Changeset 6578

Timestamp:

Oct 24, 2014, 2:15:15 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #1873: Deleting child biomaterial doesn't return the used quantity to the parent

There is no a onetimefix script for fixing this. After updating BASE it should be executed (from the bin directory):

onetimefix.sh remaining_quantity -u <root login> -p <root pwd> 

where login and password is for the root user account in BASE.

Location:

branches/3.3-stable/src

Files:

• core/net/sf/basedb/core/Update.java (modified) (3 diffs)
• install/net/sf/basedb/install/OneTimeFix.java (modified) (2 diffs)

branches/3.3-stable/src/core/net/sf/basedb/core/Update.java

@@ -40 +40 @@
 import org.hibernate.mapping.PersistentClass;
 import org.hibernate.mapping.Table;
+
 
 
@@ -74 +75 @@
 import net.sf.basedb.core.data.ItemSubtypeData;
 import net.sf.basedb.core.data.JobData;
+import net.sf.basedb.core.data.MeasuredBioMaterialData;
 import net.sf.basedb.core.data.PhysicalBioAssayData;
 import net.sf.basedb.core.data.ProjectData;
@@ -1067 +1069 @@
   
   
+  /**
+    Vefify and update the remaining quantity of all biomaterials.
+    @return The number of biomaterial fixed
+  */
+  public static int recalculateRemainingQuantity(ProgressReporter progress)
+    throws BaseException
+  {
+    org.hibernate.Session session = null;
+    org.hibernate.Transaction tx = null;
+    int numUpdated = 0;
+    try
+    {
+      session = HibernateUtil.newSession();
+      tx = HibernateUtil.newTransaction(session);
+      
+      // For temporary storing the new remaining quantities
+      Map<Integer, Double> remaining = new HashMap<Integer, Double>(); 
+      
+      // Load used quantity for all events
+      org.hibernate.Query eventQuery = HibernateUtil.createQuery(session, 
+        "SELECT evt.bioMaterial.id, evt.usedQuantity FROM BioMaterialEventData evt WHERE NOT evt.usedQuantity IS NULL");
+      
+      // Load used quantity for sources to all events
+      org.hibernate.Query sourcesQuery = HibernateUtil.createQuery(session, 
+        "SELECT src.bioMaterial.id, src.usedQuantity FROM BioMaterialEventSourceData src WHERE NOT src.usedQuantity IS NULL");
+
+      progress.display(10, "Loading biomaterial items...\n");
+      
+      List<Object[]> events = HibernateUtil.loadList(Object[].class, eventQuery, null);
+      events.addAll(HibernateUtil.loadList(Object[].class, sourcesQuery, null));
+
+      // Calculate the remaining quantity for each biomaterial
+      // o[0] = biomaterial id, o[1] = used quantity      
+      for (Object[] o : events)
+      {
+        Integer id = (Integer)o[0];
+        Float usedQuantity = (Float)o[1];
+        Double currentRemaining = remaining.get(id);
+        if (currentRemaining == null) currentRemaining = 0.0;
+        currentRemaining = currentRemaining - usedQuantity.doubleValue();
+        remaining.put(id, currentRemaining);
+      }
+      progress.display(30, "Found "+ remaining.size() + " items. Checking remaining quantity...\n");
+      
+      // Update the remaining quantity
+      org.hibernate.Query updateQuery = HibernateUtil.createQuery(session, 
+        "UPDATE MeasuredBioMaterialData mbm " +
+        "SET mbm.remainingQuantity = :remain "+
+        "WHERE mbm = :bioMaterial");
+      int numProcessed = 0;
+      for (Map.Entry<Integer, Double> entry : remaining.entrySet())
+      {
+        MeasuredBioMaterialData bioMaterial = HibernateUtil.loadData(session, MeasuredBioMaterialData.class, entry.getKey());
+        Double remainingQuantity = entry.getValue();
+        Float currentRemaining = bioMaterial.getRemainingQuantity();
+        if (currentRemaining == null || Math.abs(currentRemaining-remainingQuantity) > Math.abs(currentRemaining / 10000))
+        {
+          updateQuery.setEntity("bioMaterial", bioMaterial);
+          updateQuery.setFloat("remain", remainingQuantity.floatValue());
+          updateQuery.executeUpdate();
+          numUpdated++;
+        }
+        numProcessed++;
+        if (numProcessed % 100 == 0)
+        {
+          progress.display(30 + numProcessed * 60 / remaining.size(), "Processed " + numProcessed + " biomaterial items...                   ");
+        }
+      }
+      progress.append("\n");
+      if (numUpdated == 0)
+      {
+        progress.display(100, "Found " + numUpdated + " items to fix\n");
+      }
+      else
+      {
+        progress.display(95, "Found " + numUpdated + " items to fix. Comitting transaction...\n");
+        // Commit the changes
+        HibernateUtil.commit(tx);
+        progress.display(100, "Completeted update of " + numUpdated + " items\n");
+      }
+    }
+    catch (BaseException ex)
+    {
+      if (tx != null) HibernateUtil.rollback(tx); 
+      throw ex;
+    }
+    return numUpdated;
+  }
+
+  
   // Item type codes for item types that was removed since BASE 2
   private static final int LABELEDEXTRACT = 204;

branches/3.3-stable/src/install/net/sf/basedb/install/OneTimeFix.java

@@ -31 +31 @@
 
 
+
+
+
+
 import net.sf.basedb.core.Application;
 import net.sf.basedb.core.Config;
 import net.sf.basedb.core.ProgressReporter;
+import net.sf.basedb.core.SessionControl;
+import net.sf.basedb.core.Update;
+import net.sf.basedb.core.authentication.LoginRequest;
+import net.sf.basedb.util.ConsoleProgressReporter;
 
 /**
@@ -55 +63 @@
     try
     {
-      String cmd = args[0];   
-      if ("foo".equals(cmd))
+      String cmd = args[0];
+      if ("remaining_quantity".equals(cmd))
       {
-        showUsage();
+        String login = getOption(args, "-u", "root");
+        String pwd = getOption(args, "-p", "root");
+        
+        String msg = 
+          "-------------------------------------------------------------------\n" +
+          "This script re-calculates the remaining quantity of all biomaterial\n" +
+          "items since it may have become incorrect due to a bug.\n" +
+          "For more information see: http://base.thep.lu.se/ticket/1873\n\n" +
+          "Press ENTER to continue or CTRL+C to abort\n" +
+          "-------------------------------------------------------------------";
+        System.out.println(msg);
+        waitForEnter();
+        showDbInfo(null);
+        System.out.println("Starting BASE. Please wait...");
+        Application.start(false);
+        SessionControl sc = Application.newSessionControl(null, null, null);
+        sc.login(new LoginRequest(login, pwd));
+        int numModified = Update.recalculateRemainingQuantity(new ConsoleProgressReporter(false));
+        sc.logout();
+        sc.close();
+        Application.stop();
       }
       else