Changeset 5021

Timestamp:

Jun 26, 2009, 2:07:15 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #1340: Implement AnyToAny?.deleteStrayLinks()

The method has been implemented. It is still not called during cleanup.

Location:

trunk/src

Files:

• core/common-queries.xml (modified) (1 diff)
• core/net/sf/basedb/core/AnyToAny.java (modified) (3 diffs)
• test/TestAnyToAny.java (modified) (5 diffs)

trunk/src/core/common-queries.xml

@@ -3461 +3461 @@
     </description>
   </query>
-  <query id="SET_INTENSITYTRANSFORM_ON_BIOASSAYSETS" type="HQL">
-    <sql>
-      UPDATE BioAssaySetData bas
-      SET bas.intensityTransform = :transform
-      WHERE bas.intensityTransform IS NULL
-    </sql>
-    <description>
-      An update query that sets the intensityTransform on all 
-      bioassay sets that doesn't have a value.
+  <query id="FIND_USED_TYPES_IN_ANYTOANY" type="SQL">
+    <sql>
+      SELECT [a].[from_type] FROM [AnyToAny] [a]
+      UNION 
+      SELECT [a].[to_type] FROM [AnyToAny] [a]
+    </sql>
+    <description>
+      An SQL query that selects all used item types in any-to-any
+      links. It must select both the the 'from' and 'to' item type.
+    </description>
+  </query>
+  <query id="SELECT_STRAY_ANYTOANY" type="SQL">
+    <sql>
+      SELECT [a].[id]
+      FROM [AnyToAny] [a] 
+      LEFT JOIN [{1}] [t] 
+        ON ([t].[id] = [a].[from_id] AND [a].[from_type] = :type)
+        OR ([t].[id] = [a].[to_id] AND [a].[to_type] = :type) 
+      WHERE [t].[id] IS NULL 
+      AND ([a].[from_type] = :type OR [a].[to_type] = :type)
+    </sql>
+    <description>
+      An SQL query that selects the ID of all any-to-any links were
+      either the 'from' or 'to' item is missing. A single query
+      is used to delete all items of a specific type (both
+      'from' and 'to).
+    </description>
+  </query>
+  <query id="DELETE_STRAY_ANYTOANY" type="HQL">
+    <sql>
+      DELETE FROM AnyToAnyData
+      WHERE id IN (:ids)
+    </sql>
+    <description>
+      A HQL query that deletes all any-to-any links with the
+      id's given in the list.
     </description>
   </query>

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

@@ -22 +22 @@
 */
 package net.sf.basedb.core;
+
+import java.util.List;
+
+import org.hibernate.Hibernate;
+import org.hibernate.mapping.PersistentClass;
+import org.hibernate.mapping.Table;
 
 import net.sf.basedb.core.Transactional.Action;
@@ -28 +34 @@
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Restrictions;
+import net.sf.basedb.core.signal.ThreadSignalHandler;
 
 /**
@@ -335 +342 @@
   
   /**
-    Delete all links that are linking to non-existing applications. This method 
+    @deprecated Use {@link #deleteStrayLinks(ProgressReporter)} instead.
+  */
+  public static synchronized void deleteStrayLinks()
+  {
+    deleteStrayLinks(null);
+  }
+
+  /**
+    Delete all links that are linking to non-existing items. This method 
     is intended to be executed at regular intervals by a cleanup application.
     Although the {@link BasicItem#onBeforeCommit(Transactional.Action)} method
     tries to delete as many links as it can, it will not not delete links
     leading to items that have been deleted by Hibernate cascade.
-  */
-  public static synchronized void deleteStrayLinks()
-  {
-    
-    
-  }
-  
+    @param progress An optional progress reporter
+    @since 2.13
+  */
+  public static synchronized int deleteStrayLinks(ProgressReporter progress)
+  {
+    org.hibernate.Session session = null;
+    org.hibernate.Transaction tx = null;
+    int numDeleted = 0;
+
+    try
+    {
+      session = HibernateUtil.newSession();
+      tx = HibernateUtil.newTransaction(session);
+      
+      // Find the used items types in any-to-any links
+      if (progress != null) 
+      {
+        progress.display(5, "Finding item types used by any-to-any links...");
+      }
+      org.hibernate.Query query = HibernateUtil.getPredefinedSQLQuery(session, 
+          "FIND_USED_TYPES_IN_ANYTOANY");
+      /*
+        -- NOTE! UNION produces a distinct result by default (which is what we want)
+        SELECT [a].[from_type] FROM [AnyToAny] [a]
+        UNION 
+        SELECT [a].[to_type] FROM [AnyToAny] [a]
+      */
+      List<Integer> itemTypes = HibernateUtil.loadList(Integer.class, query, null);
+      
+      // For each item type; find and delete non-existing items
+      int index = 0;
+      int numItemTypes = itemTypes.size();
+      org.hibernate.Query deleteQuery = 
+        HibernateUtil.getPredefinedQuery(session, "DELETE_STRAY_ANYTOANY");
+      for (int itemType : itemTypes)
+      {
+        ThreadSignalHandler.checkInterrupted();
+        Item item = Item.fromValue(itemType);
+        if (progress != null)
+        {
+          int percent = 10 + (90 * index) / numItemTypes;
+          progress.display(percent, "Deleting any-to-any links referencing non-existing item: " + item);
+        }
+        PersistentClass pClass = HibernateUtil.getClassMapping(item.getDataClass().getName());
+        Table table = pClass.getTable();
+      
+        query = HibernateUtil.getPredefinedSQLQuery(session, "SELECT_STRAY_ANYTOANY", 
+            table.getName());
+        /*
+          SELECT [a].[id]
+          FROM [AnyToAny] [a] 
+          LEFT JOIN [{1}] [t] 
+            ON ([t].[id] = [a].[from_id] and [a].[from_type] = :type)
+            OR ([t].[id] = [a].[to_id] and [a].[to_type] = :type) 
+          WHERE [t].[id] is null AND ([a].[from_type = :type OR [a].[to_type] = :type)
+        */
+        query.setInteger("type", itemType);
+        List<Integer> stray = HibernateUtil.loadList(Integer.class, query, null);
+        if (stray.size() > 0)
+        {
+          deleteQuery.setParameterList("ids", stray, Hibernate.INTEGER);
+          numDeleted += HibernateUtil.executeUpdate(deleteQuery);
+        }
+        index++;
+      }
+      HibernateUtil.commit(tx);
+    }
+    catch (RuntimeException ex)
+    {
+      if (tx != null) HibernateUtil.rollback(tx);
+      throw ex;
+    }
+    finally
+    {
+      if (session != null) HibernateUtil.close(session);
+    }
+    return numDeleted;
+  }
   
   private BasicItem from;

trunk/src/test/TestAnyToAny.java

@@ -24 +24 @@
 import net.sf.basedb.core.AnyToAny;
 import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.BasicItem;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.File;
+import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemResultList;
+import net.sf.basedb.core.ProgressReporter;
 import net.sf.basedb.core.Sample;
+import net.sf.basedb.util.ConsoleProgressReporter;
 
 public class TestAnyToAny
@@ -49 +53 @@
     int fileId1 = TestFile.test_create("Linked file #1", false, true);
     int fileId2 = TestFile.test_create("Linked file #2", false, true);
-    int id = test_create(sampleId, fileId1, "first");
-    int id2 = test_create(sampleId, fileId2, "second");
+    int id = test_create(sampleId, Item.FILE, fileId1, "first", true);
+    int id2 = test_create(sampleId, Item.FILE, fileId2, "second", true);
+    // Set up test for stray links
+    int clientId = TestClient.test_create("test-stray-links", false);
+    int helpId = TestHelp.test_create(clientId, "stray-link-test", true);
+    test_create(sampleId, Item.HELP, helpId, "help", false);
     test_load(id);
-    test_list_from(sampleId, 2);
+    test_list_from(sampleId, 3);
     test_list_to(fileId1, 1);
     test_exists(sampleId, "first", true);
     test_exists(sampleId, "third", false);
+
+    // Standard test: Delete
+    if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
+    TestClient.test_delete(clientId); // Cascade deletes the help item
+    if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
     
-
-    // Extra tests:
-    if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
-
-    // Standard test: Delete
+    test_delete_stray(1);
+    test_list_from(sampleId, 2);
     test_delete(id);
     test_delete_all(sampleId, 1);
@@ -72 +82 @@
   }
 
-  static int test_create(int sampleId, int fileId, String name)
-  {
-    if (sampleId == 0 || fileId == 0) return 0;
+  static int test_create(int sampleId, Item itemType, int itemId, String name, boolean usingTo)
+  {
+    if (sampleId == 0 || itemId == 0) return 0;
     int id = 0;
     DbControl dc = null;
@@ -81 +91 @@
       dc = TestUtil.getDbControl();
       Sample s = Sample.getById(dc, sampleId);
-      File f = File.getById(dc, fileId);
-      AnyToAny a = AnyToAny.getNew(dc, s, f, name, true);
+      BasicItem item = itemType.getById(dc, itemId);
+      AnyToAny a = AnyToAny.getNew(dc, s, item, name, usingTo);
       a.setDescription("Added at "+new Date());
       dc.saveItem(a);
@@ -261 +271 @@
   }
   
+  static void test_delete_stray(int expectedResults)
+  {
+    try
+    {
+      ProgressReporter progress = TestUtil.getSilent() ? null : new ConsoleProgressReporter();
+      int deletedLinks = AnyToAny.deleteStrayLinks(progress);
+      if (expectedResults >= 0 && expectedResults != deletedLinks)
+      {
+        throw new BaseException("Expected "+expectedResults+" deletions, not "+deletedLinks);
+      }
+      if (progress != null) progress.append("\n");
+      write("--Delete stray any-to-any links OK ("+deletedLinks+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--Delete stray any-to-any links FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {}
+  }
+
+  
   static void test_exists(int sampleId, String name, boolean expected)
   {