Add sample disposition column

BimberLab · Mar 15, 2024 · 213639f · 213639f
1 parent 77aacca
commit 213639f
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Showing 9 changed files with 34 additions and 8 deletions.
diff --git a/singlecell/resources/queries/singlecell/cdna_libraries/.qview.xml b/singlecell/resources/queries/singlecell/cdna_libraries/.qview.xml
@@ -6,6 +6,7 @@
         <column name="sortId/sampleId/sampledate" />
         <column name="sortId/sampleId/stim" />
         <column name="sortId/sampleId/assayType" />
+        <column name="sortId/sampleId/disposition" />
         <column name="sortId/sampleId/tissue" />
         <column name="sortId/population" />
         <column name="sortId/replicate" />

diff --git a/singlecell/resources/queries/singlecell/cdna_libraries/Cohort Info.qview.xml b/singlecell/resources/queries/singlecell/cdna_libraries/Cohort Info.qview.xml
@@ -6,6 +6,7 @@
         <column name="sortId/sampleId/sampledate" />
         <column name="sortId/sampleId/stim" />
         <column name="sortId/sampleId/tissue" />
+        <column name="sortId/sampleId/assayType" />
         <column name="sortId/population" />
         <column name="sortId/cells" />
         <column name="sortId/hto" />

diff --git a/singlecell/resources/schemas/dbscripts/postgresql/singlecell-20.005-20.006.sql b/singlecell/resources/schemas/dbscripts/postgresql/singlecell-20.005-20.006.sql
@@ -0,0 +1 @@
+ALTER TABLE singlecell.samples ADD disposition VARCHAR(1000);
diff --git a/singlecell/resources/schemas/dbscripts/sqlserver/singlecell-20.005-20.006.sql b/singlecell/resources/schemas/dbscripts/sqlserver/singlecell-20.005-20.006.sql
@@ -0,0 +1 @@
+ALTER TABLE singlecell.samples ADD disposition VARCHAR(1000);
diff --git a/singlecell/resources/schemas/singlecell.xml b/singlecell/resources/schemas/singlecell.xml
@@ -55,6 +55,9 @@
                     <fkDisplayColumnName useRawValue="true"/>
                 </fk>
             </column>
+            <column columnName="disposition">
+                <columnTitle>Sample Disposition</columnTitle>
+            </column>
             <column columnName="assaytype">
                 <columnTitle>Assay Type</columnTitle>
                 <nullable>true</nullable>

diff --git a/singlecell/resources/web/singlecell/panel/PoolImportPanel.js b/singlecell/resources/web/singlecell/panel/PoolImportPanel.js
@@ -59,6 +59,11 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
         alwaysShow: true,
         allowBlank: false,
         transform: 'assaytype'
+    },{
+        name: 'disposition',
+        labels: ['Sample Disposition'],
+        allowRowSpan: false,
+        allowBlank: true
     },{
         name: 'tube_num',
         labels: ['Tube #', 'Stim #'],
@@ -681,6 +686,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
                 stim: r.stim,
                 celltype: r.celltype,
                 assaytype: r.assaytype || 'None',
+                disposition: r.disposition,
                 tissue: r.tissue,
                 objectId: r.objectId,
                 population: r.population,
@@ -913,6 +919,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
                     celltype: row.celltype,
                     tissue: row.tissue,
                     assaytype: row.assaytype || 'None',
+                    disposition: row.disposition,
                     objectId: guid,
                     workbook: row.workbook
                 });
@@ -1201,7 +1208,7 @@ Ext4.define('SingleCell.panel.PoolImportPanel', {
     },
 
     getSampleKey: function(data){
-        return [data.sampleId, data.subjectId, data.stim, data.assaytype, data.tissue, (Ext4.isDate(data.sampleDate) ? Ext4.Date.format(data.sampleDate, 'Y-m-d') : data.sampleDate)].join('|');
+        return [data.sampleId, data.subjectId, data.stim, data.assaytype, data.disposition, data.tissue, (Ext4.isDate(data.sampleDate) ? Ext4.Date.format(data.sampleDate, 'Y-m-d') : data.sampleDate)].join('|');
     },
 
     getSortKey: function(data){

diff --git a/singlecell/src/org/labkey/singlecell/SingleCellController.java b/singlecell/src/org/labkey/singlecell/SingleCellController.java
@@ -381,7 +381,7 @@ private static List<Map<String, Object>> parseRows(SimpleApiJsonForm form, Strin
     @RequiresPermission(ReadPermission.class)
     public static class GetMatchingSamplesAction extends ReadOnlyApiAction<SimpleApiJsonForm>
     {
-        final List<String> FIELDS = Arrays.asList("subjectId", "sampledate", "subjectid", "celltype", "tissue", "assaytype", "stim");
+        final List<String> FIELDS = Arrays.asList("subjectId", "sampledate", "subjectid", "celltype", "tissue", "assaytype", "disposition", "stim");
 
         @Override
         public Object execute(SimpleApiJsonForm form, BindException errors) throws Exception

diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
@@ -67,7 +67,7 @@ public String getName()
     @Override
     public @Nullable Double getSchemaVersion()
     {
-        return 20.005;
+        return 20.006;
     }
 
     @Override

diff --git a/singlecell/src/org/labkey/singlecell/SingleCellTableCustomizer.java b/singlecell/src/org/labkey/singlecell/SingleCellTableCustomizer.java
@@ -4,6 +4,7 @@
 import org.labkey.api.data.JdbcType;
 import org.labkey.api.data.SQLFragment;
 import org.labkey.api.data.TableInfo;
+import org.labkey.api.gwt.client.FacetingBehaviorType;
 import org.labkey.api.ldk.LDKService;
 import org.labkey.api.ldk.table.AbstractTableCustomizer;
 import org.labkey.api.query.DetailsURL;
@@ -201,11 +202,22 @@ private void customizeReadsets(AbstractTableInfo ti)
                     "END)");
             ExprColumn newCol = new ExprColumn(ti, totalCells, sql, JdbcType.INTEGER, ti.getColumn("rowid"));
             newCol.setLabel("cDNA/Total Cells");
-            UserSchema us = QueryService.get().getUserSchema(ti.getUserSchema().getUser(), (ti.getUserSchema().getContainer().isWorkbook() ? ti.getUserSchema().getContainer().getParent() : ti.getUserSchema().getContainer()), SingleCellSchema.NAME);
-            newCol.setFk(QueryForeignKey.from(us, ti.getContainerFilter())
-                    .table(SingleCellSchema.TABLE_CDNAS)
-                    .key("rowid")
-                    .display("rowid"));
+            ti.addColumn(newCol);
+        }
+
+        String assayTypes = "assayTypes";
+        if (ti.getColumn(assayTypes) == null)
+        {
+            SQLFragment sql = new SQLFragment("(SELECT ").append(
+                    ti.getSqlDialect().getGroupConcat(new SQLFragment("sm.assaytype"), true, true, new SQLFragment("','"))).append(" as expr " +
+                    " FROM " + SingleCellSchema.NAME + "." + SingleCellSchema.TABLE_CDNAS + " c " +
+                    " JOIN " + SingleCellSchema.NAME + "." + SingleCellSchema.TABLE_SORTS + " ss ON (c.sortid = ss.rowid) " +
+                    " JOIN " + SingleCellSchema.NAME + "." + SingleCellSchema.TABLE_SAMPLES + " sm ON (ss.sampleid = sm.rowid) " +
+                    " WHERE c.readsetid = " + ExprColumn.STR_TABLE_ALIAS + ".rowid OR c.tcrreadsetid = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");
+
+            ExprColumn newCol = new ExprColumn(ti, assayTypes, sql, JdbcType.VARCHAR, ti.getColumn("rowid"));
+            newCol.setLabel("cDNA/Assay Types");
+            newCol.setFacetingBehaviorType(FacetingBehaviorType.ALWAYS_OFF);
             ti.addColumn(newCol);
         }
     }
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		ALTER TABLE singlecell.samples ADD disposition VARCHAR(1000);