Merge pull request #191 from LabKey/fb_merge_23.11_to_develop

bbimber · web-flow · commit b0263e9512a8 · 2024-02-02T11:16:01.000-06:00
Merge discvr-23.11 to develop
diff --git a/LabPurchasing/resources/queries/labpurchasing/referenceItems.js b/LabPurchasing/resources/queries/labpurchasing/referenceItems.js
@@ -2,24 +2,28 @@ var LABKEY = require("labkey");
 var console = require("console");
 
 function beforeInsert(row, errors){
-    // Allow resulting vendorId from name:
-    if (row.vendorName && !row.vendorId) {
-        LABKEY.Query.selectRows({
-            schemaName: 'labpurchasing',
-            queryName: 'vendors',
-            columns: 'rowid',
-            filterArray: [LABKEY.Filter.create('vendorName', row.vendorName)],
-            sort: '-rowid',
-            maxRows: 1,
-            scope: this,
-            success: function(results) {
-                if (results.rows.length) {
-                    row.vendorId = results.rows[0].rowId;
+    // The purpose of this is to allow the user to provide a string value for
+    // vendorId or vendorName, and attempt to resolve this against known vendors:
+    if (!row.vendorId || isNaN(row.vendorId)) {
+        var vendorName = row.vendorName || row.vendorId;
+        if (vendorName) {
+            LABKEY.Query.selectRows({
+                schemaName: 'labpurchasing',
+                queryName: 'vendors',
+                columns: 'rowid',
+                filterArray: [LABKEY.Filter.create('vendorName', vendorName)],
+                sort: '-rowid',
+                maxRows: 1,
+                scope: this,
+                success: function(results) {
+                    if (results.rows.length) {
+                        row.vendorId = results.rows[0].rowId;
+                    }
+                    else {
+                        console.error("Unable to resolve vendor: " + vendorName);
+                    }
                 }
-                else {
-                    console.error("Unable to resolve vendorname: " + row.vendorName);
-                }
-            }
-        })
+            })
+        }
     }
 }
diff --git a/mGAP/resources/views/overview.html b/mGAP/resources/views/overview.html
@@ -35,7 +35,7 @@ <h4><span style="text-decoration: underline">Short Variant Catalog:</span> <img
         <br>
         <ul style="padding-top: 10px;">
             <li>Use the <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?">Genome Browser</a> to view and search data. <i class="fa-solid fa-video mgap-video-icon" data-video="genome-browser" data-video-title="Genome Browser Overview"></i></li>
-            <li class="mgap-lucene-link" hidden="hidden">Use our new <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?target=variantSearch">Full-text Search</a> tool to query variants based on gene, or using our <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-annotation.view">extensive annotations</a> <!--<i class="fa-solid fa-video mgap-video-icon" data-video="variant-search" data-video-title="Variant Full-text Search (BETA)"></i>--></li>
+            <li class="mgap-lucene-link" hidden="hidden">Use our new <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-genomeBrowser.view?target=variantSearch">Full-text Search</a> tool to query variants based on gene, or using our <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mgap-annotation.view">extensive annotations</a> <i class="fa-solid fa-video mgap-video-icon" data-video="variant-search" data-video-title="Variant Full-text Search (BETA)"></i></li>
             <li>View our list of <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/mGap-variantList.view">Predicted Damaging Variants</a>, which is a list of predicted high-impact or disease associated variants, generated from each release <i class="fa-solid fa-video mgap-video-icon" data-video="predicted-damaging-variants" data-video-title="Predicted Damaging Variants"></i></li>
             <li>Unlike many datasets, mGAP has genotype-level data, <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=clinical">often connected to living animals from pedigreed breeding colonies</a></li>
             <li>Download raw data, including <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=datasets">sequence data</a> and <a class="mgap-link" href="<%=contextPath%><%=containerPath%>/project-begin.view?pageId=variants">variant data</a></li>
diff --git a/mGAP/resources/views/releaseNotes.html b/mGAP/resources/views/releaseNotes.html
@@ -2,6 +2,7 @@ <h4>Release 2.5:</h4>
 <ul>
     <li>This release includes a major change in how we perform variant annotation, <a href="mgap-annotation.view">described in more detail here.</a></li>
     <li>This release includes 107 additional datasets. The total number of variants dropped relative to release 2.4 due to a change in our filtering. Previously, certain conditions would allow a variant to remain in the dataset, even if no subjects had this genotype. After this correction, ~4m sites were removed, although no genotype calls should be changed.</li>
+    <li>We introduced an entirely new search feature! The new 'Variant Search' page allows you to perform genome-wide queries based on variant annotations (e.g. predicted coding impact or overlap with databases of human pathogenic variants)</li>
 </ul>
 
 <h4>Release 2.4:</h4>
diff --git a/mGAP/resources/web/mGAP/DownloadWindow.js b/mGAP/resources/web/mGAP/DownloadWindow.js
@@ -68,9 +68,9 @@ Ext4.define('mGAP.window.DownloadWindow', {
                             '<pre>wget https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '<br>' +
                             'wget https://mgapdownload.ohsu.edu/' + sitesOnlyVcf + '.tbi</pre>' : '') +
                             'and genome:<br>' +
-                            '<pre>wget https://mgapdownload.ohsu.edu/' + urlFasta + '<br>' +
-                            'wget https://mgapdownload.ohsu.edu/' + urlFasta + '.fai<br>' +
-                            'wget https://mgapdownload.ohsu.edu/' + urlFasta.replace(/fasta$/, 'dict') + '</pre>'
+                            '<pre>wget https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '<br>' +
+                            'wget https://mgapdownload.ohsu.edu/genomes/' + urlFasta + '.fai<br>' +
+                            'wget https://mgapdownload.ohsu.edu/genomes/' + urlFasta.replace(/fasta$/, 'dict') + '</pre>'
                 },{
                     html: '<br><b>mGAP is an NIH funded project.  If you use these data in a publication, we ask that you please include R24OD021324 in the acknowledgements.</b>',
                     border: false,
diff --git a/mGAP/resources/web/mGAP/Utils.js b/mGAP/resources/web/mGAP/Utils.js
@@ -43,7 +43,9 @@ mGAP.Utils = (function($){
                         versionLine = '<tr><td>Current Version:</td><td>' + mGAP.Utils.getMGapReleaseVersion() + '</td></tr>';
                     }
                     var data0 = map.Counts || {};
-                    $('#' + tableId).html('<table>' + versionLine + '<tr><td>Total Variants:</td><td>' + numberWithCommas(data0.TotalVariants) + '</td></tr><tr><td>Total Animals:</td><td>' + numberWithCommas(data0.TotalSamples) + '</td></tr><tr><td style="padding-right: 20px;">Private Variants:</td><td>' + numberWithCommas(data0.TotalPrivateVariants) + '</td></tr></table>');
+                    $('#' + tableId).html('<table>' + versionLine + '<tr><td>Total Variants:</td><td>' + numberWithCommas(data0.TotalVariants) + '</td></tr><tr><td>Total Animals:</td><td>' + numberWithCommas(data0.TotalSamples) + '</td></tr><tr><td style="padding-right: 20px;">Private Variants:</td><td>' + numberWithCommas(data0.TotalPrivateVariants) + '</td></tr>' +
+                        (data0.TotalVariantsNewInRelease ? '<tr><td style="padding-right: 20px;">Variants New In Release:</td><td>' + numberWithCommas(data0.TotalVariantsNewInRelease) + '</td></tr>' : '') +
+                    '</table>');
 
                     var data1 = map.CodingPotential || {};
                     var codingLabels = ["Exonic", "Downstream<br>Gene", "Upstream<br>Gene", "Intergenic", "Intronic/<br>Non-coding"];
@@ -140,7 +142,7 @@ mGAP.Utils = (function($){
                         "name": "# Variants",
                         "mode": "markers",
                         "x": annotationData,
-                        "y": ["GWAS Associations<br>(GRASP)", "Enhancer Region<br>(FANTOM5)", "Predicted Enhancer<br>(ENCODE)", "Transcription Factor<br>Binding (ENCODE)", "Predicted High<br>Impact (SnpEff)", "Damaging<br>(Polyphen2)", "ClinVar Overlap"],
+                        "y": ["Enhancer Region<br>(FANTOM5)", "Predicted Enhancer<br>(ENCODE)", "Transcription Factor<br>Binding (ENCODE)", "Predicted High<br>Impact (SnpEff)", "Damaging<br>(Polyphen2)", "ClinVar Overlap"],
                         "type": "bar",
                         "orientation": "h",
                         "autobiny": true
diff --git a/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java b/mGAP/src/org/labkey/mgap/mGapMaintenanceTask.java
@@ -121,9 +121,9 @@ private void checkMGapFiles(Logger log, User u)
             try
             {
                 ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(genomeId, u);
-                checkSymlink(log, rg.getSourceFastaFile(), null, commandsToRun);
-                checkSymlink(log, new File(rg.getSourceFastaFile().getPath() + ".fai"), null, commandsToRun);
-                checkSymlink(log, new File(rg.getSourceFastaFile().getPath().replace(".fasta", ".dict")), null, commandsToRun);
+                checkSymlink(log, rg.getSourceFastaFile(), "genomes", commandsToRun);
+                checkSymlink(log, new File(rg.getSourceFastaFile().getPath() + ".fai"), "genomes", commandsToRun);
+                checkSymlink(log, new File(rg.getSourceFastaFile().getPath().replace(".fasta", ".dict")), "genomes", commandsToRun);
             }
             catch (PipelineJobException e)
             {
diff --git a/mcc/package-lock.json b/mcc/package-lock.json
diff --git a/mcc/resources/data/gender_codes.tsv b/mcc/resources/data/gender_codes.tsv
@@ -0,0 +1,8 @@
+code	meaning	origgender
+c	ovexed (female castrate)	f
+e	male castrate	m
+f	female	f
+h	hermaphrodite
+m	male	m
+v	vasectomized	m
+u	unknown	u
diff --git a/mcc/resources/views/nihReview.html b/mcc/resources/views/nihReview.html
@@ -7,7 +7,7 @@
             return;
 
         Ext4.get(webpart.wrapperDivId).update(
-            'Below are all MCC requests awaiting the final decision. By default this shows only pending requests; however, you can the left-hand \'Views\' button to toggle between this and all requests.' +
+            'Below are all MCC requests awaiting the final decision. By default this shows only pending requests; however, you can click the left-hand \'Views\' button to toggle between this and all requests.' +
             '<p></p>' +
             '<a class="labkey-text-link" href="/become-a-user.html#request-animals">Click Here to View Documentation on the Request Process and Scoring Criteria</a>' +
             '<br>' +
diff --git a/mcc/resources/views/populateData.html b/mcc/resources/views/populateData.html
@@ -223,7 +223,7 @@
         },{
             label: 'Gender Codes',
             populateFn: 'populateFromFile',
-            moduleName: 'ehr',
+            moduleName: 'mcc',
             schemaName: 'ehr_lookups',
             queryName: 'gender_codes',
             pk: 'rowid'
diff --git a/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx b/mcc/src/client/RequestReview/components/ReadOnlyRequest.tsx
@@ -2,7 +2,7 @@ import React from 'react';
 import { AnimalRequestModel, AnimalRequestProps } from '../../components/RequestUtils';
 import {
     existingMarmosetColonyOptions,
-    existingNHPFacilityOptions,
+    existingNHPFacilityOptions, fundingSourceOptions,
     IACUCApprovalOptions,
     institutionTypeOptions
 } from '../../AnimalRequest/components/values';
@@ -144,6 +144,18 @@ export default function ReadOnlyRequest(props: {requestData: AnimalRequestModel}
                         ])
                     }) : 'N/A'}
                 </Grid>
+                <StyledGridFieldLabel item xs={2}>
+                    <div>Funding Source(s): </div>
+                </StyledGridFieldLabel>
+                <Grid item xs={10}>
+                    {translateRawToDisplayValue(requestData.request.fundingsource, fundingSourceOptions, true)}
+                </Grid>
+                <StyledGridFieldLabel item xs={2}>
+                    <div>Grant Number(s): </div>
+                </StyledGridFieldLabel>
+                <Grid item xs={10}>
+                    {requestData.request.grantnumber}
+                </Grid>
             </Grid>
 
             <p />
diff --git a/mcc/src/client/components/RequestUtils.tsx b/mcc/src/client/components/RequestUtils.tsx
@@ -29,6 +29,8 @@ export class AnimalRequestProps {
     officiallastname: string;
     officialfirstname: string;
     officialemail: string;
+    fundingsource: string;
+    grantnumber: string;
     experimentalrationale: string;
     breedinganimals: string;
     breedingpurpose: string;
diff --git a/mcc/src/org/labkey/mcc/MccUserSchema.java b/mcc/src/org/labkey/mcc/MccUserSchema.java
@@ -22,8 +22,8 @@
 import org.labkey.mcc.security.MccRabReviewPermission;
 import org.labkey.mcc.security.MccRequestAdminPermission;
 import org.labkey.mcc.security.MccRequestorPermission;
+import org.labkey.mcc.security.MccViewRequestsPermission;
 
-import java.util.Arrays;
 import java.util.Collections;
 
 public class MccUserSchema extends SimpleUserSchema
@@ -65,9 +65,9 @@ else if (MccSchema.TABLE_REQUEST_REVIEWS.equalsIgnoreCase(name))
         else if (MccSchema.TABLE_REQUEST_SCORE.equalsIgnoreCase(name))
         {
             CustomPermissionsTable<?> ret = new CustomPermissionsTable<>(this, schemaTable, cf);
-            ret.addPermissionMapping(ReadPermission.class, MccRequestAdminPermission.class);
-            ret.addPermissionMapping(InsertPermission.class, MccRequestAdminPermission.class);
-            ret.addPermissionMapping(UpdatePermission.class, MccRequestAdminPermission.class);
+            ret.addPermissionMapping(ReadPermission.class, MccViewRequestsPermission.class);
+            ret.addPermissionMapping(InsertPermission.class, MccViewRequestsPermission.class);
+            ret.addPermissionMapping(UpdatePermission.class, MccViewRequestsPermission.class);
             ret.addPermissionMapping(DeletePermission.class, MccRequestAdminPermission.class);
 
             ret = ret.init();
diff --git a/mcc/src/org/labkey/mcc/security/MccDataAdminRole.java b/mcc/src/org/labkey/mcc/security/MccDataAdminRole.java
@@ -10,7 +10,7 @@ public class MccDataAdminRole extends AbstractRole
 {
     public MccDataAdminRole()
     {
-        super("MccDataAdmin", "These users can administer data and animal requests", ReadPermission.class, InsertPermission.class, UpdatePermission.class, MccRequestorPermission.class, MccDataAdminPermission.class, MccRequestAdminPermission.class, MccRabReviewPermission.class);
+        super("MccDataAdmin", "These users can administer data and animal requests", ReadPermission.class, InsertPermission.class, UpdatePermission.class, MccRequestorPermission.class, MccDataAdminPermission.class, MccRequestAdminPermission.class, MccViewRequestsPermission.class, MccRabReviewPermission.class);
     }
 
     @Override
diff --git a/mcc/src/org/labkey/mcc/security/MccFinalReviewerRole.java b/mcc/src/org/labkey/mcc/security/MccFinalReviewerRole.java
@@ -10,7 +10,7 @@ public class MccFinalReviewerRole extends AbstractRole
 {
     public MccFinalReviewerRole()
     {
-        super("MccFinalReviewer", "These users can enter the final reviews for MCC requests", ReadPermission.class, InsertPermission.class, UpdatePermission.class, MccRequestorPermission.class, MccRabReviewPermission.class, MccFinalReviewPermission.class);
+        super("MccFinalReviewer", "These users can enter the final reviews for MCC requests", ReadPermission.class, InsertPermission.class, UpdatePermission.class, MccRequestorPermission.class, MccRabReviewPermission.class, MccViewRequestsPermission.class, MccFinalReviewPermission.class);
     }
 
     @Override
diff --git a/mcc/src/org/labkey/mcc/security/MccRabReviewerRole.java b/mcc/src/org/labkey/mcc/security/MccRabReviewerRole.java
@@ -10,7 +10,7 @@ public class MccRabReviewerRole extends AbstractRole
 {
     public MccRabReviewerRole()
     {
-        super("MccRabReviewer", "These users can enter RAB reviews", ReadPermission.class, InsertPermission.class, UpdatePermission.class, MccRequestorPermission.class, MccRabReviewPermission.class);
+        super("MccRabReviewer", "These users can enter RAB reviews", ReadPermission.class, InsertPermission.class, UpdatePermission.class, MccRequestorPermission.class, MccViewRequestsPermission.class, MccRabReviewPermission.class);
     }
 
     @Override
diff --git a/mcc/src/org/labkey/mcc/security/MccViewRequestsPermission.java b/mcc/src/org/labkey/mcc/security/MccViewRequestsPermission.java
@@ -0,0 +1,14 @@
+package org.labkey.mcc.security;
+
+import org.labkey.api.security.permissions.AbstractPermission;
+
+/**
+ * This is required to view the data from request_scores and other approval steps.
+ */
+public class MccViewRequestsPermission extends AbstractPermission
+{
+    public MccViewRequestsPermission()
+    {
+        super("MccFinalReview", "This permission is required to enter the final decision on animal requests in the MCC");
+    }
+}
diff --git a/primeseq/resources/web/primeseq/window/DeleteJobCheckpointWindow.js b/primeseq/resources/web/primeseq/window/DeleteJobCheckpointWindow.js
@@ -0,0 +1,81 @@
+Ext4.define('Primeseq.window.DeleteJobCheckpointWindow', {
+    extend: 'Ext.window.Window',
+
+    statics: {
+        buttonHandler: function(dataRegionName){
+            const checked = LABKEY.DataRegions[dataRegionName].getChecked();
+            if (!checked.length){
+                Ext4.Msg.alert('Error', 'No rows selected');
+                return;
+            }
+
+            Ext4.create('Primeseq.window.DeleteJobCheckpointWindow', {
+                jobIds: checked,
+                dataRegionName: dataRegionName,
+                autoShow: true
+            });
+        }
+    },
+
+    initComponent: function(){
+        Ext4.QuickTips.init();
+        Ext4.apply(this, {
+            title: 'Update Job Resources',
+            width: 600,
+            bodyStyle: 'padding: 5px;',
+            items: [{
+                html: 'This will delete the checkpoint JSON file for the selected pipeline jobs, which will cause them to completely restart, instead of attempting to resume at the last checkpoint. This will only delete a checkpoint file for jobs with a status of error or cancelled.',
+                border: false,
+                style: 'padding-bottom: 20px;'
+            },{
+                xtype: 'checkbox',
+                itemId: 'restartJobs',
+                fieldLabel: 'Restart Jobs',
+                checked: true
+            }],
+            buttons: [{
+                text: 'Submit',
+                handler: this.onSubmit,
+                scope: this
+            },{
+                text: 'Cancel',
+                handler: function (btn) {
+                    btn.up('window').close();
+                }
+            }]
+        });
+
+        this.callParent(arguments);
+    },
+
+    onSubmit: function(btn){
+        Ext4.Msg.wait('Loading...');
+        var restartJobs = btn.up('window').down('#restartJobs');
+
+        LABKEY.Ajax.request({
+            method: 'POST',
+            url: LABKEY.ActionURL.buildURL('primeseq', 'deleteJobCheckpoint'),
+            jsonData: {
+                jobIds: this.jobIds.join(','),
+                restartJobs: !!restartJobs
+            },
+            scope: this,
+            success: function(response){
+                Ext4.Msg.hide();
+
+                var jsonResp = LABKEY.Utils.decode(response.responseText);
+                console.log(jsonResp);
+                var dataRegionName = this.dataRegionName;
+                this.close();
+
+                Ext4.Msg.alert('Success', 'Jobs updated: ' + jsonResp.jobsUpdated + '<br>Jobs restarted: ' + jsonResp.jobsRestarted, function(){
+                    var dataRegion = LABKEY.DataRegions[dataRegionName];
+                    if (dataRegion){
+                        dataRegion.refresh();
+                    }
+                }, this);
+            },
+            failure: LDK.Utils.getErrorCallback()
+        });
+    }
+});
diff --git a/primeseq/src/org/labkey/primeseq/PrimeseqController.java b/primeseq/src/org/labkey/primeseq/PrimeseqController.java
diff --git a/primeseq/src/org/labkey/primeseq/PrimeseqModule.java b/primeseq/src/org/labkey/primeseq/PrimeseqModule.java
diff --git a/primeseq/src/org/labkey/primeseq/pipeline/DeleteJobCheckpointButton.java b/primeseq/src/org/labkey/primeseq/pipeline/DeleteJobCheckpointButton.java
diff --git a/tcrdb/gradle.properties b/tcrdb/gradle.properties

Original file line number	Diff line number	Diff line change
`@@ -121,9 +121,9 @@ private void checkMGapFiles(Logger log, User u)`
`121`	`121`	`try`
`122`	`122`	`{`
`123`	`123`	`ReferenceGenome rg = SequenceAnalysisService.get().getReferenceGenome(genomeId, u);`
`124`		`- checkSymlink(log, rg.getSourceFastaFile(), null, commandsToRun);`
`125`		`- checkSymlink(log, new File(rg.getSourceFastaFile().getPath() + ".fai"), null, commandsToRun);`
`126`		`- checkSymlink(log, new File(rg.getSourceFastaFile().getPath().replace(".fasta", ".dict")), null, commandsToRun);`
	`124`	`+ checkSymlink(log, rg.getSourceFastaFile(), "genomes", commandsToRun);`
	`125`	`+ checkSymlink(log, new File(rg.getSourceFastaFile().getPath() + ".fai"), "genomes", commandsToRun);`
	`126`	`+ checkSymlink(log, new File(rg.getSourceFastaFile().getPath().replace(".fasta", ".dict")), "genomes", commandsToRun);`
`127`	`127`	`}`
`128`	`128`	`catch (PipelineJobException e)`
`129`	`129`	`{`