LabKey · bbimber · May 18, 2022 · Mar 11, 2022 · Mar 11, 2022 · Mar 11, 2022
diff --git a/covidseq/resources/schemas/covidseq.xml b/covidseq/resources/schemas/covidseq.xml
@@ -102,7 +102,9 @@
  <column columnName="cDNA_Plate_Location">
  <columnTitle>cDNA_Plate_Location</columnTitle>
  </column>
-
+ <column columnName="RQG_alt_ID">
+ <columnTitle>RQG_alt_ID</columnTitle>
+ </column>
  <column columnName="container">
  <isHidden>true</isHidden>
  </column>

diff --git a/covidseq/resources/schemas/dbscripts/sqlserver/covidseq-21.003-21.004.sql b/covidseq/resources/schemas/dbscripts/sqlserver/covidseq-21.003-21.004.sql
@@ -0,0 +1 @@
+ALTER TABLE covidseq.samples ADD rqg_alt_id varchar(200);
diff --git a/covidseq/resources/web/covidseq/panel/SampleImportPanel.js b/covidseq/resources/web/covidseq/panel/SampleImportPanel.js
@@ -26,9 +26,12 @@ Ext4.define('CovidSeq.panel.SampleImportPanel', {
  allowBlank: true
  },{
  name: 'cdna_plate_id',
- labels: ['cDNA_Plate_ID', 'RQG_alt_ID', 'MM Alt ID', 'Alt ID', 'MM ID', 'RQG_alt_ID'],
+ labels: ['cDNA_Plate_ID', 'MM Alt ID', 'Alt ID', 'MM ID'],
  alwaysShow: true,
  allowBlank: true
+ },{
+ name: 'RQG_alt_ID',
+ labels: ['RQG_alt_ID', 'RQG_alt_ID']
  },{
  name: 'gender',
  labels: ['Gender', 'Sex'],
@@ -226,7 +229,8 @@ Ext4.define('CovidSeq.panel.SampleImportPanel', {
 
  if (panel.COUNTY_MAP[val]) {
  if (row.state) {
- if (panel.STATE_ABBREV[val.toLowerCase()]) {
+ // Correct state, if needed:
+ if (panel.STATE_ABBREV[row.state.toLowerCase()]) {
  row.state = panel.STATE_ABBREV[row.state.toLowerCase()]
  }
 
@@ -574,6 +578,11 @@ Ext4.define('CovidSeq.panel.SampleImportPanel', {
  var errorMessages = [];
  var infoMessages = [];
  Ext4.Array.forEach(rows, function(row, rowIdx){
+ // skip blank rows:
+ if (Ext4.isEmpty(row.join(''))) {
+ return;
+ }
+
  var data = {
  objectId: LABKEY.Utils.generateUUID()
  };
@@ -640,7 +649,7 @@ Ext4.define('CovidSeq.panel.SampleImportPanel', {
 
  // CT of record is N for taqpath, N1 for CDC?
 
- data._patientid = data.patientid || data.state + '-OHSU-' + data.samplename.replaceAll('CV', '');
+ data._patientid = data.patientid || data.state + '-OHSU-' + (data.samplename ? data.samplename.replaceAll('CV', '') : 'Sample');
  ret.push(data);
  }, this);
 

diff --git a/covidseq/src/org/labkey/covidseq/CovidseqDataProvider.java b/covidseq/src/org/labkey/covidseq/CovidseqDataProvider.java
@@ -6,6 +6,7 @@
 import org.labkey.api.laboratory.AbstractDataProvider;
 import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.laboratory.NavItem;
+import org.labkey.api.laboratory.QueryCountNavItem;
 import org.labkey.api.laboratory.QueryImportNavItem;
 import org.labkey.api.laboratory.SummaryNavItem;
 import org.labkey.api.ldk.table.QueryCache;
@@ -15,6 +16,7 @@
 import org.labkey.api.view.ViewContext;
 import org.labkey.api.view.template.ClientDependency;
 
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
@@ -91,7 +93,18 @@ public Module getOwningModule()
  @Override
  public List<SummaryNavItem> getSummary(Container c, User u)
  {
- return Collections.emptyList();
+ List<SummaryNavItem> items = new ArrayList<>();
+
+ for (NavItem nav : getSampleNavItems(c, u))
+ {
+ if (nav.isVisible(c, u))
+ {
+ QueryImportNavItem item = ((QueryImportNavItem)nav);
+ items.add(new QueryCountNavItem(this, item.getSchema(), item.getQuery(), item.getItemType(), item.getReportCategory(), item.getLabel()));
+ }
+ }
+
+ return Collections.unmodifiableList(items);
  }
 
  @Override

diff --git a/covidseq/src/org/labkey/covidseq/CovidseqModule.java b/covidseq/src/org/labkey/covidseq/CovidseqModule.java
@@ -41,7 +41,7 @@ public String getName()
  @Override
  public @Nullable Double getSchemaVersion()
  {
- return 21.003;
+ return 21.004;
  }
 
  @Override

diff --git a/mGAP/resources/etls/prime-seq.xml b/mGAP/resources/etls/prime-seq.xml
@@ -94,6 +94,8 @@
  <column>liftedVcfId/library_id/name</column>
  <column>sitesOnlyVcfId/dataid/DataFileUrl</column>
  <column>sitesOnlyVcfId/name</column>
+ <column>novelSitesVcfId/dataid/DataFileUrl</column>
+ <column>novelSitesVcfId/name</column>
  <column>humanJbrowseId</column>
  <column>objectId</column>
  </sourceColumns>
@@ -104,6 +106,7 @@
  <column source="vcfId/dataid/DataFileUrl" target="vcfId" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
  <column source="variantTable/dataid/DataFileUrl" target="variantTable" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
  <column source="sitesOnlyVcfId/dataid/DataFileUrl" target="sitesOnlyVcfId" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
+ <column source="novelSitesVcfId/dataid/DataFileUrl" target="novelSitesVcfId" transformClass="org.labkey.mgap.columnTransforms.OutputFileTransform" />
  <column source="jbrowseId" transformClass="org.labkey.mgap.columnTransforms.JBrowseSessionTransform"/>
  <column source="liftedVcfId/dataid/DataFileUrl" target="liftedVcfId" transformClass="org.labkey.mgap.columnTransforms.LiftedVcfTransform" />
  <column source="humanJbrowseId" transformClass="org.labkey.mgap.columnTransforms.JBrowseHumanSessionTransform"/>

diff --git a/mGAP/resources/queries/mGAP/subjectsSource.sql b/mGAP/resources/queries/mGAP/subjectsSource.sql
@@ -3,6 +3,8 @@ SELECT
  coalesce(s.gender, d.gender) as gender,
  coalesce(s.species, d.species) as species,
  coalesce(s.geographic_origin, d.geographic_origin) as geographic_origin,
+-- TODO: geographic origin score
+
  CASE
  WHEN d.center IS NOT NULL THEN d.center
  WHEN s.subjectname IS NOT NULL THEN 'ONPRC'

diff --git a/mGAP/resources/queries/mGAP/userRequests/.qview.xml b/mGAP/resources/queries/mGAP/userRequests/.qview.xml
@@ -9,6 +9,7 @@
  <column name="userId"/>
  <column name="hasAccess"/>
  <column name="created"/>
+ <column name="userId/Active"/>
  </columns>
  <sorts>
  <sort column="created" descending="true"/>

diff --git a/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.61-16.62.sql b/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.61-16.62.sql
@@ -0,0 +1 @@
+ALTER TABLE mgap.variantList ALTER COLUMN cadd TYPE DOUBLE PRECISION USING cadd::double precision;
diff --git a/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.62-16.63.sql b/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.62-16.63.sql
@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD novelSitesVcfId int;
diff --git a/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.61-16.62.sql b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.61-16.62.sql
@@ -0,0 +1 @@
+ALTER TABLE mgap.variantList ALTER COLUMN cadd DOUBLE PRECISION;
diff --git a/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.62-16.63.sql b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.62-16.63.sql
@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD novelSitesVcfId int;
diff --git a/mGAP/resources/schemas/mgap.xml b/mGAP/resources/schemas/mgap.xml
@@ -158,6 +158,15 @@
  <fkColumnName>rowid</fkColumnName>
  </fk>
  </column>
+ <column columnName="novelSitesVcfId">
+ <columnTitle>Novel Sites For This Release</columnTitle>
+ <nullable>true</nullable>
+ <fk>
+ <fkDbSchema>sequenceanalysis</fkDbSchema>
+ <fkTable>outputfiles</fkTable>
+ <fkColumnName>rowid</fkColumnName>
+ </fk>
+ </column>
  <column columnName="humanJbrowseId">
  <columnTitle>Genome Browser (Human)</columnTitle>
  <nullable>true</nullable>

diff --git a/mGAP/resources/views/phenotypes.html b/mGAP/resources/views/phenotypes.html
@@ -41,8 +41,7 @@
  ['No Genetic Association Reported','Cardiovascular Phenotypes','Ueda, et al. 2019','https://www.ncbi.nlm.nih.gov/pubmed/30723724'],
  ['Genetic Association Reported','Retinal Disease','Moshiri, et al. 2019','https://www.ncbi.nlm.nih.gov/pubmed/30667376'],
  ['Genetic Association Reported','Bardet-Biedl Syndrome','Peterson, et al. 2019','https://www.ncbi.nlm.nih.gov/pubmed/31589838'],
- ['Genetic Association Reported','Epidermolysis Bullosa','Johnson, et al. 2019','']
-
+ ['Genetic Association Reported','Epidermolysis Bullosa','Johnson, et al. 2019','https://www.ncbi.nlm.nih.gov/pubmed/32096448']
  ];
 
  var dataMap = {};
@@ -82,6 +81,83 @@
  var rowId = mGAP.Utils.getMGapReleaseId();
  var url = LABKEY.ActionURL.buildURL('mgap', 'phenotypeList', null, {release: rowId});
  $('#traitUrl').attr('href', url);
+
+
+ //COVID data:
+ var covidRows = [
+ ['LZTFL1','SARS-CoV-2 Infection, COVID-19 severity','x','x','x','x','x','x','2:101823807..101843715'],
+ ['CXCR6','SARS-CoV-2 Infection, COVID-19 severity','x','x','x','x','x','x','2:101948255..101953190'],
+ ['CCR9','SARS-CoV-2 Infection, COVID-19 severity','x','x','x','x','x','x','2:101888276..101907994'],
+ ['CCR1','SARS-CoV-2 Infection, COVID-19 severity','x','x','x','x','x','x','2:102205536..102212086'],
+ ['CCR3','SARS-CoV-2 Infection, COVID-19 severity','x','x','x','x','x','x','2:102268893..102269960'],
+ ['RPL24','SARS-CoV-2 Infection','','','','','','x','2:174444785..174450351'],
+ ['NXPE3','SARS-CoV-2 Infection','','','','','','x','2:174323787..174365577'],
+ ['ZBTB1','SARS-CoV-2 Infection','','','','','','x','7:126570101..126598047'],
+ ['CEP97','SARS-CoV-2 Infection','','','','','','x','2:174379912..174413230'],
+ ['FOXP4','COVID-19 severity','','','','','','x','4:127783384..127837788'],
+ ['CCHCR1','COVID-19 severity','','x','','x','','','4:138774693..138790019'],
+ ['ABO','SARS-CoV-2 Infection','x','x','x','','x','x','15:7086376..7107347'],
+ ['OAS1','COVID-19 severity','x','','','x','','x','11:112632314..112654759'],
+ ['OAS2','COVID-19 severity','x','','','x','','x','11:112695363..112728626'],
+ ['OAS3','COVID-19 severity','x','','','x','','x','11:112661047..112689871'],
+ ['KANSL1','COVID-19 severity','','','','','','x','16:57818339..58014773'],
+ ['WNT3','COVID-19 severity','','','','','','x','16:57171387..57225633'],
+ ['TAC4','COVID-19 severity','','','','','','x','X:89,480,106..89,483,948'],
+ ['KAT7','COVID-19 severity','','','','','','x','16:46957860..47008121'],
+ ['DPP9','COVID-19 severity','x','x','','x','','x','19:4604356..4656762'],
+ ['TYK2','COVID-19 severity','','','','x','','x','19:10110204..10144759'],
+ ['ICAM5','COVID-19 severity','','','','x','','x','19:10044223..10051556'],
+ ['ICAM3','COVID-19 severity','','','','x','','x','19:10088945..10110262'],
+ ['ICAM4','COVID-19 severity','','','','x','','x','19:10041723..10043298'],
+ ['ICAM1','COVID-19 severity','','','','x','','x','19:10024950..10040084'],
+ ['PLEKHA4','SARS-CoV-2 Infection','','','','','','x','19:48819628..48850822'],
+ ['PPP1R15A','SARS-CoV-2 Infection','','','','','','x','19:48854619..48858778'],
+ ['TULP2','SARS-CoV-2 Infection','','','','','','x','19:48864508..48880575'],
+ ['NUCB1','SARS-CoV-2 Infection','','','','','','x','19:48881525..48906138'],
+ ['IFNAR2','COVID-19 severity','x','x','','x','','x','3:13289046..13325302'],
+ ['IL10RB','COVID-19 severity','x','x','','x','','x','3:13,254,913..13,288,351'],
+ ['TMPRSS2','COVID-19 severity','x','x','','x','','x','3:5139757..5184755'],
+ ['ACE2','SARS-CoV-2 Infection','','','','','','','X:15247646..15300547']
+ ];
+
+ covidRows = covidRows.map(function(r){
+ var publications = []
+ if (r[2]) {
+ publications.push('<a href="https://www.nature.com/articles/s41588-022-01042-x">Roberts et al.</a>')
+ }
+ if (r[3]) {
+ publications.push('<a href="https://pubmed.ncbi.nlm.nih.gov/35241825/">Horowitz et al.</a>')
+ }
+ if (r[4]) {
+ publications.push('<a href="https://doi.org/10.1038%2Fs41588-021-00854-7">Shelton et al.</a>')
+ }
+ if (r[5]) {
+ publications.push('<a href="https://doi.org/10.1038%2Fs41586-020-03065-y">Pairo-Castineira et al.</a>')
+ }
+ if (r[6]) {
+ publications.push('<a href="https://doi.org/10.1056%2FNEJMoa2020283">Ellinghaus et al.</a>')
+ }
+ if (r[7]) {
+ publications.push('<a href="https://doi.org/10.1038/s41586-021-03767-x">COVID-19 HGI</a>')
+ }
+
+ var url = LABKEY.ActionURL.buildURL('mgap', 'genomebrowser', null, {location: r[8]})
+ return ['<a href="' + url + '">' + r[0] + '</a>', r[1], publications.join('<br>')]
+ })
+
+ var table = $('#covidPublicationsTable').DataTable({
+ data: covidRows,
+ pageLength: 500,
+
+ dom: '',
+ buttons: [],
+ order: [],
+ columns: [
+ {title: 'Candidate Gene'},
+ {title: 'Phenotype', sortable: false, width: 250},
+ {title: 'Publications', sortable: false}
+ ]
+ });
  });
  })(jQuery);
 </script>
@@ -111,4 +187,15 @@ <h4 style="text-decoration: underline">Published Macaque Models:</h4>
  <span><b>Table I. Published macaque disease models with and without reported genetic associations.</b></span>
  <table id="phenotypeTable" class="stripe hover"></table>
  </div>
+</div>
+<hr>
+<h4 style="text-decoration: underline">COVID Genetic Associations:</h4>
+<div class="colDiv">
+ <div style="flex: 1;max-width: 40%;margin-right: 20px;">
+ The development of COVID-19 vaccines and therapies required extensive testing of their safety and efficacy in nonhuman primates (NHPs) before these new treatments could be used in humans (<a href="https://www.nature.com/articles/s41684-021-00760-9">reviewed in this article</a>). A growing number of human genes have been implicated in COVID-19 disease severity and hospitalization. The table to the right list many of these genes (summarized in: <a href="https://www.covid19hg.org/">https://www.covid19hg.org/</a>), and provides links to mGAP variants in each gene.
+ </div>
+ <div style="width: 600px;">
+ <span><b>Table II. Genes associated with COVID-19 severity and links to macaque variants (<a href = "https://www.nature.com/articles/s41588-021-00985-x">Based on Karlsen et al.</a>). Click the gene name to load the genome browser, showing macaque variants in that gene.</b></span>
+ <table id="covidPublicationsTable" class="stripe hover"></table>
+ </div>
 </div>
diff --git a/mGAP/src/org/labkey/mgap/mGAPModule.java b/mGAP/src/org/labkey/mgap/mGAPModule.java
@@ -61,7 +61,7 @@ public String getName()
  @Override
  public Double getSchemaVersion()
  {
- return 16.60;
+ return 16.63;
  }
 
  @Override

diff --git a/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java b/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java
@@ -120,7 +120,7 @@ private void inspectReleaseFolder(String releaseId, File baseDir, Container c, U
  expectedFiles.add(new File(f.getPath() + ".tbi"));
  });
 
- final Set<String> fields = PageFlowUtil.set("vcfId", "variantTable", "liftedVcfId", "sitesOnlyVcfId");
+ final Set<String> fields = PageFlowUtil.set("vcfId", "variantTable", "liftedVcfId", "sitesOnlyVcfId", "novelSitesVcfId");
  new TableSelector(QueryService.get().getUserSchema(u, c, mGAPSchema.NAME).getTable(mGAPSchema.TABLE_VARIANT_CATALOG_RELEASES), fields, new SimpleFilter(FieldKey.fromString("objectid"), releaseId), null).forEachResults(rs -> {
  for (String field : fields)
  {
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		ALTER TABLE covidseq.samples ADD rqg_alt_id varchar(200);
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		ALTER TABLE mgap.variantList ALTER COLUMN cadd TYPE DOUBLE PRECISION USING cadd::double precision;
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		ALTER TABLE mGAP.variantCatalogReleases ADD novelSitesVcfId int;