkey/build": { @@ -1939,32 +1939,31 @@ } }, "node_modules/@labkey/components": { - "version": "7.49.0", - "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-7.49.0.tgz", - "integrity": "sha512-vIQg37WYn5ZXo+5Gn0lJfDpqsjFpKVo+jelKxSuML+7wH6TvYBLTeBlk7wAKpLZfA5m1NDbxgf8WbViTyedmKw==", + "version": "7.62.0", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-7.62.0.tgz", + "integrity": "sha512-1py11YYqWQXpIzsSlBUIigq78eilk7Pfa7vw7SkypB9es6Xy50qCE8ZauElNxRpx7PU/KwUfUAFelJXYseulkA==", "license": "SEE LICENSE IN LICENSE.txt", "dependencies": { "@hello-pangea/dnd": "18.0.1", - "@labkey/api": "1.52.2", + "@labkey/api": "1.52.3", "@testing-library/dom": "~10.4.1", - "@testing-library/jest-dom": "~6.9.1", + "@testing-library/jest-dom": "~7.0.1", "@testing-library/react": "~16.3.2", "@testing-library/user-event": "~14.6.1", - "bootstrap": "~3.4.1", "classnames": "~2.5.1", "date-fns": "~3.6.0", "date-fns-tz": "~3.2.0", "font-awesome": "~4.7.0", - "immer": "~11.1.8", - "immutable": "~3.8.3", + "immer": "~11.1.15", + "immutable": "~3.8.4", "normalizr": "~3.6.2", "numeral": "~2.0.6", - "papaparse": "5.5.3", + "papaparse": "5.5.4", "react": "~18.3.1", "react-color": "~2.19.3", "react-datepicker": "~7.6.0", "react-dom": "~18.3.1", - "react-router-dom": "~6.30.4", + "react-router": "~7.18.2", "react-select": "~5.10.2", "react-treebeard": "~3.2.4", "vis-data": "~8.0.3", @@ -2681,15 +2680,6 @@ "url": "https://opencollective.com/popperjs" } }, - "node_modules/@remix-run/router": { - "version": "1.23.4", - "resolved": "https://registry.npmjs.org/@remix-run/router/-/router-1.23.4.tgz", - "integrity": "sha512-q7j5geK7xs3UJSdm9/iytUNclBnLmYx1EnSeCFXHPeutdqgIMeFeHtUZgS3EhlKxdBEAu8OwtJCwmLrEzpSs7Q==", - "license": "MIT", - "engines": { - "node": ">=14.0.0" - } - }, "node_modules/@rspack/binding": { "version": "2.1.7", "resolved": "https://registry.npmjs.org/@rspack/binding/-/binding-2.1.7.tgz", @@ -3015,9 +3005,9 @@ } }, "node_modules/@testing-library/jest-dom": { - "version": "6.9.1", - "resolved": "https://registry.npmjs.org/@testing-library/jest-dom/-/jest-dom-6.9.1.tgz", - "integrity": "sha512-zIcONa+hVtVSSep9UT3jZ5rizo2BsxgyDYU7WFD5eICBE7no3881HGeb/QkGfsJs6JTkY1aQhT7rIPC7e+0nnA==", + "version": "7.0.1", + "resolved": "https://registry.npmjs.org/@testing-library/jest-dom/-/jest-dom-7.0.1.tgz", + "integrity": "sha512-oMDTC3oA+6CXSO2JZnvOI7CA6oVub6kij5ggk9ohwye5slmkwxYDXcPOVxgMw/RQlticjtO0C1RZkR97HgrWMw==", "license": "MIT", "dependencies": { "@adobe/css-tools": "^4.4.0", @@ -3028,9 +3018,18 @@ "redent": "^3.0.0" }, "engines": { - "node": ">=14", + "node": ">=22", "npm": ">=6", "yarn": ">=1" + }, + "peerDependencies": { + "@testing-library/dom": ">=10 <11", + "vitest": ">= 0.32" + }, + "peerDependenciesMeta": { + "vitest": { + "optional": true + } } }, "node_modules/@testing-library/jest-dom/node_modules/dom-accessibility-api": { @@ -3897,16 +3896,6 @@ "dev": true, "license": "ISC" }, - "node_modules/bootstrap": { - "version": "3.4.1", - "resolved": "https://registry.npmjs.org/bootstrap/-/bootstrap-3.4.1.tgz", - "integrity": "sha512-yN5oZVmRCwe5aKwzRj6736nSmKDX7pLYwsXiCj/EYmo16hODaBiT4En5btW/jhBF/seV+XMx3aYwukYC3A49DA==", - "deprecated": "This version of Bootstrap is no longer supported. Please upgrade to the latest version.", - "license": "MIT", - "engines": { - "node": ">=6" - } - }, "node_modules/bootstrap-sass": { "version": "3.4.3", "resolved": "https://registry.npmjs.org/bootstrap-sass/-/bootstrap-sass-3.4.3.tgz", @@ -4256,6 +4245,19 @@ "integrity": "sha512-ASFBup0Mz1uyiIjANan1jzLQami9z1PoYSZCiiYW2FczPbenXc45FZdBZLzOT+r6+iciuEModtmCti+hjaAk0A==", "license": "MIT" }, + "node_modules/cookie": { + "version": "1.1.1", + "resolved": "https://registry.npmjs.org/cookie/-/cookie-1.1.1.tgz", + "integrity": "sha512-ei8Aos7ja0weRpFzJnEA9UHJ/7XQmqglbRwnf2ATjcB9Wq874VKH9kfjjirM6UhU2/E5fFYadylyhFldcqSidQ==", + "license": "MIT", + "engines": { + "node": ">=18" + }, + "funding": { + "type": "opencollective", + "url": "https://opencollective.com/express" + } + }, "node_modules/copy-to-clipboard": { "version": "3.3.3", "resolved": "https://registry.npmjs.org/copy-to-clipboard/-/copy-to-clipboard-3.3.3.tgz", @@ -5466,9 +5468,9 @@ } }, "node_modules/immutable": { - "version": "3.8.3", - "resolved": "https://registry.npmjs.org/immutable/-/immutable-3.8.3.tgz", - "integrity": "sha512-AUY/VyX0E5XlibOmWt10uabJzam1zlYjwiEgQSDc5+UIkFNaF9WM0JxXKaNMGf+F/ffUF+7kRKXM9A7C0xXqMg==", + "version": "3.8.4", + "resolved": "https://registry.npmjs.org/immutable/-/immutable-3.8.4.tgz", + "integrity": "sha512-ZQv17KolYrYmsDoDB8N67zhIKsNi9mGYlk96y/yuxyAqJB2hLzSGSM7k/sB0/ZvO4kx27U9+fBeD/XlLGh/uXQ==", "license": "MIT", "engines": { "node": ">=0.10.0" @@ -6470,9 +6472,9 @@ "license": "MIT" }, "node_modules/papaparse": { - "version": "5.5.3", - "resolved": "https://registry.npmjs.org/papaparse/-/papaparse-5.5.3.tgz", - "integrity": "sha512-5QvjGxYVjxO59MGU2lHVYpRWBBtKHnlIAcSe1uNFCkkptUh63NFRj0FJQm7nR67puEruUci/ZkjmEFrjCAyP4A==", + "version": "5.5.4", + "resolved": "https://registry.npmjs.org/papaparse/-/papaparse-5.5.4.tgz", + "integrity": "sha512-SwzWD9gl/ElwYLCI0nUja1mFJzjq2D8ziShfNBa7zCHzkOozeOGDwHWQ+tvCzEZcewecWZ5U7kUopDnG+DFYEQ==", "license": "MIT" }, "node_modules/param-case": { @@ -6923,35 +6925,25 @@ } }, "node_modules/react-router": { - "version": "6.30.6", - "resolved": "https://registry.npmjs.org/react-router/-/react-router-6.30.6.tgz", - "integrity": "sha512-5HfK7k5im7LTOB0EqCQmfvy4C13G92Ssj1VTmouTK3AJvyjKTnFuCV0vcMAD/JS+JC4DvDIBRrlAeJIFjh5VWg==", + "version": "7.18.3", + "resolved": "https://registry.npmjs.org/react-router/-/react-router-7.18.3.tgz", + "integrity": "sha512-gyXgtdr5uACJ5b1Q4udzjVV+tb/rlHIMJKuJ0e89R4Kzgz47z/rgP0dIKxktqIEUhDHluGTPJJH/wRha7CyqsA==", "license": "MIT", "dependencies": { - "@remix-run/router": "1.23.4" + "cookie": "^1.0.1", + "set-cookie-parser": "^2.6.0" }, "engines": { - "node": ">=14.0.0" + "node": ">=20.0.0" }, "peerDependencies": { - "react": ">=16.8" - } - }, - "node_modules/react-router-dom": { - "version": "6.30.6", - "resolved": "https://registry.npmjs.org/react-router-dom/-/react-router-dom-6.30.6.tgz", - "integrity": "sha512-0RHKZz7wwffvkU+2MFVT2NnjK44ssLEV+m0CAJaS2Ksmorrwj7WxH00jO0SOCW26/tINUnJHToXblDs33I38YQ==", - "license": "MIT", - "dependencies": { - "@remix-run/router": "1.23.4", - "react-router": "6.30.6" + "react": ">=18", + "react-dom": ">=18" }, - "engines": { - "node": ">=14.0.0" - }, - "peerDependencies": { - "react": ">=16.8", - "react-dom": ">=16.8" + "peerDependenciesMeta": { + "react-dom": { + "optional": true + } } }, "node_modules/react-select": { @@ -7358,6 +7350,12 @@ "node": ">=10" } }, + "node_modules/set-cookie-parser": { + "version": "2.7.2", + "resolved": "https://registry.npmjs.org/set-cookie-parser/-/set-cookie-parser-2.7.2.tgz", + "integrity": "sha512-oeM1lpU/UvhTxw+g3cIfxXHyJRc/uidd3yK1P242gzHds0udQBYzs3y8j4gCCW+ZJ7ad0yctld8RYO+bdurlvw==", + "license": "MIT" + }, "node_modules/set-function-length": { "version": "1.2.2", "resolved": "https://registry.npmjs.org/set-function-length/-/set-function-length-1.2.2.tgz", diff --git a/jbrowse/package.json b/jbrowse/package.json index 1ec605191..35463cf49 100644 --- a/jbrowse/package.json +++ b/jbrowse/package.json @@ -27,7 +27,7 @@ "@jbrowse/plugin-linear-genome-view": "^4.3.0", "@jbrowse/react-linear-genome-view2": "^4.3.0", "@labkey/api": "^1.52.2", - "@labkey/components": "^7.48.0", + "@labkey/components": "^7.62.0", "@mui/icons-material": "^7.3.9", "@mui/material": "^7.3.9", "@mui/utils": "^7.3.9", From aac7980491f3f593b654d6547a6eedc90137d0f6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 3 Sep 2026 06:47:14 -0700 Subject: [PATCH 12/23] Bump fast-uri in /jbrowse in the npm_and_yarn group across 1 directory (#421) Bumps the npm_and_yarn group with 1 update in the /jbrowse directory: [fast-uri](https://github.com/fastify/fast-uri). Updates `fast-uri` from 3.1.5 to 3.1.7 - [Release notes](https://github.com/fastify/fast-uri/releases) - [Commits](https://github.com/fastify/fast-uri/compare/v3.1.5...v3.1.7) --- updated-dependencies: - dependency-name: fast-uri dependency-version: 3.1.7 dependency-type: indirect dependency-group: npm_and_yarn ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- jbrowse/package-lock.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index e2e92b7c0..d9ac7c01f 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -5021,9 +5021,9 @@ "license": "MIT" }, "node_modules/fast-uri": { - "version": "3.1.5", - "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.5.tgz", - "integrity": "sha512-gHwA1O9LDIcKunMKhObS/HimwtehO1nPUECKAu5TpKgaO19fcWEl4bliWe1jWxVFvIXztJjjQ4L8XQ1EU9f7Jw==", + "version": "3.1.7", + "resolved": "https://registry.npmjs.org/fast-uri/-/fast-uri-3.1.7.tgz", + "integrity": "sha512-dOvZVzjdZdz7phd9v6jCbwxrBW3fK6n8Rc0CtdmM4bumzMnxywBYhuph6J819RRw/ku+rLbelwfMunktuzVVHg==", "dev": true, "funding": [ { From aeba6adbd1f69659541789a27643b9546e88e52f Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 3 Sep 2026 16:29:52 -0700 Subject: [PATCH 13/23] Increase logging in SequenceAnalysisMaintenanceTask --- .../SequenceAnalysisMaintenanceTask.java | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java index aabb844dc..891c6dd17 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java @@ -640,7 +640,7 @@ private void inspectLibraryDir(File child, Set expectedLibraries, Logger File f = path.toFile(); if (!expectedTracks.contains(f.getName())) { - deleteFile(path.toFile(), log); + deleteFile(path.toFile(), log, "Trigger by tracks, genome " + libraryId + ", total expected tracks: " + expectedTracks.size()); } }); } @@ -722,8 +722,18 @@ private void inspectSequenceDir(File sequenceDir, Set expectedSequences, L } private void deleteFile(File f, Logger log) + { + deleteFile(f, log, null); + } + + private void deleteFile(File f, Logger log, String msg) { log.info("deleting sequence file: " + f.getPath()); + if (msg != null) + { + log.info(msg); + } + try { if (f.isDirectory()) From 1d5c271269446358f8f5d926852d427f0997d06b Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 3 Sep 2026 18:56:43 -0700 Subject: [PATCH 14/23] Debug SequenceAnalysisMaintenanceTask --- .../sequenceanalysis/SequenceAnalysisMaintenanceTask.java | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java index 891c6dd17..15b249f5a 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java @@ -1,6 +1,7 @@ package org.labkey.sequenceanalysis; import org.apache.commons.io.FileUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.SystemUtils; import org.apache.logging.log4j.Level; import org.apache.logging.log4j.Logger; @@ -640,7 +641,9 @@ private void inspectLibraryDir(File child, Set expectedLibraries, Logger File f = path.toFile(); if (!expectedTracks.contains(f.getName())) { - deleteFile(path.toFile(), log, "Trigger by tracks, genome " + libraryId + ", total expected tracks: " + expectedTracks.size()); + log.info("Would delete track: " + f.getPath()); + log.info("Expected tracks: [" + StringUtils.join(expectedTracks, ",") + "]"); + //deleteFile(f, log, "Trigger by tracks, genome " + libraryId + ", total expected tracks: " + expectedTracks.size()); } }); } From 7c6b6d1710de8b2fce90250d6ef9ee4141feb76c Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 3 Sep 2026 19:38:50 -0700 Subject: [PATCH 15/23] Properly drop constraint --- .../dbscripts/postgresql/sequenceanalysis-12.333-12.334.sql | 1 + .../dbscripts/sqlserver/sequenceanalysis-12.333-12.334.sql | 1 + .../src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java | 2 +- 3 files changed, 3 insertions(+), 1 deletion(-) create mode 100644 SequenceAnalysis/resources/schemas/dbscripts/postgresql/sequenceanalysis-12.333-12.334.sql create mode 100644 SequenceAnalysis/resources/schemas/dbscripts/sqlserver/sequenceanalysis-12.333-12.334.sql diff --git a/SequenceAnalysis/resources/schemas/dbscripts/postgresql/sequenceanalysis-12.333-12.334.sql b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/sequenceanalysis-12.333-12.334.sql new file mode 100644 index 000000000..48b5f2499 --- /dev/null +++ b/SequenceAnalysis/resources/schemas/dbscripts/postgresql/sequenceanalysis-12.333-12.334.sql @@ -0,0 +1 @@ +ALTER TABLE sequenceanalysis.barcodes DROP CONSTRAINT IF EXISTS UNIQUE_barcodes; \ No newline at end of file diff --git a/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/sequenceanalysis-12.333-12.334.sql b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/sequenceanalysis-12.333-12.334.sql new file mode 100644 index 000000000..48b5f2499 --- /dev/null +++ b/SequenceAnalysis/resources/schemas/dbscripts/sqlserver/sequenceanalysis-12.333-12.334.sql @@ -0,0 +1 @@ +ALTER TABLE sequenceanalysis.barcodes DROP CONSTRAINT IF EXISTS UNIQUE_barcodes; \ No newline at end of file diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java index 7d5cc9d52..c5d12f175 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java @@ -213,7 +213,7 @@ public String getName() @Override public Double getSchemaVersion() { - return 12.333; + return 12.334; } @Override From 238cf5fac47afa06a9fbf846c740a4f68184cd92 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 4 Sep 2026 09:45:45 -0700 Subject: [PATCH 16/23] Bugfix to SequenceAnalysisMaintenanceTask --- .../SequenceAnalysisMaintenanceTask.java | 17 ++--------------- 1 file changed, 2 insertions(+), 15 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java index 15b249f5a..f3a95e772 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java @@ -641,9 +641,7 @@ private void inspectLibraryDir(File child, Set expectedLibraries, Logger File f = path.toFile(); if (!expectedTracks.contains(f.getName())) { - log.info("Would delete track: " + f.getPath()); - log.info("Expected tracks: [" + StringUtils.join(expectedTracks, ",") + "]"); - //deleteFile(f, log, "Trigger by tracks, genome " + libraryId + ", total expected tracks: " + expectedTracks.size()); + deleteFile(f, log); } }); } @@ -669,7 +667,7 @@ private void inspectLibraryDir(File child, Set expectedLibraries, Logger } } - try (Stream stream = Files.list(trackDir.toPath())) + try (Stream stream = Files.list(chainDir.toPath())) { stream.forEach(path -> { File f = path.toFile(); @@ -726,17 +724,6 @@ private void inspectSequenceDir(File sequenceDir, Set expectedSequences, L private void deleteFile(File f, Logger log) { - deleteFile(f, log, null); - } - - private void deleteFile(File f, Logger log, String msg) - { - log.info("deleting sequence file: " + f.getPath()); - if (msg != null) - { - log.info(msg); - } - try { if (f.isDirectory()) From 9201aafd1289506e826c7c7abc177ecf845a79b9 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 7 Sep 2026 07:08:46 -0700 Subject: [PATCH 17/23] Bugfix to ArchiveReadsetsAction --- .../sequenceanalysis/SequenceAnalysisController.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java index 57344f7d6..638f77fcf 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisController.java @@ -208,6 +208,7 @@ import java.util.List; import java.util.Map; import java.util.Set; +import java.util.stream.Collectors; import java.util.zip.GZIPInputStream; import java.util.zip.ZipEntry; import java.util.zip.ZipOutputStream; @@ -5161,14 +5162,13 @@ public ApiResponse execute(ArchiveReadsetsForm form, BindException errors) throw if (!toUpdate.isEmpty()) { - List> keys = new ArrayList<>(); - toUpdate.forEach(row -> { - keys.add(new CaseInsensitiveHashMap<>(Map.of("rowid", row.get("rowid")))); - }); + // Remove duplicates: + List> uniqueToUpdate = toUpdate.stream().distinct().toList(); + List> keys = uniqueToUpdate.stream().map(row -> new CaseInsensitiveHashMap<>(Map.of("rowid", row.get("rowid")))).collect(Collectors.toList()); try { - readData.getUpdateService().updateRows(getUser(), getContainer(), toUpdate, keys, null, null); + readData.getUpdateService().updateRows(getUser(), getContainer(), uniqueToUpdate, keys, null, null); } catch (Exception e) { From fd3a611e58a6adbc3dd24d87a1689de0a1c928c4 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Sep 2026 11:30:01 -0700 Subject: [PATCH 18/23] Update @labkey packages --- jbrowse/package-lock.json | 142 +++++++++++++------------------------- jbrowse/package.json | 4 +- 2 files changed, 50 insertions(+), 96 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index d9ac7c01f..585d8b49f 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -15,8 +15,8 @@ "@jbrowse/plugin-linear-genome-view": "^4.3.0", "@jbrowse/plugin-variants": "^4.3.0", "@jbrowse/react-linear-genome-view2": "^4.3.0", - "@labkey/api": "^1.52.2", - "@labkey/components": "^7.62.0", + "@labkey/api": "^1.52.5", + "@labkey/components": "^7.64.1", "@mui/icons-material": "^7.3.9", "@mui/material": "^7.3.9", "@mui/utils": "^7.3.9", @@ -135,6 +135,7 @@ "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.29.7.tgz", "integrity": "sha512-Nq8OhGWiZIZGV6hLHoyAKLLcJihP/xFeBMGJoUrxTX2psI8dCifzLhZISFb+VWS3wFMRDmCGw5R+dOySCqPLhw==", "license": "MIT", + "peer": true, "engines": { "node": ">=6.9.0" } @@ -207,29 +208,6 @@ "node": ">=0.8.0" } }, - "node_modules/@emnapi/core": { - "version": "1.11.2", - "resolved": "https://registry.npmjs.org/@emnapi/core/-/core-1.11.2.tgz", - "integrity": "sha512-TC8MkTuZUtcTSiFeuC0ksCh9QIJ5+F21MvZ4Wn4ORfYaFJ/0dsiudv5tVkejgwZlwQ39jL9WWDe2lz8x0WglOA==", - "dev": true, - "license": "MIT", - "optional": true, - "dependencies": { - "@emnapi/wasi-threads": "1.2.2", - "tslib": "^2.4.0" - } - }, - "node_modules/@emnapi/runtime": { - "version": "1.11.2", - "resolved": "https://registry.npmjs.org/@emnapi/runtime/-/runtime-1.11.2.tgz", - "integrity": "sha512-kyOl3X0DuTiT1h2ft8r2fYO8JYtU9a9Xis/zBSiGArNaagCOWx90N1k2wxp18czFDH+OgcWGb5ZP/XMt3dcyPA==", - "dev": true, - "license": "MIT", - "optional": true, - "dependencies": { - "tslib": "^2.4.0" - } - }, "node_modules/@emnapi/wasi-threads": { "version": "1.2.2", "resolved": "https://registry.npmjs.org/@emnapi/wasi-threads/-/wasi-threads-1.2.2.tgz", @@ -1903,9 +1881,9 @@ } }, "node_modules/@labkey/api": { - "version": "1.52.3", - "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.52.3.tgz", - "integrity": "sha512-Ac1efrlTh9/pq6ovN+L8M1Np2MXrC7IAIghRVRVbWg80gudq5Slh4NJOcnnfWmes+1D5Q+IJjI9xZ0BOZjWykw==", + "version": "1.52.5", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.52.5.tgz", + "integrity": "sha512-yEPlYvgXAQko9xMvWp0xchHWvM0gMe/PacDWBBwOvcoYJWtcGnDb5KSNMUHQNpki7shd/vB0GYKGrKalxQxEHA==", "license": "Apache-2.0" }, "node_modules/@labkey/build": { @@ -1939,13 +1917,13 @@ } }, "node_modules/@labkey/components": { - "version": "7.62.0", - "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-7.62.0.tgz", - "integrity": "sha512-1py11YYqWQXpIzsSlBUIigq78eilk7Pfa7vw7SkypB9es6Xy50qCE8ZauElNxRpx7PU/KwUfUAFelJXYseulkA==", + "version": "7.66.1", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-7.66.1.tgz", + "integrity": "sha512-abM7enKWG+NGIzqYsXfV95bJv0Qua+mssyk076uIL98dROOglstCy+ho1WuWicHj9ifMjBmYlxiwNFkLyNkuaA==", "license": "SEE LICENSE IN LICENSE.txt", "dependencies": { "@hello-pangea/dnd": "18.0.1", - "@labkey/api": "1.52.3", + "@labkey/api": "1.52.5", "@testing-library/dom": "~10.4.1", "@testing-library/jest-dom": "~7.0.1", "@testing-library/react": "~16.3.2", @@ -1975,6 +1953,7 @@ "resolved": "https://registry.npmjs.org/react/-/react-18.3.1.tgz", "integrity": "sha512-wS+hAgJShR0KhEvPJArfuPVN1+Hz1t0Y6n5jLrGQbkb4urgPE/0Rve+1kMB1v/oWgHgm4WIcV+i7F2pTVj+2iQ==", "license": "MIT", + "peer": true, "dependencies": { "loose-envify": "^1.1.0" }, @@ -2051,6 +2030,7 @@ "resolved": "https://registry.npmjs.org/@mui/material/-/material-7.3.11.tgz", "integrity": "sha512-yq8bPc3LxOwKRWpcjRgDkYFmpM6aKlARfESTmOQcvLYFeJwtHte2tw6hJDrb8sk8wcvpDprHEHVaoUU0MslIkw==", "license": "MIT", + "peer": true, "dependencies": { "@babel/runtime": "^7.28.6", "@mui/core-downloads-tracker": "^7.3.11", @@ -2161,6 +2141,7 @@ "resolved": "https://registry.npmjs.org/@mui/system/-/system-7.3.11.tgz", "integrity": "sha512-7izwGWdNawAKpBKcRlx7f2gFnAAjmASBWvMcyX4YYEeLOFsbfGRbUYGInvnAcUeql3rPxI7F9Ft4oY2OLRz44g==", "license": "MIT", + "peer": true, "dependencies": { "@babel/runtime": "^7.28.6", "@mui/private-theming": "^7.3.11", @@ -2896,6 +2877,7 @@ "integrity": "sha512-d5Ju3zXzGgbqQWvlMlLUtek2eFPIzsFe2QOF4nwTAknxo/4OZ64t+kPT9nM6fr3aZX93VK0R3v02/kZYIRrV9Q==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@rspack/binding": "2.1.7" }, @@ -2939,6 +2921,7 @@ "integrity": "sha512-WkCi6bWThVX5Ziv04srPaRoCoUY5FJolO4gqzE7xPO0XbXShsGnwn0vGD0DFfnYFcw9VSsxlmeCDV799lNYclA==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "@rspack/dev-middleware": "^2.0.3" }, @@ -2990,6 +2973,7 @@ "resolved": "https://registry.npmjs.org/@testing-library/dom/-/dom-10.4.1.tgz", "integrity": "sha512-o4PXJQidqJl82ckFaXUeoAW+XysPLauYI43Abki5hABd853iMhitooc6znOnczgbTYmEP6U6/y1ZyKAIsvMKGg==", "license": "MIT", + "peer": true, "dependencies": { "@babel/code-frame": "^7.10.4", "@babel/runtime": "^7.12.5", @@ -3169,8 +3153,7 @@ "resolved": "https://registry.npmjs.org/@types/estree/-/estree-1.0.9.tgz", "integrity": "sha512-GhdPgy1el4/ImP05X05Uw4cw2/M93BCUmnEvWZNStlCzEKME4Fkk+YpoA5OiHNQmoS7Cafb8Xa3Pya8m1Qrzeg==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@types/file-saver-es": { "version": "2.0.3", @@ -3182,8 +3165,7 @@ "version": "2.0.46", "resolved": "https://registry.npmjs.org/@types/hammerjs/-/hammerjs-2.0.46.tgz", "integrity": "sha512-ynRvcq6wvqexJ9brDMS4BnBLzmr0e14d6ZJTEShTBWKymQiHwlAyGu0ZPEFI2Fh1U53F7tN9ufClWM5KvqkKOw==", - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@types/html-minifier-terser": { "version": "6.1.0", @@ -3264,8 +3246,7 @@ "resolved": "https://registry.npmjs.org/@types/json-schema/-/json-schema-7.0.15.tgz", "integrity": "sha512-5+fP8P8MFNC+AyZCDxrB2pkZFPGzqQWUzpSeuuVLvm8VMcorNYavBqoFcxK8bQz4Qsbn4oUEEem4wDLfcysGHA==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@types/node": { "version": "26.1.2", @@ -3294,6 +3275,7 @@ "resolved": "https://registry.npmjs.org/@types/react/-/react-19.2.17.tgz", "integrity": "sha512-MXfmqaVPEVgkBT/aY0aGCkRWWtByiYQXo3xdQ8r5RzuFrPiRn8Gar2tQdXSUQ2GKV3bkXckek89V8wQBY2Q/Aw==", "license": "MIT", + "peer": true, "dependencies": { "csstype": "^3.2.2" } @@ -3304,6 +3286,7 @@ "integrity": "sha512-jp2L/eY6fn+KgVVQAOqYItbF0VY/YApe5Mz2F0aykSO8gx31bYCZyvSeYxCHKvzHG5eZjc+zyaS5BrBWya2+kQ==", "devOptional": true, "license": "MIT", + "peer": true, "peerDependencies": { "@types/react": "^19.2.0" } @@ -3360,7 +3343,6 @@ "integrity": "sha512-nuBEDgQfm1ccRp/8bCQrx1frohyufl4JlbMMZ4P1wpeOfDhF6FQkxZJ1b/e+PLwr6X1Nhw6OLme5usuBWYBvuQ==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "@webassemblyjs/helper-numbers": "1.13.2", "@webassemblyjs/helper-wasm-bytecode": "1.13.2" @@ -3371,24 +3353,21 @@ "resolved": "https://registry.npmjs.org/@webassemblyjs/floating-point-hex-parser/-/floating-point-hex-parser-1.13.2.tgz", "integrity": "sha512-6oXyTOzbKxGH4steLbLNOu71Oj+C8Lg34n6CqRvqfS2O71BxY6ByfMDRhBytzknj9yGUPVJ1qIKhRlAwO1AovA==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@webassemblyjs/helper-api-error": { "version": "1.13.2", "resolved": "https://registry.npmjs.org/@webassemblyjs/helper-api-error/-/helper-api-error-1.13.2.tgz", "integrity": "sha512-U56GMYxy4ZQCbDZd6JuvvNV/WFildOjsaWD3Tzzvmw/mas3cXzRJPMjP83JqEsgSbyrmaGjBfDtV7KDXV9UzFQ==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@webassemblyjs/helper-buffer": { "version": "1.14.1", "resolved": "https://registry.npmjs.org/@webassemblyjs/helper-buffer/-/helper-buffer-1.14.1.tgz", "integrity": "sha512-jyH7wtcHiKssDtFPRB+iQdxlDf96m0E39yb0k5uJVhFGleZFoNw1c4aeIcVUPPbXUVJ94wwnMOAqUHyzoEPVMA==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@webassemblyjs/helper-numbers": { "version": "1.13.2", @@ -3396,7 +3375,6 @@ "integrity": "sha512-FE8aCmS5Q6eQYcV3gI35O4J789wlQA+7JrqTTpJqn5emA4U2hvwJmvFRC0HODS+3Ye6WioDklgd6scJ3+PLnEA==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "@webassemblyjs/floating-point-hex-parser": "1.13.2", "@webassemblyjs/helper-api-error": "1.13.2", @@ -3408,8 +3386,7 @@ "resolved": "https://registry.npmjs.org/@webassemblyjs/helper-wasm-bytecode/-/helper-wasm-bytecode-1.13.2.tgz", "integrity": "sha512-3QbLKy93F0EAIXLh0ogEVR6rOubA9AoZ+WRYhNbFyuB70j3dRdwH9g+qXhLAO0kiYGlg3TxDV+I4rQTr/YNXkA==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@webassemblyjs/helper-wasm-section": { "version": "1.14.1", @@ -3417,7 +3394,6 @@ "integrity": "sha512-ds5mXEqTJ6oxRoqjhWDU83OgzAYjwsCV8Lo/N+oRsNDmx/ZDpqalmrtgOMkHwxsG0iI//3BwWAErYRHtgn0dZw==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "@webassemblyjs/ast": "1.14.1", "@webassemblyjs/helper-buffer": "1.14.1", @@ -3431,7 +3407,6 @@ "integrity": "sha512-4LtOzh58S/5lX4ITKxnAK2USuNEvpdVV9AlgGQb8rJDHaLeHciwG4zlGr0j/SNWlr7x3vO1lDEsuePvtcDNCkw==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "@xtuc/ieee754": "^1.2.0" } @@ -3442,7 +3417,6 @@ "integrity": "sha512-Lde1oNoIdzVzdkNEAWZ1dZ5orIbff80YPdHx20mrHwHrVNNTjNr8E3xz9BdpcGqRQbAEa+fkrCb+fRFTl/6sQw==", "dev": true, "license": "Apache-2.0", - "peer": true, "dependencies": { "@xtuc/long": "4.2.2" } @@ -3452,8 +3426,7 @@ "resolved": "https://registry.npmjs.org/@webassemblyjs/utf8/-/utf8-1.13.2.tgz", "integrity": "sha512-3NQWGjKTASY1xV5m7Hr0iPeXD9+RDobLll3T9d2AO+g3my8xy5peVyjSag4I50mR1bBSN/Ct12lo+R9tJk0NZQ==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/@webassemblyjs/wasm-edit": { "version": "1.14.1", @@ -3461,7 +3434,6 @@ "integrity": "sha512-RNJUIQH/J8iA/1NzlE4N7KtyZNHi3w7at7hDjvRNm5rcUXa00z1vRz3glZoULfJ5mpvYhLybmVcwcjGrC1pRrQ==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "@webassemblyjs/ast": "1.14.1", "@webassemblyjs/helper-buffer": "1.14.1", @@ -3479,7 +3451,6 @@ "integrity": "sha512-AmomSIjP8ZbfGQhumkNvgC33AY7qtMCXnN6bL2u2Js4gVCg8fp735aEiMSBbDR7UQIj90n4wKAFUSEd0QN2Ukg==", "dev": true, "license": "MIT", - 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"license": "BSD-3-Clause", - "peer": true + "license": "BSD-3-Clause" }, "node_modules/@xtuc/long": { "version": "4.2.2", "resolved": "https://registry.npmjs.org/@xtuc/long/-/long-4.2.2.tgz", "integrity": "sha512-NuHqBY1PB/D8xU6s/thBgOAiAP7HOYDQ32+BFZILJ8ivkUkAHQnWfn6WhL79Owj1qmUnoN/YPhktdIoucipkAQ==", "dev": true, - "license": "Apache-2.0", - "peer": true + "license": "Apache-2.0" }, "node_modules/acorn": { "version": "8.18.0", @@ -3592,6 +3558,7 @@ "integrity": "sha512-Thbli+OlOj+iMPYFBVBfJ3OmCAnaSyNn4M1vz9T6Gka5Jt9ba/HIR56joy65tY6kx/FCF5VXNB819Y7/GUrBGA==", "dev": true, "license": "MIT", + "peer": true, "dependencies": { "fast-deep-equal": "^3.1.3", "fast-uri": "^3.0.1", @@ -3609,7 +3576,6 @@ "integrity": "sha512-Wx0Kx52hxE7C18hkMEggYlEifqWZtYaRgouJor+WMdPnQyEK13vgEWyVNup7SoeeoLMsr4kf5h6dOW11I15MUA==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "ajv": "^8.0.0" }, @@ -3628,7 +3594,6 @@ "integrity": "sha512-YCS/JNFAUyr5vAuhk1DWm1CBxRHW9LbJ2ozWeemrIqpbsqKjHVxYPyi5GC0rjZIT5JxJ3virVTS8wk4i/Z+krw==", "dev": true, "license": "MIT", - 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"peer": true, "dependencies": { "@types/node": "*", "merge-stream": "^2.0.0", @@ -5890,7 +5843,6 @@ "integrity": "sha512-MpUEN2OodtUzxvKQl72cUF7RQ5EiHsGvSsVG0ia9c5RbWGL2CI4C7EpPS8UTBIplnlzZiNuV56w+FuNxy3ty2Q==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "has-flag": "^4.0.0" }, @@ -6112,8 +6064,7 @@ "resolved": "https://registry.npmjs.org/merge-stream/-/merge-stream-2.0.0.tgz", "integrity": "sha512-abv/qOcuPfk3URPfDzmZU1LKmuw8kT+0nIHvKrKgFrwifol/doWcdA4ZqsWQ8ENrFKkd67Mfpo/LovbIUsbt3w==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/mime-db": { "version": "1.54.0", @@ -6121,7 +6072,6 @@ "integrity": "sha512-aU5EJuIN2WDemCcAp2vFBfp/m4EAhWJnUNSSw0ixs7/kXbd6Pg64EmwJkNdFhB8aWt1sH2CTXrLxo/iAGV3oPQ==", "dev": true, "license": "MIT", - "peer": true, "engines": { "node": ">= 0.6" } @@ -6157,7 +6107,6 @@ "integrity": "sha512-DoeAZz8Q1C1znwsUzej1fdoi4jCf7/+Em27ouLqfK/+3m8G+D7yDhUwrc3CNhjSzGUN1kn7Iv4sWmjflQHenpw==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "@jridgewell/trace-mapping": "^0.3.25", "jest-worker": "^27.4.5", @@ -6241,6 +6190,7 @@ "resolved": "https://registry.npmjs.org/mobx/-/mobx-6.16.1.tgz", "integrity": "sha512-syNcDdX3KT+Jq3je6eGjBhuc24Z68td2VG0zNFqRswaE433D9SNH5VRy/xrGbJsUixfppLLccXhAW9JSf6n+SQ==", "license": "MIT", + "peer": true, "funding": { "type": "opencollective", "url": "https://opencollective.com/mobx" @@ -6336,8 +6286,7 @@ "resolved": "https://registry.npmjs.org/neo-async/-/neo-async-2.6.2.tgz", "integrity": "sha512-Yd3UES5mWCSqR+qNT93S3UoYUkqAZ9lLg8a7g9rimsWmYGK8cVToA4/sF3RrshdyV3sAGMXVUmpMYOw+dLpOuw==", "dev": true, - "license": "MIT", - "peer": true + "license": "MIT" }, "node_modules/no-case": { "version": "3.0.4", @@ -6371,7 +6320,6 @@ "integrity": "sha512-wRNIrw4DmVLKQlbgOMdkMx27Wrpzes2hh5Jtbi2bjPd+4wJstWIqP5A+lscnqbm0xxmT5Bpg8Lec5ItEBwx6BQ==", "dev": true, "license": "MIT", - "peer": true, "engines": { "node": ">=18" } @@ -6619,6 +6567,7 @@ } ], "license": "MIT", + "peer": true, "dependencies": { "nanoid": "^3.3.16", "picocolors": "^1.1.1", @@ -6767,6 +6716,7 @@ "resolved": "https://registry.npmjs.org/prop-types/-/prop-types-15.8.1.tgz", "integrity": "sha512-oj87CgZICdulUohogVAR7AjlC0327U4el4L6eAvOqCeudMDVU0NThNaV+b9Df4dXgSP1gXMTnPdhfe/2qDH5cg==", "license": "MIT", + "peer": true, "dependencies": { "loose-envify": "^1.4.0", "object-assign": "^4.1.1", @@ -6790,6 +6740,7 @@ "resolved": "https://registry.npmjs.org/react/-/react-19.2.8.tgz", "integrity": "sha512-PWaYA1L/q9u2u7xYQi+Y3L3Yfnie7XyLeaJICV1MGD6LprsBxcAqGjYyr0eY3p+QdsA+x/Irkt4Qif8D63+Sbw==", "license": "MIT", + "peer": true, "engines": { "node": ">=0.10.0" } @@ -6832,6 +6783,7 @@ "resolved": "https://registry.npmjs.org/react-dom/-/react-dom-19.2.8.tgz", "integrity": "sha512-rVprimfGBG3DR+Tq0IQG2DT5PxKth1WIGDmj5yPmlzr4YBe7uyE+Du4oVqTDXZSHGGGXRtTJEGSSePyQCMBglQ==", "license": "MIT", + "peer": true, "dependencies": { "scheduler": "^0.27.0" }, @@ -6920,6 +6872,7 @@ "integrity": "sha512-QgT5//D3jfjJb6Gsjxv0Slpj23ip+HtOpnNgnb2S5zU3CB26G/IDPGoy4RJB42wzFE46DRsstbW6tKHoKbhAxw==", "dev": true, "license": "MIT", + "peer": true, "engines": { "node": ">=0.10.0" } @@ -7073,7 +7026,8 @@ "version": "5.0.1", "resolved": "https://registry.npmjs.org/redux/-/redux-5.0.1.tgz", "integrity": "sha512-M9/ELqF6fy8FwmkpnF0S3YKOqMyoWJ4+CS5Efg2ct3oY9daQvd/Pc71FpGZsVsbl3Cpb+IIcjBDUnnyBdQbq4w==", - "license": "MIT" + "license": "MIT", + "peer": true }, "node_modules/regex-parser": { "version": "2.3.1", @@ -7322,7 +7276,6 @@ "integrity": "sha512-eflK8wEtyOE6+hsaRVPxvUKYCpRgzLqDTb8krvAsRIwOGlHoSgYLgBXoubGgLd2fT41/OUYdb48v4k4WWHQurA==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "@types/json-schema": "^7.0.9", "ajv": "^8.9.0", @@ -7845,7 +7798,8 @@ "version": "2.8.1", "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.8.1.tgz", "integrity": "sha512-oJFu94HQb+KVduSUQL7wnpmqnfmLsOA/nAh6b6EH0wCEoK0/mPeXU6c3wKDV83MkOuHPRHtSXKKU99IBazS/2w==", - "license": "0BSD" + "license": "0BSD", + "peer": true }, "node_modules/typescript": { "version": "6.0.3", @@ -7853,6 +7807,7 @@ "integrity": "sha512-y2TvuxSZPDyQakkFRPZHKFm+KKVqIisdg9/CZwm9ftvKXLP8NRWj38/ODjNbr43SsoXqNuAisEf1GdCxqWcdBw==", "dev": true, "license": "Apache-2.0", + "peer": true, "bin": { "tsc": "bin/tsc", "tsserver": "bin/tsserver" @@ -7912,7 +7867,6 @@ } ], "license": "MIT", - "peer": true, "dependencies": { "escalade": "^3.2.0", "picocolors": "^1.1.1" @@ -7970,6 +7924,7 @@ "https://github.com/sponsors/ctavan" ], "license": "MIT", + "peer": true, "bin": { "uuid": "dist-node/bin/uuid" } @@ -8026,6 +7981,7 @@ "resolved": "https://registry.npmjs.org/vis-data/-/vis-data-8.0.4.tgz", "integrity": "sha512-TsN0sMHqIRpdfg6TNPtfdINpkgxtnQP6JNWCaiSwvou5seXqKiP5eERkaBg+Y56wyJ4FZTeOEs/dEmWEPrpltQ==", "license": "(Apache-2.0 OR MIT)", + "peer": true, "funding": { "type": "opencollective", "url": "https://opencollective.com/visjs" @@ -8077,7 +8033,6 @@ "integrity": "sha512-6i/00NBjP4yGPs+caKSyRfpTF/8Torsu0MOW3mMzIbhgISFder8i7xbqgHlLMwJrdiN8ndBV3UA1/AfzPSr+jg==", "dev": true, "license": "MIT", - "peer": true, "dependencies": { "graceful-fs": "^4.1.2" }, @@ -8184,7 +8139,6 @@ "integrity": "sha512-jyuiGJdtvY434z5bUZrjz67v76/ePNvFZTp9Mdz29IlH4+GPsgyGjiv0fKI+M7BdkU6ADjulUcKAd3tUK3WlEw==", "dev": true, "license": "MIT", - "peer": true, "engines": { "node": ">=10.13.0" } diff --git a/jbrowse/package.json b/jbrowse/package.json index 35463cf49..64602db57 100644 --- a/jbrowse/package.json +++ b/jbrowse/package.json @@ -26,8 +26,8 @@ "@jbrowse/plugin-variants": "^4.3.0", "@jbrowse/plugin-linear-genome-view": "^4.3.0", "@jbrowse/react-linear-genome-view2": "^4.3.0", - "@labkey/api": "^1.52.2", - "@labkey/components": "^7.62.0", + "@labkey/api": "^1.52.5", + "@labkey/components": "^7.64.1", "@mui/icons-material": "^7.3.9", "@mui/material": "^7.3.9", "@mui/utils": "^7.3.9", From d2b1d128c736d8cc1cc1fc9ffce9078ea9f0abe1 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Sep 2026 11:32:39 -0700 Subject: [PATCH 19/23] JBrowse/npm audit fix --- jbrowse/package-lock.json | 52 ++++++++++++++++++++++++++++++++------- 1 file changed, 43 insertions(+), 9 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 585d8b49f..cc5a52096 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -209,9 +209,9 @@ } }, "node_modules/@emnapi/wasi-threads": { - 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"node_modules/@parcel/watcher-win32-x64": { - "version": "2.6.0", - "resolved": "https://registry.npmjs.org/@parcel/watcher-win32-x64/-/watcher-win32-x64-2.6.0.tgz", - "integrity": "sha512-cA+/pXV2YkfxlIcXOQ5fSWqAzzPyD78/x5qbK/I0vUkrlYHA8TIz+MXjAbGouguKVSI4bOmkTSJ1/poVSsgt+A==", - "cpu": [ - "x64" - ], - "dev": true, - "license": "MIT", - "optional": true, - "os": [ - "win32" - ], - "engines": { - "node": ">= 10.0.0" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/parcel" - } - }, "node_modules/@polka/url": { "version": "1.0.0-next.29", - "resolved": "https://registry.npmjs.org/@polka/url/-/url-1.0.0-next.29.tgz", - "integrity": "sha512-wwQAWhWSuHaag8c4q/KN/vCoeOJYshAIvMQwD4GpSb3OiZklFfvAgmj0VCBBImRpuF/aFgIRzllXlVX93Jevww==", "dev": true, "license": "MIT" }, "node_modules/@popperjs/core": { "version": "2.11.8", - "resolved": "https://registry.npmjs.org/@popperjs/core/-/core-2.11.8.tgz", - "integrity": "sha512-P1st0aksCrn9sGZhp8GMYwBnQsbvAWsZAX44oXNNvLHGqAOcoVxmjZiohstwQ7SqKnbR47akdNi+uleWD8+g6A==", "license": "MIT", "funding": { "type": "opencollective", @@ -2661,8 +2360,6 @@ }, "node_modules/@rspack/binding": { "version": "2.1.10", - "resolved": "https://registry.npmjs.org/@rspack/binding/-/binding-2.1.10.tgz", - "integrity": "sha512-vnu/UP5HnrND15lO9+VeG6eUrbTyycHNQNQ3XEiRiFojuoiGZkIZC3Hbzr8qQH44C6vScPODEPvvIVvLcO2LpQ==", "dev": true, "license": "MIT", "optionalDependencies": { @@ -2682,7 +2379,19 @@ "@rspack/binding-win32-x64-msvc": "2.1.10" } }, - "node_modules/@rspack/binding-darwin-arm64": { + "node_modules/@rspack/binding-win32-x64-msvc": { + "version": "2.1.10", + "cpu": [ + "x64" + ], + "dev": true, + "license": "MIT", + "optional": true, + "os": [ + "win32" + ] + }, + "node_modules/@rspack/binding/node_modules/@rspack/binding-darwin-arm64": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-darwin-arm64/-/binding-darwin-arm64-2.1.10.tgz", "integrity": "sha512-DZlcTpbIb2mjeS1aSG4k01UH33Zj7T+k8ZylPK6HmsKs4JvK4wgpWFC78WVv3p/Aj3MZS6DwtDLwpZ2Ihj/fpg==", @@ -2696,7 +2405,7 @@ "darwin" ] }, - "node_modules/@rspack/binding-darwin-x64": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-darwin-x64": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-darwin-x64/-/binding-darwin-x64-2.1.10.tgz", "integrity": "sha512-my/0h2LwxCRT6cg3oDDC2e0ZOxQLVajAdIcv0fqnQk5JRNvVuL89PuTutitnSqie1A0/JSL8OQz5XHwmoS3kow==", @@ -2710,7 +2419,7 @@ "darwin" ] }, - "node_modules/@rspack/binding-linux-arm64-gnu": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-arm64-gnu": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-arm64-gnu/-/binding-linux-arm64-gnu-2.1.10.tgz", "integrity": "sha512-laevn9g+E5PAUEGqiKe6Ju5KApsuQYp+bPI17XS3Lkl8eqL5pS/BmHYU7QMlst4GzV8+wlruVTMh//+st6Vqzg==", @@ -2724,7 +2433,7 @@ "linux" ] }, - "node_modules/@rspack/binding-linux-arm64-musl": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-arm64-musl": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-arm64-musl/-/binding-linux-arm64-musl-2.1.10.tgz", "integrity": "sha512-V71+Qz5G72+ROZXrJn5zxOszdG1AEbO8pcC/itXXtf4yRR6a3bVHKNKGhipBNxb8eI6cnD/01FH1h3ZG655jLw==", @@ -2738,7 +2447,7 @@ "linux" ] }, - "node_modules/@rspack/binding-linux-ppc64-gnu": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-ppc64-gnu": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-ppc64-gnu/-/binding-linux-ppc64-gnu-2.1.10.tgz", "integrity": "sha512-U7HlNzHcDtZ+LYOtOJmtx67kHEybZzUUAaP7aEXjGYO5WTCgh/176sW2UYP0rmZLrgUNFUuzn+B98RLaClNaVg==", @@ -2752,7 +2461,7 @@ "linux" ] }, - "node_modules/@rspack/binding-linux-riscv64-gnu": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-riscv64-gnu": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-riscv64-gnu/-/binding-linux-riscv64-gnu-2.1.10.tgz", "integrity": "sha512-GMGTJpy9/ecE+5F5IfxZH4bXv0Wx/b2TiehTlCbTksbL+pKpLHYy0rwGdjWDKbmBkhxMMqPiC7PDnn9LbdnnLA==", @@ -2766,7 +2475,7 @@ "linux" ] }, - "node_modules/@rspack/binding-linux-riscv64-musl": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-riscv64-musl": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-riscv64-musl/-/binding-linux-riscv64-musl-2.1.10.tgz", "integrity": "sha512-rkurnAWc04vIbzG1QCrPBWSJadZvaOt1mazFH3EdiJO8VUiu0I1T9zdiwuDOPrd50lOKIZlcTXbd5aaAkWEnvQ==", @@ -2780,7 +2489,7 @@ "linux" ] }, - "node_modules/@rspack/binding-linux-s390x-gnu": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-s390x-gnu": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-s390x-gnu/-/binding-linux-s390x-gnu-2.1.10.tgz", "integrity": "sha512-X+DyxkriZEAF/wihI7ERDv+CAS0mbMv36aEuQ+vXzTlvS6cSmpou/r29AHbvIF3NlG1UeAbDVlOs9QrMBZjpUQ==", @@ -2794,7 +2503,7 @@ "linux" ] }, - "node_modules/@rspack/binding-linux-x64-gnu": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-x64-gnu": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-x64-gnu/-/binding-linux-x64-gnu-2.1.10.tgz", "integrity": "sha512-Fat09V6jUuyo9qG7Wyj9cQ31VDfLmokXyBtGqKxY5OvSWHereB7QUub5btbPXHwbp6Iq4aAQyUbbLTzvR1YaBw==", @@ -2808,7 +2517,7 @@ "linux" ] }, - "node_modules/@rspack/binding-linux-x64-musl": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-linux-x64-musl": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-linux-x64-musl/-/binding-linux-x64-musl-2.1.10.tgz", "integrity": "sha512-lhHOnIJ4ClpIlA1f1L8aoxEZivYLjnjq5A6jKKz7BKsm+cHK8kqqEm6lO5KqA5xQT0Lonq1o28bmKHEj6JHInw==", @@ -2822,7 +2531,7 @@ "linux" ] }, - "node_modules/@rspack/binding-wasm32-wasi": { + "node_modules/@rspack/binding/node_modules/@rspack/binding-wasm32-wasi": { "version": "2.1.10", "resolved": "https://registry.npmjs.org/@rspack/binding-wasm32-wasi/-/binding-wasm32-wasi-2.1.10.tgz", "integrity": "sha512-KY5YbWbuvYcoaLXnV+vzZOvGRCeb6jt4EpVpKdph1h1IJjwX/ju15EQ+GOe3iecZEdf0OttQcNVcwBkLkFT9ag==", @@ -2838,7 +2547,7 @@ "@napi-rs/wasm-runtime": "1.1.6" } }, - 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} - }, - "node_modules/velocity-react/node_modules/react-transition-group": { - "version": "2.9.0", - "resolved": "https://registry.npmjs.org/react-transition-group/-/react-transition-group-2.9.0.tgz", - "integrity": "sha512-+HzNTCHpeQyl4MJ/bdE0u6XRMe9+XG/+aL4mCxVN4DnPBQ0/5bfHWPDuOZUzYdMj94daZaZdCCc1Dzt9R/xSSg==", - "license": "BSD-3-Clause", - "dependencies": { - "dom-helpers": "^3.4.0", - "loose-envify": "^1.4.0", - "prop-types": "^15.6.2", - "react-lifecycles-compat": "^3.0.4" - }, - "peerDependencies": { - "react": ">=15.0.0", - "react-dom": ">=15.0.0" - } - }, "node_modules/vis-data": { - "version": "8.0.4", - "resolved": "https://registry.npmjs.org/vis-data/-/vis-data-8.0.4.tgz", - "integrity": "sha512-TsN0sMHqIRpdfg6TNPtfdINpkgxtnQP6JNWCaiSwvou5seXqKiP5eERkaBg+Y56wyJ4FZTeOEs/dEmWEPrpltQ==", + "version": "8.0.5", "license": "(Apache-2.0 OR MIT)", "peer": true, "funding": { @@ -8017,9 +6805,7 @@ } }, "node_modules/vis-network": { - "version": "10.1.0", - "resolved": "https://registry.npmjs.org/vis-network/-/vis-network-10.1.0.tgz", - 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"integrity": "sha512-wP2EusncRGL1tZyMHC/umLkjPdYMkTL9nPEKh8G8dkYCJ9TyF6xnXFqjhdqmv5J900irN/g0P5jMvLT22krEXQ==", + "version": "5.3.3", "dev": true, "license": "MIT", "dependencies": { @@ -8137,8 +6912,6 @@ }, "node_modules/webpack-bundle-analyzer/node_modules/commander": { "version": "14.0.3", - "resolved": "https://registry.npmjs.org/commander/-/commander-14.0.3.tgz", - "integrity": "sha512-H+y0Jo/T1RZ9qPP4Eh1pkcQcLRglraJaSLoyOtHxu6AapkjWVCy2Sit1QQ4x3Dng8qDlSsZEet7g5Pq06MvTgw==", "dev": true, "license": "MIT", "engines": { @@ -8147,8 +6920,6 @@ }, "node_modules/webpack-bundle-analyzer/node_modules/escape-string-regexp": { "version": "5.0.0", - "resolved": "https://registry.npmjs.org/escape-string-regexp/-/escape-string-regexp-5.0.0.tgz", - "integrity": "sha512-/veY75JbMK4j1yjvuUxuVsiS/hr/4iHs9FTT6cgTexxdE0Ly/glccBAkloH/DofkjRbZU3bnoj38mOmhkZ0lHw==", "dev": true, "license": "MIT", "engines": { @@ -8159,9 +6930,7 @@ } }, "node_modules/webpack-sources": { - "version": "3.5.1", - "resolved": "https://registry.npmjs.org/webpack-sources/-/webpack-sources-3.5.1.tgz", - "integrity": "sha512-jyuiGJdtvY434z5bUZrjz67v76/ePNvFZTp9Mdz29IlH4+GPsgyGjiv0fKI+M7BdkU6ADjulUcKAd3tUK3WlEw==", + "version": "3.6.0", "dev": true, "license": "MIT", "engines": { @@ -8170,8 +6939,6 @@ }, "node_modules/which": { "version": "2.0.2", - "resolved": "https://registry.npmjs.org/which/-/which-2.0.2.tgz", - "integrity": "sha512-BLI3Tl1TW3Pvl70l3yq3Y64i+awpwXqsGBYWkkqMtnbXgrMD+yj7rhW0kuEDxzJaYXGjEW5ogapKNMEKNMjibA==", "dev": true, "license": "ISC", "dependencies": { @@ -8185,9 +6952,7 @@ } }, "node_modules/ws": { - "version": "8.21.1", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.21.1.tgz", - "integrity": "sha512-+0NTnW77fFN/DjQi6k/Sq/Yvk4Sgajw7urW8V+asjXnRgDs9gyGkdb7EzgfhA4goXsRIZKE28fzIXBHEzhuiWw==", + "version": "8.22.0", "dev": true, "license": "MIT", "engines": { @@ -8208,8 +6973,6 @@ }, "node_modules/yallist": { "version": "5.0.0", - "resolved": "https://registry.npmjs.org/yallist/-/yallist-5.0.0.tgz", - "integrity": "sha512-YgvUTfwqyc7UXVMrB+SImsVYSmTS8X/tSrtdNZMImM+n7+QTriRXyXim0mBrTXNeqzVF0KWGgHPeiyViFFrNDw==", "dev": true, "license": "BlueOak-1.0.0", "engines": { @@ -8218,8 +6981,6 @@ }, "node_modules/yaml": { "version": "1.10.3", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-1.10.3.tgz", - "integrity": "sha512-vIYeF1u3CjlhAFekPPAk2h/Kv4T3mAkMox5OymRiJQB0spDP10LHvt+K7G9Ny6NuuMAb25/6n1qyUjAcGNf/AA==", "license": "ISC", "engines": { "node": ">= 6" From 62ffcda3f976a8e9758821ed830ca5ddeb1b87f0 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 30 Sep 2026 07:21:10 -0700 Subject: [PATCH 22/23] Fix JB build --- .../JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts index 6bb66ce9d..434c00971 100644 --- a/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts +++ b/jbrowse/src/client/JBrowse/Browser/plugins/ExtendedVariantPlugin/index.ts @@ -218,7 +218,7 @@ export default class ExtendedVariantPlugin extends Plugin { }) }) - pluginManager.jexl.addFunction('arrayMax', (array) => { + pluginManager.jexl.addFunction('arrayMax', (array: [number]) => { return Array.isArray(array) ? Math.max(...array) : array }) From 07db9c4325c308adbd959fc1444d8be508c191df Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 30 Sep 2026 09:19:26 -0700 Subject: [PATCH 23/23] Fix JB build --- jbrowse/package-lock.json | 1371 +++++++++++++++++++++++++++++++++++-- 1 file changed, 1298 insertions(+), 73 deletions(-) diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index 427faa716..f26d28668 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -41,10 +41,14 @@ }, "node_modules/@adobe/css-tools": { "version": "4.5.0", + "resolved": "https://registry.npmjs.org/@adobe/css-tools/-/css-tools-4.5.0.tgz", + "integrity": "sha512-6OzddxPio9UiWTCemp4N8cYLV2ZN1ncRnV1cVGtve7dhPOtRkleRyx32GQCYSwDYgaHU3USMm84tNsvKzRCa1Q==", "license": "MIT" }, "node_modules/@babel/code-frame": { "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.29.7.tgz", + "integrity": "sha512-Aup7aUOfpbAUg2ROOJN6Iw5f9DMBlzu0mIkm/malLQFN/YQgO48wCj0Kxa3sEHJvPVFg7siR+qRInwXd2qhQKw==", "license": "MIT", "dependencies": { "@babel/helper-validator-identifier": "^7.29.7", @@ -57,6 +61,8 @@ }, "node_modules/@babel/generator": { "version": "7.29.8", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.29.8.tgz", + "integrity": "sha512-gZbepsdh3WDtgZKWL+vTPh71LSBrm/Y4/QDZBVCcYfmeTEEuoOYwlSy+G1StfJg+/Zy550u/3TATbm7qDbbMtg==", "license": "MIT", "dependencies": { "@babel/parser": "^7.29.8", @@ -71,6 +77,8 @@ }, "node_modules/@babel/helper-globals": { "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/helper-globals/-/helper-globals-7.29.7.tgz", + "integrity": "sha512-3nQVUAtvkKH9zahfWgw96Jc/uFOmjACE1kQz82E2lqWmHBgjzbNlsC22nuQTfahmWeQtTq5nQ/4Nnd2A1wj4zA==", "license": "MIT", "engines": { "node": ">=6.9.0" @@ -78,6 +86,8 @@ }, "node_modules/@babel/helper-module-imports": { "version": "7.29.7", + "resolved": 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