Changeset 4979

Timestamp:

Sep 24, 2018, 11:38:50 AM (4 years ago)

Author:

Nicklas Nordborg

Message:

References #1054: Even more functionality in the Flagged alignment wizard

When a RNA is selected for DoNotUse we should also find the corresponding DNA and FlowThrough. This is done by looking for the other items that have the same Lysate parent and same Qiacube date and run number.

File:

• extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/GenotypeServlet.java (modified) (3 diffs)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/GenotypeServlet.java

@@ -38 +38 @@
 import net.sf.basedb.core.SimpleProgressReporter;
 import net.sf.basedb.core.Subtypable;
+import net.sf.basedb.core.Type;
 import net.sf.basedb.core.query.Annotations;
 import net.sf.basedb.core.query.Expressions;
@@ -506 +507 @@
         ItemList flaggedAlignments = BiomaterialList.FLAGGED_ALIGNMENT.get(dc);
         
+        ItemQuery<Extract> dnaFtQuery = Extract.getQuery();
+        dnaFtQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
+        // We find ALL child items to a specific Lysate with the same Qiacube date and run number
+        dnaFtQuery.join(Hql.innerJoin("parent", "lys"));
+        dnaFtQuery.join(Annotations.innerJoin(Annotationtype.QIACUBE_DATE.load(dc), "qcDate"));
+        dnaFtQuery.join(Annotations.innerJoin(Annotationtype.QIACUBE_RUN_NO.load(dc), "qcRun"));
+        dnaFtQuery.restrict(Restrictions.eq(Hql.alias("lys"), Hql.entityParameter("lysate", Item.EXTRACT)));
+        dnaFtQuery.restrict(Restrictions.eq(Hql.alias("qcDate"), Expressions.parameter("qcDate", Type.DATE)));
+        dnaFtQuery.restrict(Restrictions.eq(Hql.alias("qcRun"), Expressions.parameter("qcRun", Type.INT)));
+        
         GenoTypeChecker checker = new GenoTypeChecker();
         checker.preloadVcfForFlaggedAlignments(dc);
@@ -547 +558 @@
           // Load all downstream items (by matching the name)
           List<BasicItem> allChildItems = getAllChildItems(dc, rootItem);
+          if ("RNA".equals(doNotUse))
+          {
+            Extract rna = (Extract)rootItem;
+            Extract lysate = (Extract)rna.getParent();
+            Date qcDate = (Date)Annotationtype.QIACUBE_DATE.getAnnotationValue(dc, rna);
+            Integer qcRun = (Integer)Annotationtype.QIACUBE_RUN_NO.getAnnotationValue(dc, rna);
+            // Also include DNA and FlowThrough from the same Qiacube run
+            if (lysate != null && qcDate != null && qcRun != null)
+            {
+              dnaFtQuery.setEntityParameter("lysate", lysate);
+              dnaFtQuery.setParameter("qcDate", qcDate, Type.DATE);
+              dnaFtQuery.setParameter("qcRun", qcRun, Type.INT);
+              for (Extract e : dnaFtQuery.list(dc))
+              {
+                if (!e.equals(rootItem)) // The query return all children for the lysate but we do not need to process the RNA twice
+                {
+                  List<BasicItem> dnaFtItems = getAllChildItems(dc, e);
+                  allChildItems.addAll(dnaFtItems);
+                  jsonDebug.add("[Debug]Added " + dnaFtItems.size() + " items related to " + e);
+                }
+              }
+            }
+          }
           
           for (BasicItem basicItem : allChildItems)