From 865a27d434d02aeadcac901400cbbd3ec0d7ee1f Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Fri, 16 Jan 2026 16:33:16 -0800
Subject: [PATCH 1/6] Merge pull request #210 from
 bimberlabinternal/25.11_fb_sbtperf

Use query parameters in alignment_summary queries
---
 .../resources/views/bulkHaplotype.html        |  8 ++---
 GenotypeAssays/resources/views/sbtReview.html | 14 ++++++---
 .../resources/web/genotypeassays/buttons.js   |  7 ++++-
 .../genotypeassays/panel/HaplotypePanel.js    | 15 +++++----
 .../window/PublishResultsWindow.js            | 25 ++++++---------
 .../GenotypeAssaysController.java             | 13 +++++++-
 .../genotypeassays/GenotypeAssaysManager.java |  5 +--
 .../pipeline/MhcCleanupPipelineJob.java       | 31 ++++++++++++++-----
 8 files changed, 77 insertions(+), 41 deletions(-)

diff --git a/GenotypeAssays/resources/views/bulkHaplotype.html b/GenotypeAssays/resources/views/bulkHaplotype.html
index 2fe394f38..2d82ad0bf 100644
--- 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
index 2f2dff68e..695e7fd1d 100644
--- 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
index 35744801d..f2c022429 100644
--- 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
index 735ae2ac8..aacc05bdc 100644
--- 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
index 1e5d754ec..d2969f4b3 100644
--- 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
index c025e29f1..eb14a4194 100644
--- 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
index bf43c9f8b..a4425d0a0 100644
--- 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
index 7df7f1c0c..05a526ae6 100644
--- 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;

From ee229511378108e4c9727f184d8248ba58b44d60 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 20 Jan 2026 11:39:10 -0800
Subject: [PATCH 2/6] Add column for cognate CDR3s

---
 .../schemas/dbscripts/postgresql/tcrdb-15.62-15.63.sql         | 1 +
 .../schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql          | 1 +
 tcrdb/resources/schemas/tcrdb.xml                              | 3 +++
 tcrdb/src/org/labkey/tcrdb/TCRdbModule.java                    | 2 +-
 4 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.62-15.63.sql
 create mode 100644 tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql

diff --git a/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.62-15.63.sql b/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.62-15.63.sql
new file mode 100644
index 000000000..973c4e081
--- /dev/null
+++ b/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.62-15.63.sql
@@ -0,0 +1 @@
+ALTER TABLE tcrdb.clone_responses ADD COLUMN cognateCdr3s varchar(4000);
\ No newline at end of file
diff --git a/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql
new file mode 100644
index 000000000..973c4e081
--- /dev/null
+++ b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql
@@ -0,0 +1 @@
+ALTER TABLE tcrdb.clone_responses ADD COLUMN cognateCdr3s varchar(4000);
\ No newline at end of file
diff --git a/tcrdb/resources/schemas/tcrdb.xml b/tcrdb/resources/schemas/tcrdb.xml
index 0a81bc9d5..11912c1df 100644
--- a/tcrdb/resources/schemas/tcrdb.xml
+++ b/tcrdb/resources/schemas/tcrdb.xml
@@ -164,6 +164,9 @@
             <column columnName="cdr3WithSegments">
                 <columnTitle>CDR3 With Segments</columnTitle>
             </column>
+            <column columnName="cognateCdr3s">
+                <columnTitle>Cognate CDR3s</columnTitle>
+            </column>
             <column columnName="comments">
 
             </column>
diff --git a/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java b/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
index 93c758e86..6fabf709a 100644
--- a/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
+++ b/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
@@ -46,7 +46,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 15.62;
+        return 15.63;
     }
 
     @Override

From ad7ac5dece561b330034fa056c528fff0900effa Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 20 Jan 2026 12:33:27 -0800
Subject: [PATCH 3/6] Fix SQL error

---
 .../resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql
index 973c4e081..afec68ce2 100644
--- a/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql
+++ b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.62-15.63.sql
@@ -1 +1 @@
-ALTER TABLE tcrdb.clone_responses ADD COLUMN cognateCdr3s varchar(4000);
\ No newline at end of file
+ALTER TABLE tcrdb.clone_responses ADD cognateCdr3s varchar(4000);
\ No newline at end of file

From 60b329160981029b9cd33984c0b8f8a30d77c01e Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Tue, 20 Jan 2026 16:17:38 -0800
Subject: [PATCH 4/6] Add new field

---
 tcrdb/resources/queries/tcrdb/clone_responses/.qview.xml       | 1 +
 .../queries/tcrdb/clone_responses/Cohort Info.qview.xml        | 1 +
 .../schemas/dbscripts/postgresql/tcrdb-15.63-15.64.sql         | 1 +
 .../schemas/dbscripts/sqlserver/tcrdb-15.63-15.64.sql          | 1 +
 tcrdb/resources/schemas/tcrdb.xml                              | 3 +++
 tcrdb/src/org/labkey/tcrdb/TCRdbModule.java                    | 2 +-
 6 files changed, 8 insertions(+), 1 deletion(-)
 create mode 100644 tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.63-15.64.sql
 create mode 100644 tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.63-15.64.sql

diff --git a/tcrdb/resources/queries/tcrdb/clone_responses/.qview.xml b/tcrdb/resources/queries/tcrdb/clone_responses/.qview.xml
index 0ac2d820a..40599d784 100644
--- a/tcrdb/resources/queries/tcrdb/clone_responses/.qview.xml
+++ b/tcrdb/resources/queries/tcrdb/clone_responses/.qview.xml
@@ -17,6 +17,7 @@
         <column name="oddsRatio" />
         <column name="enrichmentFDR" />
         <column name="comments"/>
+        <column name="status"/>
     </columns>
     <sorts>
         <sort column="cDNA_ID" descending="false" />
diff --git a/tcrdb/resources/queries/tcrdb/clone_responses/Cohort Info.qview.xml b/tcrdb/resources/queries/tcrdb/clone_responses/Cohort Info.qview.xml
index 192d75857..d8c498918 100644
--- a/tcrdb/resources/queries/tcrdb/clone_responses/Cohort Info.qview.xml	
+++ b/tcrdb/resources/queries/tcrdb/clone_responses/Cohort Info.qview.xml	
@@ -17,6 +17,7 @@
         <column name="oddsRatio" />
         <column name="enrichmentFDR" />
         <column name="comments"/>
+        <column name="status"/>
         <column name="cDNA_ID/sortId/sampleId/allProjects/projects" />
     </columns>
     <sorts>
diff --git a/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.63-15.64.sql b/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.63-15.64.sql
new file mode 100644
index 000000000..2ba85ac8b
--- /dev/null
+++ b/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.63-15.64.sql
@@ -0,0 +1 @@
+ALTER TABLE tcrdb.clone_responses ADD COLUMN status varchar(4000);
\ No newline at end of file
diff --git a/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.63-15.64.sql b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.63-15.64.sql
new file mode 100644
index 000000000..2d8afd906
--- /dev/null
+++ b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.63-15.64.sql
@@ -0,0 +1 @@
+ALTER TABLE tcrdb.clone_responses ADD status varchar(4000);
\ No newline at end of file
diff --git a/tcrdb/resources/schemas/tcrdb.xml b/tcrdb/resources/schemas/tcrdb.xml
index 11912c1df..f0b4d71dd 100644
--- a/tcrdb/resources/schemas/tcrdb.xml
+++ b/tcrdb/resources/schemas/tcrdb.xml
@@ -167,6 +167,9 @@
             <column columnName="cognateCdr3s">
                 <columnTitle>Cognate CDR3s</columnTitle>
             </column>
+            <column columnName="status">
+                <columnTitle>Status</columnTitle>
+            </column>
             <column columnName="comments">
 
             </column>
diff --git a/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java b/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
index 6fabf709a..b2521391c 100644
--- a/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
+++ b/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
@@ -46,7 +46,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 15.63;
+        return 15.64;
     }
 
     @Override

From 0fc29ef7cde0da397f1d43840cd62752e6acaf5d Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Wed, 28 Jan 2026 11:59:29 -0800
Subject: [PATCH 5/6] Add linked schemas for PMR and mGAP

---
 .../queries/study/exportedDemographics.sql          | 13 +++++++++++++
 PMR/resources/schemas/PMR_Data.template.xml         | 12 ++++++++++++
 mGAP/resources/queries/mGAP/subjectsSource.sql      | 10 +++++-----
 mGAP/resources/schemas/mGAP_Data.template.xml       |  6 ++++++
 4 files changed, 36 insertions(+), 5 deletions(-)
 create mode 100644 PMR/resources/queries/study/exportedDemographics.sql
 create mode 100644 PMR/resources/schemas/PMR_Data.template.xml
 create mode 100644 mGAP/resources/schemas/mGAP_Data.template.xml

diff --git a/PMR/resources/queries/study/exportedDemographics.sql b/PMR/resources/queries/study/exportedDemographics.sql
new file mode 100644
index 000000000..c72b04637
--- /dev/null
+++ b/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
\ No newline at end of file
diff --git a/PMR/resources/schemas/PMR_Data.template.xml b/PMR/resources/schemas/PMR_Data.template.xml
new file mode 100644
index 000000000..a9b154c67
--- /dev/null
+++ b/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>
\ No newline at end of file
diff --git a/mGAP/resources/queries/mGAP/subjectsSource.sql b/mGAP/resources/queries/mGAP/subjectsSource.sql
index ce5a82461..39b9dae63 100644
--- a/mGAP/resources/queries/mGAP/subjectsSource.sql
+++ b/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)
\ No newline at end of file
diff --git a/mGAP/resources/schemas/mGAP_Data.template.xml b/mGAP/resources/schemas/mGAP_Data.template.xml
new file mode 100644
index 000000000..d017f79a1
--- /dev/null
+++ b/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>
\ No newline at end of file

From 555c017fae912d639187104d79d8d5fdff3b8ef6 Mon Sep 17 00:00:00 2001
From: bbimber <bbimber@gmail.com>
Date: Mon, 2 Feb 2026 09:18:03 -0800
Subject: [PATCH 6/6] Store cdr3WithProductive with response data

---
 .../schemas/dbscripts/postgresql/tcrdb-15.64-15.65.sql         | 1 +
 .../schemas/dbscripts/sqlserver/tcrdb-15.64-15.65.sql          | 1 +
 tcrdb/resources/schemas/tcrdb.xml                              | 3 +++
 tcrdb/src/org/labkey/tcrdb/TCRdbModule.java                    | 2 +-
 4 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.64-15.65.sql
 create mode 100644 tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.64-15.65.sql

diff --git a/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.64-15.65.sql b/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.64-15.65.sql
new file mode 100644
index 000000000..0e003a631
--- /dev/null
+++ b/tcrdb/resources/schemas/dbscripts/postgresql/tcrdb-15.64-15.65.sql
@@ -0,0 +1 @@
+ALTER TABLE tcrdb.clone_responses ADD COLUMN cdr3WithProductive varchar(4000);
\ No newline at end of file
diff --git a/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.64-15.65.sql b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.64-15.65.sql
new file mode 100644
index 000000000..6e8259e72
--- /dev/null
+++ b/tcrdb/resources/schemas/dbscripts/sqlserver/tcrdb-15.64-15.65.sql
@@ -0,0 +1 @@
+ALTER TABLE tcrdb.clone_responses ADD cdr3WithProductive varchar(4000);
\ No newline at end of file
diff --git a/tcrdb/resources/schemas/tcrdb.xml b/tcrdb/resources/schemas/tcrdb.xml
index f0b4d71dd..0df8f0916 100644
--- a/tcrdb/resources/schemas/tcrdb.xml
+++ b/tcrdb/resources/schemas/tcrdb.xml
@@ -164,6 +164,9 @@
             <column columnName="cdr3WithSegments">
                 <columnTitle>CDR3 With Segments</columnTitle>
             </column>
+            <column columnName="cdr3WithProductive">
+                <description>CDR3 With Productivity</description>
+            </column>
             <column columnName="cognateCdr3s">
                 <columnTitle>Cognate CDR3s</columnTitle>
             </column>
diff --git a/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java b/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
index b2521391c..a23163596 100644
--- a/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
+++ b/tcrdb/src/org/labkey/tcrdb/TCRdbModule.java
@@ -46,7 +46,7 @@ public String getName()
     @Override
     public Double getSchemaVersion()
     {
-        return 15.64;
+        return 15.65;
     }
 
     @Override