diff --git a/.github/workflows/branch_release.yml b/.github/workflows/branch_release.yml index e0b4cfc12..23e4616bf 100644 --- a/.github/workflows/branch_release.yml +++ b/.github/workflows/branch_release.yml @@ -19,7 +19,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v7 - name: Create branches and PRs uses: LabKey/gitHubActions/branch-release@develop diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 7a01ac2f6..b50a98f37 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -56,9 +56,13 @@ jobs: LK_VERSION=$(cat /home/runner/work/_temp/_github_home/lkDist/release.txt | sed 's/-SNAPSHOT//g') cd /home/runner/work/_temp/_github_home/labkey_build/${LK_VERSION}/server/server/modules/DiscvrLabKeyModules COUNT=$(gh release list | grep 'latest' | wc -l) - if [ $COUNT != '0' ];then gh release delete 'latest' --cleanup-tag -y; fi + if [ $COUNT != '0' ];then + echo 'Deleting existing release' + gh release delete 'latest' --cleanup-tag -y; + fi - git push -f origin "latest" + git push -f origin 'latest' + sleep 100 # gh release periodically fails due to a missing tag. gh release create 'latest' --verify-tag --generate-notes --prerelease --title "Development Build: ${{ env.DEFAULT_BRANCH }}" gh release upload 'latest' /home/runner/work/_temp/_github_home/lkDist/discvr/DISCVR-* \ No newline at end of file diff --git a/.github/workflows/merge_release.yml b/.github/workflows/merge_release.yml index f6d8d6ea0..2eee13940 100644 --- a/.github/workflows/merge_release.yml +++ b/.github/workflows/merge_release.yml @@ -21,7 +21,7 @@ jobs: steps: - name: Checkout - uses: actions/checkout@v3 + uses: actions/checkout@v7 - name: Merge PR uses: LabKey/gitHubActions/merge-release@develop diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java index da250d486..82e76b851 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisMaintenanceTask.java @@ -8,6 +8,8 @@ import org.labkey.api.data.CompareType; import org.labkey.api.data.Container; import org.labkey.api.data.ContainerManager; +import org.labkey.api.data.DbSchema; +import org.labkey.api.data.DbSchemaType; import org.labkey.api.data.SimpleFilter; import org.labkey.api.data.Sort; import org.labkey.api.data.TableInfo; @@ -16,7 +18,9 @@ import org.labkey.api.exp.api.ExpRun; import org.labkey.api.exp.api.ExperimentService; import org.labkey.api.ldk.LDKService; +import org.labkey.api.pipeline.CancelledException; import org.labkey.api.pipeline.PipeRoot; +import org.labkey.api.pipeline.PipelineJob; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.api.pipeline.PipelineService; import org.labkey.api.pipeline.PipelineStatusFile; @@ -57,6 +61,9 @@ */ public class SequenceAnalysisMaintenanceTask implements MaintenanceTask { + private static final String SYSTEM_MAINTENANCE_DESCRIPTION = "System Maintenance"; + private static final String JOB_TABLE = "statusfiles"; + public SequenceAnalysisMaintenanceTask() { @@ -74,6 +81,31 @@ public String getName() return "DeleteSequenceAnalysisArtifacts"; } + // NOTE: if there is a more direct way to locate the JobID this hack should be replaced + private void checkJobCancelled(Logger log) + { + // Make the assumption there is only one active maintenance job at a time: + SimpleFilter filter = new SimpleFilter(FieldKey.fromString("description"), SYSTEM_MAINTENANCE_DESCRIPTION). + addCondition(FieldKey.fromString("container"), ContainerManager.getRoot().getId()). + addCondition(FieldKey.fromString("modified"), new Date(), CompareType.DATE_EQUAL); + int rowId = new TableSelector(DbSchema.get("pipeline", DbSchemaType.Module).getTable(JOB_TABLE), PageFlowUtil.set("RowId", "Status"), filter, null).getMapCollection().stream().filter(map -> { + String val = String.valueOf(map.get("status")); + return val != null && (val.toLowerCase().startsWith(PipelineJob.TaskStatus.cancelling.name()) || val.toLowerCase().startsWith(PipelineJob.TaskStatus.running.name())); + }).map(rs -> Integer.parseInt(String.valueOf(rs.get("rowid")))).max(Integer::compareTo).orElse(-1); + + if (rowId == -1) + { + log.warn("Unable to find rowId for job", new Exception("Unable to find rowId for job")); + return; + } + + PipelineStatusFile sf = PipelineService.get().getStatusFile(rowId); + if (PipelineJob.TaskStatus.cancelling.name().equalsIgnoreCase(sf.getStatus())) + { + throw new CancelledException(); + } + } + @Override public void run(Logger log) { @@ -158,6 +190,7 @@ private void verifySequenceDataPresent(Logger log) if (i % 1000 == 0) { log.info("readdata " + i + " of " + readDatas.size() + ". Current container: " + ContainerManager.getForId(rd.getContainer()).getPath()); + checkJobCancelled(log); } if (rd.getFileId1() != null) @@ -221,6 +254,7 @@ else if (!d.getFile().exists()) if (i % 1000 == 0) { log.info("analysis " + i + " of " + analyses.size() + ". Current container: " + ContainerManager.getForId(m.getContainer()).getPath()); + checkJobCancelled(log); } if (m.getAlignmentFile() != null) @@ -296,7 +330,11 @@ else if (sf.getFilePath() == null) private void processContainer(Container c, Logger log) throws IOException, PipelineJobException { if (!c.isWorkbook()) + { log.info("processing container: " + c.getPath()); + } + + checkJobCancelled(log); PipeRoot root = PipelineService.get().getPipelineRootSetting(c); if (root != null && !root.isCloudRoot()) diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java index b085af33e..7d5cc9d52 100644 --- a/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/SequenceAnalysisModule.java @@ -152,6 +152,7 @@ import org.labkey.sequenceanalysis.run.preprocessing.FastqcProcessingStep; import org.labkey.sequenceanalysis.run.preprocessing.FilterReadsStep; import org.labkey.sequenceanalysis.run.preprocessing.FlashPipelineStep; +import org.labkey.sequenceanalysis.run.preprocessing.Kraken2Step; import org.labkey.sequenceanalysis.run.preprocessing.PrintReadsContainingStep; import org.labkey.sequenceanalysis.run.preprocessing.TagPcrSummaryStep; import org.labkey.sequenceanalysis.run.preprocessing.TrimmomaticWrapper; @@ -291,7 +292,7 @@ public static void registerPipelineSteps() SequencePipelineService.get().registerPipelineStep(new CutadaptWrapper.Provider()); SequencePipelineService.get().registerPipelineStep(new FastqcProcessingStep.Provider()); SequencePipelineService.get().registerPipelineStep(new CutadaptCropWrapper.Provider()); - //SequencePipelineService.get().registerPipelineStep(new BlastFilterPipelineStep.Provider()); + SequencePipelineService.get().registerPipelineStep(new Kraken2Step.Provider()); //ref library SequencePipelineService.get().registerPipelineStep(new DNAReferenceLibraryStep.Provider()); diff --git a/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/Kraken2Step.java b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/Kraken2Step.java new file mode 100644 index 000000000..5842b4228 --- /dev/null +++ b/SequenceAnalysis/src/org/labkey/sequenceanalysis/run/preprocessing/Kraken2Step.java @@ -0,0 +1,212 @@ +package org.labkey.sequenceanalysis.run.preprocessing; + +import org.apache.logging.log4j.Logger; +import org.jetbrains.annotations.Nullable; +import org.json.JSONObject; +import org.labkey.api.pipeline.PipelineJobException; +import org.labkey.api.pipeline.PipelineJobService; +import org.labkey.api.sequenceanalysis.SequenceAnalysisService; +import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider; +import org.labkey.api.sequenceanalysis.pipeline.CommandLineParam; +import org.labkey.api.sequenceanalysis.pipeline.PipelineContext; +import org.labkey.api.sequenceanalysis.pipeline.PipelineStepProvider; +import org.labkey.api.sequenceanalysis.pipeline.PreprocessingStep; +import org.labkey.api.sequenceanalysis.pipeline.SequencePipelineService; +import org.labkey.api.sequenceanalysis.pipeline.ToolParameterDescriptor; +import org.labkey.api.sequenceanalysis.run.AbstractCommandPipelineStep; +import org.labkey.api.sequenceanalysis.run.AbstractCommandWrapper; +import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper; +import org.labkey.api.util.Compress; +import org.labkey.api.util.FileUtil; +import org.labkey.api.util.Pair; + +import java.io.File; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.List; + +public class Kraken2Step extends AbstractCommandPipelineStep implements PreprocessingStep +{ + private static final String DB_PARAM = "db"; + private static final String MODE_PARAM = "mode"; + + public Kraken2Step(PipelineStepProvider provider, PipelineContext ctx) + { + super(provider, ctx, new Kraken2Wrapper(ctx.getLogger())); + } + + public static class Provider extends AbstractPipelineStepProvider + { + public Provider() + { + super("Kraken2", "Kraken2", "Kraken2", "This step aligns input reads against a reference using BWA-mem and will only return read pairs without a passing hit in either read.", Arrays.asList( + ToolParameterDescriptor.create(DB_PARAM, "Database", "This determines the DB for positive or negative selection", "ldk-simplecombo", new JSONObject(){{ + put("storeValues", "kraken2_bv;kraken2_standard"); + put("multiSelect", false); + put("allowBlank", false); + put("joinReturnValue", true); + put("delimiter", ";"); + }}, "kraken2_bv"), + ToolParameterDescriptor.create(MODE_PARAM, "Reads To Retain", "This determines which set of reads is passed to the next step. If 'Retain Classified' is selected, then reads matching the DB are retained. if 'Retain Unclassified' is selected, then reads that do not match the DB are retained", "ldk-simplecombo", new JSONObject(){{ + put("storeValues", "Classified;Unclassified"); + put("multiSelect", false); + put("allowBlank", false); + put("joinReturnValue", true); + put("delimiter", ";"); + }}, null), + ToolParameterDescriptor.createCommandLineParam(CommandLineParam.createSwitch("--memory-mapping"), "memoryMapping", "Memory Mapping", "If checked, the DB will not be read into memory, reducing RAM", "checkbox", null, false), + ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--minimum-hit-groups"), "minimumHitGroups", "Minimum Hit Groups", "Minimum number of hit groups (overlapping k-mers sharing the same minimizer) needed to make a call", "ldk-integerfield", new JSONObject(){{ + put("minValue", 0); + }}, 2), + ToolParameterDescriptor.createCommandLineParam(CommandLineParam.create("--confidence"), "confidence", "Confidence", "Confidence score threshold (0-1)", "ldk-numberfield", new JSONObject(){{ + put("minValue", 0); + put("maxValue", 1); + put("decimalPrecision", 2); + }}, 0) + ), null, "https://github.com/DerrickWood/kraken2"); + } + + @Override + public Kraken2Step create(PipelineContext context) + { + return new Kraken2Step(this, context); + } + } + + @Override + public Output processInputFile(File inputFile, @Nullable File inputFile2, File outputDir) throws PipelineJobException + { + PreprocessingOutputImpl output = new PreprocessingOutputImpl(inputFile, inputFile2); + + List args = new ArrayList<>(); + args.add(getWrapper().getExe().getPath()); + + if (inputFile2 != null) + { + args.add("--paired"); + } + + if (inputFile.getName().toLowerCase().endsWith(".gz")) + { + args.add("--gzip-compressed"); + } + + Integer threads = SequencePipelineService.get().getMaxThreads(getPipelineCtx().getLogger()); + if (threads != null) + { + args.add("--threads"); + args.add(threads.toString()); + } + + String dbName = getProvider().getParameterByName(DB_PARAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class); + if (dbName == null) + { + throw new PipelineJobException("Missing DB name"); + } + + File binDir = FileUtil.appendName(new File(PipelineJobService.get().getAppProperties().getToolsDirectory()), "kraken2_dbs"); + if (!binDir.exists()) + { + throw new PipelineJobException("Unable to find kraken2 DB dir, expected: " + binDir.getAbsolutePath()); + } + + File dbDir = FileUtil.appendName(binDir, dbName); + if (!dbDir.exists()) + { + throw new PipelineJobException("Unable to find kraken2 DB dir, expected: " + dbDir.getAbsolutePath()); + } + + args.add("--use-names"); + + args.add("--db"); + args.add(dbDir.getAbsolutePath()); + + args.addAll(getClientCommandArgs()); + + args.add("--output"); + args.add("-"); + + String mode = getProvider().getParameterByName(MODE_PARAM).extractValue(getPipelineCtx().getJob(), getProvider(), getStepIdx(), String.class); + + File classifiedOutputBase = FileUtil.appendName(outputDir, SequenceAnalysisService.get().getUnzippedBaseName(inputFile.getName()) + ".classified"); + File unclassifiedOutputBase = FileUtil.appendName(outputDir, SequenceAnalysisService.get().getUnzippedBaseName(inputFile.getName()) + ".unclassified"); + if ("Classified".equals(mode)) + { + args.add("--classified-out"); + args.add(classifiedOutputBase.getPath() + "#.fq"); + } + else + { + args.add("--unclassified-out"); + args.add(unclassifiedOutputBase.getPath() + "#.fq"); + } + + File reportFile = FileUtil.appendName(outputDir, SequencePipelineService.get().getUnzippedBaseName(inputFile.getName()) + ".kraken2.report.txt"); + args.add("--report"); + args.add(reportFile.getPath()); + + args.add(inputFile.getPath()); + if (inputFile2 != null) + { + args.add(inputFile2.getPath()); + } + + getWrapper().execute(args); + + if ("Classified".equals(mode)) + { + File classified1 = new File(classifiedOutputBase.getPath() + "_1.fq"); + File classified2 = inputFile2 == null ? null : new File(classifiedOutputBase.getPath() + "_2.fq"); + if (!classified1.exists()) + { + throw new PipelineJobException("Classified file does not exist: " + classified1.getAbsolutePath()); + } + + File compressed1 = Compress.compressGzip(classified1); + output.addIntermediateFile(classified1); + + File compressed2 = classified2 == null ? null : Compress.compressGzip(classified2); + if (classified2 != null) + { + output.addIntermediateFile(classified2); + } + + output.setProcessedFastq(Pair.of(compressed1, compressed2)); + } + else + { + File unclassified1 = new File(unclassifiedOutputBase.getPath() + "_1.fq"); + File unclassified2 = inputFile2 == null ? null : new File(unclassifiedOutputBase.getPath() + "_2.fq"); + if (!unclassified1.exists()) + { + throw new PipelineJobException("Unclassified file does not exist: " + unclassified1.getAbsolutePath()); + } + + File compressed1 = Compress.compressGzip(unclassified1); + output.addIntermediateFile(unclassified1); + + File compressed2 = unclassified2 == null ? null : Compress.compressGzip(unclassified2); + if (unclassified2 != null) + { + output.addIntermediateFile(unclassified2); + } + + output.setProcessedFastq(Pair.of(compressed1, compressed2)); + } + + return output; + } + + public static class Kraken2Wrapper extends AbstractCommandWrapper + { + public Kraken2Wrapper(Logger log) + { + super(log); + } + + public File getExe() + { + return SimpleScriptWrapper.resolveFileInPath("kraken2", null, true); + } + } +} diff --git a/SequenceAnalysis/test/src/org/labkey/test/tests/external/labModules/SequenceTest.java b/SequenceAnalysis/test/src/org/labkey/test/tests/external/labModules/SequenceTest.java index 6c8f67114..a8c49a0c7 100644 --- a/SequenceAnalysis/test/src/org/labkey/test/tests/external/labModules/SequenceTest.java +++ b/SequenceAnalysis/test/src/org/labkey/test/tests/external/labModules/SequenceTest.java @@ -611,7 +611,7 @@ private void analysisPanelTest() throws Exception waitForElementToDisappear(Ext4Helper.Locators.window("Add Steps")); Map fieldsetMap = new HashMap<>(); - String[] setNames = {"Adapter Trimming (Trimmomatic)", "Average Quality Filter", "Crop Reads", "Downsample Reads", "Filter Reads Matching Reference", "Head Crop", "Quality Trimming (Adaptive)", "Quality Trimming (Sliding Window)", "Read Length Filter"}; + String[] setNames = {"Adapter Trimming (Trimmomatic)", "Average Quality Filter", "Crop Reads", "Downsample Reads", "Filter Reads Matching Reference", "Head Crop", "Quality Trimming (Adaptive)", "Quality Trimming (Sliding Window)", "Read Length Filter", "Kraken2"}; isPresentInThisOrder(setNames); for (String name : setNames) @@ -628,6 +628,9 @@ private void analysisPanelTest() throws Exception waitAndClick(Locator.id(fieldsetMap.get("Head Crop").down("ldk-linkbutton[text='Remove']", Ext4CmpRef.class).getId()).append(Locator.tag("a"))); waitForElementToDisappear(Locator.id(fieldsetMap.get("Head Crop").getId())); + waitAndClick(Locator.id(fieldsetMap.get("Kraken2").down("ldk-linkbutton[text='Remove']", Ext4CmpRef.class).getId()).append(Locator.tag("a"))); + waitForElementToDisappear(Locator.id(fieldsetMap.get("Kraken2").getId())); + Integer overlapLength = 6; Double errorRate = 0.2; Integer cropLength = 500; diff --git a/Studies/resources/views/studiesOverview.html b/Studies/resources/views/studiesOverview.html index 5fd144f1e..b2cb492ee 100644 --- a/Studies/resources/views/studiesOverview.html +++ b/Studies/resources/views/studiesOverview.html @@ -26,37 +26,43 @@ // } // }) - LABKEY.Query.selectRows({ - schemaName: 'study', - queryName: 'datasets', - columns: 'Name,Label,CategoryId/Label', - scope: this, - failure: LDK.Utils.getErrorCallback(), - success: function (results) { - let div = $('
') + // timepointType is an indirect test for whether a study exists: + if (LABKEY.moduleContext.study.timepointType) { + LABKEY.Query.selectRows({ + schemaName: 'study', + queryName: 'datasets', + columns: 'Name,Label,CategoryId/Label', + scope: this, + failure: LDK.Utils.getErrorCallback(), + success: function (results) { + let div = $('
') - const dataByCategory = {} - results.rows.sort((a, b) => a.Label.localeCompare(b.Label)).forEach(row => { - const dsUrl = LABKEY.ActionURL.buildURL('query', 'executeQuery', null, { - schemaName: 'study', - queryName: row.Name - }); + const dataByCategory = {} + results.rows.sort((a, b) => a.Label.localeCompare(b.Label)).forEach(row => { + const dsUrl = LABKEY.ActionURL.buildURL('query', 'executeQuery', null, { + schemaName: 'study', + queryName: row.Name + }); - dataByCategory[row['CategoryId/Label']] = dataByCategory[row['CategoryId/Label']] || [] - dataByCategory[row['CategoryId/Label']].push($(`
  • ${row.Label}
    • `)) - }) + dataByCategory[row['CategoryId/Label']] = dataByCategory[row['CategoryId/Label']] || [] + dataByCategory[row['CategoryId/Label']].push($(`
  • ${row.Label}
    • `)) + }) - Object.keys(dataByCategory).sort().forEach(category => { - div.append('

    ' + category + '

    ').append('
      ') - const ul = div.children('ul')[0] - dataByCategory[category].forEach(item => { - ul.append(item[0]) + Object.keys(dataByCategory).sort().forEach(category => { + div.append('

      ' + category + '

      ').append('
        ') + const ul = div.children('ul')[0] + dataByCategory[category].forEach(item => { + ul.append(item[0]) + }) }) - }) - $('#' + webpart.wrapperDivId).append(div) - } - }) + $('#' + webpart.wrapperDivId).append(div) + } + }) + } else { + let div = $('
        There are no studies in the current folder
        ') + $('#' + webpart.wrapperDivId).append(div) + } }) }); }(jQuery, LABKEY)); diff --git a/jbrowse/package-lock.json b/jbrowse/package-lock.json index e0be57a60..6bbcb9fb9 100644 --- a/jbrowse/package-lock.json +++ b/jbrowse/package-lock.json @@ -18,13 +18,12 @@ "@jbrowse/product-core": "^4.1.13", "@jbrowse/react-linear-genome-view2": "^4.1.13", "@labkey/api": "^1.51.0", - "@labkey/components": "^7.35.0", + "@labkey/components": "^7.42.1", "@mui/x-data-grid": "^7.28.1", "assert": "^2.1.0", "browserify-zlib": "^0.2.0", "buffer": "^6.0.3", "child_process": "^1.0.2", - "fs": "^0.0.2", "jquery": "^3.7.1", "jspdf": "^4.2.1", "jspdf-autotable": "^5.0.7", @@ -84,21 +83,20 @@ } }, "node_modules/@babel/core": { - "version": "7.29.0", - "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.29.0.tgz", - "integrity": "sha512-CGOfOJqWjg2qW/Mb6zNsDm+u5vFQ8DxXfbM09z69p5Z6+mE1ikP2jUXw+j42Pf1XTYED2Rni5f95npYeuwMDQA==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.29.7.tgz", + "integrity": "sha512-RgHBCvtjbOK2gXSNBNIkNoEc9qoVEtau3hj8gEqKQuL3HZAibKarWFEI3Lfm6EYKkLalOh8eSrj9b+ch9H/VBA==", "dev": true, - "license": "MIT", "dependencies": { - "@babel/code-frame": "^7.29.0", - "@babel/generator": "^7.29.0", - "@babel/helper-compilation-targets": "^7.28.6", - "@babel/helper-module-transforms": "^7.28.6", - "@babel/helpers": "^7.28.6", - "@babel/parser": "^7.29.0", - "@babel/template": "^7.28.6", - "@babel/traverse": "^7.29.0", - "@babel/types": "^7.29.0", + "@babel/code-frame": "^7.29.7", + "@babel/generator": "^7.29.7", + "@babel/helper-compilation-targets": "^7.29.7", + "@babel/helper-module-transforms": "^7.29.7", + "@babel/helpers": "^7.29.7", + "@babel/parser": "^7.29.7", + "@babel/template": "^7.29.7", + "@babel/traverse": "^7.29.7", + "@babel/types": "^7.29.7", "@jridgewell/remapping": "^2.3.5", "convert-source-map": "^2.0.0", "debug": "^4.1.0", @@ -375,14 +373,13 @@ } }, "node_modules/@babel/helpers": { - "version": "7.28.6", - "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.28.6.tgz", - "integrity": "sha512-xOBvwq86HHdB7WUDTfKfT/Vuxh7gElQ+Sfti2Cy6yIWNW05P8iUslOVcZ4/sKbE+/jQaukQAdz/gf3724kYdqw==", + "version": "7.29.7", + "resolved": "https://registry.npmjs.org/@babel/helpers/-/helpers-7.29.7.tgz", + "integrity": "sha512-1k2lAGRMfHTcwuNYcCNUmaUffmQv8KWMfh2iJUUeRlwlwH4FdNG7mfPI10NPfLHJFThE4Tyr4mv7kTNZOiPuBg==", "dev": true, - "license": "MIT", "dependencies": { - "@babel/template": "^7.28.6", - "@babel/types": "^7.28.6" + "@babel/template": "^7.29.7", + "@babel/types": "^7.29.7" }, "engines": { "node": ">=6.9.0" @@ -3575,9 +3572,9 @@ } }, "node_modules/@labkey/api": { - "version": "1.51.3", - "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.51.3.tgz", - "integrity": "sha512-rs0idz4TLQuDatYBnLHFTL8ljpvCaCVynRA1KukTWD8yoZOGnMipX4m6+2CmoUaatZPFbiEIYvEqGU8WKLWrpg==" + "version": "1.51.4", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/api/-/@labkey/api-1.51.4.tgz", + "integrity": "sha512-D8Rs1yd8dKnmLxGzMaTtOg3S7EpQRSGMCGPRNTPqICTukYwlHhi39UViiF9b7s3knlK4gtp9D64CHbQcehgw+w==" }, "node_modules/@labkey/build": { "version": "9.1.4", @@ -3616,12 +3613,12 @@ } }, "node_modules/@labkey/components": { - "version": "7.41.0", - "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-7.41.0.tgz", - "integrity": "sha512-lqYxEPIk0lyVFqA+mc+cJn+LUIuIQJrJNc3U0x3TDpKwt3OUbzsuhl51MrZwB21a1skM37HiYE5utysnQI48Ug==", + "version": "7.42.1", + "resolved": "https://labkey.jfrog.io/artifactory/api/npm/libs-client/@labkey/components/-/@labkey/components-7.42.1.tgz", + "integrity": "sha512-y9sVFxdqCQDBnWCSW4BqtpauFMbjuTmywXDT1O6Zh31PopyyWhGiEA99K+zPxGzn7QRKh6BLcm0QrlTFPh0+jA==", "dependencies": { "@hello-pangea/dnd": "18.0.1", - "@labkey/api": "1.51.3", + "@labkey/api": "1.51.4", "@testing-library/dom": "~10.4.1", "@testing-library/jest-dom": "~6.9.1", "@testing-library/react": "~16.3.2", @@ -3631,7 +3628,7 @@ "date-fns": "~3.6.0", "date-fns-tz": "~3.2.0", "font-awesome": "~4.7.0", - "immer": "~10.1.3", + "immer": "~11.1.8", "immutable": "~3.8.3", "normalizr": "~3.6.2", "numeral": "~2.0.6", @@ -3640,11 +3637,11 @@ "react-color": "~2.19.3", "react-datepicker": "~7.6.0", "react-dom": "~18.3.1", - "react-router-dom": "~6.30.1", + "react-router-dom": "~6.30.4", "react-select": "~5.10.2", "react-treebeard": "~3.2.4", "vis-data": "~8.0.3", - "vis-network": "~10.0.2" + "vis-network": "~10.1.0" } }, "node_modules/@labkey/components/node_modules/immutable": { @@ -7139,9 +7136,9 @@ } }, "node_modules/dompurify": { - "version": "3.4.2", - "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-3.4.2.tgz", - "integrity": "sha512-lHeS9SA/IKeIFFyYciHBr2n0v1VMPlSj843HdLOwjb2OxNwdq9Xykxqhk+FE42MzAdHvInbAolSE4mhahPpjXA==", + "version": "3.4.11", + "resolved": "https://registry.npmjs.org/dompurify/-/dompurify-3.4.11.tgz", + "integrity": "sha512-zhlUV12GsaRzMsf9q5M254YhA4+VuF0fG+QFqu6aYpoGlKtz+w8//jBcGVYBgQkR5GHjUomejY84AV+/uPbWdw==", "optionalDependencies": { "@types/trusted-types": "^2.0.7" } @@ -7865,11 +7862,6 @@ "node": ">= 0.6" } }, - "node_modules/fs": { - "version": "0.0.2", - "resolved": "https://registry.npmjs.org/fs/-/fs-0.0.2.tgz", - "integrity": "sha512-YAiVokMCrSIFZiroB1oz51hPiPRVcUtSa4x2U5RYXyhS9VAPdiFigKbPTnOSq7XY8wd3FIVPYmXpo5lMzFmxgg==" - }, "node_modules/fs-extra": { "version": "11.3.1", "resolved": "https://registry.npmjs.org/fs-extra/-/fs-extra-11.3.1.tgz", @@ -8336,11 +8328,10 @@ } }, "node_modules/http-proxy-middleware": { - "version": "2.0.9", - "resolved": "https://registry.npmjs.org/http-proxy-middleware/-/http-proxy-middleware-2.0.9.tgz", - "integrity": "sha512-c1IyJYLYppU574+YI7R4QyX2ystMtVXZwIdzazUIPIJsHuWNd+mho2j+bKoHftndicGj9yh+xjd+l0yj7VeT1Q==", + "version": "2.0.10", + "resolved": "https://registry.npmjs.org/http-proxy-middleware/-/http-proxy-middleware-2.0.10.tgz", + "integrity": "sha512-RKzRWNPxUZqbuk3BC5mGVJbBnWgr+diEnjJexIOytFbBzDy88Fbh/YvBr3DsNrl1jYAfjWfpATEv0NO35FDuPQ==", "dev": true, - "license": "MIT", "dependencies": { "@types/http-proxy": "^1.17.8", "http-proxy": "^1.18.1", @@ -8426,9 +8417,9 @@ "license": "BSD-3-Clause" }, "node_modules/immer": { - "version": "10.1.3", - "resolved": "https://registry.npmjs.org/immer/-/immer-10.1.3.tgz", - "integrity": "sha512-tmjF/k8QDKydUlm3mZU+tjM6zeq9/fFpPqH9SzWmBnVVKsPBg/V66qsMwb3/Bo90cgUN+ghdVBess+hPsxUyRw==", + "version": "11.1.8", + "resolved": "https://registry.npmjs.org/immer/-/immer-11.1.8.tgz", + "integrity": "sha512-/tbkHMW7y10Lx6i1crLjD4/OhNkRG+Fo7byZHtah0547nIeXYcpIXaUh0IAQY6gO5459qpGGYapcEOHtFXkIuA==", "funding": { "type": "opencollective", "url": "https://opencollective.com/immer" @@ -8839,10 +8830,20 @@ "license": "MIT" }, "node_modules/js-yaml": { - "version": "4.1.1", - "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.1.1.tgz", - "integrity": "sha512-qQKT4zQxXl8lLwBtHMWwaTcGfFOZviOJet3Oy/xmGk2gZH677CJM9EvtfdSkgWcATZhj/55JZ0rmy3myCT5lsA==", + "version": "4.2.0", + "resolved": "https://registry.npmjs.org/js-yaml/-/js-yaml-4.2.0.tgz", + "integrity": "sha512-ePWsvanv0DWuDRsW8dnt+R4jQ31SCRCQ7hhNcPXZPsoBZiemuZNYGf7adZdqX2D86j6rvKp3RpCxVTSb8WQlOw==", "dev": true, + "funding": [ + { + "type": "github", + "url": "https://github.com/sponsors/puzrin" + }, + { + "type": "github", + "url": "https://github.com/sponsors/nodeca" + } + ], "dependencies": { "argparse": "^2.0.1" }, @@ -8981,14 +8982,13 @@ } }, "node_modules/launch-editor": { - "version": "2.12.0", - "resolved": "https://registry.npmjs.org/launch-editor/-/launch-editor-2.12.0.tgz", - "integrity": "sha512-giOHXoOtifjdHqUamwKq6c49GzBdLjvxrd2D+Q4V6uOHopJv7p9VJxikDsQ/CBXZbEITgUqSVHXLTG3VhPP1Dg==", + "version": "2.14.1", + "resolved": "https://registry.npmjs.org/launch-editor/-/launch-editor-2.14.1.tgz", + "integrity": "sha512-QWBrQsMpH7gPr965dsKD/3cKWiNoTjpATQf++Xq63N6sKRGMwlVXz41O1IZTMfZQgBctD/K5Zt06+/I6pP6+HA==", "dev": true, - "license": "MIT", "dependencies": { "picocolors": "^1.1.1", - "shell-quote": "^1.8.3" + "shell-quote": "^1.8.4" } }, "node_modules/librpc-web-mod": { @@ -11577,11 +11577,10 @@ } }, "node_modules/shell-quote": { - "version": "1.8.3", - "resolved": "https://registry.npmjs.org/shell-quote/-/shell-quote-1.8.3.tgz", - "integrity": "sha512-ObmnIF4hXNg1BqhnHmgbDETF8dLPCggZWBjkQfhZpbszZnYur5DUljTcCHii5LC3J5E0yeO/1LIMyH+UvHQgyw==", + "version": "1.8.4", + "resolved": "https://registry.npmjs.org/shell-quote/-/shell-quote-1.8.4.tgz", + "integrity": "sha512-VsC6n6vz1ihYYyZZwX7YZSF5l5x36ca17OC+a69h94YqB7X6XLwf+5MOgynYir2SLFUbl8gIYvBo8K8RoNQ6bQ==", "dev": true, - "license": "MIT", "engines": { "node": ">= 0.4" }, @@ -11969,11 +11968,10 @@ } }, "node_modules/tar": { - "version": "7.5.11", - "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.11.tgz", - "integrity": "sha512-ChjMH33/KetonMTAtpYdgUFr0tbz69Fp2v7zWxQfYZX4g5ZN2nOBXm1R2xyA+lMIKrLKIoKAwFj93jE/avX9cQ==", + "version": "7.5.16", + "resolved": "https://registry.npmjs.org/tar/-/tar-7.5.16.tgz", + "integrity": "sha512-56adEpPMouktRlBLXiaYFFzZ/3+JXa8P9n7WbR+ibIjtviN55mEaOkiysCnPnWm+7kkui1Dn8J9l+g6zV8731w==", "dev": true, - "license": "BlueOak-1.0.0", "dependencies": { "@isaacs/fs-minipass": "^4.0.0", "chownr": "^3.0.0", @@ -12570,9 +12568,9 @@ } }, "node_modules/vis-network": { - "version": "10.0.3", - "resolved": "https://registry.npmjs.org/vis-network/-/vis-network-10.0.3.tgz", - "integrity": "sha512-Sk8qoyY4oi8o5dh8bHsKTTtHi8wWZABbLpH0Ac95ULqVuBIFbMng95QJmEKP8kIQlkjbq3ChJrk1bPmig9Cxig==", + "version": "10.1.0", + "resolved": "https://registry.npmjs.org/vis-network/-/vis-network-10.1.0.tgz", + "integrity": "sha512-D7b5p/C6SwWv1BlH9EDdtP0Tje/PJzSBWKef9qy2DyTC14QB7KBcnAZxIyW2m7mFYyfoeR+k5GF747zDcIhaKA==", "funding": { "type": "opencollective", "url": "https://opencollective.com/visjs" @@ -12870,11 +12868,10 @@ } }, "node_modules/webpack-dev-server": { - "version": "5.2.4", - "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.4.tgz", - "integrity": "sha512-GqDPGZN9bRqKBTkp4aWkobDDHMsrXKoGSdOH56smIri8qR0JG8gfL8/v/f/OZR3/OKXjG8uwJbFVhKm/FNU/UA==", + "version": "5.2.5", + "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.5.tgz", + "integrity": "sha512-4wZtCquSuv9CKX8oybo+mqxtxZqWz47uM1Ch94lxowBztOhWCbhqvRbfC/mODOwxgV2brY+JGZpHq58/SuVFYg==", "dev": true, - "license": "MIT", "dependencies": { "@types/bonjour": "^3.5.13", "@types/connect-history-api-fallback": "^1.5.4", diff --git a/jbrowse/package.json b/jbrowse/package.json index 31c0c43e2..bd5a2a5e6 100644 --- a/jbrowse/package.json +++ b/jbrowse/package.json @@ -24,13 +24,12 @@ "@jbrowse/product-core": "^4.1.13", "@jbrowse/react-linear-genome-view2": "^4.1.13", "@labkey/api": "^1.51.0", - "@labkey/components": "^7.35.0", + "@labkey/components": "^7.42.1", "@mui/x-data-grid": "^7.28.1", "assert": "^2.1.0", "browserify-zlib": "^0.2.0", "buffer": "^6.0.3", "child_process": "^1.0.2", - "fs": "^0.0.2", "jquery": "^3.7.1", "jspdf": "^4.2.1", "jspdf-autotable": "^5.0.7", diff --git a/jbrowse/tools/buildStandaloneCli.js b/jbrowse/tools/buildStandaloneCli.js deleted file mode 100644 index fbfd342e9..000000000 --- a/jbrowse/tools/buildStandaloneCli.js +++ /dev/null @@ -1,68 +0,0 @@ -// This script is a workaround until pkg supports ES modules: https://github.com/vercel/pkg/issues/1291 -// See also: https://nodejs.org/api/single-executable-applications.html -// This should be replaced once a better solution is available -const fs = require('fs'); -const { exec, execSync } = require('child_process'); - -function convertEs6ToCommonJS(packageName) { - const sourceFile = './buildCli/node_modules/@isaacs/cliui/node_modules/' + packageName + '/index.js'; - const origFile = sourceFile + '.orig'; - if (fs.existsSync(origFile)) { - console.log('File exists, skipping: ' + origFile); - } else { - console.log('Updating: ' + sourceFile); - if (!fs.existsSync(sourceFile)) { - throw new Error('Missing file: ' + sourceFile); - } - - if (fs.existsSync('./buildCli/' + packageName)) { - console.log('Deleting existing index.js file') - fs.unlinkSync('./buildCli/' + packageName) - } - - try { - execSync('npx esbuild --outdir=./buildCli/' + packageName + ' --target=es6 --format=cjs ' + sourceFile) - } catch (err) { - throw new Error('ERROR: ' + err.message); - } - - try { - fs.renameSync(sourceFile, origFile) - } catch (err){ - throw new Error('ERROR: ' + err); - } - - try { - fs.renameSync('./buildCli/' + packageName + '/index.js', sourceFile) - } catch (err){ - throw new Error('ERROR: ' + err); - } - } -} - -convertEs6ToCommonJS('ansi-regex') -convertEs6ToCommonJS('ansi-styles') -convertEs6ToCommonJS('strip-ansi') -convertEs6ToCommonJS('wrap-ansi') -convertEs6ToCommonJS('string-width') - -const child = exec('npx pkg --outdir=./resources/external/jb-cli ./buildCli/node_modules/@jbrowse/cli', (err, stdout, stderr) => { - if (err) { - throw new Error('Unable to run pkg: ' + err) - } -}); - -child.stdout.setEncoding('utf8'); -child.stdout.on('data', function(data) { - console.log(data); -}); - -child.stderr.setEncoding('utf8'); -child.stderr.on('data', function(data) { - console.log(data); -}); - -child.on('close', function(code) { - console.log('closing pkg: ' + code); -}); - diff --git a/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R b/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R index 46bdb584f..ee5de2b82 100644 --- a/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R +++ b/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R @@ -17,6 +17,7 @@ for (datasetId in names(seuratObjects)) { } Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRA', storeStimLevelData = FALSE, minEDS = minEDS) + Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRD', storeStimLevelData = FALSE, minEDS = minEDS) Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRB', minEDS = minEDS) saveData(seuratObj, datasetId) diff --git a/singlecell/resources/chunks/RunRiraClassification.R b/singlecell/resources/chunks/RunRiraClassification.R index 89740793e..eeded9f15 100644 --- a/singlecell/resources/chunks/RunRiraClassification.R +++ b/singlecell/resources/chunks/RunRiraClassification.R @@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) { printName(datasetId) seuratObj <- readSeuratRDS(seuratObjects[[datasetId]]) - seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown) + seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown, filterDisallowedClasses = filterDisallowedClasses) seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix) diff --git a/singlecell/resources/chunks/UpdateSeuratPrototype.R b/singlecell/resources/chunks/UpdateSeuratPrototype.R index 56e48e7d5..2da10f1ac 100644 --- a/singlecell/resources/chunks/UpdateSeuratPrototype.R +++ b/singlecell/resources/chunks/UpdateSeuratPrototype.R @@ -26,7 +26,7 @@ for (datasetId in names(seuratObjects)) { } if (runRira) { - seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE, maxAllowedUnknown = maxAllowedUnknown) + seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE, maxAllowedUnknown = maxAllowedUnknown, filterDisallowedClasses = filterDisallowedClasses) seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE) seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE) } diff --git a/singlecell/resources/queries/singlecell/cdna_libraries/.qview.xml b/singlecell/resources/queries/singlecell/cdna_libraries/.qview.xml index 3226dbcf0..93d777b34 100644 --- a/singlecell/resources/queries/singlecell/cdna_libraries/.qview.xml +++ b/singlecell/resources/queries/singlecell/cdna_libraries/.qview.xml @@ -14,6 +14,7 @@ + diff --git a/singlecell/resources/queries/singlecell/cdna_libraries/Cohort Info.qview.xml b/singlecell/resources/queries/singlecell/cdna_libraries/Cohort Info.qview.xml index 692e8d8e6..eecc93482 100644 --- a/singlecell/resources/queries/singlecell/cdna_libraries/Cohort Info.qview.xml +++ b/singlecell/resources/queries/singlecell/cdna_libraries/Cohort Info.qview.xml @@ -16,6 +16,7 @@ + diff --git a/singlecell/resources/web/singlecell/panel/PoolImportPanel.js b/singlecell/resources/web/singlecell/panel/PoolImportPanel.js index 5ee0ccfd5..8fd230b87 100644 --- a/singlecell/resources/web/singlecell/panel/PoolImportPanel.js +++ b/singlecell/resources/web/singlecell/panel/PoolImportPanel.js @@ -149,8 +149,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', { allowRowSpan: true },{ name: 'kitType', - labels: ['Kit Type', 'V1.1/V2/HT', 'V1.1/HT', 'HT/V1.1/V2', 'V2/HT'], - transform: 'kitType' + labels: ['Kit Type', 'V1.1/V2/HT', 'V1.1/HT', 'HT/V1.1/V2', 'V2/HT'] }], IGNORED_COLUMNS: [], @@ -1045,7 +1044,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', { LDK.Assert.assertNotEmpty('Expected non-null workbook', row.workbook); var cDNA = Ext4.apply({ sortGUID: sortMap[sortKey], - chemistry: null, + chemistry: row.kitType, plateId: row.plateId, well: row.well || 'Pool', citeseqpanel: row.citeseqpanel, diff --git a/singlecell/resources/web/singlecell/panel/cDNAImportPanel.js b/singlecell/resources/web/singlecell/panel/cDNAImportPanel.js index a02351135..a76717c2d 100644 --- a/singlecell/resources/web/singlecell/panel/cDNAImportPanel.js +++ b/singlecell/resources/web/singlecell/panel/cDNAImportPanel.js @@ -403,6 +403,10 @@ Ext4.define('SingleCell.panel.cDNAImportPanel', { citeseqReadsetId: row.citeseqReadsetId }; + if (row.kitType) { + baseRow.chemistry = row.kitType + } + var gexReadsetId = readsetMap[row.plateId + '-GEX']; if (gexReadsetId) { baseRow.readsetId = gexReadsetId; diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java index 9ee51c7b0..fa518d0b7 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/RunRiraClassification.java @@ -28,6 +28,10 @@ public Provider() {{ put("checked", true); }}, true), + SeuratToolParameter.create("filterDisallowedClasses", "Filter Disallowed Classes", "If true, then cells will be filtered based on expression of common contaminants, such as RBC or platelet genes ", "checkbox", new JSONObject() + {{ + put("checked", true); + }}, true), SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown", "If provided, this step will throw an error is more than this fraction of cells fail the check for disallowed UCell combinations", "ldk-numberfield", new JSONObject() {{ put("minValue", 0); diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java index 2518b0d1a..63d597ef8 100644 --- a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java +++ b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/UpdateSeuratPrototype.java @@ -64,6 +64,10 @@ public Provider() {{ put("checked", false); }}, false), + SeuratToolParameter.create("filterDisallowedClasses", "Filter Disallowed Classes (RIRA)", "This applies to RIRA classification. If true, then cells will be filtered based on expression of common contaminants, such as RBC or platelet genes ", "checkbox", new JSONObject() + {{ + put("checked", true); + }}, true), SeuratToolParameter.create("maxAllowedUnknown", "Max Allowed Unknown (RIRA)", "If provided, this step will throw an error is more than this fraction of cells fail the check for disallowed UCell combinations", "ldk-numberfield", new JSONObject() {{ put("minValue", 0);