diff --git a/covidseq/resources/schemas/covidseq.xml b/covidseq/resources/schemas/covidseq.xml
index 6de4c263e..29da021be 100644
--- a/covidseq/resources/schemas/covidseq.xml
+++ b/covidseq/resources/schemas/covidseq.xml
@@ -102,7 +102,9 @@
cDNA_Plate_Location
-
+
+ RQG_alt_ID
+ true
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
new file mode 100644
index 000000000..98cc10388
--- /dev/null
+++ 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);
\ No newline at end of file
diff --git a/covidseq/resources/web/covidseq/panel/SampleImportPanel.js b/covidseq/resources/web/covidseq/panel/SampleImportPanel.js
index 772477723..f496d68b9 100644
--- 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
index b685df28e..90cf16863 100644
--- 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 getSummary(Container c, User u)
{
- return Collections.emptyList();
+ List 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
index b5796d777..e1fa71e8c 100644
--- 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
index c6a31d3b6..a8f394aa7 100644
--- a/mGAP/resources/etls/prime-seq.xml
+++ b/mGAP/resources/etls/prime-seq.xml
@@ -94,6 +94,8 @@
liftedVcfId/library_id/namesitesOnlyVcfId/dataid/DataFileUrlsitesOnlyVcfId/name
+ novelSitesVcfId/dataid/DataFileUrl
+ novelSitesVcfId/namehumanJbrowseIdobjectId
@@ -104,6 +106,7 @@
+
diff --git a/mGAP/resources/queries/mGAP/subjectsSource.sql b/mGAP/resources/queries/mGAP/subjectsSource.sql
index d30fba46d..e81d5be2b 100644
--- 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
index da6852317..5fff46319 100644
--- a/mGAP/resources/queries/mGAP/userRequests/.qview.xml
+++ b/mGAP/resources/queries/mGAP/userRequests/.qview.xml
@@ -9,6 +9,7 @@
+
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
new file mode 100644
index 000000000..1575f958f
--- /dev/null
+++ 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;
\ No newline at end of file
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
new file mode 100644
index 000000000..93bde7eb1
--- /dev/null
+++ b/mGAP/resources/schemas/dbscripts/postgresql/mgap-16.62-16.63.sql
@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD novelSitesVcfId int;
\ No newline at end of file
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
new file mode 100644
index 000000000..f3df21a83
--- /dev/null
+++ b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.61-16.62.sql
@@ -0,0 +1 @@
+ALTER TABLE mgap.variantList ALTER COLUMN cadd DOUBLE PRECISION;
\ No newline at end of file
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
new file mode 100644
index 000000000..93bde7eb1
--- /dev/null
+++ b/mGAP/resources/schemas/dbscripts/sqlserver/mgap-16.62-16.63.sql
@@ -0,0 +1 @@
+ALTER TABLE mGAP.variantCatalogReleases ADD novelSitesVcfId int;
\ No newline at end of file
diff --git a/mGAP/resources/schemas/mgap.xml b/mGAP/resources/schemas/mgap.xml
index 96b65a274..ee022ea76 100644
--- a/mGAP/resources/schemas/mgap.xml
+++ b/mGAP/resources/schemas/mgap.xml
@@ -158,6 +158,15 @@
rowid
+
+ Novel Sites For This Release
+ true
+
+ sequenceanalysis
+ outputfiles
+ rowid
+
+ Genome Browser (Human)true
diff --git a/mGAP/resources/views/phenotypes.html b/mGAP/resources/views/phenotypes.html
index 5b200d4e6..8a03b9ac1 100644
--- 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('Roberts et al.')
+ }
+ if (r[3]) {
+ publications.push('Horowitz et al.')
+ }
+ if (r[4]) {
+ publications.push('Shelton et al.')
+ }
+ if (r[5]) {
+ publications.push('Pairo-Castineira et al.')
+ }
+ if (r[6]) {
+ publications.push('Ellinghaus et al.')
+ }
+ if (r[7]) {
+ publications.push('COVID-19 HGI')
+ }
+
+ var url = LABKEY.ActionURL.buildURL('mgap', 'genomebrowser', null, {location: r[8]})
+ return ['' + r[0] + '', r[1], publications.join(' ')]
+ })
+
+ 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);
@@ -111,4 +187,15 @@
Published Macaque Models:
Table I. Published macaque disease models with and without reported genetic associations.
+
+
+
COVID Genetic Associations:
+
+
+ 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 (reviewed in this article). 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: https://www.covid19hg.org/), and provides links to mGAP variants in each gene.
+
+
+ Table II. Genes associated with COVID-19 severity and links to macaque variants (Based on Karlsen et al.). Click the gene name to load the genome browser, showing macaque variants in that gene.
+
