LabKey · bbimber · Feb 13, 2021 · Jan 25, 2021 · Jan 25, 2021 · Jan 26, 2021
diff --git a/mGAP/resources/folderTypes/mGAP.folderType.xml b/mGAP/resources/folderTypes/mGAP.folderType.xml
@@ -84,6 +84,10 @@
  <name>mGAP Variant Releases</name>
  <location>body</location>
  </webPart>
+ <webPart>
+ <name>mGAP Release Notes</name>
+ <location>body</location>
+ </webPart>
  <webPart>
  <name>mGAP Gene Search</name>
  <location>right</location>

diff --git a/mGAP/resources/views/contact.html b/mGAP/resources/views/contact.html
@@ -49,7 +49,7 @@
  success: function(response){
  console.log(response);
 
- Ext4.Msg.alert('Success', 'An account has been requested.  You should receive a reply shortly.', function(){
+ Ext4.Msg.alert('Success', 'Your request has been sent. You should receive a reply shortly.', function(){
  window.location = LABKEY.ActionURL.getContextPath() + '/';
  });
  },

diff --git a/mGAP/resources/views/releaseNotes.html b/mGAP/resources/views/releaseNotes.html
@@ -0,0 +1,12 @@
+<h4>Release 2.0:</h4>
+<ul>
+ <li>Substantial revamp of all data. All samples have been realigned to the <a href="https://www.ncbi.nlm.nih.gov/assembly/GCF_003339765.1/">MMul_10 reference genome</a>, followed by our <a href="mgap-dataProcessing.view">standard GenotypeGVCFs pipeline</a>. The MMul_10 is the most complete rhesus macaque assembly to date, and we expect this should improve accuracy of variant calls. Further, because our data are now aligned to the same assembly as NCBI/Ensembl, it should be easier to translate between mGAP and other databases.</li>
+ <li>Our internal variant calling process has switched to use GATK's GenomicsDB to pre-aggregate data prior to calling with GenotypeGVCFs, as opposed to CombineGVCFs, which was used in prior releases. This should be a purely technical difference with no change in the resulting data</li>
+</ul>
+
+<h4>Future Plans:</h4>
+<ul>
+ <li>We expect to upgrade the genome browser to use the redesigned <a href="https://jbrowse.org/jb2/">JBrowse 2</a> browser. This should provide general performance improvements and will make future mGAP-specific customization easier.</li>
+ <li>We will support other modes of viewing and downloading variant data, in particular tabular views by gene.</li>
+ <li>We recognize that the mGAP release VCF can be enormous, particularly because of all the site-specific functional annotation. To support different types of users, upcoming releases will include 'slim' versions of the data, which will be downloadable files with certain information removed to save file size.</li>
+</ul>
diff --git a/mGAP/resources/views/releaseNotes.view.xml b/mGAP/resources/views/releaseNotes.view.xml
@@ -0,0 +1,8 @@
+<view xmlns="http://labkey.org/data/xml/view" title="mGAP Release Notes">
+ <permissions>
+ <permission name="read"/>
+ </permissions>
+ <dependencies>
+ <dependency path="ldk.context"/>
+ </dependencies>
+</view>
diff --git a/mGAP/resources/views/releaseNotes.webpart.xml b/mGAP/resources/views/releaseNotes.webpart.xml
@@ -0,0 +1,6 @@
+<webpart xmlns="http://labkey.org/data/xml/webpart" title="mGAP Release Notes">
+ <view name="releaseNotes"/>
+ <locations>
+ <location name="body"/>
+ </locations>
+</webpart>
diff --git a/mGAP/resources/views/variants.html b/mGAP/resources/views/variants.html
@@ -9,7 +9,7 @@
  title: 'Variant Catalog Releases',
  schemaName: 'mgap',
  queryName: 'variantCatalogReleases',
- maxRows: 50,
+ maxRows: 3,
  showRecordSelectors: false,
  showDetailsColumn: false,
  buttonBar: {position: 'none', includeStandardButtons: false, items: []}

diff --git a/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java b/mGAP/src/org/labkey/mgap/pipeline/mGapReleaseGenerator.java
@@ -953,7 +953,7 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
  File interestingVariantTable = getVariantTableName(ctx, vcfInput);
  try (VCFFileReader reader = new VCFFileReader(vcfInput); CloseableIterator<VariantContext> 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", "CADD_PH"});
+ writer.writeNext(new String[]{"Chromosome", "Position", "Reference", "Allele", "Source", "Reason", "Description", "Overlapping Gene(s)", "OMIM Entries", "OMIM Phenotypes", "AF", "Identifier", "CADD_PH"});
  while (it.hasNext())
  {
  Set<List<String>> queuedLines = new LinkedHashSet<>();
@@ -1113,7 +1113,7 @@ private void inspectAndSummarizeVcf(JobContext ctx, File vcfInput, GeneToNameTra
  try
  {
  String allele = clnAlleles.get(i);
- maybeWriteVariantLine(queuedLines, vc, allele, "ClinVar", diseaseSplit.get(j), description, overlappingGenes, omims, omimds, ctx.getLogger(), "ClinVar:" + clnAlleleIds.get(j));
+ maybeWriteVariantLine(queuedLines, vc, allele, "ClinVar", diseaseSplit.get(j), description, overlappingGenes, omims, omimds, ctx.getLogger(), "ClinVar:" + clnAlleleIds.get(i));
 
  }
  catch (IndexOutOfBoundsException e)

diff --git a/mcc/resources/etls/snprc.xml b/mcc/resources/etls/snprc.xml
@@ -1,14 +1,121 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <etl xmlns="http://labkey.org/etl/xml">
  <name>SNPRC_Data</name>
+ <!--NOTE: folder is: /Marmoset R24-->
+ <!--See also: https://github.com/LabKey/snprcEHRModules/blob/develop/snprc_r24/resources/referenceStudy/datasets/datasets_metadata.xml-->
  <description>SNPRC Clinical/Demographics Data</description>
  <transforms>
- <transform type="RemoteQueryTransformStep" id="step1">
+ <transform type="RemoteQueryTransformStep" id="demographics">
  <description>Copy to target</description>
- <source remoteSource="snprcEHR" schemaName="study" queryName="R24DemographicsSrc" />
- <destination schemaName="study" queryName="Demographics" targetOption="merge"/>
+ <source remoteSource="SNPRC" schemaName="study" queryName="Demographics">
+ <sourceColumns>
+ <column>AnimalId</column>
+ <column>date</column>
+ <column>gender</column>
+ <column>geographic_origin</column>
+ <column>birth</column>
+ <column>death</column>
+ <column>species</column>
+ <column>objectid</column>
+ </sourceColumns>
+ </source>
+ <destination schemaName="study" queryName="Demographics" targetOption="truncate" bulkLoad="true">
+ <columnTransforms>
+ <column source="AnimalId" target="Id"/>
+ </columnTransforms>
+ <alternateKeys>
+ <column name="objectid"/>
+ </alternateKeys>
+ </destination>
+
  </transform>
+
+ <!--<transform type="RemoteQueryTransformStep" id="parentage">-->
+ <!--<description>Copy to target</description>-->
+ <!--<source remoteSource="SNPRC" schemaName="study" queryName="parentage">-->
+ <!--<sourceColumns>-->
+ <!--<column>AnimalId</column>-->
+ <!--<column>date</column>-->
+ <!--<column>parent</column>-->
+ <!--<column>relationship</column>-->
+ <!--<column>method</column>-->
+ <!--<column>objectid</column>-->
+ <!--</sourceColumns>-->
+ <!--</source>-->
+ <!--<destination schemaName="study" queryName="parentage" targetOption="merge" bulkLoad="true">-->
+ <!--<columnTransforms>-->
+ <!--<column source="AnimalId" target="Id"/>-->
+ <!--</columnTransforms>-->
+ <!--</destination>-->
+
+ <!--</transform>-->
+
+ <!--NOTE: restore once we can filter on date is not null-->
+ <!--<transform type="RemoteQueryTransformStep" id="birth">-->
+ <!--<description>Copy to target</description>-->
+ <!--<source remoteSource="SNPRC" schemaName="study" queryName="Demographics">-->
+ <!--<sourceColumns>-->
+ <!--<column>AnimalId</column>-->
+ <!--<column>birth</column>-->
+ <!--<column>gender</column>-->
+ <!--<column>species</column>-->
+ <!--<column>dam</column>-->
+ <!--<column>sire</column>-->
+ <!--<column>objectid</column>-->
+ <!--</sourceColumns>-->
+ <!--</source>-->
+ <!--<destination schemaName="study" queryName="birth" targetOption="truncate" bulkLoad="true">-->
+ <!--<columnTransforms>-->
+ <!--<column source="AnimalId" target="Id"/>-->
+ <!--<column source="birth" target="date" />-->
+ <!--</columnTransforms>-->
+ <!--</destination>-->
+
+ <!--</transform>-->
+
+ <transform type="RemoteQueryTransformStep" id="weight">
+ <description>Copy to target</description>
+ <source remoteSource="SNPRC" schemaName="study" queryName="weight">
+ <sourceColumns>
+ <column>AnimalId</column>
+ <column>date</column>
+ <column>weight</column>
+ <column>objectid</column>
+ </sourceColumns>
+ </source>
+ <destination schemaName="study" queryName="weight" targetOption="truncate" bulkLoad="true">
+ <columnTransforms>
+ <column source="AnimalId" target="Id"/>
+ </columnTransforms>
+ <alternateKeys>
+ <column name="objectid"/>
+ </alternateKeys>
+ </destination>
+
+ </transform>
+
+ <!--<transform type="RemoteQueryTransformStep" id="deaths">-->
+ <!--<description>Copy to target</description>-->
+ <!--<source remoteSource="SNPRC" schemaName="study" queryName="deaths">-->
+ <!--<sourceColumns>-->
+ <!--<column>AnimalId</column>-->
+ <!--<column>date</column>-->
+ <!--<column>cause</column>-->
+ <!--<column>objectid</column>-->
+ <!--</sourceColumns>-->
+ <!--</source>-->
+ <!--<destination schemaName="study" queryName="deaths" targetOption="merge" bulkLoad="true">-->
+ <!--<columnTransforms>-->
+ <!--<column source="AnimalId" target="Id"/>-->
+ <!--</columnTransforms>-->
+ <!--<alternateKeys>-->
+ <!--<column name="objectid"/>-->
+ <!--</alternateKeys>-->
+ <!--</destination>-->
+
+ <!--</transform>-->
  </transforms>
+
  <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified" />
  <schedule>
  <!--11PM-->

diff --git a/mcc/resources/etls/wnprc.xml b/mcc/resources/etls/wnprc.xml
@@ -3,17 +3,108 @@
  <name>WNPRC_Data</name>
  <description>WNPRC Clinical/Demographics Data</description>
  <transforms>
- <transform type="RemoteQueryTransformStep" id="step1">
+ <transform type="RemoteQueryTransformStep" id="demographics">
  <description>Copy to target</description>
- <source remoteSource="wnprcEHR" schemaName="study" queryName="Demographics"/>
- <destination schemaName="study" queryName="Demographics" targetOption="merge"/>
+ <source remoteSource="WNPRC" schemaName="study" queryName="Demographics">
+ <sourceColumns>
+ <column>Id</column>
+ <column>date</column>
+ <column>gender</column>
+ <column>geographic_origin</column>
+ <column>birth</column>
+ <column>death</column>
+ <column>species</column>
+ <column>objectid</column>
+ </sourceColumns>
+ </source>
+ <destination schemaName="study" queryName="Demographics" targetOption="truncate" bulkLoad="true">
+ <alternateKeys>
+ <column name="objectid"/>
+ </alternateKeys>
+ </destination>
 
  </transform>
+
+ <transform type="RemoteQueryTransformStep" id="parentage">
+ <description>Copy to target</description>
+ <source remoteSource="WNPRC" schemaName="study" queryName="parentage">
+ <sourceColumns>
+ <column>Id</column>
+ <column>date</column>
+ <column>parent</column>
+ <column>relationship</column>
+ <column>method</column>
+ <column>objectid</column>
+ </sourceColumns>
+ </source>
+ <destination schemaName="study" queryName="parentage" targetOption="truncate" bulkLoad="true">
+ <alternateKeys>
+ <column name="objectid"/>
+ </alternateKeys>
+ </destination>
+
+ </transform>
+
+ <transform type="RemoteQueryTransformStep" id="birth">
+ <description>Copy to target</description>
+ <source remoteSource="WNPRC" schemaName="study" queryName="birth">
+ <sourceColumns>
+ <column>Id</column>
+ <column>date</column>
+ <column>gender</column>
+ <column>species</column>
+ <column>geographic_origin</column>
+ <column>dam</column>
+ <column>sire</column>
+ <column>objectid</column>
+ </sourceColumns>
+ </source>
+ <destination schemaName="study" queryName="birth" targetOption="truncate" bulkLoad="true">
+ <alternateKeys>
+ <column name="objectid"/>
+ </alternateKeys>
+ </destination>
+
+ </transform>
+
+ <transform type="RemoteQueryTransformStep" id="weight">
+ <description>Copy to target</description>
+ <source remoteSource="WNPRC" schemaName="study" queryName="weight">
+ <sourceColumns>
+ <column>Id</column>
+ <column>date</column>
+ <column>weight</column>
+ <column>objectid</column>
+ </sourceColumns>
+ </source>
+ <destination schemaName="study" queryName="weight" targetOption="truncate" bulkLoad="true">
+ <alternateKeys>
+ <column name="objectid"/>
+ </alternateKeys>
+ </destination>
+ </transform>
+
+ <transform type="RemoteQueryTransformStep" id="deaths">
+ <description>Copy to target</description>
+ <source remoteSource="WNPRC" schemaName="study" queryName="deaths">
+ <sourceColumns>
+ <column>Id</column>
+ <column>date</column>
+ <column>cause</column>
+ <column>objectid</column>
+ </sourceColumns>
+ </source>
+ <destination schemaName="study" queryName="deaths" targetOption="truncate" bulkLoad="true">
+ <alternateKeys>
+ <column name="objectid"/>
+ </alternateKeys>
+ </destination>
+ </transform>
  </transforms>
- <!--species~eq=Marmoset-->
+
  <incrementalFilter className="ModifiedSinceFilterStrategy" timestampColumnName="modified" />
  <schedule>
- <!--101PM-->
- <cron expression="0 0 20 * * ?"/>
+ <!--9PM-->
+ <cron expression="0 0 21 * * ?"/>
  </schedule>
 </etl>
diff --git a/mcc/resources/module.xml b/mcc/resources/module.xml
@@ -0,0 +1,21 @@
+<module xmlns="http://labkey.org/moduleProperties/xml/">
+ <properties>
+ <propertyDescriptor name="MCCContainer">
+ <canSetPerContainer>false</canSetPerContainer>
+ <description>This is the path to the container holding the primary MCC Study. Use of slashes is very important - it should be in the format '/myProject/mcc'</description>
+ <editPermissions>
+ <permission>ADMIN</permission>
+ </editPermissions>
+ </propertyDescriptor>
+ <propertyDescriptor name="MCCContactUsers">
+ <canSetPerContainer>false</canSetPerContainer>
+ <description>This is a comma separated list of LabKey user names of users that should be notified by email when requests are submitted through MCC.</description>
+ <editPermissions>
+ <permission>ADMIN</permission>
+ </editPermissions>
+ </propertyDescriptor>
+ </properties>
+ <clientDependencies>
+
+ </clientDependencies>
+</module>
diff --git a/mcc/resources/queries/study/animalGroupMembership.js b/mcc/resources/queries/study/animalGroupMembership.js
@@ -0,0 +1,14 @@
+/*
+ * Copyright (c) 2011-2014 LabKey Corporation
+ *
+ * Licensed under the Apache License, Version 2.0: http://www.apache.org/licenses/LICENSE-2.0
+ */
+
+require("ehr/triggers").initScript(this);
+
+function onInit(event, helper){
+ helper.setScriptOptions({
+ allowFutureDates: true,
+ removeTimeFromDate: true
+ });
+}