Add calculated columns

Author: bbimber

tcrdb/src/org/labkey/tcrdb/TCRdbModule.java

@@ -72,6 +72,8 @@ protected void doStartupAfterSpringConfig(ModuleContext moduleContext)
         LaboratoryService.get().registerTableCustomizer(this, TCRdbTableCustomizer.class, TCRdbSchema.SEQUENCE_ANALYSIS, "sequence_readsets");
         LaboratoryService.get().registerTableCustomizer(this, TCRdbTableCustomizer.class, TCRdbSchema.SEQUENCE_ANALYSIS, "sequence_analyses");
         LaboratoryService.get().registerTableCustomizer(this, TCRdbTableCustomizer.class, TCRdbSchema.NAME, TCRdbSchema.TABLE_CLONES);
+        LaboratoryService.get().registerTableCustomizer(this, TCRdbTableCustomizer.class, TCRdbSchema.NAME, TCRdbSchema.TABLE_CLONE_RESPONSES);
+        LaboratoryService.get().registerTableCustomizer(this, TCRdbTableCustomizer.class, TCRdbSchema.NAME, TCRdbSchema.TABLE_STIM_EXPERIMENTS);
         LaboratoryService.get().registerTableCustomizer(this, TCRdbTableCustomizer.class, TCRdbSchema.SINGLE_CELL, TCRdbSchema.TABLE_CDNAS);
 
         LDKService.get().registerQueryButton(new ChangeStatusButton(), TCRdbSchema.SINGLE_CELL, "samples");

tcrdb/src/org/labkey/tcrdb/TCRdbTableCustomizer.java

@@ -12,13 +12,15 @@
 import org.labkey.api.data.SimpleFilter;
 import org.labkey.api.data.Table;
 import org.labkey.api.data.TableInfo;
+import org.labkey.api.data.WrappedColumn;
 import org.labkey.api.exp.api.ExpProtocol;
 import org.labkey.api.laboratory.LaboratoryService;
 import org.labkey.api.ldk.LDKService;
 import org.labkey.api.ldk.table.AbstractTableCustomizer;
 import org.labkey.api.query.DetailsURL;
 import org.labkey.api.query.ExprColumn;
 import org.labkey.api.query.FieldKey;
+import org.labkey.api.query.QueryForeignKey;
 import org.labkey.api.query.QueryService;
 
 import java.util.Arrays;
@@ -48,6 +50,14 @@ else if (matches(ti, TCRdbSchema.NAME, TCRdbSchema.TABLE_CLONES))
             {
                 customizeClones(ti);
             }
+            else if (matches(ti, TCRdbSchema.NAME, TCRdbSchema.TABLE_CLONE_RESPONSES))
+            {
+                customizeCloneResponses(ti);
+            }
+            else if (matches(ti, TCRdbSchema.NAME, TCRdbSchema.TABLE_STIM_EXPERIMENTS))
+            {
+                customizeStims(ti);
+            }
             else if (ti instanceof AssayResultTable)
             {
                 customizeAssayData(ti);
@@ -223,6 +233,34 @@ private void addClonotypeForLocusCol(AbstractTableInfo ti, SQLFragment selectSql
         ti.addColumn(newCol);
     }
 
+    private void customizeCloneResponses(AbstractTableInfo ti)
+    {
+        if (ti.getColumn("stimId") == null)
+        {
+            WrappedColumn col = new WrappedColumn(ti.getColumn("cDNA_ID"), "stimId");
+            col.setReadOnly(true);
+            col.setUserEditable(false);
+            col.setLabel("Stim Experiment");
+            col.setFk(new QueryForeignKey(ti.getUserSchema(), null, ti.getUserSchema(), null, TCRdbSchema.TABLE_STIM_EXPERIMENTS, "cdna_id", "cdna_id"));
+
+            ti.addColumn(col);
+        }
+    }
+
+    private void customizeStims(AbstractTableInfo ti)
+    {
+        if (ti.getColumn("controlStim") == null)
+        {
+            WrappedColumn col = new WrappedColumn(ti.getColumn("controlStimId"), "controlStim");
+            col.setReadOnly(true);
+            col.setUserEditable(false);
+            col.setLabel("Control Stim Info");
+            col.setFk(new QueryForeignKey(ti.getUserSchema(), null, ti.getUserSchema(), null, TCRdbSchema.TABLE_STIM_EXPERIMENTS, "cdna_id", "cdna_id"));
+
+            ti.addColumn(col);
+        }
+    }
+
     private void customizeClones(AbstractTableInfo ti)
     {
         LDKService.get().applyNaturalSort(ti, "cloneName");

tcrdb/src/org/labkey/tcrdb/TCRdbUserSchema.java

@@ -6,6 +6,7 @@
 import org.labkey.api.data.ContainerFilter;
 import org.labkey.api.data.DbSchema;
 import org.labkey.api.data.TableInfo;
+import org.labkey.api.ldk.table.ContainerScopedTable;
 import org.labkey.api.ldk.table.SharedDataTable;
 import org.labkey.api.module.Module;
 import org.labkey.api.query.DefaultSchema;
@@ -43,9 +44,12 @@ protected TableInfo createWrappedTable(String name, @NotNull TableInfo sourceTab
     {
         if (TCRdbSchema.TABLE_MIXCR_LIBRARIES.equalsIgnoreCase(name))
         {
-            // TODO: assert cf is null or not default?
             return new SharedDataTable<>(this, sourceTable).init();
         }
+        else if (TCRdbSchema.TABLE_STIM_EXPERIMENTS.equalsIgnoreCase(name))
+        {
+            return new ContainerScopedTable<>(this, sourceTable, null, "cdna_id").init();
+        }
 
         return super.createWrappedTable(name, sourceTable, cf);
     }