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 77b8db42a..85aef954b 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); diff --git a/mGAP/resources/module.xml b/mGAP/resources/module.xml index fe178cbe4..8f95a1d13 100644 --- a/mGAP/resources/module.xml +++ b/mGAP/resources/module.xml @@ -25,7 +25,7 @@ - + diff --git a/mGAP/resources/views/admin.html b/mGAP/resources/views/admin.html index 250f925f7..4f719f502 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', diff --git a/mGAP/resources/views/annotation.html b/mGAP/resources/views/annotation.html index 9fc544f86..4f18ac9f8 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
    • -
    diff --git a/mGAP/resources/views/overview.html b/mGAP/resources/views/overview.html index a5a06f46c..65ada0fff 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/overview.view.xml b/mGAP/resources/views/overview.view.xml index 7b1027159..0c08a328c 100644 --- a/mGAP/resources/views/overview.view.xml +++ b/mGAP/resources/views/overview.view.xml @@ -5,7 +5,7 @@ - + diff --git a/mGAP/resources/views/quickLinks.html b/mGAP/resources/views/quickLinks.html index c486c8bbf..26bbe219f 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 03bfa8b13..10b3bcf33 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/columnTransforms/AbstractVariantTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/AbstractVariantTransform.java index 5345e4fc3..04530b420 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; @@ -112,51 +118,60 @@ 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) - { - 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()) + if (!EtlQueueManager.get().isFileInQueue(getContainerUser().getContainer(), f)) { - 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); + if (localCopy == null) + { + // TODO + } + + //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) { @@ -190,12 +205,22 @@ 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()); + 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"); + if (f.equals(localCopy)) + { + getStatusLogger().debug("Attempting to copy file that is already a child of the target: " + f.getPath(), new Exception()); + return localCopy; + } + boolean doCopy = true; if (localCopy.exists()) { @@ -206,15 +231,47 @@ 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()); + if (localCopy.exists()) + { + throw new PipelineJobException("Unable to delete file: " + localCopy.getPath()); + } + } + catch (IOException e) + { + throw new PipelineJobException("Unable to delete file: " + localCopy.getPath(), e); + } } } + else + { + getStatusLogger().info("existing file not found: " + localCopy.getPath()); + } if (doCopy) { - getStatusLogger().info("queueing file copy: " + localCopy.getPath()); - EtlQueueManager.get().queueFileCopy(getContainerUser().getContainer(), f, localCopy); + getStatusLogger().info("Creating symlink: " + f.getPath() + " / " + localCopy.getPath()); + try + { + if (!Files.isReadable(f.toPath())) + { + throw new PipelineJobException("Unable to read file: " + f.getPath()); + } + + if (localCopy.exists()) + { + throw new PipelineJobException("File should have been deleted: " + localCopy.getPath()); + } + + Files.createSymbolicLink(localCopy.toPath(), f.toPath()); + } + catch (IOException e) + { + throw new PipelineJobException("Failed to create symlink: " + localCopy.getPath(), e); + } } File index = new File(f.getPath() + ".tbi"); @@ -223,14 +280,25 @@ 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.getPath()); indexLocal.delete(); } if (!indexLocal.exists()) { - getStatusLogger().info("queueing copy of index: " + indexLocal.getPath()); - EtlQueueManager.get().queueFileCopy(getContainerUser().getContainer(), index, indexLocal); + getStatusLogger().info("Creating symlink copy of VCF index: " + index.getPath() + " / " + indexLocal.getPath()); + try + { + Files.createSymbolicLink(indexLocal.toPath(), index.toPath()); + } + catch (IOException e) + { + getStatusLogger().error("Failed to create symlink: " + indexLocal.getPath(), e); + } + } + else + { + getStatusLogger().info("Local index already exists: " + indexLocal.getPath()); } } diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java index f3b0ca462..e489595de 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; @@ -149,7 +151,10 @@ 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); @@ -175,6 +180,34 @@ 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("container"), new SimpleFilter(FieldKey.fromString("objectid"), objectId), null); + if (!ts1.exists()) + { + getStatusLogger().error("expected jsonfile to exist: " + objectId); + return; + } + + try + { + String containerId = ts1.getObject(String.class); + + Map row = new CaseInsensitiveHashMap<>(); + row.put("objectid", objectId); + row.put("container", containerId); + row.put("trackJson", getTrackJson(true)); + + 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) + { + 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); @@ -244,20 +277,33 @@ 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")); + String value = rs.getString(FieldKey.fromString(fieldKey)); + if (value == null) + { + getStatusLogger().info(fieldKey + " is null, skipping in getOrCreateJsonFile()"); + return null; + } + + 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); - return ts1.getArrayList(String.class).get(0); + String objectId = ts1.getArrayList(String.class).get(0); + 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()); @@ -271,9 +317,18 @@ 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 { diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/LuceneIndexTransform.java index 55fb8c77e..ae7ad050a 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()); } diff --git a/mGAP/src/org/labkey/mgap/columnTransforms/TrackOutputFileTransform.java b/mGAP/src/org/labkey/mgap/columnTransforms/TrackOutputFileTransform.java index a396b4ba2..6855be884 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; } diff --git a/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java b/mGAP/src/org/labkey/mgap/etl/EtlQueueManager.java index 950454383..bdb8f60f0 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)) @@ -106,6 +121,7 @@ private void copyFile(File source, File destination, Logger log) { if (destination.exists()) { + log.info("Deleting destination file: " + source.getPath()); destination.delete(); } diff --git a/mGAP/src/org/labkey/mgap/jbrowse/mGAPLuceneDetector.java b/mGAP/src/org/labkey/mgap/jbrowse/mGAPLuceneDetector.java index 91e51971c..5e0e458a7 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; } diff --git a/mGAP/src/org/labkey/mgap/mGAPController.java b/mGAP/src/org/labkey/mgap/mGAPController.java index 0b5378b4f..09d8cde8c 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 840d419ec..fdff5e3e3 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 86e2a4c69..9375e0a70 100644 --- a/mGAP/src/org/labkey/mgap/mGAPModule.java +++ b/mGAP/src/org/labkey/mgap/mGAPModule.java @@ -158,10 +158,13 @@ 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).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"), 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 -> { String jbrowseId = rs.getString(FieldKey.fromString("jbrowseId")); diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java index a6a03642c..0a8833abd 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; @@ -86,6 +87,7 @@ 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; @@ -129,8 +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); @@ -377,7 +380,7 @@ public void complete(JobContext ctx, List inputs, List outputVCFMap = new HashMap<>(); Map outputTableMap = new HashMap<>(); @@ -386,8 +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"); @@ -405,11 +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")) @@ -442,6 +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) @@ -450,7 +456,7 @@ 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); } @@ -458,7 +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); @@ -486,11 +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')) @@ -522,7 +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) @@ -543,7 +555,10 @@ 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()); @@ -572,6 +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]); @@ -596,7 +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: @@ -936,7 +956,7 @@ 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 { @@ -1023,13 +1043,22 @@ 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: " + 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 @@ -1104,18 +1133,15 @@ 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; } @@ -1148,35 +1174,32 @@ 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 +1228,7 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra if (sampleCount == 1) { - totalPrivateVariants++; + totalPrivateVariants.getAndIncrement(); } } @@ -1342,7 +1365,6 @@ 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 +1444,14 @@ 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 +1466,7 @@ 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 @@ -1487,14 +1509,22 @@ 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 ced520a20..8ed255fff 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<>(); diff --git a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java index 7e73046d8..e34d61a27 100644 --- a/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java +++ b/mGAP/src/org/labkey/mgap/query/TracksPerReleaseGenomeBrowserDisplayColumnFactory.java @@ -5,10 +5,13 @@ 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.LinkBuilder; import org.labkey.api.util.PageFlowUtil; import org.labkey.api.writer.HtmlWriter; +import java.util.Set; + /** * Created by bimber on 5/17/2017. */ @@ -25,13 +28,26 @@ public void renderGridCellContents(RenderContext ctx, HtmlWriter out) 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(LinkBuilder.labkeyLink("View In Genome Browser", url.getActionURL())); } } + + @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")); + } }; } } diff --git a/mcc/package-lock.json b/mcc/package-lock.json index 20e3cdd47..7ad10c48b 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", - 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"https://github.com/sponsors/sindresorhus" + } } } } diff --git a/mcc/src/client/components/dashboard/BarChart.tsx b/mcc/src/client/components/dashboard/BarChart.tsx index 92f5f99b1..e994ab435 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)