Changeset 5734

Timestamp:

Sep 13, 2011, 11:41:48 AM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #1591: Upgrade script for BASE 2.17 --> 3.0

• The file for an image can be null, skip those when updating
• Deprecated batch importers that have been replaced with new ones (labeled extract, hybridization and scan importer). The update will disable the old plug-ins.
• Disable BioAssaySetExporter? if it is still present in the database. The plug-in no longer exists in the api.
• Remove role keys and plug-in keys for item types that no longer exists (labeled extract, hyb, scan, software type, hardware type, etc.)

Location:

trunk/src

Files:

• core/common-queries.xml (modified) (2 diffs)
• core/net/sf/basedb/core/Install.java (modified) (2 diffs)
• core/net/sf/basedb/core/PluginDefinition.java (modified) (6 diffs)
• core/net/sf/basedb/core/Update.java (modified) (8 diffs)
• core/net/sf/basedb/core/data/PluginDefinitionData.java (modified) (1 diff)
• core/net/sf/basedb/util/extensions/manager/processor/PluginInstallationProcessor.java (modified) (1 diff)
• plugins/core/core-plugins.xml (modified) (5 diffs)
• plugins/core/net/sf/basedb/plugins/batchimport/HybridizationImporter.java (modified) (1 diff)
• plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java (modified) (1 diff)
• plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java (modified) (1 diff)

trunk/src/core/common-queries.xml

@@ -3267 +3267 @@
 
 
-  <query id="DELETE_PLUGINGUICONTEXTS_ITEMTYPE" type="SQL">
-    <sql>
-      DELETE FROM PluginDefinitionGuiContexts 
-      WHERE item_type={1}
+  <query id="DELETE_PLUGINGUICONTEXTS_FOR_ITEMTYPE" type="SQL">
+    <sql>
+      DELETE FROM [PluginDefinitionGuiContexts] 
+      WHERE [item_type] = :itemType
     </sql>
     <description>
@@ -3277 +3277 @@
     </description>
   </query>
+
+  <query id="DELETE_PLUGINKEYS_FOR_ITEMTYPE" type="SQL">
+    <sql>
+      DELETE FROM [PluginKeys] 
+      WHERE [key_id] IN (
+        SELECT k.[id]
+        FROM [Keys] k
+        WHERE k.[item_type] = :itemType
+      )
+    </sql>
+    <description>
+      An SQL query that delete plug-in keys referencing keys
+      for a given item type.
+    </description>
+  </query>
+
 
   <query id="GET_SUBTYPABLE_ITEMS_FOR_SUBTYPE_OF_CLASS" type="HQL">

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

@@ -2356 +2356 @@
       dc = sessionControl.newDbControl();
       plugin = PluginDefinition.installOrUpdate(dc, info, null, shareToEveryone);
-      boolean isNew = !plugin.isInDatabase();
-      
-      if (isNew)
-      {
-        plugin.setTrusted(true);
-      }
-      dc.commit();
-      
-      if (isNew)
-      {
-        log.info("createPluginDefinition: OK [class="+className+"]");
+      if (plugin != null)
+      {
+        boolean isNew = !plugin.isInDatabase();
+        if (isNew)
+        {
+          plugin.setTrusted(true);
+        }
+        dc.commit();
+        if (isNew)
+        {
+          log.info("createPluginDefinition: OK [class="+className+"]");
+        }
+        else
+        {
+          log.info("createPluginDefinition: UPDATED [class="+className+"]");
+        }
       }
       else
       {
-        log.info("createPluginDefinition: UPDATED [class="+className+"]");
+        log.info("createPluginDefinition: SKIPPED [class="+className+"]");
       }
     }
@@ -2649 +2654 @@
       {
         log.info("createDataFileType: EXISTS [externalId="+externalId+"]");
-        /*
-        TODO #1591: Make sure that updating create proper file type links
-        if (itemSubtypes != null && schemaVersion.getSchemaVersion() < 100)
-        {
-          for (ItemSubtypeFT sft : itemSubtypes)
-          {
-            ItemSubtypeFileTypeData subtypeFile = new ItemSubtypeFileTypeData();
-            subtypeFile.setItemSubtype(sft.subtype);
-            subtypeFile.setDataFileType(fileType);
-            subtypeFile.setRequired(sft.required);
-            subtypeFile.setAllowMultiple(sft.multiple);
-            HibernateUtil.saveData(session, subtypeFile);
-          }
-        }
-        */
         HibernateUtil.commit(tx);
       }

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

@@ -376 +376 @@
   /**
     Install or update the plug-in definition with information from the info
-    object. Existing plug-ins will be updated and the disabled flag is cleared.
+    object. Existing plug-ins will be updated and the disabled flag is cleared
+    (unless it is deprecated).
     New plug-ins are configured with additional options from the info object:
     <ul>
@@ -383 +384 @@
     <li>immediate-execution: If the plug-in is allowed to bypass the job queue.
     <li>everyone-use: If the plug-in should be shared with USE permission to everyone.
+    <li>deprecated: Disable the plug-in if it is already installed, do not install
+      if it is missing
     </ul>
+    @return The plugin definition or null if no plug-in was installed
     @since 3.0
   */
@@ -390 +394 @@
     PluginDefinition plugin = null;
     String className = info.getClassName();
+    boolean deprecated = Values.getBoolean(info.getProperty("deprecated"));
     try
     {
@@ -397 +402 @@
     catch (ItemNotFoundException ex)
     {
-      plugin = PluginDefinition.getNew(dc, className, jarFile, true);
-      plugin.setMaxMemory(Values.getLong(info.getProperty("max-memory"), null));
-      plugin.setAllowImmediateExecution(Values.getBoolean(info.getProperty("immediate-execution")));
-      if (Values.getBoolean(info.getProperty("everyone-use")))
+      if (!deprecated)
       {
-        plugin.setItemKey(shareToEveryone);
+        plugin = PluginDefinition.getNew(dc, className, jarFile, true);
+        plugin.setMaxMemory(Values.getLong(info.getProperty("max-memory"), null));
+        plugin.setAllowImmediateExecution(Values.getBoolean(info.getProperty("immediate-execution")));
+        if (Values.getBoolean(info.getProperty("everyone-use")))
+        {
+          plugin.setItemKey(shareToEveryone);
+        }
+        dc.saveItem(plugin);
+        plugin.info = info; // So that we can set an ID on the info object after commit.
       }
-      dc.saveItem(plugin);
-      plugin.info = info; // So that we can set an ID on the info object after commit.
-    }
-    plugin.setAbout(info.getAbout(), true);
-    plugin.setDisabled(false);
+    }
+    if (plugin != null)
+    {
+      plugin.setAbout(info.getAbout(), true);
+      plugin.setDisabled(deprecated);
+    }
     return plugin;
   }
@@ -801 +812 @@
     Checks if this plugin is disabled or not. A disabled plugin
     can't be used.
-    @return
+    @since 3.0
   */
   public boolean isDisabled()
@@ -809 +820 @@
   
   /**
-    Disabled or enabled this plugin.
+    Disabled or enable this plugin.
+    @since 3.0
   */
   public void setDisabled(boolean disabled)

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

@@ -50 +50 @@
 import net.sf.basedb.core.data.ItemSubtypeData;
 import net.sf.basedb.core.data.PhysicalBioAssayData;
+import net.sf.basedb.core.data.PluginDefinitionData;
 import net.sf.basedb.core.data.ProjectKeyData;
 import net.sf.basedb.core.data.PropertyFilterData;
 import net.sf.basedb.core.data.ProtocolData;
+import net.sf.basedb.core.data.RoleKeyData;
 import net.sf.basedb.core.data.SchemaVersionData;
 import net.sf.basedb.core.data.UserData;
@@ -333 +335 @@
       session.delete(tmpType);
       
-      // Update the shcema version number
+      // Disable the 'BioAssaySetExporter' plug-in since it is no longer included in the code
+      query = HibernateUtil.getPredefinedQuery(session, "GET_PLUGINDEFINITION_FOR_CLASSNAME");
+      query.setString("className", "net.sf.basedb.plugins.BioAssaySetExporter");
+      PluginDefinitionData plugin = HibernateUtil.loadData(PluginDefinitionData.class, query);
+      if (plugin != null)
+      {
+        plugin.setDisabled(true);
+      }
+      
+      // Update the schema version number
       setSchemaVersion(session, schemaVersion);
   
@@ -411 +422 @@
       progress.display(30, "--Converting hybridizations to bioassays");
       Map<Integer, Integer> hybMap = copyHybridizations(session);
+      cleanContextFromProperty(session, Item.ARRAYSLIDE, "hybridization", "physicalBioAssay", false);     
       removeContext(session, HYBRIDIZATION);
-      cleanContextFromProperty(session, Item.ARRAYSLIDE, "hybridization", "physicalBioAssay", false);     
       
       progress.display(35, "--Converting scans to bioassays");
@@ -446 +457 @@
       cleanContextFromProperty(session, Item.DATAFILETYPE, "genericType", "genericType", true);
       removeContext(session, FILETYPE);
-      
+    
       // 2: remove unused columns/tables
       progress.display(80, "--Dropping old database objects");
@@ -646 +657 @@
     }
   }
-
+  
+  /**
+    Remove context-related information for the given item type.
+  */
   private static void removeContext(org.hibernate.Session session, int itemType)
   {
@@ -661 +675 @@
       {
         session.delete(ctx);
+      }
+
+      // DELETE FROM PluginDefinitionGuiContexts WHERE item_type=?
+      query = HibernateUtil.getPredefinedSQLQuery(session, 
+        "DELETE_PLUGINGUICONTEXTS_FOR_ITEMTYPE");
+      query.setInteger("itemType", itemType);
+      query.executeUpdate();
+      
+      log.debug("Removing role key for item: " + itemType);
+      // DELETE FROM PluginKeys WHERE item_type=?
+      query = HibernateUtil.getPredefinedSQLQuery(session, 
+        "DELETE_PLUGINKEYS_FOR_ITEMTYPE");
+      query.setInteger("itemType", itemType);
+      query.executeUpdate();
+
+      query = HibernateUtil.createQuery(session, "SELECT key FROM RoleKeyData key WHERE key.itemType = :itemType");
+      query.setInteger("itemType", itemType);
+      for (RoleKeyData key : HibernateUtil.loadList(RoleKeyData.class, query, null))
+      {
+        session.delete(key);
       }
       
@@ -913 +947 @@
         {
           Object[] imgRow = (Object[])it2.next();
-          
-          if (fileSet == null)
+          Integer fileId = (Integer)imgRow[2];
+          if (fileId != null)
           {
-            fileSet = new FileSetData();
-            fileSet.setItemType(Item.DERIVEDBIOASSAY.getValue());
-            session.save(fileSet);
-            bioAssay.setFileSet(fileSet);
+            if (fileSet == null)
+            {
+              fileSet = new FileSetData();
+              fileSet.setItemType(Item.DERIVEDBIOASSAY.getValue());
+              session.save(fileSet);
+              bioAssay.setFileSet(fileSet);
+            }
+            if (fileType == null)
+            {
+              // Create a temporary file type, which will be removed
+              // once the install has created the correct one
+              fileType = new DataFileTypeData();
+              fileType.setName("Temporary file type for scanned images");
+              fileType.setExternalId("tmp.image");
+              fileType.setItemType(Item.DERIVEDBIOASSAY.getValue());
+              session.save(fileType);
+            }
+            
+            FileSetMemberData member = new FileSetMemberData();
+            member.setFile(load(session, FileData.class, fileId));
+            member.setFileSet(fileSet);
+            member.setDataFileType(fileType);
+            session.save(member);
           }
-          if (fileType == null)
-          {
-            // Create a temporary file type, which will be removed
-            // once the install has created the correct one
-            fileType = new DataFileTypeData();
-            fileType.setName("Temporary file type for scanned images");
-            fileType.setExternalId("tmp.image");
-            fileType.setItemType(Item.DERIVEDBIOASSAY.getValue());
-            session.save(fileType);
-          }
-          
-          FileSetMemberData member = new FileSetMemberData();
-          member.setFile(load(session, FileData.class, imgRow[2]));
-          member.setFileSet(fileSet);
-          member.setDataFileType(fileType);
-          session.save(member);
         }
         
@@ -1456 +1493 @@
     HibernateUtil.getPredefinedSQLQuery(session, "UPDATE_ITEMTYPE", 
       "BioPlateTypes", "biomaterial_type", oldTypeS, newTypeS).executeUpdate();
-    // DELETE FROM PluginDefinitionGuiContexts WHERE item_type={1}
-    HibernateUtil.getPredefinedSQLQuery(session, 
-      "DELETE_PLUGINGUICONTEXTS_ITEMTYPE", oldTypeS).executeUpdate();
     
   }

trunk/src/core/net/sf/basedb/core/data/PluginDefinitionData.java

@@ -292 +292 @@
     If the plugin is enabled or disabled.
     // Mapped in hibernate-properties-PluginDefinitionData.xml since annotation doesn't support a default value
+    @since 3.0
   */
   public boolean isDisabled()

trunk/src/core/net/sf/basedb/util/extensions/manager/processor/PluginInstallationProcessor.java

@@ -137 +137 @@
           {
             PluginDefinition plugin = PluginDefinition.installOrUpdate(dc, info, jarFile, shareToEveryone);
-            allPlugins.put(info.getClassName(), plugin);
-            if (plugin.isInDatabase())
+            if (plugin != null)
             {
-              numUpdated++;
-            }
-            else
-            {
-              numInstalled++;
+              allPlugins.put(info.getClassName(), plugin);
+              if (plugin.isInDatabase())
+              {
+                numUpdated++;
+              }
+              else
+              {
+                numInstalled++;
+              }
             }
           }

trunk/src/plugins/core/core-plugins.xml

@@ -555 +555 @@
   </plugin-definition>
 
-  <!-- 
-  Used for backwards compatibility with older server installations
+  <!-- Used for backwards compatibility with older server installations -->
   <plugin-definition id="LabeledExtractImporter">
     <about>
-      <name>Labeled extract importer</name>
+      <name>Labeled extract importer (deprecated)</name>
       <description>
         Imports and updates labeled extracts in a batch.
@@ -567 +566 @@
     <settings>
       <property name="everyone-use">1</property>
-    </settings>
-  </plugin-definition>
-  -->
-  <!-- 
-  Used for backwards compatibility with older server installations
+      <property name="deprecated">1</property>
+    </settings>
+  </plugin-definition>
+
+  <!-- Used for backwards compatibility with older server installations -->
   <plugin-definition id="HybridizationImporter">
     <about>
-      <name>Hybridization importer</name>
+      <name>Hybridization importer (deprecated)</name>
       <description>
         Imports and updates hybridizations in a batch.
@@ -582 +581 @@
     <settings>
       <property name="everyone-use">1</property>
-    </settings>
-  </plugin-definition>
-  -->
+      <property name="deprecated">1</property>
+    </settings>
+  </plugin-definition>
+
   <plugin-definition id="PhysicalBioAssayImporter">
     <about>
@@ -598 +598 @@
   </plugin-definition>
   
-  <!-- 
-  Used for backwards compatibility with older server installations
+  <!-- Used for backwards compatibility with older server installations -->
   <plugin-definition id="ScanImporter">
     <about>
-      <name>Scan importer</name>
+      <name>Scan importer (deprecated)</name>
       <description>
         Imports and updates scans in a batch.
@@ -610 +609 @@
     <settings>
       <property name="everyone-use">1</property>
-    </settings>
-  </plugin-definition>
-  -->
+      <property name="deprecated">1</property>
+    </settings>
+  </plugin-definition>
   
   <plugin-definition id="DerivedBioAssayImporter">

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/HybridizationImporter.java

@@ -58 +58 @@
   @version 2.8
   @base.modified $Date$
+  @deprecated In 3.0, use {@link PhysicalBioAssayImporter} instead
 */
+@Deprecated
 public class HybridizationImporter
   extends AbstractItemImporter<PhysicalBioAssay>

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java

@@ -53 +53 @@
   @version 2.8
   @base.modified $Date$
+  @deprecated In 3.0, use {@link ExtractImporter} instead
 */
+@Deprecated
 public class LabeledExtractImporter
   extends AbstractItemImporter<Extract>

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ScanImporter.java

@@ -54 +54 @@
   @version 2.8
   @base.modified $Date$
+  @deprecated In 3.0, use {@link DerivedBioAssayImporter} instead
 */
+@Deprecated
 public class ScanImporter
   extends AbstractItemImporter<DerivedBioAssay>