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Merge discvr-24.3 to develop
2 parents e45f8b4 + 7d89782 commit 95a6c4b

23 files changed

Lines changed: 293 additions & 785 deletions

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

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@@ -26,6 +26,7 @@
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<column name="Id/MostRecentWeight/MostRecentWeightGrams"/>
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<column name="Id/MostRecentWeight/MostRecentWeightDate"/>
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<column name="alternateIds"/>
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<column name="litterId"/>
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<column name="excludeFromCensus"/>
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<column name="Id/mostRecentObservations/availability::observation">
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<properties>

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

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@@ -1,14 +1,11 @@
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package org.labkey.mgap.columnTransforms;
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3-
import org.apache.commons.io.FileUtils;
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import org.jetbrains.annotations.Nullable;
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import org.labkey.api.jbrowse.JBrowseService;
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import org.labkey.api.pipeline.PipelineJobException;
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import org.labkey.api.sequenceanalysis.run.SimpleScriptWrapper;
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import org.labkey.mgap.etl.EtlQueueManager;
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import java.io.File;
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import java.io.IOException;
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import java.util.Arrays;
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public class LuceneIndexTransform extends OutputFileTransform
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{
@@ -27,6 +24,7 @@ protected File doFileCopy(File f, File subdir, @Nullable String name) throws Pip
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// NOTE: lucene is a special case since the DB tracks one file, but we need this whole folder:
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File sourceDir = f.getParentFile();
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File targetDir = new File(subdir, "LuceneIndex");
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JBrowseService.get().clearLuceneCacheEntry(targetDir);
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EtlQueueManager.get().queueRsyncCopy(getContainerUser().getContainer(), sourceDir, targetDir);
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return new File(targetDir, sourceDir.getName() + "/" + f.getName());

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

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@@ -174,7 +174,7 @@ private static class FieldData
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public static void filterCodingPotential(Set<String> codingPotential)
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{
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//due to overlapping transcripts, this is often added. remove these less-specific terms in order
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for (String type : Arrays.asList("intragenic_variant", "non_coding_transcript_variant", "intron_variant"))
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for (String type : Arrays.asList("custom", "intergenic_variant", "intragenic_variant"))
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{
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if (codingPotential.size() > 1)
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{
@@ -184,9 +184,8 @@ public static void filterCodingPotential(Set<String> codingPotential)
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if (codingPotential.contains("synonymous_variant") || codingPotential.contains("missense_variant"))
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{
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codingPotential.remove("intergenic_variant");
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codingPotential.remove("intragenic_variant");
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codingPotential.remove("non_coding_transcript_variant");
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codingPotential.remove("intron_variant");
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}
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}
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‎mcc/package-lock.json‎

Lines changed: 7 additions & 7 deletions
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‎mcc/resources/etls/mcc.xml‎

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@@ -38,7 +38,7 @@
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="Demographics" targetOption="truncate" bulkLoad="true">
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<destination schemaName="study" queryName="Demographics" targetOption="truncate" bulkLoad="true" batchSize="5000">
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<alternateKeys>
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<column name="objectid"/>
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</alternateKeys>
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<column>objectid</column>
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</sourceColumns>
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</source>
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<destination schemaName="study" queryName="kinship" targetOption="truncate" bulkLoad="true">
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<destination schemaName="study" queryName="kinship" targetOption="truncate" bulkLoad="true" batchSize="5000">
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<alternateKeys>
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<column name="objectid"/>
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</alternateKeys>
@@ -72,7 +72,7 @@
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<column>objectid</column>
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</sourceColumns>
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</source>
75-
<destination schemaName="study" queryName="weight" targetOption="truncate" bulkLoad="true">
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<destination schemaName="study" queryName="weight" targetOption="truncate" bulkLoad="true" batchSize="5000">
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<alternateKeys>
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<column name="objectid"/>
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</alternateKeys>
@@ -89,7 +89,7 @@
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<column>objectid</column>
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</sourceColumns>
9191
</source>
92-
<destination schemaName="study" queryName="genomicDatasets" targetOption="truncate" bulkLoad="true">
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<destination schemaName="study" queryName="genomicDatasets" targetOption="truncate" bulkLoad="true" batchSize="5000">
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<alternateKeys>
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<column name="objectid"/>
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</alternateKeys>
@@ -106,7 +106,7 @@
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<column>objectid</column>
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</sourceColumns>
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</source>
109-
<destination schemaName="study" queryName="clinical_observations" targetOption="truncate" bulkLoad="true">
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<destination schemaName="study" queryName="clinical_observations" targetOption="truncate" bulkLoad="true" batchSize="5000">
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<alternateKeys>
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<column name="objectid"/>
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</alternateKeys>
@@ -127,7 +127,7 @@
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<column>marmosetsShipped</column>
128128
</sourceColumns>
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</source>
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<destination schemaName="mcc" queryName="census" targetOption="truncate" bulkLoad="true">
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<destination schemaName="mcc" queryName="census" targetOption="truncate" bulkLoad="true" batchSize="5000">
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</destination>
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</transform>

‎mcc/resources/queries/mcc/aggregatedDemographics.sql‎

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@@ -19,6 +19,7 @@ SELECT
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WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/SNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
2020
ELSE false
2121
END as u24_status,
22+
d.litterId,
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d.Id.mostRecentDeparture.mostRecentDeparture,
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o.availability,
2425
o.current_housing_status,
@@ -67,6 +68,7 @@ SELECT
6768
WHEN d.calculated_status = 'Alive' AND (SELECT COUNT(f.flag.value) as total FROM "/data/Colonies/WNPRC/".study.flags f WHERE f.Id = d.Id AND f.isActive = true) > 0 THEN true
6869
ELSE false
6970
END as u24_status,
71+
d.litterId,
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d.Id.mostRecentDeparture.mostRecentDeparture,
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o.availability,
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o.current_housing_status,
@@ -112,6 +114,7 @@ SELECT
112114
d.objectid,
113115
d.calculated_status,
114116
d.u24_status,
117+
d.litterId,
115118
d.Id.mostRecentDeparture.mostRecentDeparture,
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o.availability,
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o.current_housing_status,
@@ -160,6 +163,7 @@ SELECT
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d.objectid,
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d.calculated_status,
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d.u24_status,
166+
d.litterId,
163167
d.Id.mostRecentDeparture.mostRecentDeparture,
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o.availability,
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o.current_housing_status,

‎mcc/resources/queries/study/demographics.js‎

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@@ -111,6 +111,13 @@ function onUpsert(helper, scriptErrors, row, oldRow){
111111
}
112112
}
113113

114+
if (oldRow && oldRow.Id) {
115+
var existingId = triggerHelper.getMccAlias(oldRow.Id);
116+
if (existingId) {
117+
idToMccAlias[row.Id] = existingId;
118+
}
119+
}
120+
114121
if (!row.date) {
115122
row.date = new Date();
116123
}

‎mcc/resources/queries/study/demographics.query.xml‎

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<deleteUrl />
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<columns>
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<column columnName="Id">
12-
<url></url>
12+
<url />
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</column>
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<column columnName="date">
1515
<isHidden>true</isHidden>
@@ -121,6 +121,13 @@
121121
<column columnName="alternateIds">
122122
<columnTitle>Alternate IDs</columnTitle>
123123
</column>
124+
<column columnName="litterId">
125+
<columnTitle>Litter ID</columnTitle>
126+
<url>/query/executeQuery.view?schemaName=study&amp;
127+
query.queryName=Demographics&amp;
128+
query.litterId~eq=${litterId}
129+
</url>
130+
</column>
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<column columnName="remark">
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</column>

‎mcc/resources/queries/study/demographics/.qview.xml‎

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@@ -36,6 +36,7 @@
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<column name="usage_current"/>
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<column name="usage_future"/>
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<column name="date_of_observations"/>
39+
<column name="litterId"/>
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</columns>
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<sorts>
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<sort column="Id" descending="false"/>

‎mcc/resources/queries/study/demographicsLittermates.query.xml‎

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@@ -0,0 +1,23 @@
1+
<query xmlns="http://labkey.org/data/xml/query">
2+
<description>Littermates of Any Animal</description>
3+
<metadata>
4+
<tables xmlns="http://labkey.org/data/xml">
5+
<table tableName="demographicsLittermates" tableDbType="NOT_IN_DB">
6+
<description>Littermates of Any Animal</description>
7+
<columns>
8+
<column columnName="Id">
9+
<isKeyField>true</isKeyField>
10+
<isHidden>true</isHidden>
11+
</column>
12+
<column columnName="litterId">
13+
14+
</column>
15+
<column columnName="litterMates">
16+
<columnTitle>Littermate(s)</columnTitle>
17+
</column>
18+
</columns>
19+
<titleColumn>Relationship</titleColumn>
20+
</table>
21+
</tables>
22+
</metadata>
23+
</query>

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