Merge discvr-25.11 to develop

GenotypeAssays/resources/views/bulkHaplotype.html

@@ -1,10 +1,10 @@
 <script type="text/javascript" nonce="<%=scriptNonce%>">
 
     Ext4.onReady(function () {
-        var analysisIds = LABKEY.ActionURL.getParameter('analysisIds');
+        var analysisId = LABKEY.ActionURL.getParameter('analysisId');
 
-        if (!analysisIds) {
-            alert('Must Provide At Least One Analysis Id');
+        if (!analysisId) {
+            alert('Must Provide An Analysis Id');
             return;
         }
 
@@ -15,7 +15,7 @@
             title: 'Haplotype Matches',
             items: [{
                 xtype: 'genotypeassays-haplotypepanel',
-                analysisIds: analysisIds.split(';'),
+                analysisIds: analysisId,
                 showCheckBoxes: true
             }]
         }).render(webpart.wrapperDivId);

GenotypeAssays/resources/views/sbtReview.html

@@ -155,13 +155,15 @@
                             allowHeaderLock: false,
                             schemaName: 'sequenceanalysis',
                             queryName: 'alignment_summary_grouped',
-                            //viewName: 'With Haplotype Matches',
+                            viewName: 'With Haplotype Matches',
                             //sort: '-percent',
                             containerPath: Laboratory.Utils.getQueryContainerPath(),
-                            filterArray: [LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)],
                             removeableFilters: [
                                 LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE)
                             ],
+                            parameters: {
+                                AnalysisId: analysisId
+                            },
                             scope: this,
                             success: this.onDataRegionLoad
                         })
@@ -173,15 +175,17 @@
                             allowHeaderLock: false,
                             schemaName: 'sequenceanalysis',
                             queryName: 'alignment_summary_by_lineage',
-                            //viewName: 'With Haplotype Matches',
+                            viewName: 'With Haplotype Matches',
                             sort: '-percent',
                             containerPath: Laboratory.Utils.getQueryContainerPath(),
-                            filterArray: [LABKEY.Filter.create('analysis_id', analysisId, LABKEY.Filter.Types.EQUAL)],
                             removeableFilters: [
                                 LABKEY.Filter.create('percent_from_locus', 0.25, LABKEY.Filter.Types.GTE),
                                 LABKEY.Filter.create('total_reads', 5, LABKEY.Filter.Types.GT),
                                 LABKEY.Filter.create('totalLineages', 1, LABKEY.Filter.Types.EQUAL)
                             ],
+                            parameters: {
+                                AnalysisId: analysisId
+                            },
                             scope: this,
                             success: this.onDataRegionLoad
                         })
@@ -191,7 +195,7 @@
                         title: 'Haplotype Matches',
                         items: [{
                             xtype: 'genotypeassays-haplotypepanel',
-                            analysisIds: [analysisId]
+                            analysisId: [analysisId]
                         }]
                     },{
                         xtype: 'ldk-querypanel',

GenotypeAssays/resources/web/genotypeassays/buttons.js

@@ -21,9 +21,14 @@ GenotypeAssays.buttons = new function(){
                 return;
             }
 
+            if (checked.length !== 1) {
+                alert('Only one row at a time can be selected');
+                return;
+            }
+
             var newForm = Ext4.DomHelper.append(document.getElementsByTagName('body')[0],
                     '<form method="POST" action="' + LABKEY.ActionURL.buildURL("genotypeassays", "bulkHaplotype", null) + '">' +
-                    '<input type="hidden" name="analysisIds" value="' + Ext4.htmlEncode(checked.join(';')) + '" />' +
+                    '<input type="hidden" name="analysisId" value="' + Ext4.htmlEncode(checked[0]) + '" />' +
                     '</form>');
             newForm.submit();
         }

GenotypeAssays/resources/web/genotypeassays/panel/HaplotypePanel.js

@@ -1,7 +1,7 @@
 Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
     extend: 'Ext.panel.Panel',
     alias: 'widget.genotypeassays-haplotypepanel',
-    analysisIds: null,
+    analysisId: null,
     showCheckBoxes: false,
 
     initComponent: function(){
@@ -266,10 +266,11 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
                             }
                         }, this);
 
-                        Ext4.Msg.confirm('Publish Selected?', 'You have chosen to published the following haplotypes:<br><br>' + (haplotypeNames.length > 8 ? 'Too many to display' : haplotypeNames.join('<br>')) + '<br><br>Continue?', function (val) {
+                        Ext4.Msg.confirm('Publish Selected?', 'You have chosen to publish the following haplotypes:<br><br>' + (haplotypeNames.length > 8 ? 'Too many to display' : haplotypeNames.join('<br>')) + '<br><br>Continue?', function (val) {
                             if (val == 'yes') {
                                 Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
                                     actionName: 'cacheHaplotypes',
+                                    analysisId: this.analysisId,
                                     json: json
                                 }).show();
                             }
@@ -460,10 +461,12 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
             schemaName: 'sequenceanalysis',
             queryName: 'alignment_summary_by_lineage',
             columns: 'analysis_id,analysis_id/readset,analysis_id/readset/subjectId,lineages,loci,total,total_reads,percent,total_reads_from_locus,percent_from_locus',
+            parameters: {
+                AnalysisId: this.analysisId
+            },
             apiVersion: 13.2,
             scope: this,
             filterArray: [
-                LABKEY.Filter.create('analysis_id', this.analysisIds.join(';'), LABKEY.Filter.Types.IN),
                 LABKEY.Filter.create('percent_from_locus', minPct || 0, LABKEY.Filter.Types.GTE)
             ],
             failure: LDK.Utils.getErrorCallback(),
@@ -502,9 +505,9 @@ Ext4.define('GenotypeAssays.panel.HaplotypePanel', {
             sort: 'analysis_id',
             apiVersion: 13.2,
             scope: this,
-            filterArray: [
-                LABKEY.Filter.create('analysis_id', this.analysisIds.join(';'), LABKEY.Filter.Types.IN)
-            ],
+            parameters: {
+                AnalysisId: this.analysisId
+            },
             failure: LDK.Utils.getErrorCallback(),
             success: function(results){
                 this.lineageToAlleleMap = {};

GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js

@@ -11,26 +11,20 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
                 return;
             }
 
+            const analysisId = dr.getParameters()?.AnalysisId;
+            if (!analysisId) {
+                Ext4.Msg.alert('Error', 'Error: unable to find analysisId. This should not occur.');
+                LDK.Assert.assertNotEmpty('Unable to find AnalysisId parameter from the DataRegion in PublishResultsWindow');
+
+                return;
+            }
+
             Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
                 dataRegionName: dataRegionName,
+                analysisId: analysisId,
                 actionName: 'cacheAnalyses'
             }).show();
         }
-
-        // haplotypeButtonHandler: function(dataRegionName){
-        //     var dr = LABKEY.DataRegions[dataRegionName];
-        //     LDK.Assert.assertNotEmpty('Unable to find dataregion in PublishResultsWindow', dr);
-        //
-        //     if (!dr.getChecked().length) {
-        //         Ext4.Msg.alert('Error', 'No rows selected');
-        //         return;
-        //     }
-        //
-        //     Ext4.create('GenotypeAssays.window.PublishResultsWindow', {
-        //         dataRegionName: dataRegionName,
-        //         actionName: 'cacheHaplotypes'
-        //     }).show();
-        // }
     },
 
     initComponent: function(){
@@ -122,6 +116,7 @@ Ext4.define('GenotypeAssays.window.PublishResultsWindow', {
             scope: this,
             jsonData: {
                 alleleNames: alleleNames,
+                analysisId: this.analysisId,
                 json: Ext4.encode(this.json),
                 protocolId: protocol
             },

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java

@@ -133,7 +133,7 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors)
                     }
 
                     String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);
-                    Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);
+                    Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), form.getAnalysisId(), protocol, alleleNames);
                     resultProperties.put("runsCreated", ret.first);
                     resultProperties.put("runsDeleted", ret.second);
                 }
@@ -159,6 +159,7 @@ public static class CacheAnalysesForm
     {
         private String[] _alleleNames;
         private String _json;
+        private int _analysisId;
         private int _protocolId;
 
         public String[] getAlleleNames()
@@ -190,6 +191,16 @@ public void setJson(String json)
         {
             _json = json;
         }
+
+        public int getAnalysisId()
+        {
+            return _analysisId;
+        }
+
+        public void setAnalysisId(int analysisId)
+        {
+            _analysisId = analysisId;
+        }
     }
 
     @RequiresPermission(UpdatePermission.class)

GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java

@@ -90,8 +90,7 @@ public static GenotypeAssaysManager get()
         return _instance;
     }
 
-
-    public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
+    public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final int analysisId, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException
     {
         final User u = ctx.getUser();
         final List<Long> runsCreated = new ArrayList<>();
@@ -126,6 +125,8 @@ public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final E
 
             AtomicInteger records = new AtomicInteger();
             TableSelector tsAlignments = new TableSelector(tableAlignments, cols.values(), new SimpleFilter(FieldKey.fromString("key"), Arrays.asList(pks), CompareType.IN), null);
+            tsAlignments.setNamedParameters(Map.of("AnalysisId", analysisId));
+
             tsAlignments.forEach(new Selector.ForEachBlock<ResultSet>()
             {
                 @Override

PMR/resources/queries/study/exportedDemographics.sql

@@ -0,0 +1,13 @@
+SELECT
+    d.Id,
+    d.date,
+    d.gender,
+    d.species,
+    d.geographic_origin,
+    d.birth,
+    d.death,
+    d.calculated_status,
+    d.Id.parents.dam as dam,
+    d.Id.parents.sire as sire
+
+FROM study.demographics d

PMR/resources/schemas/PMR_Data.template.xml

@@ -0,0 +1,12 @@
+<templateSchema sourceSchemaName="study" xmlns="http://labkey.org/data/xml/externalSchema" xmlns:cv="http://labkey.org/data/xml/queryCustomView">
+    <tables>
+        <tableName>exportedDemographics</tableName>
+    </tables>
+    <metadata>
+        <tables xmlns="http://labkey.org/data/xml">
+            <table tableName="exportedDemographics" tableDbType="NOT_IN_DB">
+                <tableTitle>Demographics</tableTitle>
+            </table>
+        </tables>
+    </metadata>
+</templateSchema>

mGAP/resources/queries/mGAP/subjectsSource.sql

@@ -12,13 +12,13 @@ SELECT
   d.status as status,
   m.subjectname as originalId,
   p1.externalAlias as sire,
-  coalesce(s.Id.parents.sire, d.sire) as originalSire,
+  coalesce(s.sire, d.sire) as originalSire,
   p2.externalAlias as dam,
-  coalesce(s.Id.parents.dam, d.dam) as originalDam,
+  coalesce(s.dam, d.dam) as originalDam,
 
 FROM mgap.animalMapping m
-LEFT JOIN "/Internal/PMR/".study.demographics s ON (m.subjectname = s.Id)
+LEFT JOIN PMR_Data.exportedDemographics s ON (m.subjectname = s.Id)
 LEFT JOIN mgap.demographics d ON (m.subjectname = d.subjectname)
-LEFT JOIN mgap.animalMapping p1 ON (p1.subjectname = coalesce(s.Id.parents.sire, d.sire))
-LEFT JOIN mgap.animalMapping p2 ON (p2.subjectname = coalesce(s.Id.parents.dam, d.dam))
+LEFT JOIN mgap.animalMapping p1 ON (p1.subjectname = coalesce(s.sire, d.sire))
+LEFT JOIN mgap.animalMapping p2 ON (p2.subjectname = coalesce(s.dam, d.dam))
 WHERE (s.Id IS NOT NULL OR d.subjectname IS NOT NULL)

mGAP/resources/schemas/mGAP_Data.template.xml

@@ -0,0 +1,6 @@
+<templateSchema sourceSchemaName="mGAP" xmlns="http://labkey.org/data/xml/externalSchema" xmlns:cv="http://labkey.org/data/xml/queryCustomView">
+    <tables>
+        <tableName>subjectsSource</tableName>
+        <tableName>sequenceDatasetsSource</tableName>
+    </tables>
+</templateSchema>