Add field to show if readset has raw reads archived

Author: bbimber

SequenceAnalysis/resources/queries/sequenceanalysis/sequence_readsets/SRA Info.qview.xml

@@ -0,0 +1,25 @@
+<customView xmlns="http://labkey.org/data/xml/queryCustomView" label="SRA Info" canOverride="true">
+   <columns>
+       <column name="rowid" />
+       <column name="name" />
+       <column name="subjectid" />
+       <column name="sampledate"/>
+       <column name="platform" />
+       <column name="librarytype" />
+       <column name="application" />
+       <column name="sampletype" />
+       <column name="comments" />
+
+       <column name="runIds"/>
+       <column name="jobIds"/>
+       <column name="created" />
+       <column name="status" />
+       <column name="workbook" />
+       <column name="sraRuns" />
+       <column name="isArchived" />
+       <column name="files" />
+   </columns>
+   <sorts>
+       <sort column="rowid" descending="true"/>
+   </sorts>
+</customView>

SequenceAnalysis/src/org/labkey/sequenceanalysis/query/SequenceAnalysisUserSchema.java

@@ -262,6 +262,15 @@ public void renderGridCellContents(RenderContext ctx, Writer out) throws IOExcep
             ret.addColumn(newCol3);
         }
 
+        if (ret.getColumn("isArchived") == null)
+        {
+            SQLFragment sql = new SQLFragment("CASE WHEN (select count(*) as expr from " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_READ_DATA + " rd where rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid and rd.archived = " + ret.getSqlDialect().getBooleanTRUE() + ") > 0 THEN " + ret.getSqlDialect().getBooleanTRUE() + " ELSE " + ret.getSqlDialect().getBooleanFALSE() + " END");
+            ExprColumn newCol = new ExprColumn(ret, "isArchived", sql, JdbcType.INTEGER, sourceTable.getColumn("rowid"));
+            newCol.setURL(DetailsURL.fromString("/query/executeQuery.view?schemaName=sequenceanalysis&query.queryName=readData&query.readset~eq=${rowid}"));
+            newCol.setLabel("Archived To SRA?");
+            ret.addColumn(newCol);
+        }
+
         if (ret.getColumn("totalAlignments") == null)
         {
             SQLFragment sql = new SQLFragment("(SELECT COUNT(rd.rowid) FROM " + SequenceAnalysisSchema.SCHEMA_NAME + "." + SequenceAnalysisSchema.TABLE_ANALYSES + " rd WHERE rd.readset = " + ExprColumn.STR_TABLE_ALIAS + ".rowid)");