Merge pull request #210 from bimberlabinternal/25.11_fb_sbtperf

bbimber · web-flow · commit 865a27d434d0 · 2026-01-16T16:33:16.000-08:00
Use query parameters in alignment_summary queries
diff --git a/GenotypeAssays/resources/views/bulkHaplotype.html b/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);
diff --git a/GenotypeAssays/resources/views/sbtReview.html b/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',
diff --git a/GenotypeAssays/resources/web/genotypeassays/buttons.js b/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();
         }
diff --git a/GenotypeAssays/resources/web/genotypeassays/panel/HaplotypePanel.js b/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 = {};
diff --git a/GenotypeAssays/resources/web/genotypeassays/window/PublishResultsWindow.js b/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
             },
diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysController.java b/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)
diff --git a/GenotypeAssays/src/org/labkey/genotypeassays/GenotypeAssaysManager.java b/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
diff --git a/primeseq/src/org/labkey/primeseq/pipeline/MhcCleanupPipelineJob.java b/primeseq/src/org/labkey/primeseq/pipeline/MhcCleanupPipelineJob.java
@@ -283,7 +283,11 @@ private void processAnalysis(int analysisId)
                 final Map<String, Double> existingData = new HashMap<>();
                 SimpleFilter dataFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
                 dataFilter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getLineageThreshold(), CompareType.GT);
-                new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null).forEachResults(rs -> {
+
+                TableSelector ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null);
+                ts.setNamedParameters(Map.of("AnalysisId", analysisId));
+
+                ts.forEachResults(rs -> {
                     existingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
                 });
 
@@ -311,7 +315,10 @@ private void processAnalysis(int analysisId)
                     SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
                     filter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getLineageThreshold(), CompareType.LT);
 
-                    List<String> lowFreqRowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
+                    ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("rowids"), filter, null);
+                    ts.setNamedParameters(Map.of("AnalysisId", analysisId));
+
+                    List<String> lowFreqRowIdList = ts.getArrayList(String.class);
                     if (!lowFreqRowIdList.isEmpty())
                     {
                         getJob().getLogger().info("Analysis: " + analysisId + ", low freq lineages: " + lowFreqRowIdList.size());
@@ -329,7 +336,9 @@ private void processAnalysis(int analysisId)
                     SimpleFilter filter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
                     filter.addCondition(FieldKey.fromString("percent_from_locus"), getPipelineJob().getAlleleGroupThreshold(), CompareType.LT);
 
-                    List<String> lowFreqRowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
+                    ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null);
+                    ts.setNamedParameters(Map.of("AnalysisId", analysisId));
+                    List<String> lowFreqRowIdList = ts.getArrayList(String.class);
                     if (!lowFreqRowIdList.isEmpty())
                     {
                         getJob().getLogger().info("Analysis: " + analysisId + ", low freq allele groups: " + lowFreqRowIdList.size());
@@ -363,7 +372,9 @@ private void processAnalysis(int analysisId)
                     filter.addCondition(FieldKey.fromString("totalLineages"), 1, CompareType.GT);
                     filter.addCondition(FieldKey.fromString("loci"), "MHC", CompareType.CONTAINS);
 
-                    List<String> rowIdList = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null).getArrayList(String.class);
+                    ts  = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), filter, null);
+                    ts.setNamedParameters(Map.of("AnalysisId", analysisId));
+                    List<String> rowIdList = ts.getArrayList(String.class);
                     if (!rowIdList.isEmpty())
                     {
                         getJob().getLogger().info("Analysis: " + analysisId + ", multi-lineage records: " + rowIdList.size());
@@ -380,7 +391,9 @@ private void processAnalysis(int analysisId)
                 {
                     SimpleFilter nAlignmentFilter = new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId, CompareType.EQUAL);
                     nAlignmentFilter.addCondition(FieldKey.fromString("nAlignments"), 1, CompareType.GT);
-                    List<String> redundantAlignmentSets = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), nAlignmentFilter, null).getArrayList(String.class);
+                    ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("rowids"), nAlignmentFilter, null);
+                    ts.setNamedParameters(Map.of("AnalysisId", analysisId));
+                    List<String> redundantAlignmentSets = ts.getArrayList(String.class);
                     if (!redundantAlignmentSets.isEmpty())
                     {
                         getJob().getLogger().info("Analysis: " + analysisId + ", redundant alignment sets: " + redundantAlignmentSets.size());
@@ -446,7 +459,9 @@ private void processAnalysis(int analysisId)
 
                 // verify ending data:
                 final Map<String, Double> endingData = new HashMap<>();
-                new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null).forEachResults(rs -> {
+                ts = new TableSelector(QueryService.get().getUserSchema(getJob().getUser(), getJob().getContainer(), "sequenceanalysis").getTable("alignment_summary_by_lineage"), PageFlowUtil.set("lineages", "percent_from_locus"), dataFilter, null);
+                ts.setNamedParameters(Map.of("AnalysisId", analysisId));
+                ts.forEachResults(rs -> {
                     endingData.put(rs.getString(FieldKey.fromString("lineages")), rs.getDouble(FieldKey.fromString("percent_from_locus")));
                 });
 
@@ -515,7 +530,9 @@ public AlignmentGroupCompare(final int analysisId, Container c, User u)
         {
             this.analysisId = analysisId;
 
-            new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null).forEachResults(rs -> {
+            TableSelector ts = new TableSelector(QueryService.get().getUserSchema(u, c, "sequenceanalysis").getTable("alignment_summary_grouped"), PageFlowUtil.set("analysis_id", "alleles", "lineages", "totalLineages", "total_reads", "total_forward", "total_reverse", "valid_pairs", "rowids"), new SimpleFilter(FieldKey.fromString("analysis_id"), analysisId), null);
+            ts.setNamedParameters(Map.of("AnalysisId", analysisId));
+            ts.forEachResults(rs -> {
                 if (rs.getString(FieldKey.fromString("alleles")) == null)
                 {
                     return;

Original file line number	Diff line number	Diff line change
`@@ -133,7 +133,7 @@ public ApiResponse execute(CacheAnalysesForm form, BindException errors)`
`133`	`133`	`}`
`134`	`134`
`135`	`135`	`String[] alleleNames = Arrays.stream(form.getAlleleNames()).map(StringEscapeUtils::unescapeHtml4).toArray(String[]::new);`
`136`		`- Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), protocol, alleleNames);`
	`136`	`+ Pair<List<Long>, List<Long>> ret = GenotypeAssaysManager.get().cacheAnalyses(getViewContext(), form.getAnalysisId(), protocol, alleleNames);`
`137`	`137`	`resultProperties.put("runsCreated", ret.first);`
`138`	`138`	`resultProperties.put("runsDeleted", ret.second);`
`139`	`139`	`}`
`@@ -159,6 +159,7 @@ public static class CacheAnalysesForm`
`159`	`159`	`{`
`160`	`160`	`private String[] _alleleNames;`
`161`	`161`	`private String _json;`
	`162`	`+ private int _analysisId;`
`162`	`163`	`private int _protocolId;`
`163`	`164`
`164`	`165`	`public String[] getAlleleNames()`
`@@ -190,6 +191,16 @@ public void setJson(String json)`
`190`	`191`	`{`
`191`	`192`	`_json = json;`
`192`	`193`	`}`
	`194`	`+`
	`195`	`+ public int getAnalysisId()`
	`196`	`+ {`
	`197`	`+ return _analysisId;`
	`198`	`+ }`
	`199`	`+`
	`200`	`+ public void setAnalysisId(int analysisId)`
	`201`	`+ {`
	`202`	`+ _analysisId = analysisId;`
	`203`	`+ }`
`193`	`204`	`}`
`194`	`205`
`195`	`206`	`@RequiresPermission(UpdatePermission.class)`
Original file line number	Diff line number	Diff line change
`@@ -90,8 +90,7 @@ public static GenotypeAssaysManager get()`
`90`	`90`	`return _instance;`
`91`	`91`	`}`
`92`	`92`
`93`		`-`
`94`		`- public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException`
	`93`	`+ public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final int analysisId, final ExpProtocol protocol, String[] pks) throws IllegalArgumentException`
`95`	`94`	`{`
`96`	`95`	`final User u = ctx.getUser();`
`97`	`96`	`final List<Long> runsCreated = new ArrayList<>();`
`@@ -126,6 +125,8 @@ public Pair<List<Long>, List<Long>> cacheAnalyses(final ViewContext ctx, final E`
`126`	`125`
`127`	`126`	`AtomicInteger records = new AtomicInteger();`
`128`	`127`	`TableSelector tsAlignments = new TableSelector(tableAlignments, cols.values(), new SimpleFilter(FieldKey.fromString("key"), Arrays.asList(pks), CompareType.IN), null);`
	`128`	`+ tsAlignments.setNamedParameters(Map.of("AnalysisId", analysisId));`
	`129`	`+`
`129`	`130`	`tsAlignments.forEach(new Selector.ForEachBlock<ResultSet>()`
`130`	`131`	`{`
`131`	`132`	`@Override`