From 30ede6c5416e4e6957d46dc55c8efed442371360 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 7 Apr 2025 12:18:42 -0700 Subject: [PATCH 01/30] Parallel stream in mGapReleaseGenerator --- .../mgap/pipeline/mGapReleaseGenerator.java | 31 +++++++++---------- 1 file changed, 14 insertions(+), 17 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index a6a03642..7d640252 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -86,6 +86,7 @@ import java.util.Set; import java.util.TreeSet; import java.util.concurrent.atomic.AtomicBoolean; +import java.util.concurrent.atomic.AtomicLong; import java.util.regex.Matcher; import java.util.regex.Pattern; @@ -1148,35 +1149,32 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra String releaseVersion = ctx.getParams().optString("releaseVersion"); - long sitesInspected = 0L; - long totalVariants = 0L; - long totalPrivateVariants = 0L; - long newInThisRelease = 0L; + AtomicLong sitesInspected = new AtomicLong(); + AtomicLong totalVariants = new AtomicLong(); + AtomicLong totalPrivateVariants = new AtomicLong(); + AtomicLong newInThisRelease = new AtomicLong(); Map typeCounts = new HashMap<>(); File interestingVariantTable = getVariantTableName(ctx, vcfInput); try (VCFFileReader reader = new VCFFileReader(vcfInput); CloseableIterator it = reader.iterator(); CSVWriter writer = new CSVWriter(PrintWriters.getPrintWriter(interestingVariantTable), '\t', CSVWriter.NO_QUOTE_CHARACTER)) { writer.writeNext(new String[]{"Chromosome", "Position", "Reference", "Allele", "Source", "Reason", "Description", "Overlapping Gene(s)", "OMIM Entries", "OMIM Phenotypes", "AF", "Identifier", "CADD_Score"}); - while (it.hasNext()) - { + it.stream().parallel().forEachOrdered(vc -> { Set> queuedLines = new LinkedHashSet<>(); - sitesInspected++; - - if (sitesInspected % 1000000 == 0) + sitesInspected.getAndIncrement(); + if (sitesInspected.get() % 1000000 == 0) { ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Inspected " + sitesInspected + " variants"); ctx.getLogger().info("inspected " + sitesInspected + " variants"); } - VariantContext vc = it.next(); if (vc.isFiltered()) { - continue; + return; } - totalVariants++; + totalVariants.getAndIncrement(); //track total by variant type Long typeCount = typeCounts.get(vc.getType()); @@ -1205,7 +1203,7 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra if (sampleCount == 1) { - totalPrivateVariants++; + totalPrivateVariants.getAndIncrement(); } } @@ -1342,7 +1340,6 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra try { maybeWriteVariantLine(queuedLines, vc, a.getBaseString(), "ClinVar", diseaseSplit.get(j), description, overlappingGenes, omimIds, omimPhenotypes, ctx.getLogger(), "ClinVar:" + clnAlleleIds.get(i)); - } catch (IndexOutOfBoundsException e) { @@ -1422,14 +1419,14 @@ else if (maxScore > 0.0) if (vc.getAttribute("mGAPV") != null && releaseVersion.equals(vc.getAttributeAsString("mGAPV", null))) { - newInThisRelease++; + newInThisRelease.getAndIncrement(); } for (List line : queuedLines) { writer.writeNext(line.toArray(new String[0])); } - } + }); } catch (IOException e) { @@ -1444,7 +1441,7 @@ else if (maxScore > 0.0) totalSubjects = reader.getFileHeader().getSampleNamesInOrder().size(); } - generateSummaries(ctx, vcfInput, genome, totalVariants, totalPrivateVariants, newInThisRelease, totalSubjects, typeCounts); + generateSummaries(ctx, vcfInput, genome, totalVariants.get(), totalPrivateVariants.get(), newInThisRelease.get(), totalSubjects, typeCounts); } try From ca0d6ea447f6ff73001a54190b1e0f0f37d0d1a2 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 7 Apr 2025 15:25:03 -0700 Subject: [PATCH 02/30] Debug/test date parsing --- .../test/tests/external/labModules/ELISPOT_AssayTest.java | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/elispot_assay/test/src/org/labkey/test/tests/external/labModules/ELISPOT_AssayTest.java b/elispot_assay/test/src/org/labkey/test/tests/external/labModules/ELISPOT_AssayTest.java index 77b8db42..85aef954 100644 --- a/elispot_assay/test/src/org/labkey/test/tests/external/labModules/ELISPOT_AssayTest.java +++ b/elispot_assay/test/src/org/labkey/test/tests/external/labModules/ELISPOT_AssayTest.java @@ -177,6 +177,10 @@ private void createPlateTemplate() String originalID = TEMPLATE_DATA[1][1]; TEMPLATE_DATA[1][1] = ""; + // Debug client date parsing + String clientFormattedString = (String)executeScript("return Ext4.Date.format(LDK.ConvertUtils.parseDate('2012-02-09'), 'Y-m-d');"); + assertEquals("Incorrect date parsing", clientFormattedString, "2012-02-09"); + _helper.addRecordsToAssayTemplate(TEMPLATE_DATA, expectedCols); waitForElement(_helper.getAssayWell("A1", LabModuleHelper.UNKNOWN_COLOR), WAIT_FOR_PAGE); From c6df6a4d7e88d7a5032d3b721c1dd5e48a96bd1b Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 10 Apr 2025 12:38:14 -0700 Subject: [PATCH 03/30] Add gzip to mGAP VariantsToTable --- .../mgap/pipeline/mGapReleaseGenerator.java | 20 ++++++++++++------- .../labkey/mgap/pipeline/mGapSummarizer.java | 2 +- 2 files changed, 14 insertions(+), 8 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index 7d640252..f4d93519 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -57,6 +57,7 @@ import org.labkey.api.sequenceanalysis.run.GeneToNameTranslator; import org.labkey.api.sequenceanalysis.run.LiftoverBcfToolsWrapper; import org.labkey.api.sequenceanalysis.run.SelectVariantsWrapper; +import org.labkey.api.util.Compress; import org.labkey.api.util.FileType; import org.labkey.api.util.FileUtil; import org.labkey.api.util.GUID; @@ -1105,18 +1106,15 @@ private File liftToHuman(JobContext ctx, File primaryTrackVcf, File noGenotypes, ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Running Liftover"); File liftedToGRCh37 = getLiftedVcfName(ctx.getOutputDir(), primaryTrackVcf); - File liftoverRejects = new File(ctx.getOutputDir(), SequenceAnalysisService.get().getUnzippedBaseName(primaryTrackVcf.getName()) + ".liftoverRejectGRCh37.vcf.gz"); - if (!indexExists(liftoverRejects)) + if (!indexExists(liftedToGRCh37)) { LiftoverBcfToolsWrapper liftoverVcfRunner = new LiftoverBcfToolsWrapper(ctx.getLogger()); - liftoverVcfRunner.doLiftover(noGenotypes, chainFile, sourceGenome.getWorkingFastaFile(), grch37Genome.getWorkingFastaFile(), liftoverRejects, liftedToGRCh37); + liftoverVcfRunner.doLiftover(noGenotypes, chainFile, sourceGenome.getWorkingFastaFile(), grch37Genome.getWorkingFastaFile(), null, liftedToGRCh37); } else { ctx.getLogger().info("resuming with existing file: " + liftedToGRCh37.getPath()); } - ctx.getFileManager().addIntermediateFile(liftoverRejects); - ctx.getFileManager().addIntermediateFile(new File(liftoverRejects.getPath() + ".tbi")); return liftedToGRCh37; } @@ -1484,14 +1482,22 @@ private static void generateSummaries(JobContext ctx, File vcf, ReferenceGenome //variants to table ctx.getLogger().info("Running VariantsToTable"); ctx.getJob().setStatus(PipelineJob.TaskStatus.running, "Running VariantsToTable"); - File variantsToTable = new File(ctx.getOutputDir(), SequenceAnalysisService.get().getUnzippedBaseName(vcf.getName()) + ".variantsToTable.txt"); + + File variantsToTableNoGz = new File(ctx.getOutputDir(), SequenceAnalysisService.get().getUnzippedBaseName(vcf.getName()) + ".variantsToTable.txt"); + File variantsToTable = new File(variantsToTableNoGz.getPath() + ".gz"); File tableCheck = new File(variantsToTable.getPath() + ".done"); if (!tableCheck.exists()) { VariantsToTableRunner vtt = new VariantsToTableRunner(ctx.getLogger()); List fields = new ArrayList<>(Arrays.asList("POS", "REF", "ALT", "FILTER")); fields.addAll(mGapSummarizer.SUMMARY_FIELDS); - vtt.execute(vcf, variantsToTable, genome.getWorkingFastaFile(), fields); + vtt.execute(vcf, variantsToTableNoGz, genome.getWorkingFastaFile(), fields); + + if (variantsToTable.exists()) + { + variantsToTable.delete(); + } + Compress.compressGzip(variantsToTableNoGz); try { diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapSummarizer.java b/mGAP/src/org/labkey/mgap/pipeline/mGapSummarizer.java index ced520a2..8ed255ff 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapSummarizer.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapSummarizer.java @@ -193,7 +193,7 @@ public void generateSummary(SequenceOutputHandler.JobContext ctx, File variantsT { ctx.getLogger().info("reading variant table"); FieldTracker tracker = new FieldTracker(130); - try (BufferedReader reader = Readers.getReader(variantsToTable)) + try (BufferedReader reader = IOUtil.openFileForBufferedUtf8Reading(variantsToTable)) { String lineStr; List header = new ArrayList<>(); From dff2355682e43e8db7e0fd964266a8a9dac7a790 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 11 Apr 2025 10:15:35 -0700 Subject: [PATCH 04/30] Temporary fix for mGAP and multi-species --- mGAP/src/org/labkey/mgap/mGAPModule.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mGAP/src/org/labkey/mgap/mGAPModule.java b/mGAP/src/org/labkey/mgap/mGAPModule.java index e94cdaa1..fa768faa 100644 --- a/mGAP/src/org/labkey/mgap/mGAPModule.java +++ b/mGAP/src/org/labkey/mgap/mGAPModule.java @@ -161,7 +161,8 @@ public JSONObject getPageContextJson(ContainerUser context) SimpleFilter filter = new SimpleFilter(); filter.addClause(ContainerFilter.current(context.getContainer()).createFilterClause(mGAPSchema.getInstance().getSchema(), FieldKey.fromString("container"))); - TableSelector ts = new TableSelector(mGAPSchema.getInstance().getSchema().getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES), PageFlowUtil.set("rowid", "objectid", "version", "jbrowseId", "humanJbrowseId", "luceneIndex"), filter, new Sort("-releaseDate")); + filter.addCondition(FieldKey.fromString("species"), "Rhesus macaque"); + TableSelector ts = new TableSelector(mGAPSchema.getInstance().getSchema().getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES), PageFlowUtil.set("rowid", "objectid", "species", "version", "jbrowseId", "humanJbrowseId", "luceneIndex"), filter, new Sort("-releaseDate")); ts.setMaxRows(1); ts.forEachResults(rs -> { String jbrowseId = rs.getString(FieldKey.fromString("jbrowseId")); From 0f73845787052b9d2f7a656df04bd0829e32b8fc Mon Sep 17 00:00:00 2001 From: bbimber Date: Sat, 12 Apr 2025 07:04:44 -0700 Subject: [PATCH 05/30] Support scatter/gather for liftover --- mGAP/resources/views/admin.html | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/mGAP/resources/views/admin.html b/mGAP/resources/views/admin.html index 250f925f..4f719f50 100644 --- a/mGAP/resources/views/admin.html +++ b/mGAP/resources/views/admin.html @@ -18,6 +18,10 @@ xtype: 'ldk-linkbutton', text: 'Manage Genomes', href: LABKEY.ActionURL.buildURL('query', 'executeQuery', null, {schemaName: 'sequenceanalysis', queryName: 'reference_libraries'}) + },{ + xtype: 'ldk-linkbutton', + text: 'Manage Sequence Outputs', + href: LABKEY.ActionURL.buildURL('query', 'executeQuery', null, {schemaName: 'sequenceanalysis', queryName: 'outputfiles'}) },{ xtype: 'ldk-linkbutton', text: 'Manage JBrowse Tracks', From 091cb5d02c8be7cb5c8ff12a4ba3585cbb131283 Mon Sep 17 00:00:00 2001 From: bbimber Date: Mon, 14 Apr 2025 10:23:27 -0700 Subject: [PATCH 06/30] Support scatter/gather for liftover --- mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index f4d93519..1e1148d6 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -938,7 +938,7 @@ public void processFilesRemote(List inputFiles, JobContext c String species = ctx.getParams().getString("species"); String releaseVersion = ctx.getParams().optString("releaseVersion", "0.0"); - File primaryTrackVcf = new File(ctx.getOutputDir(), "mGap." + species + ".v" + FileUtil.makeLegalName(releaseVersion).replaceAll(" ", "_") + ".vcf.gz"); + File primaryTrackVcf = new File(ctx.getOutputDir(), "mGap." + species.replaceAll(" ", "_") + ".v" + FileUtil.makeLegalName(releaseVersion).replaceAll(" ", "_") + ".vcf.gz"); try { From 4e388dcc7e0af51958c43ef786743932f087e133 Mon Sep 17 00:00:00 2001 From: bbimber Date: Wed, 16 Apr 2025 13:49:40 -0700 Subject: [PATCH 07/30] Add null check --- mcc/src/client/components/dashboard/BarChart.tsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mcc/src/client/components/dashboard/BarChart.tsx b/mcc/src/client/components/dashboard/BarChart.tsx index 92f5f99b..e994ab43 100644 --- a/mcc/src/client/components/dashboard/BarChart.tsx +++ b/mcc/src/client/components/dashboard/BarChart.tsx @@ -31,7 +31,7 @@ export default function BarChart(props: {demographics: [], fieldName: string, gr const indexAxis: 'x' | 'y' = props.indexAxis || 'y' - const collectedData = demographics.reduce((acc, curr: {}, idx) => { + const collectedData = (demographics ?? []).reduce((acc, curr: {}, idx) => { const value = curr[fieldName] === null ? 'Unknown' : curr[fieldName]; const group = groupField == null ? 'counts' : curr[groupField] || missingDataTerm @@ -46,7 +46,7 @@ export default function BarChart(props: {demographics: [], fieldName: string, gr } return acc; - }, {}); + }, {}) const labels = [...new Set(Object.keys(collectedData).flatMap(groupName => Object.keys(collectedData[groupName])))].sort(Intl.Collator().compare) const groupNames = Object.keys(collectedData).sort(Intl.Collator().compare) From 70aed840d5bb200fccae7c033e24152477c0ee27 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 25 Apr 2025 16:56:05 -0700 Subject: [PATCH 08/30] Make liftover optional in mGapReleaseGenerator --- .../mgap/pipeline/mGapReleaseGenerator.java | 28 ++++++++++++------- 1 file changed, 18 insertions(+), 10 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index 1e1148d6..22521e1b 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -131,8 +131,9 @@ public mGapReleaseGenerator() put("filterArray", "js:[LABKEY.Filter.create('datedisabled', null, LABKEY.Filter.Types.ISBLANK)]"); put("displayField", "name"); put("valueField", "rowid"); - put("allowBlank", false); + put("allowBlank", true); }}, null), + ToolParameterDescriptor.create("doLiftover", "Do Liftover?", "If true, the data will be lifted to GRCh37", "checkbox", null, false), ToolParameterDescriptor.create("luceneIndex", "Lucene Index", "A pre-made lucene index created from this VCF.", "sequenceanalysis-sequenceoutputfileselectorfield", new JSONObject() {{ put("allowBlank", false); @@ -452,7 +453,7 @@ else if (so.getCategory().endsWith("Release Track")) } SequenceOutputFile liftedVcf = liftedVcfMap.get(release); - if (liftedVcf == null) + if (ctx.getParams().optBoolean("doLiftover", false) && liftedVcf == null) { throw new PipelineJobException("Unable to find lifted VCF for release: " + release); } @@ -545,7 +546,10 @@ else if (so.getCategory().endsWith("Release Track")) row.put("releaseDate", new Date()); row.put("species", species); row.put("vcfId", so.getRowid()); - row.put("liftedVcfId", liftedVcf.getRowid()); + if (liftedVcf != null) + { + row.put("liftedVcfId", liftedVcf.getRowid()); + } row.put("sitesOnlyVcfId", sitesOnlyVcf.getRowid()); row.put("novelSitesVcfId", novelSitesVcf.getRowid()); row.put("luceneIndex", luceneIndex.getRowid()); @@ -1025,13 +1029,17 @@ public void processFilesRemote(List inputFiles, JobContext c File sitesOnlyVcf = getSitesOnlyVcf(ctx, primaryTrackVcf, genome); - File lifted = liftToHuman(ctx, primaryTrackVcf, sitesOnlyVcf, genome, grch37Genome); - SequenceOutputFile output3 = new SequenceOutputFile(); - output3.setFile(lifted); - output3.setName("mGAP Release: " + species + " " + releaseVersion + " Lifted to Human"); - output3.setCategory((testOnly ? "Test " : "") + "mGAP Release Lifted to Human"); - output3.setLibrary_id(grch37Genome.getGenomeId()); - ctx.getFileManager().addSequenceOutput(output3); + boolean doLiftover = ctx.getParams().optBoolean("doLiftover", false); + if (doLiftover) + { + File lifted = liftToHuman(ctx, primaryTrackVcf, sitesOnlyVcf, genome, grch37Genome); + SequenceOutputFile output3 = new SequenceOutputFile(); + output3.setFile(lifted); + output3.setName("mGAP Release: " + species + " " + releaseVersion + " Lifted to Human"); + output3.setCategory((testOnly ? "Test " : "") + "mGAP Release Lifted to Human"); + output3.setLibrary_id(grch37Genome.getGenomeId()); + ctx.getFileManager().addSequenceOutput(output3); + } } private void checkVcfAnnotationsAndSamples(File vcfInput, boolean skipAnnotationChecks) throws PipelineJobException From 4118eb7c578e3347427499c45214053b44682e65 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Apr 2025 06:19:58 -0700 Subject: [PATCH 09/30] npm dependency updates --- mcc/package-lock.json | 1863 +++++++++++++++++++++-------------------- 1 file changed, 945 insertions(+), 918 deletions(-) diff --git a/mcc/package-lock.json b/mcc/package-lock.json index 20e3cdd4..7ad10c48 100644 --- a/mcc/package-lock.json +++ b/mcc/package-lock.json @@ -37,13 +37,13 @@ } }, "node_modules/@ampproject/remapping": { - "version": "2.2.1", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz", - "integrity": "sha512-lFMjJTrFL3j7L9yBxwYfCq2k6qqwHyzuUl/XBnif78PWTJYyL/dfowQHWE3sp6U6ZzqWiiIZnpTMO96zhkjwtg==", + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.3.0.tgz", + "integrity": "sha512-30iZtAPgz+LTIYoeivqYo853f02jBYSd5uGnGpkFV0M3xOt9aN73erkgYAmZU43x4VfqcnLxW9Kpg3R5LC4YYw==", "dev": true, "dependencies": { - "@jridgewell/gen-mapping": "^0.3.0", - "@jridgewell/trace-mapping": "^0.3.9" + "@jridgewell/gen-mapping": "^0.3.5", + "@jridgewell/trace-mapping": "^0.3.24" }, "engines": { "node": ">=6.0.0" @@ -72,22 +72,21 @@ } }, "node_modules/@babel/core": { - "version": "7.26.8", - "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.8.tgz", - "integrity": "sha512-l+lkXCHS6tQEc5oUpK28xBOZ6+HwaH7YwoYQbLFiYb4nS2/l1tKnZEtEWkD0GuiYdvArf9qBS0XlQGXzPMsNqQ==", + "version": "7.26.10", + "resolved": "https://registry.npmjs.org/@babel/core/-/core-7.26.10.tgz", + "integrity": "sha512-vMqyb7XCDMPvJFFOaT9kxtiRh42GwlZEg1/uIgtZshS5a/8OaduUfCi7kynKgc3Tw/6Uo2D+db9qBttghhmxwQ==", "dev": true, "dependencies": { "@ampproject/remapping": "^2.2.0", "@babel/code-frame": "^7.26.2", - "@babel/generator": "^7.26.8", + "@babel/generator": "^7.26.10", "@babel/helper-compilation-targets": "^7.26.5", "@babel/helper-module-transforms": "^7.26.0", - "@babel/helpers": "^7.26.7", - "@babel/parser": "^7.26.8", - "@babel/template": "^7.26.8", - "@babel/traverse": "^7.26.8", - "@babel/types": "^7.26.8", - "@types/gensync": "^1.0.0", + "@babel/helpers": "^7.26.10", + "@babel/parser": "^7.26.10", + "@babel/template": "^7.26.9", + "@babel/traverse": "^7.26.10", + "@babel/types": "^7.26.10", "convert-source-map": "^2.0.0", "debug": "^4.1.0", "gensync": "^1.0.0-beta.2", @@ -109,12 +108,12 @@ "dev": true }, "node_modules/@babel/generator": { - "version": "7.26.8", - "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.26.8.tgz", - "integrity": "sha512-ef383X5++iZHWAXX0SXQR6ZyQhw/0KtTkrTz61WXRhFM6dhpHulO/RJz79L8S6ugZHJkOOkUrUdxgdF2YiPFnA==", + "version": "7.27.0", + "resolved": "https://registry.npmjs.org/@babel/generator/-/generator-7.27.0.tgz", + "integrity": "sha512-VybsKvpiN1gU1sdMZIp7FcqphVVKEwcuj02x73uvcHE0PTihx1nlBcowYWhDwjpoAXRv43+gDzyggGnn1XZhVw==", "dependencies": { - "@babel/parser": "^7.26.8", - "@babel/types": "^7.26.8", + "@babel/parser": "^7.27.0", + "@babel/types": "^7.27.0", "@jridgewell/gen-mapping": "^0.3.5", "@jridgewell/trace-mapping": "^0.3.25", "jsesc": "^3.0.2" @@ -136,12 +135,12 @@ } }, "node_modules/@babel/helper-compilation-targets": { - "version": "7.26.5", - "resolved": "https://registry.npmjs.org/@babel/helper-compilation-targets/-/helper-compilation-targets-7.26.5.tgz", - "integrity": "sha512-IXuyn5EkouFJscIDuFF5EsiSolseme1s0CZB+QxVugqJLYmKdxI1VfIBOst0SUu4rnk2Z7kqTwmoO1lp3HIfnA==", + "version": "7.27.0", + "resolved": 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"sha512-CNqKBRMQjwcmKR0idID5va1qlhrqVUKpovi+Ec79ksW8ux7iS1+A6VqzfZXgVYCFRKl7XL5ap3ZoMpwBJxcg0w==", "dev": true, "dependencies": { "@types/eslint-scope": "^3.7.7", "@types/estree": "^1.0.6", - "@webassemblyjs/ast": "^1.12.1", - "@webassemblyjs/wasm-edit": "^1.12.1", - "@webassemblyjs/wasm-parser": "^1.12.1", + "@types/json-schema": "^7.0.15", + "@webassemblyjs/ast": "^1.14.1", + "@webassemblyjs/wasm-edit": "^1.14.1", + "@webassemblyjs/wasm-parser": "^1.14.1", "acorn": "^8.14.0", "browserslist": "^4.24.0", "chrome-trace-event": "^1.0.2", @@ -8619,9 +8598,9 @@ "loader-runner": "^4.2.0", "mime-types": "^2.1.27", "neo-async": "^2.6.2", - "schema-utils": "^3.2.0", + "schema-utils": "^4.3.2", "tapable": "^2.1.1", - "terser-webpack-plugin": "^5.3.10", + "terser-webpack-plugin": "^5.3.11", "watchpack": "^2.4.1", "webpack-sources": "^3.2.3" }, @@ -8698,42 +8677,39 @@ } }, "node_modules/webpack-cli": { - "version": "5.1.4", - "resolved": 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"webpack-merge": "^6.0.1" }, "bin": { "webpack-cli": "bin/cli.js" }, "engines": { - "node": ">=14.15.0" + "node": ">=18.12.0" }, "funding": { "type": "opencollective", "url": "https://opencollective.com/webpack" }, "peerDependencies": { - "webpack": "5.x.x" + "webpack": "^5.82.0" }, "peerDependenciesMeta": { - "@webpack-cli/generators": { - "optional": true - }, "webpack-bundle-analyzer": { "optional": true }, @@ -8742,13 +8718,22 @@ } } }, + "node_modules/webpack-cli/node_modules/@discoveryjs/json-ext": { + "version": "0.6.3", + "resolved": "https://registry.npmjs.org/@discoveryjs/json-ext/-/json-ext-0.6.3.tgz", + "integrity": "sha512-4B4OijXeVNOPZlYA2oEwWOTkzyltLao+xbotHQeqN++Rv27Y6s818+n2Qkp8q+Fxhn0t/5lA5X1Mxktud8eayQ==", + "dev": true, + "engines": { + "node": ">=14.17.0" + } + }, "node_modules/webpack-cli/node_modules/commander": { - "version": "10.0.1", - "resolved": "https://registry.npmjs.org/commander/-/commander-10.0.1.tgz", - "integrity": "sha512-y4Mg2tXshplEbSGzx7amzPwKKOCGuoSRP/CjEdwwk0FOGlUbq6lKuoyDZTNZkmxHdJtp54hdfY/JUrdL7Xfdug==", + "version": "12.1.0", + "resolved": "https://registry.npmjs.org/commander/-/commander-12.1.0.tgz", + "integrity": "sha512-Vw8qHK3bZM9y/P10u3Vib8o/DdkvA2OtPtZvD871QKjy74Wj1WSKFILMPRPSdUSx5RFK1arlJzEtA4PkFgnbuA==", "dev": true, "engines": { - "node": ">=14" + "node": ">=18" } }, "node_modules/webpack-dev-middleware": { @@ -8800,14 +8785,15 @@ } }, "node_modules/webpack-dev-server": { - "version": "5.1.0", - "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.1.0.tgz", - "integrity": "sha512-aQpaN81X6tXie1FoOB7xlMfCsN19pSvRAeYUHOdFWOlhpQ/LlbfTqYwwmEDFV0h8GGuqmCmKmT+pxcUV/Nt2gQ==", + "version": "5.2.1", + "resolved": "https://registry.npmjs.org/webpack-dev-server/-/webpack-dev-server-5.2.1.tgz", + "integrity": "sha512-ml/0HIj9NLpVKOMq+SuBPLHcmbG+TGIjXRHsYfZwocUBIqEvws8NnS/V9AFQ5FKP+tgn5adwVwRrTEpGL33QFQ==", "dev": true, "dependencies": { "@types/bonjour": "^3.5.13", "@types/connect-history-api-fallback": "^1.5.4", "@types/express": "^4.17.21", + "@types/express-serve-static-core": "^4.17.21", "@types/serve-index": "^1.9.4", "@types/serve-static": "^1.15.5", "@types/sockjs": "^0.3.36", @@ -8818,10 +8804,9 @@ "colorette": "^2.0.10", "compression": "^1.7.4", "connect-history-api-fallback": "^2.0.0", - "express": "^4.19.2", + "express": "^4.21.2", "graceful-fs": "^4.2.6", - "html-entities": "^2.4.0", - "http-proxy-middleware": "^2.0.3", + "http-proxy-middleware": "^2.0.7", "ipaddr.js": "^2.1.0", "launch-editor": "^2.6.1", "open": "^10.0.3", @@ -8856,18 +8841,66 @@ } } }, + "node_modules/webpack-dev-server/node_modules/chokidar": { + "version": "3.6.0", + "resolved": "https://registry.npmjs.org/chokidar/-/chokidar-3.6.0.tgz", + "integrity": "sha512-7VT13fmjotKpGipCW9JEQAusEPE+Ei8nl6/g4FBAmIm0GOOLMua9NDDo/DWp0ZAxCr3cPq5ZpBqmPAQgDda2Pw==", + "dev": true, + "dependencies": { + "anymatch": "~3.1.2", + "braces": "~3.0.2", + "glob-parent": "~5.1.2", + "is-binary-path": "~2.1.0", + "is-glob": "~4.0.1", + "normalize-path": "~3.0.0", + "readdirp": "~3.6.0" + }, + "engines": { + "node": ">= 8.10.0" + }, + "funding": { + "url": "https://paulmillr.com/funding/" + }, + "optionalDependencies": { + "fsevents": "~2.3.2" + } + }, + "node_modules/webpack-dev-server/node_modules/glob-parent": { + "version": "5.1.2", + "resolved": "https://registry.npmjs.org/glob-parent/-/glob-parent-5.1.2.tgz", + "integrity": "sha512-AOIgSQCepiJYwP3ARnGx+5VnTu2HBYdzbGP45eLw1vr3zB3vZLeyed1sC9hnbcOc9/SrMyM5RPQrkGz4aS9Zow==", + "dev": true, + "dependencies": { + "is-glob": "^4.0.1" + }, + "engines": { + "node": ">= 6" + } + }, + "node_modules/webpack-dev-server/node_modules/readdirp": { + "version": "3.6.0", + "resolved": "https://registry.npmjs.org/readdirp/-/readdirp-3.6.0.tgz", + "integrity": "sha512-hOS089on8RduqdbhvQ5Z37A0ESjsqz6qnRcffsMU3495FuTdqSm+7bhJ29JvIOsBDEEnan5DPu9t3To9VRlMzA==", + "dev": true, + "dependencies": { + "picomatch": "^2.2.1" + }, + "engines": { + "node": ">=8.10.0" + } + }, "node_modules/webpack-merge": { - "version": "5.10.0", - "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-5.10.0.tgz", - "integrity": "sha512-+4zXKdx7UnO+1jaN4l2lHVD+mFvnlZQP/6ljaJVb4SZiwIKeUnrT5l0gkT8z+n4hKpC+jpOv6O9R+gLtag7pSA==", + "version": "6.0.1", + "resolved": "https://registry.npmjs.org/webpack-merge/-/webpack-merge-6.0.1.tgz", + "integrity": "sha512-hXXvrjtx2PLYx4qruKl+kyRSLc52V+cCvMxRjmKwoA+CBbbF5GfIBtR6kCvl0fYGqTUPKB+1ktVmTHqMOzgCBg==", "dev": true, "dependencies": { "clone-deep": "^4.0.1", "flat": "^5.0.2", - "wildcard": "^2.0.0" + "wildcard": "^2.0.1" }, "engines": { - "node": ">=10.0.0" + "node": ">=18.0.0" } }, "node_modules/webpack-sources": { @@ -8879,24 +8912,6 @@ "node": ">=10.13.0" } }, - "node_modules/webpack/node_modules/schema-utils": { - "version": "3.3.0", - "resolved": "https://registry.npmjs.org/schema-utils/-/schema-utils-3.3.0.tgz", - "integrity": "sha512-pN/yOAvcC+5rQ5nERGuwrjLlYvLTbCibnZ1I7B1LaiAz9BRBlE9GMgE/eqV30P7aJQUf7Ddimy/RsbYO/GrVGg==", - "dev": true, - "dependencies": { - "@types/json-schema": "^7.0.8", - "ajv": "^6.12.5", - "ajv-keywords": "^3.5.2" - }, - "engines": { - "node": ">= 10.13.0" - }, - "funding": { - "type": "opencollective", - "url": "https://opencollective.com/webpack" - } - }, "node_modules/websocket-driver": { "version": "0.7.4", "resolved": "https://registry.npmjs.org/websocket-driver/-/websocket-driver-0.7.4.tgz", @@ -8966,9 +8981,9 @@ "dev": true }, "node_modules/ws": { - "version": "8.18.0", - "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.0.tgz", - "integrity": "sha512-8VbfWfHLbbwu3+N6OKsOMpBdT4kXPDDB9cJk2bJ6mh9ucxdlnNvH1e+roYkKmN9Nxw2yjz7VzeO9oOz2zJ04Pw==", + "version": "8.18.1", + "resolved": "https://registry.npmjs.org/ws/-/ws-8.18.1.tgz", + "integrity": "sha512-RKW2aJZMXeMxVpnZ6bck+RswznaxmzdULiBr6KY7XkTnW8uvt0iT9H5DkHUChXrc+uurzwa0rVI16n/Xzjdz1w==", "dev": true, "engines": { "node": ">=10.0.0" @@ -8999,6 +9014,18 @@ "engines": { "node": ">= 6" } + }, + "node_modules/yocto-queue": { + "version": "0.1.0", + "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", + "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", + "dev": true, + "engines": { + "node": ">=10" + }, + "funding": { + "url": "https://github.com/sponsors/sindresorhus" + } } } } From 94db65ab63c596b94f75749a02d607176c673889 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Apr 2025 08:18:33 -0700 Subject: [PATCH 10/30] Account for species in mGapReleaseGenerator --- .../mgap/pipeline/mGapReleaseGenerator.java | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index 22521e1b..d80f36a7 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -380,7 +380,7 @@ public void complete(JobContext ctx, List inputs, List outputVCFMap = new HashMap<>(); Map outputTableMap = new HashMap<>(); @@ -389,8 +389,10 @@ public void complete(JobContext ctx, List inputs, List novelSitesVcfMap = new HashMap<>(); Map trackVCFMap = new HashMap<>(); + ctx.getLogger().debug("Total outputs created: " + outputsCreated.size()); for (SequenceOutputFile so : outputsCreated) { + ctx.getLogger().debug("Inspecting: " + so.getName() + " / " + so.getCategory()); if (so.getRowid() == null || so.getRowid() == 0) { throw new PipelineJobException("No rowId found for sequence output"); @@ -408,11 +410,11 @@ else if (so.getCategory().contains("Lifted")) } else if (so.getCategory().contains("mGAP Release: Sites Only")) { - sitesOnlyVcfMap.put("mGAP Release: " + releaseVersion, so); + sitesOnlyVcfMap.put("mGAP Release: " + releaseVersionString, so); } else if (so.getCategory().contains("Release Track") && so.getName().contains("Novel Sites")) { - novelSitesVcfMap.put("mGAP Release: " + releaseVersion, so); + novelSitesVcfMap.put("mGAP Release: " + releaseVersionString, so); trackVCFMap.put(so.getName(), so); } else if (so.getCategory().endsWith("Release")) @@ -445,6 +447,7 @@ else if (so.getCategory().endsWith("Release Track")) String releaseId = new GUID().toString(); for (String release : outputVCFMap.keySet()) { + ctx.getLogger().debug("Preparing release: " + release); SequenceOutputFile so = outputVCFMap.get(release); SequenceOutputFile so2 = outputTableMap.get(release); if (so2 == null) @@ -461,7 +464,7 @@ else if (so.getCategory().endsWith("Release Track")) SequenceOutputFile sitesOnlyVcf = sitesOnlyVcfMap.get(release); if (sitesOnlyVcf == null) { - throw new PipelineJobException("Unable to find sites-only VCF for release: " + release); + throw new PipelineJobException("Unable to find sites-only VCF for release: " + release + ". Total map size: " + sitesOnlyVcfMap.size()); } SequenceOutputFile novelSitesVcf = novelSitesVcfMap.get(release); @@ -1035,13 +1038,18 @@ public void processFilesRemote(List inputFiles, JobContext c File lifted = liftToHuman(ctx, primaryTrackVcf, sitesOnlyVcf, genome, grch37Genome); SequenceOutputFile output3 = new SequenceOutputFile(); output3.setFile(lifted); - output3.setName("mGAP Release: " + species + " " + releaseVersion + " Lifted to Human"); + output3.setName("mGAP Release: " + getVersionString(species, releaseVersion) + " Lifted to Human"); output3.setCategory((testOnly ? "Test " : "") + "mGAP Release Lifted to Human"); output3.setLibrary_id(grch37Genome.getGenomeId()); ctx.getFileManager().addSequenceOutput(output3); } } + private static String getVersionString(String species, String releaseVersion) + { + return species + " " + releaseVersion; + } + private void checkVcfAnnotationsAndSamples(File vcfInput, boolean skipAnnotationChecks) throws PipelineJobException { try (VCFFileReader reader = new VCFFileReader(vcfInput)) From f930f240a4a942644eff5d735ffbe958c2c3b3ed Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Apr 2025 12:41:51 -0700 Subject: [PATCH 11/30] Improve error message --- .../org/labkey/mgap/pipeline/mGapReleaseGenerator.java | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index d80f36a7..5e1e3250 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -492,11 +492,17 @@ else if (so.getCategory().endsWith("Release Track")) totalSubjects = reader.getFileHeader().getSampleNamesInOrder().size(); } - // NOTE: this can be rather slow. Consider caching remotely or using VCF index? String totalVariants = null; try { File releaseStats = new File(so.getFile().getParentFile(), SequenceAnalysisService.get().getUnzippedBaseName(so.getFile().getName()) + ".summaryByField.txt"); + + // NOTE: this is a one-off fix when there is mis-alignment between remote workdir and local dir. Should not normally be needed: + if (! releaseStats.exists()) + { + releaseStats = new File(ctx.getOutputDir(), releaseStats.getName()); + } + if (releaseStats.exists()) { try (CSVReader reader = new CSVReader(IOUtil.openFileForBufferedReading(releaseStats), '\t')) @@ -528,7 +534,7 @@ else if (so.getCategory().endsWith("Release Track")) } else { - job.getLogger().error("unable to find release stats file: " + releaseStats.getPath()); + throw new PipelineJobException("Unable to find release stats file: " + releaseStats.getPath() + ", for VCF: " + so.getRowid() + ", " + so.getFile().getPath()); } } catch (IOException e) From 6853f47ce43e7280e59d44dc16a74866788b43ee Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Apr 2025 15:01:37 -0700 Subject: [PATCH 12/30] Improve error message --- .../mgap/columnTransforms/JBrowseSessionTransform.java | 7 ++++++- .../src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index f3b0ca46..9cc39140 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -244,7 +244,12 @@ private TableInfo getDatabases() private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLException { - int outputFileId = getOrCreateOutputFile(rs.getString(FieldKey.fromString(fieldKey)), getInputValue("objectId"), rs.getString("label")); + Integer outputFileId = getOrCreateOutputFile(rs.getString(FieldKey.fromString(fieldKey)), getInputValue("objectId"), rs.getString("label")); + if (outputFileId == null) + { + getStatusLogger().info("outputFileId is null, skipping in getOrCreateJsonFile()"); + return null; + } //determine if there is already a JSONfile for this outputfile TableSelector ts1 = new TableSelector(getJsonFiles(), PageFlowUtil.set("objectid"), new SimpleFilter(FieldKey.fromString("outputfile"), outputFileId), null); diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index 5e1e3250..0a8833ab 100644 --- a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java +++ b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java @@ -587,6 +587,11 @@ else if (so.getCategory().endsWith("Release Track")) continue; //header } + if (lineNo % 5000 == 0) + { + job.getLogger().info("Inspected {} sites", lineNo); + } + Map map = new CaseInsensitiveHashMap<>(); map.put("releaseId", releaseId); map.put("contig", line[0]); @@ -611,7 +616,7 @@ else if (so.getCategory().endsWith("Release Track")) } else { - job.getLogger().error("unable to find release stats file: " + variantTable.getPath()); + throw new PipelineJobException("Unable to find variant table for output: " + so2.getRowid() + ", " + variantTable.getPath()); } //also tracks: From 48aa6525f498a8e1b204af88f79b66c667fe0523 Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Apr 2025 15:17:00 -0700 Subject: [PATCH 13/30] Bugfix to seurat prototype update action --- mGAP/resources/module.xml | 2 +- mGAP/resources/views/overview.view.xml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/mGAP/resources/module.xml b/mGAP/resources/module.xml index fe178cbe..8f95a1d1 100644 --- a/mGAP/resources/module.xml +++ b/mGAP/resources/module.xml @@ -25,7 +25,7 @@ - + diff --git a/mGAP/resources/views/overview.view.xml b/mGAP/resources/views/overview.view.xml index 7b102715..0c08a328 100644 --- a/mGAP/resources/views/overview.view.xml +++ b/mGAP/resources/views/overview.view.xml @@ -5,7 +5,7 @@ - + From 5203e6a3743d57fcadcc55bfcb902f71b187e87f Mon Sep 17 00:00:00 2001 From: bbimber Date: Tue, 29 Apr 2025 16:01:34 -0700 Subject: [PATCH 14/30] Bugfixes to mGAP ETL --- .../AbstractVariantTransform.java | 83 ++++++++++--------- .../JBrowseSessionTransform.java | 8 +- .../org/labkey/mgap/etl/EtlQueueManager.java | 15 ++++ 3 files changed, 64 insertions(+), 42 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index 5345e4fc..d3d0e692 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java @@ -112,51 +112,56 @@ protected Integer getOrCreateOutputFile(Object dataFileUrl, Object folderName, S File f = new File(uri); if (!f.exists()) { - getStatusLogger().error("File not found: " + uri); - return null; - } - else - { - File subDir = getLocalSubdir(folderName); - File localCopy = doFileCopy(f, subDir, name); - - //first create the ExpData - ExpData d = ExperimentService.get().getExpDataByURL(localCopy, getContainerUser().getContainer()); - if (d == null) + if (!EtlQueueManager.get().isFileInQueue(getContainerUser().getContainer(), f)) { - d = ExperimentService.get().createData(getContainerUser().getContainer(), new DataType("Variant Catalog")); - d.setDataFileURI(localCopy.toURI()); - d.setName(localCopy.getName()); - d.save(getContainerUser().getUser()); - } - - //then the outputfile - TableSelector ts = new TableSelector(getOutputFilesTableInfo(), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("dataId"), d.getRowId()), null); - if (ts.exists()) - { - getStatusLogger().info("existing record found for outputfile: " + d.getDataFileUrl()); - return ts.getObject(Integer.class); + getStatusLogger().error("File not found: " + uri); + return null; } else { - Map row = new CaseInsensitiveHashMap<>(); - row.put("category", getOutputFileCategory()); - row.put("dataid", d.getRowId()); - row.put("name", name == null ? "mGAP Variants, Version: " + getInputValue("version") : name); - row.put("description", getDescription()); - row.put("library_id", getLibraryId()); - row.put("container", getContainerUser().getContainer().getId()); - row.put("created", new Date()); - row.put("createdby", getContainerUser().getUser().getUserId()); - row.put("modified", new Date()); - row.put("modifiedby", getContainerUser().getUser().getUserId()); - - List> rows = getOutputFilesTableInfo().getUpdateService().insertRows(getContainerUser().getUser(), getContainerUser().getContainer(), List.of(row), new BatchValidationException(), null, new HashMap<>()); - getStatusLogger().info("created outputfile: " + rows.get(0).get("rowid")); - - return (Integer)rows.get(0).get("rowid"); + getStatusLogger().debug("File is in ETL queue: " + f.getPath()); } } + + File subDir = getLocalSubdir(folderName); + File localCopy = doFileCopy(f, subDir, name); + + //first create the ExpData + ExpData d = ExperimentService.get().getExpDataByURL(localCopy, getContainerUser().getContainer()); + if (d == null) + { + d = ExperimentService.get().createData(getContainerUser().getContainer(), new DataType("Variant Catalog")); + d.setDataFileURI(localCopy.toURI()); + d.setName(localCopy.getName()); + d.save(getContainerUser().getUser()); + } + + //then the outputfile + TableSelector ts = new TableSelector(getOutputFilesTableInfo(), PageFlowUtil.set("rowid"), new SimpleFilter(FieldKey.fromString("dataId"), d.getRowId()), null); + if (ts.exists()) + { + getStatusLogger().info("existing record found for outputfile: " + d.getDataFileUrl()); + return ts.getObject(Integer.class); + } + else + { + Map row = new CaseInsensitiveHashMap<>(); + row.put("category", getOutputFileCategory()); + row.put("dataid", d.getRowId()); + row.put("name", name == null ? "mGAP Variants, Version: " + getInputValue("version") : name); + row.put("description", getDescription()); + row.put("library_id", getLibraryId()); + row.put("container", getContainerUser().getContainer().getId()); + row.put("created", new Date()); + row.put("createdby", getContainerUser().getUser().getUserId()); + row.put("modified", new Date()); + row.put("modifiedby", getContainerUser().getUser().getUserId()); + + List> rows = getOutputFilesTableInfo().getUpdateService().insertRows(getContainerUser().getUser(), getContainerUser().getContainer(), List.of(row), new BatchValidationException(), null, new HashMap<>()); + getStatusLogger().info("created outputfile: " + rows.get(0).get("rowid")); + + return (Integer)rows.get(0).get("rowid"); + } } catch (Exception e) { diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index 9cc39140..f691df79 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -244,13 +244,15 @@ private TableInfo getDatabases() private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLException { - Integer outputFileId = getOrCreateOutputFile(rs.getString(FieldKey.fromString(fieldKey)), getInputValue("objectId"), rs.getString("label")); - if (outputFileId == null) + String value = rs.getString(FieldKey.fromString(fieldKey)); + if (value == null) { - getStatusLogger().info("outputFileId is null, skipping in getOrCreateJsonFile()"); + getStatusLogger().info(fieldKey + " is null, skipping in getOrCreateJsonFile()"); return null; } + Integer outputFileId = getOrCreateOutputFile(value, getInputValue("objectId"), rs.getString("label")); + //determine if there is already a JSONfile for this outputfile TableSelector ts1 = new TableSelector(getJsonFiles(), PageFlowUtil.set("objectid"), new SimpleFilter(FieldKey.fromString("outputfile"), outputFileId), null); if (ts1.exists()) diff --git a/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java b/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java index 95045438..3ea174d3 100644 --- a/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java +++ b/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java @@ -76,6 +76,21 @@ public void queueFileCopy(Container c, File source, File destination) _pendingFileCopy.get(c).add(Pair.of(source, destination)); } + public boolean isFileInQueue(Container c, final File destination) + { + if (_pendingFileCopy.containsKey(c) && _pendingFileCopy.get(c).stream().anyMatch(p -> destination.equals(p.getRight()))) + { + return true; + } + + if (_pendingRsyncCopy.containsKey(c) && _pendingRsyncCopy.get(c).stream().anyMatch(p -> destination.equals(p.getRight()))) + { + return true; + } + + return false; + } + public void queueRsyncCopy(Container c, File source, File destination) { if (!_pendingRsyncCopy.containsKey(c)) From 004679a3e3a1cf4618f275180bb425d6f3f96e38 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 1 May 2025 08:02:39 -0700 Subject: [PATCH 15/30] Bugfixes to mGAP browser action with multiple species --- mGAP/resources/views/overview.html | 2 +- mGAP/resources/views/quickLinks.html | 2 +- mGAP/resources/views/releaseNotes.html | 2 +- mGAP/src/org/labkey/mgap/mGAPController.java | 50 +++++++++++++------- mGAP/src/org/labkey/mgap/mGAPManager.java | 5 ++ mGAP/src/org/labkey/mgap/mGAPModule.java | 4 +- 6 files changed, 45 insertions(+), 20 deletions(-) diff --git a/mGAP/resources/views/overview.html b/mGAP/resources/views/overview.html index a5a06f46..65ada0ff 100644 --- a/mGAP/resources/views/overview.html +++ b/mGAP/resources/views/overview.html @@ -46,7 +46,7 @@

Structural Variant Catalog: We have released a draft dataset with structural variants generated from PacBio sequencing of 44 Rhesus macaques. These data complement the short variant catalog by detecting categories of variants not readily accomplished with short read Illumina data.

NHP Models of Human Disease: Phenotypes

diff --git a/mGAP/resources/views/quickLinks.html b/mGAP/resources/views/quickLinks.html index c486c8bb..26bbe219 100644 --- a/mGAP/resources/views/quickLinks.html +++ b/mGAP/resources/views/quickLinks.html @@ -18,7 +18,7 @@ '
  • Predicted Damaging Variants
    • ' + (jbrowseId ? '
  • Genome Browser (Macaque)
    • ' : '') + (humanJbrowseId ? '
  • Genome Browser (Human)
    • ' : '') + - (releaseHasLuceneIndex ? '
  • Full-text Variant Search (BETA)
    • ' : '') + + (releaseHasLuceneIndex ? '
  • Full-text Variant Search
    • ' : '') + '' ); } diff --git a/mGAP/resources/views/releaseNotes.html b/mGAP/resources/views/releaseNotes.html index 03bfa8b1..10b3bcf3 100644 --- a/mGAP/resources/views/releaseNotes.html +++ b/mGAP/resources/views/releaseNotes.html @@ -1,7 +1,7 @@

    Release 3.0:

    • This release involves a major change in the processing of variants. All prior releases omitted variants in complex or repetitive regions. We originally excluded these because genotypes can be less accurate; however, we made this change because some repetitive regions overlap coding regions and can contain valuable information. This also results in a significant increase in the total number of variants.
      • -
    • This is the first release to include a second species. The dataset now contains both Rhesus macaques and Japanese macaques (which are separated into a separate track).
      • +
    • This is the first release to include a second species. The dataset now contains both Rhesus macaques and Japanese macaques (which are separated into a separate VCF / browser track).

    Release 2.5:

    diff --git a/mGAP/src/org/labkey/mgap/mGAPController.java b/mGAP/src/org/labkey/mgap/mGAPController.java index 52991080..002afba7 100644 --- a/mGAP/src/org/labkey/mgap/mGAPController.java +++ b/mGAP/src/org/labkey/mgap/mGAPController.java @@ -898,7 +898,8 @@ public void validateCommand(Object o, Errors errors) public static class GenomeBrowserForm { private String _databaseId; - private String _species; + private String _nhpSpecies; + private String _browserSpecies; private String _trackName; private String _target = "browser"; @@ -912,14 +913,24 @@ public void setDatabaseId(String databaseId) _databaseId = databaseId; } - public String getSpecies() + public String getNhpSpecies() { - return _species; + return _nhpSpecies; } - public void setSpecies(String species) + public void setNhpSpecies(String nhpSpecies) { - _species = species; + _nhpSpecies = nhpSpecies; + } + + public String getBrowserSpecies() + { + return _browserSpecies; + } + + public void setBrowserSpecies(String browserSpecies) + { + _browserSpecies = browserSpecies; } public String getTrackName() @@ -967,10 +978,16 @@ public URLHelper getRedirectURL(GenomeBrowserForm form) } String jbrowseDatabaseId = StringUtils.trimToNull(form.getDatabaseId()); - String species = StringUtils.trimToNull(form.getSpecies()); + String browserSpecies = StringUtils.trimToNull(form.getBrowserSpecies()); + String nhpSpecies = StringUtils.trimToNull(form.getNhpSpecies()); + if (nhpSpecies == null) + { + nhpSpecies = mGAPManager.get().getDefaultSpecies(); + } + if (jbrowseDatabaseId == null) { - jbrowseDatabaseId = ctx.getString("human".equals(species) ? "mgapJBrowseHuman" : "mgapJBrowse"); + jbrowseDatabaseId = ctx.getString("human".equals(browserSpecies) ? "mgapJBrowseHuman" : "mgapJBrowse"); } if (jbrowseDatabaseId == null) @@ -990,7 +1007,7 @@ public URLHelper getRedirectURL(GenomeBrowserForm form) // This requires trackId if ("variantSearch".equals(actionName)) { - String trackGUID = getPrimaryTrackUUID(target, jbrowseDatabaseId, ctx.getString("mgapReleaseGUID")); + String trackGUID = getPrimaryTrackUUID(target, jbrowseDatabaseId, ctx.getString("mgapReleaseGUID"), nhpSpecies); if (trackGUID != null) { params.put("trackId", new String[]{trackGUID}); @@ -1036,25 +1053,26 @@ public URLHelper getRedirectURL(GenomeBrowserForm form) return ret; } - public String getPrimaryTrackUUID(Container target, String jbrowseSession, String releaseId) + public String getPrimaryTrackUUID(Container target, String jbrowseSession, String releaseId, String species) { - final String trackName = "mGAP Release"; - UserSchema mgap = QueryService.get().getUserSchema(getUser(), target, mGAPSchema.NAME); UserSchema jbrowse = QueryService.get().getUserSchema(getUser(), target, "jbrowse"); //find the selected track: SimpleFilter trackFilter = new SimpleFilter(FieldKey.fromString("releaseId"), releaseId); - trackFilter.addCondition(FieldKey.fromString("trackName"), trackName, CompareType.EQUAL); + trackFilter.addCondition(FieldKey.fromString("trackName"), species, CompareType.STARTS_WITH); + trackFilter.addCondition(FieldKey.fromString("isprimarytrack"), true, CompareType.EQUAL); + trackFilter.addCondition(FieldKey.fromString("category"), "Species Dataset", CompareType.EQUAL); + List outputFileIds = new TableSelector(mgap.getTable(mGAPSchema.TABLE_TRACKS_PER_RELEASE), PageFlowUtil.set("vcfId"), trackFilter, null).getArrayList(Integer.class); if (outputFileIds.isEmpty()) { - _log.error("Unable to find track: " + jbrowseSession + " / " + releaseId + " / " + trackName); + _log.error("Unable to find track for species: " + jbrowseSession + " / " + releaseId + " / " + species); return null; } else if (outputFileIds.size() > 1) { - _log.error("More than one matching outputfile found, using first: " + jbrowseSession + " / " + releaseId + " / " + trackName); + _log.error("More than one matching outputfile found for species, using first: " + jbrowseSession + " / " + releaseId + " / " + species); } //now database members from these outputFileIds: @@ -1064,12 +1082,12 @@ else if (outputFileIds.size() > 1) List guids = new TableSelector(databaseMembers, PageFlowUtil.set("jsonfile"), dbFilter, null).getArrayList(String.class); if (guids.isEmpty()) { - _log.error("No database_members found for track: " + jbrowseSession + " / " + releaseId + " / " + trackName + " / " + outputFileIds.get(0)); + _log.error("No database_members found for track: " + jbrowseSession + " / " + releaseId + " / " + species + " / " + outputFileIds.get(0)); return null; } else if (guids.size() > 1) { - _log.error("More than one matching database_member record found, using first: " + jbrowseSession + " / " + releaseId + " / " + trackName + " / " + outputFileIds.get(0)); + _log.error("More than one matching database_member record found, using first: " + jbrowseSession + " / " + releaseId + " / " + species + " / " + outputFileIds.get(0)); } return guids.get(0); diff --git a/mGAP/src/org/labkey/mgap/mGAPManager.java b/mGAP/src/org/labkey/mgap/mGAPManager.java index 840d419e..fdff5e3e 100644 --- a/mGAP/src/org/labkey/mgap/mGAPManager.java +++ b/mGAP/src/org/labkey/mgap/mGAPManager.java @@ -110,4 +110,9 @@ public Set getNotificationUsers() return ret; } + + public String getDefaultSpecies() + { + return "Rhesus macaque"; + } } \ No newline at end of file diff --git a/mGAP/src/org/labkey/mgap/mGAPModule.java b/mGAP/src/org/labkey/mgap/mGAPModule.java index fa768faa..763c5a09 100644 --- a/mGAP/src/org/labkey/mgap/mGAPModule.java +++ b/mGAP/src/org/labkey/mgap/mGAPModule.java @@ -158,10 +158,12 @@ public PipelineStartup() public JSONObject getPageContextJson(ContainerUser context) { JSONObject ret = super.getPageContextJson(context); + ret.put("defaultSpecies", mGAPManager.get().getDefaultSpecies()); SimpleFilter filter = new SimpleFilter(); filter.addClause(ContainerFilter.current(context.getContainer()).createFilterClause(mGAPSchema.getInstance().getSchema(), FieldKey.fromString("container"))); - filter.addCondition(FieldKey.fromString("species"), "Rhesus macaque"); + filter.addCondition(FieldKey.fromString("species"), mGAPManager.get().getDefaultSpecies()); + TableSelector ts = new TableSelector(mGAPSchema.getInstance().getSchema().getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES), PageFlowUtil.set("rowid", "objectid", "species", "version", "jbrowseId", "humanJbrowseId", "luceneIndex"), filter, new Sort("-releaseDate")); ts.setMaxRows(1); ts.forEachResults(rs -> { From 35866df4186a944c5e50d6c372b574a44787fcad Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 1 May 2025 08:39:35 -0700 Subject: [PATCH 16/30] Debug mGAP ETL --- .../mgap/columnTransforms/AbstractVariantTransform.java | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index d3d0e692..485fe025 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java @@ -201,6 +201,12 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx //Copy file locally, plus index if exists: File localCopy = new File(subdir, name == null || f.getName().startsWith("mGap.v") ? f.getName() : FileUtil.makeLegalName(name).replaceAll(" ", "_") + ".vcf.gz"); + if (f.getAbsolutePath().equals(localCopy)) + { + getStatusLogger().error("Attempting to copy file that is already a child of the target: " + f.getPath(), new Exception()); + return localCopy; + } + boolean doCopy = true; if (localCopy.exists()) { From d67d77c2fce2ffdc0e7752f737243a5ffd57d5b0 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 1 May 2025 09:24:59 -0700 Subject: [PATCH 17/30] Debug mGAP ETL --- .../mgap/columnTransforms/AbstractVariantTransform.java | 8 ++++++-- .../mgap/columnTransforms/TrackOutputFileTransform.java | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index 485fe025..38ab49e8 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java @@ -201,7 +201,7 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx //Copy file locally, plus index if exists: File localCopy = new File(subdir, name == null || f.getName().startsWith("mGap.v") ? f.getName() : FileUtil.makeLegalName(name).replaceAll(" ", "_") + ".vcf.gz"); - if (f.getAbsolutePath().equals(localCopy)) + if (f.equals(localCopy)) { getStatusLogger().error("Attempting to copy file that is already a child of the target: " + f.getPath(), new Exception()); return localCopy; @@ -221,6 +221,10 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx localCopy.delete(); } } + else + { + getStatusLogger().info("existing file not found: " + localCopy.getPath()); + } if (doCopy) { @@ -234,7 +238,7 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx File indexLocal = new File(localCopy.getPath() + ".tbi"); if (doCopy && indexLocal.exists()) { - getStatusLogger().info("deleting local copy of index since file was re-copied"); + getStatusLogger().info("deleting local copy of index since file will be re-copied"); indexLocal.delete(); } diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/TrackOutputFileTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/TrackOutputFileTransform.java index a396b4ba..6855be88 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/TrackOutputFileTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/TrackOutputFileTransform.java @@ -12,7 +12,7 @@ protected Object doTransform(Object inputValue) { if (null == inputValue) { - getStatusLogger().warn("value was null for track outputfile"); + getStatusLogger().debug("inputValue was null for TrackOutputFileTransform"); return null; } From d905e9c3d2be9f5147cd7acd474d321c39b931e5 Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 1 May 2025 10:02:53 -0700 Subject: [PATCH 18/30] More logging --- mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java | 1 + 1 file changed, 1 insertion(+) diff --git a/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java b/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java index 3ea174d3..bdb8f60f 100644 --- a/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java +++ b/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java @@ -121,6 +121,7 @@ private void copyFile(File source, File destination, Logger log) { if (destination.exists()) { + log.info("Deleting destination file: " + source.getPath()); destination.delete(); } From b3404cd12d189b42c52faee79db24468ffd905dd Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 1 May 2025 10:24:44 -0700 Subject: [PATCH 19/30] Avoid logging error --- .../labkey/mgap/columnTransforms/AbstractVariantTransform.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index 38ab49e8..fc154e9c 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java @@ -203,7 +203,7 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx File localCopy = new File(subdir, name == null || f.getName().startsWith("mGap.v") ? f.getName() : FileUtil.makeLegalName(name).replaceAll(" ", "_") + ".vcf.gz"); if (f.equals(localCopy)) { - getStatusLogger().error("Attempting to copy file that is already a child of the target: " + f.getPath(), new Exception()); + getStatusLogger().debug("Attempting to copy file that is already a child of the target: " + f.getPath(), new Exception()); return localCopy; } From 180be0c4658254e3a39b1c6ed938a4735575988f Mon Sep 17 00:00:00 2001 From: bbimber Date: Thu, 1 May 2025 13:08:11 -0700 Subject: [PATCH 20/30] Include species in TracksPerReleaseGenomeBrowserDisplayColumnFactory --- ...eleaseGenomeBrowserDisplayColumnFactory.java | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java index 9ec97544..d08d57d3 100644 --- a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java @@ -5,10 +5,12 @@ import org.labkey.api.data.DisplayColumn; import org.labkey.api.data.RenderContext; import org.labkey.api.query.DetailsURL; +import org.labkey.api.query.FieldKey; import org.labkey.api.util.PageFlowUtil; import java.io.IOException; import java.io.Writer; +import java.util.Set; /** * Created by bimber on 5/17/2017. @@ -26,13 +28,26 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep String jbrowseId = ctx.get(getBoundKey("releaseId", "jbrowseId"), String.class); String containerId = ctx.get(getBoundKey("releaseId", "container"), String.class); String trackName = ctx.get(getBoundKey("trackName"), String.class); + String species = ctx.get(getBoundKey("releaseId", "species"), String.class); if (jbrowseId != null && trackName != null) { - DetailsURL url = DetailsURL.fromString("/mgap/genomeBrowser.view?database=" + jbrowseId + "&activeTracks=" + trackName, ContainerManager.getForId(containerId)); + DetailsURL url = DetailsURL.fromString("/mgap/genomeBrowser.view?database=" + jbrowseId + "&activeTracks=" + trackName + (species == null ? "" : "&nhpSpecies=" + species), ContainerManager.getForId(containerId)); out.write("View In Genome Browser"); } } + + @Override + public void addQueryFieldKeys(Set keys) + { + super.addQueryFieldKeys(keys); + + keys.add(getBoundKey("species")); + keys.add(getBoundKey("trackName")); + keys.add(getBoundKey("releaseId", "jbrowseId")); + keys.add(getBoundKey("releaseId", "container")); + keys.add(getBoundKey("releaseId", "species")); + } }; } } From c2e843cc0fb31780a41bd3787c908b6499bda383 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 2 May 2025 07:43:54 -0700 Subject: [PATCH 21/30] Use symlinks in mGAP ETL rather than copy --- .../AbstractVariantTransform.java | 45 ++++++++++++++++--- 1 file changed, 39 insertions(+), 6 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index fc154e9c..a59b12ad 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java @@ -1,6 +1,9 @@ package org.labkey.mgap.columnTransforms; import org.apache.commons.lang3.StringUtils; +import org.jetbrains.annotations.Nullable; +import org.junit.Assert; +import org.junit.Test; import org.labkey.api.collections.CaseInsensitiveHashMap; import org.labkey.api.data.Results; import org.labkey.api.data.Selector; @@ -24,7 +27,10 @@ import org.labkey.mgap.mGAPManager; import java.io.File; +import java.io.IOException; import java.net.URI; +import java.nio.file.Files; +import java.nio.file.Path; import java.sql.SQLException; import java.util.Date; import java.util.HashMap; @@ -195,7 +201,7 @@ protected File getLocalSubdir(Object folderName) throws PipelineJobException return subdir; } - protected File doFileCopy(File f, File subdir, String name) throws PipelineJobException + protected File doFileCopy(File f, File subdir, @Nullable String name) throws PipelineJobException { getStatusLogger().info("preparing to copy file: " + f.getPath()); @@ -217,8 +223,15 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx } else { - getStatusLogger().info("source file has been modified, deleting copy and re-syncing"); - localCopy.delete(); + getStatusLogger().info("source file has been modified, deleting copy and re-syncing: " + localCopy.getPath()); + try + { + Files.delete(localCopy.toPath()); + } + catch (IOException e) + { + throw new PipelineJobException("Unable to delete file: " + localCopy.getPath(), e); + } } } else @@ -229,7 +242,20 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx if (doCopy) { getStatusLogger().info("queueing file copy: " + localCopy.getPath()); - EtlQueueManager.get().queueFileCopy(getContainerUser().getContainer(), f, localCopy); + try + { + if (!Files.isReadable(f.toPath())) + { + throw new PipelineJobException("Unable to read file: " + f.getPath()); + } + + Files.createSymbolicLink(f.toPath(), localCopy.toPath()); + } + catch (IOException e) + { + getStatusLogger().error("Failed to create symlink: " + localCopy.getPath(), e); + return null; + } } File index = new File(f.getPath() + ".tbi"); @@ -238,14 +264,21 @@ protected File doFileCopy(File f, File subdir, String name) throws PipelineJobEx File indexLocal = new File(localCopy.getPath() + ".tbi"); if (doCopy && indexLocal.exists()) { - getStatusLogger().info("deleting local copy of index since file will be re-copied"); + getStatusLogger().info("deleting local copy of index since file will be re-copied: " + indexLocal.getPath()); indexLocal.delete(); } if (!indexLocal.exists()) { getStatusLogger().info("queueing copy of index: " + indexLocal.getPath()); - EtlQueueManager.get().queueFileCopy(getContainerUser().getContainer(), index, indexLocal); + try + { + Files.createSymbolicLink(f.toPath(), localCopy.toPath()); + } + catch (IOException e) + { + getStatusLogger().error("Failed to create symlink: " + localCopy.getPath(), e); + } } } From f92cf41a6aba70160945a77b8ee8c51f4081d819 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 2 May 2025 07:49:16 -0700 Subject: [PATCH 22/30] Expand mGAPLuceneDetector --- mGAP/src/org/labkey/mgap/jbrowse/mGAPLuceneDetector.java | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/mGAP/src/org/labkey/mgap/jbrowse/mGAPLuceneDetector.java b/mGAP/src/org/labkey/mgap/jbrowse/mGAPLuceneDetector.java index 91e51971..5e0e458a 100644 --- a/mGAP/src/org/labkey/mgap/jbrowse/mGAPLuceneDetector.java +++ b/mGAP/src/org/labkey/mgap/jbrowse/mGAPLuceneDetector.java @@ -34,6 +34,14 @@ public SequenceOutputFile findMatchingLuceneIndex(SequenceOutputFile vcfFile, Li return SequenceOutputFile.getForId(ts.getObject(Integer.class)); } + SimpleFilter filter2 = new SimpleFilter(FieldKey.fromString("vcfId"), vcfFile.getRowid(), CompareType.EQUAL); + filter2.addCondition(FieldKey.fromString("vcfIndexId"), null, CompareType.NONBLANK); + TableSelector ts2 = new TableSelector(QueryService.get().getUserSchema(u, target, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_TRACKS_PER_RELEASE), PageFlowUtil.set("vcfIndexId"), filter2, null); + if (ts2.exists()) + { + return SequenceOutputFile.getForId(ts2.getObject(Integer.class)); + } + return null; } From 7a1440bfb5707e885d790b71622f0713a2577200 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 2 May 2025 08:27:48 -0700 Subject: [PATCH 23/30] Add more logging in ETL --- .../AbstractVariantTransform.java | 34 +++++++++++++++---- .../LuceneIndexTransform.java | 11 +++++- 2 files changed, 37 insertions(+), 8 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index a59b12ad..0779f1b5 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java @@ -131,6 +131,10 @@ protected Integer getOrCreateOutputFile(Object dataFileUrl, Object folderName, S File subDir = getLocalSubdir(folderName); File localCopy = doFileCopy(f, subDir, name); + if (localCopy == null) + { + // TODO + } //first create the ExpData ExpData d = ExperimentService.get().getExpDataByURL(localCopy, getContainerUser().getContainer()); @@ -203,7 +207,11 @@ protected File getLocalSubdir(Object folderName) throws PipelineJobException protected File doFileCopy(File f, File subdir, @Nullable String name) throws PipelineJobException { - getStatusLogger().info("preparing to copy file: " + f.getPath()); + getStatusLogger().info("preparing to copy file: " + f.getPath() + ", with name: " + name); + if (f.getName().equals("write.lock")) + { + return LuceneIndexTransform.doLuceneCopy(f, subdir, name, getStatusLogger(), getContainerUser().getContainer()); + } //Copy file locally, plus index if exists: File localCopy = new File(subdir, name == null || f.getName().startsWith("mGap.v") ? f.getName() : FileUtil.makeLegalName(name).replaceAll(" ", "_") + ".vcf.gz"); @@ -227,6 +235,10 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip try { Files.delete(localCopy.toPath()); + if (localCopy.exists()) + { + throw new PipelineJobException("Unable to delete file: " + localCopy.getPath()); + } } catch (IOException e) { @@ -241,7 +253,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip if (doCopy) { - getStatusLogger().info("queueing file copy: " + localCopy.getPath()); + getStatusLogger().info("Creating symlink: " + f.getPath() + " / " + localCopy.getPath()); try { if (!Files.isReadable(f.toPath())) @@ -249,12 +261,16 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip throw new PipelineJobException("Unable to read file: " + f.getPath()); } + if (localCopy.exists()) + { + throw new PipelineJobException("File should have been deleted: " + localCopy.getPath()); + } + Files.createSymbolicLink(f.toPath(), localCopy.toPath()); } catch (IOException e) { - getStatusLogger().error("Failed to create symlink: " + localCopy.getPath(), e); - return null; + throw new PipelineJobException("Failed to create symlink: " + localCopy.getPath(), e); } } @@ -270,16 +286,20 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip if (!indexLocal.exists()) { - getStatusLogger().info("queueing copy of index: " + indexLocal.getPath()); + getStatusLogger().info("Creating symlink copy of VCF index: " + index.getPath() + " / " + indexLocal.getPath()); try { - Files.createSymbolicLink(f.toPath(), localCopy.toPath()); + Files.createSymbolicLink(index.toPath(), indexLocal.toPath()); } catch (IOException e) { - getStatusLogger().error("Failed to create symlink: " + localCopy.getPath(), e); + getStatusLogger().error("Failed to create symlink: " + indexLocal.getPath(), e); } } + else + { + getStatusLogger().info("Local index already exists: " + indexLocal.getPath()); + } } return localCopy; diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java index 55fb8c77..ae7ad050 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java @@ -1,6 +1,8 @@ package org.labkey.mgap.columnTransforms; +import org.apache.logging.log4j.Logger; import org.jetbrains.annotations.Nullable; +import org.labkey.api.data.Container; import org.labkey.api.jbrowse.JBrowseService; import org.labkey.api.pipeline.PipelineJobException; import org.labkey.mgap.etl.EtlQueueManager; @@ -21,11 +23,18 @@ protected Object doTransform(Object inputValue) @Override protected File doFileCopy(File f, File subdir, @Nullable String name) throws PipelineJobException { + return doLuceneCopy(f, subdir, name, getStatusLogger(), getContainerUser().getContainer()); + } + + public static File doLuceneCopy(File f, File subdir, @Nullable String name, Logger log, Container container) throws PipelineJobException + { + log.info("preparing to copy lucene index: " + f.getPath() + ", with name: " + name); + // NOTE: lucene is a special case since the DB tracks one file, but we need this whole folder: File sourceDir = f.getParentFile(); File targetDir = new File(subdir, "LuceneIndex"); JBrowseService.get().clearLuceneCacheEntry(targetDir); - EtlQueueManager.get().queueRsyncCopy(getContainerUser().getContainer(), sourceDir, targetDir); + EtlQueueManager.get().queueRsyncCopy(container, sourceDir, targetDir); return new File(targetDir, sourceDir.getName() + "/" + f.getName()); } From 0fe26b1bea28e57eff6f61a016727010dd4b6220 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 2 May 2025 09:20:52 -0700 Subject: [PATCH 24/30] Bugfix to mGAP ETL --- .../mgap/columnTransforms/AbstractVariantTransform.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index 0779f1b5..04530b42 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java @@ -266,7 +266,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip throw new PipelineJobException("File should have been deleted: " + localCopy.getPath()); } - Files.createSymbolicLink(f.toPath(), localCopy.toPath()); + Files.createSymbolicLink(localCopy.toPath(), f.toPath()); } catch (IOException e) { @@ -289,7 +289,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip getStatusLogger().info("Creating symlink copy of VCF index: " + index.getPath() + " / " + indexLocal.getPath()); try { - Files.createSymbolicLink(index.toPath(), indexLocal.toPath()); + Files.createSymbolicLink(indexLocal.toPath(), index.toPath()); } catch (IOException e) { From fc38d5868ee62b54403e1fb378cb875ae3704d39 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 2 May 2025 11:22:53 -0700 Subject: [PATCH 25/30] Update HTML margins --- mGAP/resources/views/annotation.html | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/mGAP/resources/views/annotation.html b/mGAP/resources/views/annotation.html index 9fc544f8..4f18ac9f 100644 --- a/mGAP/resources/views/annotation.html +++ b/mGAP/resources/views/annotation.html @@ -18,7 +18,7 @@ })(jQuery); -
    +
    Assigning significance to genetics variants is often a challenge, and this is particularly problematic for model organisms like macaques, which have few sources of genomic annotations, relative to human or mouse. @@ -34,7 +34,6 @@
  • dbNSFP: Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs
  • SnpEff: variant annotation and effect prediction tool
  • VariantAnnotation: a custom Funcotator-compatible set of annotation sources
    • -
    From 24841a5bb401646caaccc634af1bf2a8acd65c65 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 2 May 2025 11:38:47 -0700 Subject: [PATCH 26/30] Debug mGAP indexes in ETL --- .../JBrowseSessionTransform.java | 20 +++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index f691df79..66d1c58a 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -149,7 +149,10 @@ protected void addTracks(final String databaseId, String releaseId) FieldKey.fromString("description"), FieldKey.fromString("isprimarytrack"), FieldKey.fromString("vcfId/dataid/DataFileUrl"), - FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl") + FieldKey.fromString("releaseId/luceneIndex"), + FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl"), + FieldKey.fromString("vcfIndexId"), + FieldKey.fromString("vcfIndexId/dataid/DataFileUrl") ); TableInfo tracksPerRelease = QueryService.get().getUserSchema(getContainerUser().getUser(), getContainerUser().getContainer(), mGAPSchema.NAME).getTable(mGAPSchema.TABLE_TRACKS_PER_RELEASE); @@ -278,9 +281,18 @@ private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLExcept if (isDefaultTrack) { - boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl"))) != null; - getStatusLogger().info("Creating track JSON for primary track, has lucene index: " + hasLuceneIndex); - row.put("trackJson", getTrackJson(hasLuceneIndex)); + boolean expectIndex = rs.getObject(FieldKey.fromString("releaseId/luceneIndex")) != null || rs.getObject(FieldKey.fromString("vcfIndexId")) != null; + + boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl"))) != null || + StringUtils.trimToNull(rs.getString(FieldKey.fromString("vcfIndexId/dataid/DataFileUrl"))) != null; + + if (expectIndex && !hasLuceneIndex) + { + getStatusLogger().warn("Expected VCF index but did not find one for outputId: " + outputFileId); + } + + getStatusLogger().info("Creating track JSON for primary track, has lucene index: " + expectIndex + " / " + hasLuceneIndex); + row.put("trackJson", getTrackJson(expectIndex)); } else { From 924d5ae8c237c1c4a97742d1aa33e5f8000cd6c2 Mon Sep 17 00:00:00 2001 From: bbimber Date: Fri, 2 May 2025 13:41:52 -0700 Subject: [PATCH 27/30] Force lucene config creation in mGAP ETL --- .../JBrowseSessionTransform.java | 40 ++++++++++++++++++- 1 file changed, 39 insertions(+), 1 deletion(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index 66d1c58a..ab1bfb30 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -17,7 +17,9 @@ import org.labkey.api.pipeline.PipelineValidationException; import org.labkey.api.query.BatchValidationException; import org.labkey.api.query.FieldKey; +import org.labkey.api.query.InvalidKeyException; import org.labkey.api.query.QueryService; +import org.labkey.api.query.QueryUpdateServiceException; import org.labkey.api.query.UserSchema; import org.labkey.api.util.GUID; import org.labkey.api.util.PageFlowUtil; @@ -178,6 +180,39 @@ protected void addTracks(final String databaseId, String releaseId) }); } + private void ensureLuceneData(String objectId) + { + //determine if there is already a JSONfile for this outputfile + TableSelector ts1 = new TableSelector(getJsonFiles(), PageFlowUtil.set("isprimarytrack", "container"), new SimpleFilter(FieldKey.fromString("objectid"), objectId), null); + if (!ts1.exists()) + { + getStatusLogger().error("expected jsonfile to exist: " + objectId); + return; + } + + try (Results rs = ts1.getResults()) + { + boolean isDefaultTrack = rs.getBoolean(FieldKey.fromString("isprimarytrack")); + if (!isDefaultTrack) + { + return; + } + + String containerId = rs.getString(FieldKey.fromString("container")); + + Map row = new CaseInsensitiveHashMap<>(); + row.put("objectid", objectId); + row.put("container", containerId); + row.put("trackJson", getTrackJson(true)); + + getJsonFiles().getUpdateService().updateRows(getContainerUser().getUser(), getContainerUser().getContainer(), Arrays.asList(row), Arrays.asList(new CaseInsensitiveHashMap<>(Map.of("objectid", objectId))), new BatchValidationException(), null, null); + } + catch (SQLException | QueryUpdateServiceException | BatchValidationException | InvalidKeyException e) + { + getStatusLogger().error("Unable to update lucene config", e); + } + } + protected void getOrCreateDatabaseMember(String databaseId, String jsonFileId) throws Exception { SimpleFilter filter = new SimpleFilter(FieldKey.fromString("database"), databaseId); @@ -261,7 +296,10 @@ private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLExcept if (ts1.exists()) { getStatusLogger().info("jsonfile already exists for output: " + outputFileId); - return ts1.getArrayList(String.class).get(0); + String objectId = ts1.getArrayList(String.class).get(0); + ensureLuceneData(objectId); + + return objectId; } try From 58723ec5ad9adac63154126b9514e19a70f2ae30 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 4 May 2025 08:05:45 -0700 Subject: [PATCH 28/30] Bugfix to mGAP ETL --- .../JBrowseSessionTransform.java | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index ab1bfb30..a0006f54 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -183,7 +183,7 @@ protected void addTracks(final String databaseId, String releaseId) private void ensureLuceneData(String objectId) { //determine if there is already a JSONfile for this outputfile - TableSelector ts1 = new TableSelector(getJsonFiles(), PageFlowUtil.set("isprimarytrack", "container"), new SimpleFilter(FieldKey.fromString("objectid"), objectId), null); + TableSelector ts1 = new TableSelector(getJsonFiles(), PageFlowUtil.set("container"), new SimpleFilter(FieldKey.fromString("objectid"), objectId), null); if (!ts1.exists()) { getStatusLogger().error("expected jsonfile to exist: " + objectId); @@ -192,12 +192,6 @@ private void ensureLuceneData(String objectId) try (Results rs = ts1.getResults()) { - boolean isDefaultTrack = rs.getBoolean(FieldKey.fromString("isprimarytrack")); - if (!isDefaultTrack) - { - return; - } - String containerId = rs.getString(FieldKey.fromString("container")); Map row = new CaseInsensitiveHashMap<>(); @@ -291,21 +285,24 @@ private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLExcept Integer outputFileId = getOrCreateOutputFile(value, getInputValue("objectId"), rs.getString("label")); + boolean isDefaultTrack = rs.getObject(FieldKey.fromString("isprimarytrack")) != null && rs.getBoolean(FieldKey.fromString("isprimarytrack")); + //determine if there is already a JSONfile for this outputfile TableSelector ts1 = new TableSelector(getJsonFiles(), PageFlowUtil.set("objectid"), new SimpleFilter(FieldKey.fromString("outputfile"), outputFileId), null); if (ts1.exists()) { getStatusLogger().info("jsonfile already exists for output: " + outputFileId); String objectId = ts1.getArrayList(String.class).get(0); - ensureLuceneData(objectId); + if (isDefaultTrack) + { + ensureLuceneData(objectId); + } return objectId; } try { - boolean isDefaultTrack = rs.getObject(FieldKey.fromString("isprimarytrack")) != null && rs.getBoolean(FieldKey.fromString("isprimarytrack")); - TableInfo jsonFiles = getJbrowseUserSchema().getTable("jsonfiles"); CaseInsensitiveHashMap row = new CaseInsensitiveHashMap<>(); row.put("objectid", new GUID().toString()); From 68677f3498369103373240ca79e486693653224d Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 4 May 2025 12:40:24 -0700 Subject: [PATCH 29/30] Bugfix to mGAP ETL --- .../labkey/mgap/columnTransforms/JBrowseSessionTransform.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index a0006f54..76541b9d 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -190,9 +190,9 @@ private void ensureLuceneData(String objectId) return; } - try (Results rs = ts1.getResults()) + try { - String containerId = rs.getString(FieldKey.fromString("container")); + String containerId = ts1.getObject(String.class); Map row = new CaseInsensitiveHashMap<>(); row.put("objectid", objectId); From 79c3f50a89dd80d3e92acc67d5f378dbb7a0a2c2 Mon Sep 17 00:00:00 2001 From: bbimber Date: Sun, 4 May 2025 13:12:18 -0700 Subject: [PATCH 30/30] Need UserSchema not DbSchema --- .../labkey/mgap/columnTransforms/JBrowseSessionTransform.java | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index 76541b9d..e489595d 100644 --- a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java +++ b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java @@ -199,7 +199,8 @@ private void ensureLuceneData(String objectId) row.put("container", containerId); row.put("trackJson", getTrackJson(true)); - getJsonFiles().getUpdateService().updateRows(getContainerUser().getUser(), getContainerUser().getContainer(), Arrays.asList(row), Arrays.asList(new CaseInsensitiveHashMap<>(Map.of("objectid", objectId))), new BatchValidationException(), null, null); + TableInfo jsonFiles = getJbrowseUserSchema().getTable("jsonfiles"); + jsonFiles.getUpdateService().updateRows(getContainerUser().getUser(), getContainerUser().getContainer(), Arrays.asList(row), Arrays.asList(new CaseInsensitiveHashMap<>(Map.of("objectid", objectId))), new BatchValidationException(), null, null); } catch (SQLException | QueryUpdateServiceException | BatchValidationException | InvalidKeyException e) {