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Merge 24.7 to develop #218

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Merged
bbimber merged 20 commits into from
Sep 25, 2024
Merged

Merge 24.7 to develop #218

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c47e3a3
Increase memory allowed for CacheAlignerIndexesTask
bbimber Aug 31, 2024
d7d5bab
Query syntax
bbimber Sep 3, 2024
cf54a9e
Improve mGAP ETL
bbimber Sep 8, 2024
c885048
Update JBrowse version
bbimber Sep 8, 2024
aa1eef7
Improve MCC request/data linkage
bbimber Sep 11, 2024
15790d0
Update MCC color scheme
bbimber Sep 11, 2024
0a17d4f
Add calculated fields to MCC for linking requests and data
bbimber Sep 11, 2024
9cebdbe
Bugfix to MCC sql
bbimber Sep 11, 2024
7ace23c
Show shipments in MCC request details
bbimber Sep 11, 2024
70b6d1c
Update MCC fields
bbimber Sep 11, 2024
89a5fad
Update MCC fields to ETL
bbimber Sep 11, 2024
51c7d03
Ensure request details uses correct containerpath
bbimber Sep 11, 2024
4546771
Store source colony
bbimber Sep 13, 2024
42a34ee
UpdateSeuratPrototype now updates DB record
bbimber Sep 13, 2024
a3dd846
Improve MCC plots
bbimber Sep 13, 2024
7bb1ef1
Bugfix to MCC RequestUtils.tsx, primarily exposed during testing when…
bbimber Sep 13, 2024
c2c6d0b
Add cases to MCC and IDR studies
bbimber Sep 17, 2024
a366625
Update permission on views
bbimber Sep 20, 2024
da36dc9
Update permission on more views
bbimber Sep 20, 2024
8820176
Fix merge conflicts
bbimber Sep 24, 2024
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2 changes: 1 addition & 1 deletion GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js
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Expand Up @@ -100,7 +100,7 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
});
}, this);

if (results.length == 1){
if (results.length === 1){
field.setValue(results[0].id);
}
field.setDisabled(false);
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3 changes: 3 additions & 0 deletions IDR/resources/referenceStudy/study/datasets/datasets_manifest.xml
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Expand Up @@ -10,6 +10,9 @@
<dataset name="birth" id="1007" category="Colony Management" demographicData="true" type="Standard">
<tags/>
</dataset>
<dataset name="cases" id="5012" category="Clinical" type="Standard">
<tags/>
</dataset>
<dataset name="encounters" id="1067" showByDefault="false" category="Clinical" type="Standard">
<tags/>
</dataset>
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57 changes: 57 additions & 0 deletions IDR/resources/referenceStudy/study/datasets/datasets_metadata.xml
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Expand Up @@ -1035,4 +1035,61 @@
</columns>
<tableTitle>Kinship</tableTitle>
</table>
<table tableName="cases" tableDbType="TABLE">
<columns>
<column columnName="Id">
<datatype>varchar</datatype>
<propertyURI>http://cpas.labkey.com/Study#ParticipantId</propertyURI>
<importAliases>
<importAlias>ptid</importAlias>
</importAliases>
</column>
<column columnName="date">
<datatype>timestamp</datatype>
<propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
<conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
</column>
<column columnName="enddate">
<datatype>timestamp</datatype>
<propertyURI>urn:ehr.labkey.org/#EndDate</propertyURI>
</column>
<column columnName="caseid">
<datatype>varchar</datatype>
<propertyURI>urn:ehr.labkey.org/#CaseId</propertyURI>
</column>
<column columnName="reviewdate">
<datatype>timestamp</datatype>
</column>
<column columnName="category">
<datatype>varchar</datatype>
</column>
<column columnName="project">
<datatype>integer</datatype>
<propertyURI>urn:ehr.labkey.org/#Project</propertyURI>
</column>
<column columnName="assignedvet">
<datatype>integer</datatype>
</column>
<column columnName="plan">
<datatype>varchar</datatype>
</column>
<column columnName="objectid">
<datatype>entityid</datatype>
<propertyURI>urn:ehr.labkey.org/#ObjectId</propertyURI>
<isKeyField>true</isKeyField>
</column>
<column columnName="vetreview">
<datatype>varchar</datatype>
<propertyURI>urn:ehr.labkey.org/#VetReview</propertyURI>
</column>
<column columnName="vetreviewdate">
<datatype>timestamp</datatype>
<propertyURI>urn:ehr.labkey.org/#VetReviewDate</propertyURI>
</column>
<column columnName="problem">
<datatype>varchar</datatype>
</column>
</columns>
<tableTitle>Cases</tableTitle>
</table>
</tables>
2 changes: 1 addition & 1 deletion MccColony/resources/queries/study/departure/.qview.xml
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Expand Up @@ -5,7 +5,7 @@
<column name="date"/>
<column name="source"/>
<column name="destination"/>
<column name="mccTransfer"/>
<column name="mccRequestId"/>
<column name="remark"/>
<column name="qcstate" />
</columns>
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6 changes: 4 additions & 2 deletions mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java
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Expand Up @@ -148,7 +148,8 @@ protected void addTracks(final String databaseId, String releaseId)
FieldKey.fromString("url"),
FieldKey.fromString("description"),
FieldKey.fromString("isprimarytrack"),
FieldKey.fromString("vcfId/dataid/DataFileUrl")
FieldKey.fromString("vcfId/dataid/DataFileUrl"),
FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl")
);

TableInfo tracksPerRelease = QueryService.get().getUserSchema(getContainerUser().getUser(), getContainerUser().getContainer(), mGAPSchema.NAME).getTable(mGAPSchema.TABLE_TRACKS_PER_RELEASE);
Expand Down Expand Up @@ -270,7 +271,8 @@ private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLExcept

if (isDefaultTrack)
{
boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("luceneIndex/dataid/DataFileUrl"))) != null;
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));
}
else
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2 changes: 1 addition & 1 deletion mGAP/src/org/labkey/mgap/mGAPController.java
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Expand Up @@ -996,7 +996,7 @@ public URLHelper getRedirectURL(GenomeBrowserForm form)
}
else
{
throw new IllegalArgumentException("Unable to find primary track for release: " + ctx.getString("mgapReleaseGUID"));
throw new IllegalArgumentException("Unable to find primary track for release: " + ctx.getString("mgapReleaseGUID") + ", with JBrowse ID: " + jbrowseDatabaseId);
}
}

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5 changes: 3 additions & 2 deletions mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java
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Expand Up @@ -133,9 +133,10 @@ private void checkMGapFiles(Logger log, User u)

if (!commandsToRun.isEmpty())
{
log.error("There are missing symlinks. Please run makeSymlinks.sh");
File bashFile = new File(baseDir, "makeSymlinks.sh");
log.error("There are missing symlinks. Please run " + bashFile.getPath());

try (PrintWriter writer = PrintWriters.getPrintWriter(new File(baseDir, "makeSymlinks.sh")))
try (PrintWriter writer = PrintWriters.getPrintWriter(bashFile))
{
writer.println("#!/bin/bash");
writer.println("set -e");
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3 changes: 2 additions & 1 deletion mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java
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Expand Up @@ -353,8 +353,9 @@ private File getTrackListFile(File outputDir)
}

@Override
public void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException
public void complete(JobContext ctx, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated) throws PipelineJobException
{
PipelineJob job = ctx.getJob();
if (outputsCreated.isEmpty())
{
job.getLogger().error("no outputs found");
Expand Down
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