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Fix merge conflicts
2 parents d00b2a0 + da36dc9 commit 8820176

40 files changed

Lines changed: 878 additions & 367 deletions

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‎GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -100,7 +100,7 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
100100
});
101101
}, this);
102102

103-
if (results.length == 1){
103+
if (results.length === 1){
104104
field.setValue(results[0].id);
105105
}
106106
field.setDisabled(false);

‎IDR/resources/referenceStudy/study/datasets/datasets_manifest.xml‎

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Original file line numberDiff line numberDiff line change
@@ -10,6 +10,9 @@
1010
<dataset name="birth" id="1007" category="Colony Management" demographicData="true" type="Standard">
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<tags/>
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</dataset>
13+
<dataset name="cases" id="5012" category="Clinical" type="Standard">
14+
<tags/>
15+
</dataset>
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<dataset name="encounters" id="1067" showByDefault="false" category="Clinical" type="Standard">
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<tags/>
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</dataset>

‎IDR/resources/referenceStudy/study/datasets/datasets_metadata.xml‎

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Original file line numberDiff line numberDiff line change
@@ -1035,4 +1035,61 @@
10351035
</columns>
10361036
<tableTitle>Kinship</tableTitle>
10371037
</table>
1038+
<table tableName="cases" tableDbType="TABLE">
1039+
<columns>
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<column columnName="Id">
1041+
<datatype>varchar</datatype>
1042+
<propertyURI>http://cpas.labkey.com/Study#ParticipantId</propertyURI>
1043+
<importAliases>
1044+
<importAlias>ptid</importAlias>
1045+
</importAliases>
1046+
</column>
1047+
<column columnName="date">
1048+
<datatype>timestamp</datatype>
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<propertyURI>http://cpas.labkey.com/Study#VisitDate</propertyURI>
1050+
<conceptURI>http://cpas.labkey.com/Study#VisitDate</conceptURI>
1051+
</column>
1052+
<column columnName="enddate">
1053+
<datatype>timestamp</datatype>
1054+
<propertyURI>urn:ehr.labkey.org/#EndDate</propertyURI>
1055+
</column>
1056+
<column columnName="caseid">
1057+
<datatype>varchar</datatype>
1058+
<propertyURI>urn:ehr.labkey.org/#CaseId</propertyURI>
1059+
</column>
1060+
<column columnName="reviewdate">
1061+
<datatype>timestamp</datatype>
1062+
</column>
1063+
<column columnName="category">
1064+
<datatype>varchar</datatype>
1065+
</column>
1066+
<column columnName="project">
1067+
<datatype>integer</datatype>
1068+
<propertyURI>urn:ehr.labkey.org/#Project</propertyURI>
1069+
</column>
1070+
<column columnName="assignedvet">
1071+
<datatype>integer</datatype>
1072+
</column>
1073+
<column columnName="plan">
1074+
<datatype>varchar</datatype>
1075+
</column>
1076+
<column columnName="objectid">
1077+
<datatype>entityid</datatype>
1078+
<propertyURI>urn:ehr.labkey.org/#ObjectId</propertyURI>
1079+
<isKeyField>true</isKeyField>
1080+
</column>
1081+
<column columnName="vetreview">
1082+
<datatype>varchar</datatype>
1083+
<propertyURI>urn:ehr.labkey.org/#VetReview</propertyURI>
1084+
</column>
1085+
<column columnName="vetreviewdate">
1086+
<datatype>timestamp</datatype>
1087+
<propertyURI>urn:ehr.labkey.org/#VetReviewDate</propertyURI>
1088+
</column>
1089+
<column columnName="problem">
1090+
<datatype>varchar</datatype>
1091+
</column>
1092+
</columns>
1093+
<tableTitle>Cases</tableTitle>
1094+
</table>
10381095
</tables>

‎MccColony/resources/queries/study/departure/.qview.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -5,7 +5,7 @@
55
<column name="date"/>
66
<column name="source"/>
77
<column name="destination"/>
8-
<column name="mccTransfer"/>
8+
<column name="mccRequestId"/>
99
<column name="remark"/>
1010
<column name="qcstate" />
1111
</columns>

‎mGAP/src/org/labkey/mgap/columnTransforms/JBrowseSessionTransform.java‎

Lines changed: 4 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -148,7 +148,8 @@ protected void addTracks(final String databaseId, String releaseId)
148148
FieldKey.fromString("url"),
149149
FieldKey.fromString("description"),
150150
FieldKey.fromString("isprimarytrack"),
151-
FieldKey.fromString("vcfId/dataid/DataFileUrl")
151+
FieldKey.fromString("vcfId/dataid/DataFileUrl"),
152+
FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl")
152153
);
153154

154155
TableInfo tracksPerRelease = QueryService.get().getUserSchema(getContainerUser().getUser(), getContainerUser().getContainer(), mGAPSchema.NAME).getTable(mGAPSchema.TABLE_TRACKS_PER_RELEASE);
@@ -270,7 +271,8 @@ private String getOrCreateJsonFile(Results rs, String fieldKey) throws SQLExcept
270271

271272
if (isDefaultTrack)
272273
{
273-
boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("luceneIndex/dataid/DataFileUrl"))) != null;
274+
boolean hasLuceneIndex = StringUtils.trimToNull(rs.getString(FieldKey.fromString("releaseId/luceneIndex/dataid/DataFileUrl"))) != null;
275+
getStatusLogger().info("Creating track JSON for primary track, has lucene index: " + hasLuceneIndex);
274276
row.put("trackJson", getTrackJson(hasLuceneIndex));
275277
}
276278
else

‎mGAP/src/org/labkey/mgap/mGAPController.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -996,7 +996,7 @@ public URLHelper getRedirectURL(GenomeBrowserForm form)
996996
}
997997
else
998998
{
999-
throw new IllegalArgumentException("Unable to find primary track for release: " + ctx.getString("mgapReleaseGUID"));
999+
throw new IllegalArgumentException("Unable to find primary track for release: " + ctx.getString("mgapReleaseGUID") + ", with JBrowse ID: " + jbrowseDatabaseId);
10001000
}
10011001
}
10021002

‎mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -133,9 +133,10 @@ private void checkMGapFiles(Logger log, User u)
133133

134134
if (!commandsToRun.isEmpty())
135135
{
136-
log.error("There are missing symlinks. Please run makeSymlinks.sh");
136+
File bashFile = new File(baseDir, "makeSymlinks.sh");
137+
log.error("There are missing symlinks. Please run " + bashFile.getPath());
137138

138-
try (PrintWriter writer = PrintWriters.getPrintWriter(new File(baseDir, "makeSymlinks.sh")))
139+
try (PrintWriter writer = PrintWriters.getPrintWriter(bashFile))
139140
{
140141
writer.println("#!/bin/bash");
141142
writer.println("set -e");

‎mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -353,8 +353,9 @@ private File getTrackListFile(File outputDir)
353353
}
354354

355355
@Override
356-
public void complete(PipelineJob job, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated, SequenceAnalysisJobSupport support) throws PipelineJobException
356+
public void complete(JobContext ctx, List<SequenceOutputFile> inputs, List<SequenceOutputFile> outputsCreated) throws PipelineJobException
357357
{
358+
PipelineJob job = ctx.getJob();
358359
if (outputsCreated.isEmpty())
359360
{
360361
job.getLogger().error("no outputs found");

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