Changeset 3850

Timestamp:

Oct 17, 2007, 8:45:22 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #788: Select project default platforms / variant

The update must also change the value for project with 'affymetrix' as the current default
raw data type to 'platform.affymetrix'. It also sets the default platform.

Location:

trunk

Files:

• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/Update.java (modified) (3 diffs)
• www/my_base/projects/edit_project.jsp (modified) (5 diffs)

trunk/src/core/common-queries.xml

@@ -2943 +2943 @@
   </query>
 
+  <query id="GET_PROJECTS_WITH_DEFAULT" type="HQL">
+    <sql>
+      SELECT prj
+      FROM ProjectData prj
+      WHERE prj.projectDefaults[:name] = :value
+    </sql>
+    <description>
+      A HQL query that loads all projects which has a given default value
+      for a setting.
+    </description>
+  </query>
+
 
 </predefined-queries>

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

@@ -51 +51 @@
 import net.sf.basedb.core.data.PluginConfigurationData;
 import net.sf.basedb.core.data.PluginDefinitionData;
+import net.sf.basedb.core.data.ProjectData;
 import net.sf.basedb.core.data.RawBioAssayData;
 import net.sf.basedb.core.data.SchemaVersionData;
@@ -1663 +1664 @@
     <li>Set a platform for array designs and raw bioassays
     <li>Change experiment raw data type if it is "affymetrix" to "platform.affymetrix"
+    <li>Change project default raw data type if it is "affymetrix" to "platform.affymetrix"
     <li>Move CEL and CDF files into FileSet:s
     <li>Remove filters on ArrayDesign.isAffyChip property
@@ -1772 +1774 @@
       query.setString("newRawDataType", affyRaw.getId());
       HibernateUtil.executeUpdate(query);
-      
+    
+      // Change raw data type for 'affymetrix' projects to 'platform.affymetrix'
+      query = HibernateUtil.getPredefinedQuery(session, 
+        "GET_PROJECTS_WITH_DEFAULT");
+      /**
+        SELECT prj
+        FROM ProjectData prj
+        WHERE prj.projectDefaults[:name] = :value
+      */
+      query.setString("name", "raw_data_type");
+      query.setString("value", "affymetrix");
+      List<ProjectData> projects = HibernateUtil.loadList(ProjectData.class, query);
+      for (ProjectData project : projects)
+      {
+        Project p = dc.getItem(Project.class, project);
+        p.setDefaultRawDataType(affyRaw);
+        p.setDefaultItem(dc, affymetrix, Project.Default.PLATFORM);
+      }
+    
       // Update property filters on 'rawDataType=affymetrix' to 'platform.affymetrix'
       query = HibernateUtil.getPredefinedSQLQuery(session, 

trunk/www/my_base/projects/edit_project.jsp

@@ -110 +110 @@
   Platform currentPlatform = null;
   PlatformVariant currentVariant = null;
+  RawDataType currentRawDataType = null;
   
   if (itemId == 0)
@@ -121 +122 @@
     cc.setObject("item", project);
     title = "Edit project -- " + HTML.encodeTags(project.getName());
+    currentRawDataType = project.getDefaultRawDataType();
     
     try
@@ -126 +128 @@
       currentPlatform = (Platform)project.getDefaultItem(dc, Project.Default.PLATFORM);
       currentVariant = (PlatformVariant)project.getDefaultItem(dc, Project.Default.PLATFORM_VARIANT);
+      if (currentRawDataType != null)
+      {
+        if (currentPlatform == null) currentPlatform = currentRawDataType.getPlatform(dc);
+        if (currentVariant == null) currentVariant = currentRawDataType.getVariant(dc);
+      }
     }
     catch (PermissionDeniedException ex)
@@ -131 +138 @@
       deniedPlatform = true;
     }
+    
+    if (currentRawDataType == null && currentVariant != null) currentRawDataType = currentVariant.getRawDataType();
+    if (currentRawDataType == null && currentPlatform != null) currentRawDataType = currentPlatform.getRawDataType();
+    if (currentRawDataType == null) currentRawDataType = project.getDefaultRawDataType();
     
     groupQuery = project.getGroups();
@@ -141 +152 @@
     throw new PermissionDeniedException(Permission.WRITE, itemType.toString());
   }
-  RawDataType currentRawDataType = project != null ? 
-    project.getDefaultRawDataType() : null;
   
   ItemQuery<Platform> platformQuery = Platform.getQuery();