Changeset 1503

Timestamp:

Jan 18, 2012, 1:10:02 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #334: Use item subtypes - step 2

Make sure that the subtype id has been loaded before it is used by a filter. Otherwise the query will not find any items.

Location:

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie

Files:

• dao/Case.java (modified) (4 diffs)
• dao/Patient.java (modified) (1 diff)
• dao/SpecimenTube.java (modified) (5 diffs)
• dao/Subtype.java (modified) (2 diffs)
• servlet/PersonalRegistrationServlet.java (modified) (1 diff)
• servlet/SampleReportServlet.java (modified) (1 diff)

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Case.java

@@ -49 +49 @@
     // Look for a case with the given name (primary case)
     ItemQuery<Sample> caseQuery = Sample.getQuery();
-    Subtype.CASE.addFilter(caseQuery);
+    Subtype.CASE.addFilter(dc, caseQuery);
     caseQuery.restrict(Restrictions.eq(Hql.property("name"), Expressions.parameter("name", name, Type.STRING)));
     List<Sample> cases = caseQuery.list(dc);
@@ -67 +67 @@
       merged = true;
       caseQuery = Sample.getQuery();
-      Subtype.CASE.addFilter(caseQuery);
+      Subtype.CASE.addFilter(dc, caseQuery);
       caseQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
       caseQuery.join(Hql.innerJoin("cce", "event", "evt"));
       caseQuery.join(Hql.innerJoin("evt", "bioMaterial", "sp")); // 'sp' should now reference a specimen tube
-      Subtype.SPECIMEN.addFilter(caseQuery, "sp");
+      Subtype.SPECIMEN.addFilter(dc, caseQuery, "sp");
       caseQuery.restrict(Restrictions.like(Hql.property("sp", "name"), Expressions.parameter("name", name + ".%", Type.STRING)));
       caseQuery.setDistinct(true);
@@ -92 +92 @@
         AnnotationType reasonIfNoSpecimenType = Reggie.findAnnotationType(dc, Item.SAMPLE, Reggie.ANNOTATION_REASON_IF_NO_SPECIMEN, true);
         caseQuery = Sample.getQuery();
-        Subtype.CASE.addFilter(caseQuery);
+        Subtype.CASE.addFilter(dc, caseQuery);
         caseQuery.restrict(Annotations.like(null, reasonIfNoSpecimenType, "[" + name + "]%", false));
         cases = caseQuery.list(dc);
@@ -126 +126 @@
   {
     ItemQuery<Sample> caseQuery = patient.getBioSource().getSamples();
-    Subtype.CASE.addFilter(caseQuery);
+    Subtype.CASE.addFilter(dc, caseQuery);
     caseQuery.include(Include.ALL);
     caseQuery.order(Orders.asc(Hql.property("name")));

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Patient.java

@@ -38 +38 @@
     AnnotationType pnrType = Reggie.findAnnotationType(dc, Item.BIOSOURCE, Reggie.ANNOTATION_PERSONAL_NUMBER, true);
     ItemQuery<BioSource> patientQuery = BioSource.getQuery();
-    Subtype.PATIENT.addFilter(patientQuery);
+    Subtype.PATIENT.addFilter(dc, patientQuery);
     patientQuery.restrict(Annotations.eq(null, pnrType, pnr, false));
     List<BioSource> patients = patientQuery.list(dc);

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/SpecimenTube.java

@@ -38 +38 @@
   {
     ItemQuery<Sample> specimenQuery = theCase.getSample().getChildSamples();
-    Subtype.SPECIMEN.addFilter(specimenQuery);
+    Subtype.SPECIMEN.addFilter(dc, specimenQuery);
     if (limitToOriginal)
     {
@@ -63 +63 @@
   {
     ItemQuery<Sample> specimenQuery = Sample.getQuery();
-    Subtype.SPECIMEN.addFilter(specimenQuery);
+    Subtype.SPECIMEN.addFilter(dc, specimenQuery);
     specimenQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.parameter("name", name + ".%", Type.STRING)));
     specimenQuery.order(Orders.asc(Hql.property("name")));
@@ -85 +85 @@
     
     ItemQuery<Sample> tubeQuery = Sample.getQuery();
-    Subtype.SPECIMEN.addFilter(tubeQuery);
+    Subtype.SPECIMEN.addFilter(dc, tubeQuery);
     tubeQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string(tubeName)));
     tubeQuery.order(Orders.desc(Hql.property("name")));       
@@ -114 +114 @@
     
     ItemQuery<Sample> tubeQuery = Sample.getQuery();
-    Subtype.SPECIMEN.addFilter(tubeQuery);
+    Subtype.SPECIMEN.addFilter(dc, tubeQuery);
     tubeQuery.restrict(Restrictions.eq(Hql.property("originalQuantity"), null));
     tubeQuery.order(Orders.desc(Hql.property("id")));
     tubeQuery.include(Include.ALL);
     tubeQuery.exclude(Include.REMOVED);
-    
     List<Sample> tubes = tubeQuery.list(dc);
     for (Sample tube : tubes)
@@ -125 +124 @@
       BioWell well = tube.getBioWell();
       String boxNamePrefix = null;
+
       if (well != null)
       {

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Subtype.java

@@ -110 +110 @@
     @since 2.1
   */
-  public void addFilter(ItemQuery<? extends Subtypable> query)
+  public void addFilter(DbControl dc, ItemQuery<? extends Subtypable> query)
   {
-    addFilter(query, null);
+    addFilter(dc, query, null);
   }
 
@@ -127 +127 @@
     @since 2.1
   */
-  public void addFilter(ItemQuery<? extends Subtypable> query, String alias)
+  public void addFilter(DbControl dc, ItemQuery<? extends Subtypable> query, String alias)
   {
+    if (id==0) load(dc); // Ensure that the subtype has been loaded
     query.restrict(Restrictions.eq(Hql.property(alias, "itemSubtype"), Expressions.integer(id)));
   }

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

@@ -193 +193 @@
           // No patient was found -- try to find the highest existing patient number
           ItemQuery<BioSource> patientQuery = BioSource.getQuery();
-          Subtype.PATIENT.addFilter(patientQuery);
+          Subtype.PATIENT.addFilter(dc, patientQuery);
           patientQuery.restrict(Restrictions.like(Hql.property("name"), Expressions.string("PAT%")));
           patientQuery.order(Orders.desc(Hql.property("name")));

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

@@ -112 +112 @@
         
         sampleQuery.restrict(Restrictions.and(restr));
-        Subtype.SPECIMEN.addFilter(sampleQuery);
+        Subtype.SPECIMEN.addFilter(dc, sampleQuery);
 
         sampleQuery.include(Include.ALL);