Changeset 7290

Timestamp:

Jan 31, 2017, 1:13:44 PM (6 years ago)

Author:

Nicklas Nordborg

Message:

Merged pre-3.10 release changes back to trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• config/dist/mysql-queries.xml (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/AnnotationUtil.java (modified) (1 diff)
• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/HibernateUtil.java (modified) (1 diff)
• src/test/TestAnnotation.java (modified) (7 diffs)
• src/test/TestAnnotationType.java (modified) (1 diff)
• src/test/TestFileServer.java (modified) (2 diffs)
• src/test/data/base.onk.lu.se.crt (modified) (2 diffs)
• www/views/jobs/list_jobs.jsp (modified) (2 diffs)

trunk/config/dist/mysql-queries.xml

@@ -87 +87 @@
   </query>
 
+  <query id="PS_FIND_OVERRIDE_ID_FOR_PROJECT_ANNOTATION" type="SQL">
+    <sql>
+      UPDATE [Annotations] 
+      SET [override_id] = COALESCE(
+        (SELECT [tmp].[id] FROM (
+          SELECT [id] FROM [Annotations] 
+          WHERE [annotationset_id] = :annotationSetId
+          AND [annotationtype_id] = :annotationTypeId
+          AND [source] = 0 AND [project_id] = 0
+        ) [tmp] ) 
+        , 0)
+      WHERE id = :annotationId
+    </sql>
+    <description>
+      Updates the "override_id" column on a newly created project-specific 
+      (PRIMARY) annotation to point to the existing default annotation id
+      or 0 if no default annotation exists. To make this query work in MySQL
+      we need a double inner subselect to force a temporary table for the
+      single value we are after.
+    </description>
+  </query>
+  
+  <query id="PS_UPDATE_PROJECT_ANNOTATION_OVERRIDE_REF_INHERITED" type="HQL">
+    <sql>
+      UPDATE [Annotations] 
+      SET [override_id] = :annotationId
+      WHERE [annotationset_id] = :annotationSetId
+      AND [inherited_id] IN (
+        SELECT [tmp].[id] FROM (
+          SELECT [id] FROM [Annotations]
+          WHERE [annotationset_id] = :parentSetId
+          AND [override_id] = :parentId
+        ) [tmp]
+      )
+    </sql>
+    <description>
+      Updates the "override_id" column on project-specific annotations
+      to point to a newly created default annotation (INHERITED and 
+      CLONED annotations). The subquery will find project-specific annotation
+      on the parent annotation set that is overriding the inherited annotation.
+      
+      To make this query work in MySQL we need a double inner subselect 
+      to force a temporary table for the values we are after.
+    </description>
+  </query>
+  
+  <query id="PS_FIND_OVERRIDE_ID_FOR_PROJECT_ANNOTATION_INHERITED" type="SQL">
+    <sql>
+      UPDATE [Annotations] 
+      SET [override_id] = COALESCE(
+        (SELECT [tmp].[id] FROM (
+          SELECT [id] FROM [Annotations] 
+          WHERE [annotationset_id] = :annotationSetId
+          AND [inherited_id] = :parentOverrideId
+          AND [source] &lt;&gt; 0 
+          AND [project_id] = 0
+        ) [tmp])
+        , 0)
+      WHERE id = :annotationId
+    </sql>
+    <description>
+      Updates the "override_id" column on a newly created project-specific 
+      (CLONED or INHERITED) annotation to point to the existing default 
+      annotation id or 0 if no default annotation exists.
+      
+      To make this query work in MySQL we need a double inner subselect 
+      to force a temporary table for the values we are after.
+    </description>
+  </query>
 
+  <query id="PS_RESET_OVERRIDE_ON_PROJECT_ANNOTATIONS" type="HQL">
+    <sql>
+      UPDATE [Annotations]  
+      SET [override_id] = 0
+      WHERE [override_id] IN (:deletedAnnotations)
+      OR [inherited_id] IN (
+        SELECT [tmp].[id] FROM (
+          SELECT [id] FROM [Annotations] 
+          WHERE [override_id] IN (:deletedPrimaryAnnotations)
+        ) [tmp]
+      )
+    </sql>
+    <description>
+      Reset the "override_id" column on project-specific annotations
+      that points to a default annotation that has been removed.
+
+      To make this query work in MySQL we need a double inner subselect 
+      to force a temporary table for the values we are after.
+    </description>
+  </query>
+  
 </predefined-queries>

trunk/src/clients/web/net/sf/basedb/clients/web/AnnotationUtil.java

@@ -167 +167 @@
     // The base object has 'id', 'source', 'annotationType' and 'annotation'
     JSONObject json = new JSONObject();
-    json.put("id", ""+at.getId() + (a!=null ? "-" + a.getId() : ""));
+    String id = ""+at.getId();
+    if (a != null) id += "-" + a.getId();
+    if (inherited != null) id += "-" + inherited.getId();
+    json.put("id", id);
     // If 'a' is null this is a primary annotation that has no current values
     json.put("source", a == null ? (inherited == null ? "PRIMARY" : "INHERITED") : a.getSource().name());

trunk/src/core/common-queries.xml

@@ -3823 +3823 @@
     <description>
       Updates the "override_id" column on a newly created project-specific 
-      (PRIMARY) annotation to point to the existing default annotation id
-      or 0 if no default annotation exists.
+      (CLONED or INHERITED) annotation to point to the existing default 
+      annotation id or 0 if no default annotation exists.
     </description>
   </query>

trunk/src/core/net/sf/basedb/core/HibernateUtil.java

@@ -1402 +1402 @@
       session.flush();
     }
-    catch(HibernateException ex)
+    catch (ConstraintViolationException ex)
+    {
+      // This is the best we can do... I think...
+      throw new DatabaseException(ex.getSQLException());
+    }
+    catch (StaleStateException ex)
+    {
+      throw new ItemModifiedException(ex);
+    }
+    catch (HibernateException ex)
     {
       throw new BaseException(ex);

trunk/src/test/TestAnnotation.java

@@ -100 +100 @@
     // Test: inherit and clone annotations
     int rawBioAssayId = TestRawBioAssay.test_create(Platform.GENERIC, "genepix", null, 0, 0, 0, 0, arrayDesignId, false);
+    int rawBioAssayId2 = TestRawBioAssay.test_create(Platform.GENERIC, "genepix", null, 0, 0, 0, 0, arrayDesignId2, false);
     test_inherit_annotation(Item.RAWBIOASSAY, rawBioAssayId, intAnnotationId, false);
     int clonedId = test_inherit_annotation(Item.RAWBIOASSAY, rawBioAssayId, stringAnnotationId, true);
@@ -110 +111 @@
     // Test project specific annotations -- set a default value and a project-specific for "Project #1"
     int defaultProjectAnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId2, projectSpecificId, 0, "default value");
+    test_inherit_annotation(Item.RAWBIOASSAY, rawBioAssayId2, defaultProjectAnnotationId, false);
+    
     TestProject.test_activate_project(project1, null);
     int project1AnnotationId = test_annotatate(Item.ARRAYDESIGN, arrayDesignId2, projectSpecificId, 0, "project 1 value");
+    test_inherit_annotation(Item.RAWBIOASSAY, rawBioAssayId2, project1AnnotationId, false);
     TestProject.test_noactive_project();
+    
+    if (defaultProjectAnnotationId == project1AnnotationId)
+    {
+      write("--Create project-specific annotation value FAILED (test returns the default value");
+      ok = false;
+    }
 
     // Check that the annotation values are as expected
@@ -120 +130 @@
     TestProject.test_activate_project(project2, null);
     test_project_annotation(Item.ARRAYDESIGN, arrayDesignId2, projectSpecificId, "default value", "project 1 value");
+
+    
+    if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
+    
+    // Remove project-specific annotation
+    test_remove_annotation(Item.ARRAYDESIGN, arrayDesignId2, projectSpecificId);
     TestProject.test_noactive_project();
-    
-    if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
+    test_remove_annotation(Item.ARRAYDESIGN, arrayDesignId2, projectSpecificId);
+    
     // Remove an annotation that is inherited
     test_remove_annotation(Item.ARRAYDESIGN, arrayDesignId, intId);
@@ -128 +144 @@
     
     TestRawBioAssay.test_delete(rawBioAssayId);
+    TestRawBioAssay.test_delete(rawBioAssayId2);
 
     // Remove the annotations
@@ -184 +201 @@
         l.addAll(Arrays.asList(value));
         Unit unit = unitId != 0 ? Unit.getById(dc, unitId) : null;
-        a.setValuesIfDifferent(l, unit);
+        boolean changed = a.setValuesIfDifferent(l, unit);
+        if (changed && at.getProjectAnnotations() && dc.getSessionControl().getActiveProjectId() != a.getProjectId())
+        {
+          // We have created  a different (project-specific) annotation
+          a = as.getAnnotation(at);
+        }
       }
       dc.commit();
@@ -368 +390 @@
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tAnnotation type\tAnnotation set\tSource\tParent\tValues\tUnit\tRaw values");
-      write("-- \t-- \t---------------\t--------------\t------\t------\t------\t----\t----------");
+      write("   \tID \tAnnotation type\tAnnotation set\tSource\tProject\tParent\tValues\tUnit\tRaw values");
+      write("-- \t-- \t---------------\t--------------\t------\t-------\t------\t------\t----\t----------");
     }
   }
@@ -387 +409 @@
     }
     write(i+":\t"+a.getId()+"\t"+a.getAnnotationType()+"\t"+a.getAnnotationSet()+"\t"+
-        a.getSource()+"\t"+a.getInheritedFrom()+"\t" +
+        a.getSource()+"\t"+a.getProjectId()+"\t"+a.getInheritedFrom()+"\t" +
         values + "\t" + a.getUnit() + "\t" + a.getValues());
   }

trunk/src/test/TestAnnotationType.java

@@ -107 +107 @@
     test_delete(id_boolean);
     test_delete(id_enum);
+    test_delete(id2_enum);
     write("++Testing annotation types "+(ok ? "OK" : "Failed")+"\n");
     return ok;

trunk/src/test/TestFileServer.java

@@ -79 +79 @@
         out.close();
         fs.setServerCertificate(out.toByteArray());
+        fs.getServerX509Certificate().checkValidity();
       }
       if (clientCertificateFile != null)
@@ -87 +88 @@
         fs.setClientCertificate(out.toByteArray());
         fs.setClientCertificatePassword(clientCertificatePassword);
+        fs.getClientX509Certificate().checkValidity();
       }
       dc.saveItem(fs);

trunk/src/test/data/base.onk.lu.se.crt

@@ -1 +1 @@
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@@ -26 +26 @@
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trunk/www/views/jobs/list_jobs.jsp

@@ -196 +196 @@
         exportable="true"
       />
-      <%
-      Enumeration<String, String> jobTypes = new Enumeration<String, String>();
-      for (ItemSubtype subtype : typeQuery.list(dc))
-      {
-        jobTypes.add(Integer.toString(subtype.getId()), HTML.encodeTags(subtype.getName()));
-      }
-      %>    
       <tbl:columndef 
         id="itemSubtype"
@@ -209 +202 @@
         exportproperty="itemSubtype.name:string"
         datatype="int"
-        enumeration="<%=jobTypes%>"
+        enumeration="<%=Enumeration.fromItems(typeQuery.list(dc), "-none-")%>"
         title="Subtype"
         sortable="true"