Changeset 6600

Timestamp:

Nov 17, 2014, 8:41:18 AM (8 years ago)

Author:

Nicklas Nordborg

Message:

Merge BASE 3.3.3 to the trunk.

There is a test failure in "TestFile?" for the https file. I guess this due to updates to the Http client library in #1809 and that it existed already in BASE 3.3.2 when the urls changed due to server move.

Location:

trunk

Files:

• . (modified) (1 prop)
• config/dist/base.config (modified) (1 diff)
• credits.txt (modified) (1 diff)
• doc/src/docbook/appendix/update_warnings.xml (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/extensions/ExtensionsControl.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/path/Path.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/taglib/path/PathElement.java (modified) (1 diff)
• src/core/net/sf/basedb/core/BioMaterialEvent.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/BioMaterialEventSource.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/HibernateUtil.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (8 diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (3 diffs)
• src/install/net/sf/basedb/install/OneTimeFix.java (modified) (2 diffs)
• src/test/TestChangeHistory.java (modified) (2 diffs)
• www/WEB-INF/path.tld (modified) (3 diffs)
• www/admin/pluginconfigurations/configurations.js (modified) (1 diff)
• www/admin/pluginconfigurations/view_configuration.jsp (modified) (1 diff)
• www/admin/plugindefinitions/plugins.js (modified) (1 diff)
• www/admin/plugindefinitions/view_plugin.jsp (modified) (1 diff)
• www/common/annotations/list.js (modified) (1 diff)
• www/common/history/history.js (modified) (1 diff)
• www/common/overview/overview.js (modified) (3 diffs)
• www/common/plugin/parse_file.jsp (modified) (1 diff)
• www/views/jobs/index.jsp (modified) (2 diffs)
• www/views/jobs/jobs.js (modified) (2 diffs)
• www/views/jobs/list_jobs.jsp (modified) (1 diff)
• www/views/rawbioassays/index.jsp (modified) (1 diff)

trunk/config/dist/base.config

@@ -41 +41 @@
 #db.driver           = org.postgresql.Driver
 #db.url              = jdbc:postgresql:base2
-#db.dynamic.catalog  = base2
 #db.dynamic.schema   = dynamic
 #db.queries          = /postgres-queries.xml

trunk/credits.txt

@@ -1 +1 @@
 $Id$
 
-The current BASE team is (at BASE 3.3.2 release)
+The current BASE team is (at BASE 3.3.3 release)
 {{{
 Jari Häkkinen

trunk/doc/src/docbook/appendix/update_warnings.xml

@@ -61 +61 @@
       since the <classname>org.hibernate.dialect.PostgreSQLDialect</classname> has
       been deprecated.
+    </para>
+    
+  </sect1>
+
+  <sect1 id="appendix.update_warnings.3.3.3">
+    <title>BASE 3.3.3</title>
+  
+    <bridgehead>Remaining quantity</bridgehead>
+    <para>
+      A bug that affected remaining quantity calculations for 
+      biomaterial item has been fixed. Existing items may have been
+      saved with incorrect remaining quantity and must be fixed.
+      After installing the BASE 3.3.3 update, the existing
+      remaining quantity values are fix by running a special script.
+      Change directory to <filename class="directory">&lt;base-dir&gt;/bin/</filename> 
+      and issue
+<programlisting>
+./onetimefix.sh remaining_quantity -u &lt;root login&gt; -p &lt;root pwd&gt;
+</programlisting>
     </para>
     

trunk/src/clients/web/net/sf/basedb/clients/web/extensions/ExtensionsControl.java

@@ -804 +804 @@
   {
     ExtensionPoint<?> ep = getExtensionPoint(ex.getExtends());
+    if (ep == null) return false;
     // The extension point cant violoate the policy
     if (!ep.getActionClass().isAnnotationPresent(UnsafeScriptable.class)) return false;

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/path/Path.java

@@ -146 +146 @@
     sb.append("<h1");
     addIdAndStyles(sb);
+    addDynamicAttributes(sb);
     sb.append(">");
 

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/path/PathElement.java

@@ -225 +225 @@
     sb.append("<span");
     addIdAndStyles(sb);
+    addDynamicAttributes(sb);
     sb.append(">");
     if (getHref() != null && isEnabled())

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

@@ -26 +26 @@
 import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.core.query.Hql;
-
 import net.sf.basedb.core.data.BioMaterialData;
 import net.sf.basedb.core.data.BioMaterialEventData;
@@ -719 +718 @@
     checkPermission(Permission.RESTRICTED_WRITE);
     if (bioMaterial == null) throw new InvalidUseOfNullException("bioMaterial");
-    BioMaterialData data = (BioMaterialData)bioMaterial.getData();
+    BioMaterialData data = (BioMaterialData)HibernateUtil.unwrapIfProxy(getDbControl().getHibernateSession(), bioMaterial.getData());
     Map<BioMaterialData, BioMaterialEventSourceData> sources = getData().getSources();
     BioMaterialEventSourceData src = sources.remove(data);
@@ -858 +857 @@
     Map<BioMaterialData, BioMaterialEventSourceData> sources = getData().getSources();
     int parentId = parent == null ? 0 : parent.getId();
-    
+
     Iterator<Map.Entry<BioMaterialData, BioMaterialEventSourceData>> it = sources.entrySet().iterator();
     while (it.hasNext())
@@ -865 +864 @@
       
       BioMaterialEventSourceData src = entry.getValue();
-      BioMaterialData bioMaterial = entry.getKey();
+      BioMaterialData bioMaterial = (BioMaterialData)HibernateUtil.unwrapIfProxy(dc.getHibernateSession(), entry.getKey());
       
       if (bioMaterial.getId() != parentId)

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

@@ -25 +25 @@
 import java.util.Set;
 
+import net.sf.basedb.core.data.BioMaterialData;
 import net.sf.basedb.core.data.BioMaterialEventSourceData;
 import net.sf.basedb.core.data.MeasuredBioMaterialData;
@@ -167 +168 @@
   {
     checkPermission(Permission.RESTRICTED_WRITE);
-    if (data.getBioMaterial() instanceof MeasuredBioMaterialData)
-    {
-      MeasuredBioMaterialData mbData = (MeasuredBioMaterialData)data.getBioMaterial();
+    BioMaterialData bm = (BioMaterialData)HibernateUtil.unwrapIfProxy(dc.getHibernateSession(), data.getBioMaterial());
+    if (bm instanceof MeasuredBioMaterialData)
+    {
+      MeasuredBioMaterialData mbData = (MeasuredBioMaterialData)bm;
       Float delta = 0.0f;
       if (data.getUsedQuantity() != null)

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

@@ -1453 +1453 @@
       throw new BaseException(ex);
     }   
+  }
+  
+  /**
+    If the given data object is a proxy, load the real data object instead.
+    @since 3.3.3
+  */
+  static BasicData unwrapIfProxy(Session session, BasicData data)
+  {
+    if (data instanceof org.hibernate.proxy.HibernateProxy)
+    {
+      org.hibernate.proxy.HibernateProxy proxy = (org.hibernate.proxy.HibernateProxy)data;
+      org.hibernate.proxy.LazyInitializer li = proxy.getHibernateLazyInitializer();
+      if (li.isUninitialized())
+      {
+        if (session instanceof SessionWrapper)
+        {
+          session = ((SessionWrapper)session).getParentSession();
+        }
+        li.setSession((org.hibernate.internal.SessionImpl)session);
+      }
+      data = (BasicData)li.getImplementation();
+    }
+
+    return data;
   }
   

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

@@ -39 +39 @@
 import java.util.Set;
 import java.sql.SQLException;
+
 
 /**
@@ -161 +162 @@
     @see FeatureIdentificationMethod
   */
-  private final Map<Object, FeatureData> preloaded;
+  private Map<Object, FeatureInfo> preloaded;
+  
+  private ReporterProxy reporterProxy;
+  private FeatureProxy featureProxy;
   
   /**
@@ -230 +234 @@
     }
     
-    // Preload features 
-    if (arrayDesign != null && arrayDesign.getHasFeatures() && rawBioAssay.getNumDbSpots() == 0)
-    {
-      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(dc.getStatelessSession(), "COUNT_FEATURES_FOR_ARRAYDESIGN");
-      /*
-        SELECT count(*)
-        FROM FeatureData f
-        WHERE f.arrayDesignBlock.arrayDesign = :arrayDesign
-      */
-      query.setInteger("arrayDesign", arrayDesign.getId());
-      int numFeatures = HibernateUtil.loadData(Long.class, query).intValue();
-      preloaded = new HashMap<Object, FeatureData>(numFeatures);
-      query = HibernateUtil.getPredefinedQuery(dc.getStatelessSession(), "PRELOAD_FEATURES");
-      /*
-        SELECT f 
-        FROM FeatureData f 
-        JOIN FETCH f.arrayDesignBlock b 
-        LEFT JOIN FETCH f.reporter 
-        WHERE b.arrayDesign = :arrayDesign
-      */
-      query.setInteger("arrayDesign", arrayDesign.getId());
-      ScrollIterator<FeatureData> si = null;
-      try
-      {
-        si = QueryExecutor.loadIterator(FeatureData.class, query, 
-            dc.getStatelessSession(), dc.getSessionControl());
-      }
-      catch (InterruptedException ex)
-      {
-        throw new SignalException("Aborted by user", ex);
-      }
-      while (si.hasNext())
-      {
-        ThreadSignalHandler.checkInterrupted();
-        FeatureData feature = si.next();
-        Object featureId = fiMethod.getIdentifier(feature);
-        if (preloaded.put(featureId, feature) != null)
-        {
-          throw new InvalidDataException("Can't identify features with " + fiMethod + 
-            ". Found duplicate feature: " + featureId);
-        }
-      }
-      si.close();
-    }
-    else
-    {
-      this.preloaded = null;
-    }
-    this.usedFeatures = new HashSet<Object>(preloaded == null ? 100 : preloaded.size());
     setDbControl(dc);
   }
@@ -529 +484 @@
     throws BaseException
   {
+    if (usedFeatures == null) preloadFeatures();
     if (externalReporterId != null) externalReporterId = externalReporterId.trim();
     if (preloaded == null)
@@ -571 +527 @@
           "] has already been used by another spot.");
       }
-      FeatureData feature = preloaded.get(featureId);
+      FeatureInfo feature = preloaded.get(featureId);
       if (feature == null)
       {
@@ -579 +535 @@
             "=" + featureId + "] doesn't exist on array design");
       }
-      ReporterData reporterOnFeature = feature.getReporter();
+      ReporterData reporterOnFeature = feature.getReporter(reporterProxy);
       if (reporterOnFeature == null && acceptInsertIfNullReporterOnFeature)
       {
@@ -595 +551 @@
       }
       data.setPosition(feature.getPosition());
-      setPropertyValue(data, "feature", feature);
+      setPropertyValue(data, "feature", feature.getFeature(featureProxy));
       data.setReporter(reporterOnFeature);
     }
     super.insert(data);
+  }
+  
+  private void preloadFeatures()
+  {
+    // Preload features 
+    if (arrayDesign != null && arrayDesign.getHasFeatures() && rawBioAssay.getNumDbSpots() == 0)
+    {
+      DbControl dc = getDbControl();
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(dc.getStatelessSession(), "COUNT_FEATURES_FOR_ARRAYDESIGN");
+      /*
+        SELECT count(*)
+        FROM FeatureData f
+        WHERE f.arrayDesignBlock.arrayDesign = :arrayDesign
+      */
+      query.setInteger("arrayDesign", arrayDesign.getId());
+      int numFeatures = HibernateUtil.loadData(Long.class, query).intValue();
+      preloaded = new HashMap<Object, FeatureInfo>(numFeatures);
+      reporterProxy = new ReporterProxy();
+      featureProxy = new FeatureProxy();
+      query = HibernateUtil.getPredefinedQuery(dc.getStatelessSession(), "PRELOAD_FEATURES");
+      /*
+        SELECT f 
+        FROM FeatureData f 
+        JOIN FETCH f.arrayDesignBlock b 
+        LEFT JOIN FETCH f.reporter 
+        WHERE b.arrayDesign = :arrayDesign
+      */
+      query.setInteger("arrayDesign", arrayDesign.getId());
+      ScrollIterator<FeatureData> si = null;
+      try
+      {
+        si = QueryExecutor.loadIterator(FeatureData.class, query, 
+            dc.getStatelessSession(), dc.getSessionControl());
+      }
+      catch (InterruptedException ex)
+      {
+        throw new SignalException("Aborted by user", ex);
+      }
+      while (si.hasNext())
+      {
+        ThreadSignalHandler.checkInterrupted();
+        FeatureData feature = si.next();
+        Object featureId = fiMethod.getIdentifier(feature);
+        if (preloaded.put(featureId, new FeatureInfo(feature)) != null)
+        {
+          throw new InvalidDataException("Can't identify features with " + fiMethod + 
+            ". Found duplicate feature: " + featureId);
+        }
+      }
+      si.close();
+    }
+    else
+    {
+      this.preloaded = null;
+    }
+    this.usedFeatures = new HashSet<Object>(preloaded == null ? 100 : preloaded.size());
   }
   
@@ -646 +658 @@
   }
 
+
+  static class FeatureInfo
+  {
+    private final int featureId;
+    private final int position;
+    private final int reporterId;
+    private final String externalReporterId;
+
+    FeatureInfo(FeatureData feature)
+    {
+      featureId = feature.getId();
+      position = feature.getPosition();
+      ReporterData reporter = feature.getReporter();
+      if (reporter != null)
+      {
+        reporterId = reporter.getId();
+        externalReporterId = reporter.getExternalId();
+      }
+      else
+      {
+        reporterId = 0;
+        externalReporterId = null;
+      }
+    }
+    
+    int getPosition()
+    {
+      return position;
+    }
+    
+    ReporterData getReporter(ReporterProxy proxy)
+    {
+      return reporterId == 0 ? null : proxy.setTheId(reporterId, externalReporterId);
+    }
+    
+    FeatureData getFeature(FeatureProxy proxy)
+    {
+      return proxy.setTheId(featureId);
+    }
+    
+  }
+
+  static class ReporterProxy
+    extends ReporterData
+  {
+    private int id;
+    private String externalId;
+    
+    ReporterProxy()
+    {}
+    
+    ReporterProxy setTheId(int id, String externalId)
+    {
+      this.id = id;
+      this.externalId = externalId;
+      return this;
+    }
+    @Override
+    public int getId()
+    {
+      return id;
+    }
+    
+    @Override
+    public String getExternalId()
+    {
+      return externalId;
+    }
+  }
+
+  static class FeatureProxy
+    extends FeatureData
+  {
+    private int id;
+    
+    FeatureProxy()
+    {
+      super(null, (ReporterData)null);
+    }
+    
+    FeatureProxy setTheId(int id)
+    {
+      this.id = id;
+      return this;
+    }
+    @Override
+    public int getId()
+    {
+      return id;
+    }
+  }
+  
 }

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

@@ -26 +26 @@
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Iterator;
@@ -49 +50 @@
 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.PropertyFilterData;
 import net.sf.basedb.core.data.ReporterCloneTemplateData;
@@ -930 +932 @@
   }
   
+  /**
+    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;
+  }
+
   
 

trunk/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

trunk/src/test/TestChangeHistory.java

@@ -95 +95 @@
     TestExtract.test_delete(extractId);
     
+    // 1 CREATE event only
     test_list_by_item(Item.BIOSOURCE, bioSourceId, 1);
-    test_list_by_item(Item.SAMPLE, sampleId, 7);
+    
+    /*
+      1 CREATE
+      2 UPDATE (name and externalId)
+      3 ADD+UPDATE+REMOVE ('change' annotation)
+      2 UPDATE (remainingQuantity when creating/deleting extract)
+    */
+    test_list_by_item(Item.SAMPLE, sampleId, 8);
     /*
       Total change log events:
-      5 CREATE (biosource, sample, annotationtype, extract, annotation)
-      4 UPDATE (when updating and removing the annotation from the sample)
-      2 DELETE (extract, annotation)
+      4 CREATE (biosource, sample, annotationtype, extract)
+      1 ADD (annotation)
+      5 UPDATE (when updating the sample, it's annotation and child extract)
+      1 REMOVE (annotation)
+      1 DELETE (extract)
     */
-    test_list_by_user(TestUtil.getSessionControl().getLoggedInUserId(), since, 11);
+    test_list_by_user(TestUtil.getSessionControl().getLoggedInUserId(), since, 12);
     
     if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
@@ -110 +120 @@
     TestBioSource.test_delete(bioSourceId);
     TestAnnotationType.test_delete(annotationTypeId);
-    // 14 = The original 11 create+update + 3 delete
-    test_delete_stray(14);
+    // 15 = The original 12 create+update + 3 delete
+    test_delete_stray(15);
     
     xtRegistry.unregisterExtension("test.db-logger");

trunk/www/WEB-INF/path.tld

@@ -45 +45 @@
     </attribute>
     <attribute>
+      <name>subclass</name>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>style</name>
       <rtexprvalue>true</rtexprvalue>
     </attribute>
+    <dynamic-attributes>true</dynamic-attributes>
   </tag>
 
@@ -60 +65 @@
     <attribute>
       <name>clazz</name>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>subclass</name>
       <rtexprvalue>true</rtexprvalue>
     </attribute>
@@ -87 +96 @@
       <rtexprvalue>true</rtexprvalue>
     </attribute>
+    <dynamic-attributes>true</dynamic-attributes>
   </tag>
 </taglib>

trunk/www/admin/pluginconfigurations/configurations.js

@@ -69 +69 @@
       Buttons.addClickHandler('btnConfigure', configurations.configurePlugin, attributes);
       
+      if (Doc.element('main.annotations'))
+      {
+        TabControl.addTabActivateListener('main.annotations', AnnotationsList.loadOnce);
+      }
       TabControl.addTabActivateListener('main.history', History.loadOnce);
     }

trunk/www/admin/pluginconfigurations/view_configuration.jsp

@@ -404 +404 @@
       <t:tab id="annotations" title="Annotations" 
         tooltip="View annotation values" clazz="white"
-        visible="<%=plugin != null && plugin.supports("net.sf.basedb.core.plugin.AnnotationSetterPlugin") %>"
-        activate="AnnotationsList.loadOnce()">
+        visible="<%=plugin != null && plugin.supports("net.sf.basedb.core.plugin.AnnotationSetterPlugin") %>">
         <jsp:include page="../../common/annotations/list_frameset.jsp">
           <jsp:param name="item_type" value="<%=itemType.name()%>" />

trunk/www/admin/plugindefinitions/plugins.js

@@ -118 +118 @@
       Buttons.addClickHandler('btnUnload', plugins.unloadPlugin, attributes);
       Buttons.addClickHandler('btnToggleDisabled', plugins.toggleDisabled);
-      
+
+      if (Doc.element('main.annotations'))
+      {
+        TabControl.addTabActivateListener('main.annotations', AnnotationsList.loadOnce);
+      }
       TabControl.addTabActivateListener('main.history', History.loadOnce);
     }

trunk/www/admin/plugindefinitions/view_plugin.jsp

@@ -675 +675 @@
     <t:tab id="annotations" title="Annotations" 
       tooltip="View annotation values" clazz="white"
-      visible="<%=!plugin.requiresConfiguration() && plugin.supports("net.sf.basedb.core.plugin.AnnotationSetterPlugin") %>"
-      activate="AnnotationsList.loadOnce()">
+      visible="<%=!plugin.requiresConfiguration() && plugin.supports("net.sf.basedb.core.plugin.AnnotationSetterPlugin") %>">
       <jsp:include page="../../common/annotations/list_frameset.jsp">
         <jsp:param name="item_type" value="<%=itemType.name()%>" />

trunk/www/common/annotations/list.js

@@ -71 +71 @@
     url += '&item_type='+Data.get('annotate-data', 'item-type');
     url += '&item_id='+Data.get('annotate-data', 'item-id');
-    frames['annotations'].location.href = url;
+    frames['annotations'].location.replace(url);
     loaded = true;
   }

trunk/www/common/history/history.js

@@ -60 +60 @@
     url += '&source_type='+Data.get('history-data', 'source-type');
     url += '&source_id='+Data.get('history-data', 'source-id');
-    frames['history-frame'].location.href = url;
+    frames['history-frame'].location.replace(url);
     loaded = true;
   }

trunk/www/common/overview/overview.js

@@ -41 +41 @@
     url += '&item_type='+Data.get('overview-data', 'item-type');
     url += '&item_id='+Data.get('overview-data', 'item-id');
-    frames['overview'].location.href = url;
+    frames['overview'].location.replace(url);
     loaded = true;
   }
@@ -51 +51 @@
     url += '&item_type='+Data.get('overview-data', 'item-type');
     url += '&item_id='+Data.get('overview-data', 'item-id');
-    frames['overview'].location.href = url;
+    frames['overview'].location.replace(url);
   }
   
@@ -60 +60 @@
     url += '&item_type='+Data.get('overview-data', 'item-type');
     url += '&item_id='+Data.get('overview-data', 'item-id');
-    frames['overview'].location.href = url;
+    frames['overview'].location.replace(url);
   }
 

trunk/www/common/plugin/parse_file.jsp

@@ -197 +197 @@
     id="parsedFile"
     subclass="absolutefull dialogtabcontrol"
-    position="top"
+    position="top" active="filedata"
     >
   <t:tab

trunk/www/views/jobs/index.jsp

@@ -58 +58 @@
   import="java.util.List"
   import="java.util.ArrayList"
+  import="java.util.Collection"
   import="java.util.Collections"
 %>
@@ -278 +279 @@
     redirect = viewPage;
   }
+  else if ("AbortJobs".equals(cmd))
+  {
+    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    dc = sc.newDbControl();
+    int numAborted = 0;
+    int numSelected = 0;
+    for (int jobId : cc.getSelected())
+    {
+      numSelected++;
+      Job job = Job.getById(dc, jobId);
+      SignalTransporter signalTransporter = job.getSignalTransporter();
+      if (signalTransporter == null)
+      {
+        if (job.getStatus() == Job.Status.WAITING)
+        {
+          job.doneError("Aborted by user");
+          numAborted++;
+        }
+      }
+      else
+      {
+        Collection<Signal> supportedSignals = signalTransporter.getSupportedSignals();
+        if (supportedSignals == null || supportedSignals.contains(Signal.ABORT))
+        {
+          signalTransporter.send(Signal.ABORT);
+          numAborted++;
+        }
+      }
+    }
+    dc.commit();
+    
+    message = numAborted + " of " + numSelected + " jobs have been aborted ";
+    Thread.sleep(500);
+    redirect = listPage;
+  }
   else if ("AbortJob".equals(cmd))
   {

trunk/www/views/jobs/jobs.js

@@ -62 +62 @@
       Buttons.addClickHandler('btnDeleteItems', Buttons.deleteItems, tableAttributes);
       Buttons.addClickHandler('btnRestoreItems', Buttons.restoreItems, tableAttributes);
+      Buttons.addClickHandler('btnAbort', jobs.abortJobs, tableAttributes);
       Buttons.addClickHandler('btnShareItems', Buttons.shareItems, tableAttributes);
       Buttons.addClickHandler('btnSetOwner', Buttons.setOwnerOfItems, tableAttributes);
@@ -80 +81 @@
   }
 
+  
+  jobs.abortJobs = function()
+  {
+    var frm = document.forms['jobs'];
+    var numSelected = Table.checkIfSelected('jobs');
+    if (numSelected == 0) return;
+    if (!confirm('You are about to abort '+numSelected+' jobs. This can\'t be undone. Continue?'))
+    {
+      return;
+    }
+    frm.cmd.value = 'AbortJobs';
+    frm.submit();
+  }
   
   jobs.abortJob = function()

trunk/www/views/jobs/list_jobs.jsp

@@ -413 +413 @@
             title="Restore" 
             tooltip="Restore the selected (deleted) items"
+          />
+          <tbl:button 
+            id="btnAbort"
+            image="abort.png"
+            title="Abort&hellip;" 
+            tooltip="Abort the selected items"
           />
           <tbl:button 

trunk/www/views/rawbioassays/index.jsp

@@ -347 +347 @@
       {
         ad = arrayDesignId == 0 ? null : ArrayDesign.getById(dc, arrayDesignId);
-        if (!rba.isSameArrayDesign(ad))
+        if (!rba.isSameArrayDesign(ad) || !rba.isInDatabase())
         {
           if (rba.hasData())