Changeset 3775

Timestamp:

Sep 25, 2007, 11:12:36 AM (16 years ago)

Author:

Johan Enell

Message:

Merged the 2.4.2 release

log:branches/2.4-stable#3694:3770

Location:

trunk

Files:

• doc/src/docbook/admindoc/installation_upgrade.xml (modified) (6 diffs)
• doc/src/docbook/overviewdoc/resources.xml (modified) (2 diffs)
• doc/src/docbook/userdoc/analyse_mev.xml (modified) (1 diff)
• src/clients/migrate/net/sf/basedb/clients/migrate/QuotaTransfer.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (4 diffs)
• src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/AbstractBatcher.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/BasicBatcher.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/DbControl.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/FeatureBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/FilterBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/MappingBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Operator.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PluginConfiguration.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PositionBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PositionExtraValueBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawBioAssay.java (modified) (1 diff)
• src/core/net/sf/basedb/core/RawDataBatcher.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/ReporterBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/SpotBatcher.java (modified) (1 diff)
• src/core/net/sf/basedb/core/SpotExtraValueBatcher.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (30 diffs)
• src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java (modified) (2 diffs)
• www/admin/jobagents/view_agent.jsp (modified) (2 diffs)
• www/admin/pluginconfigurations/list_configurations.jsp (modified) (2 diffs)
• www/admin/pluginconfigurations/view_configuration.jsp (modified) (3 diffs)
• www/common/import/no_fileformat.jsp (modified) (1 diff)
• www/exception/exception.jsp (modified) (2 diffs)
• www/lims/arraydesigns/features/index.jsp (modified) (2 diffs)

trunk/doc/src/docbook/admindoc/installation_upgrade.xml

@@ -343 +343 @@
             </listitem>
           </varlistentry>
-          <varlistentry>
-            <term id="installation_upgrade.jobagent.user_account">Enable the job agent user account</term>
+          <varlistentry id="installation_upgrade.jobagent.user_account">
+            <term>Enable the job agent user account</term>
             <listitem>
               <para>
@@ -367 +367 @@
       <para>
         <variablelist>
-          <varlistentry>
-            <term id="installation_upgrade.jobagent.database">Create a user account on the database</term>
+          <varlistentry id="installation_upgrade.jobagent.database">
+            <term>Create a user account on the database</term>
             <listitem>
               <para>
@@ -413 +413 @@
             </listitem>
           </varlistentry>
-          <varlistentry>
-            <term id="installation_upgrade.jobagent.client.config">Edit the <filename>base.config</filename> file</term>
+          <varlistentry id="installation_upgrade.jobagent.client.config">
+            <term>Edit the <filename>base.config</filename> file</term>
             <listitem>
               <para>
@@ -462 +462 @@
             </listitem>
           </varlistentry>
-          <varlistentry>
-            <term id="installation_upgrade.jobagent.client.properties">Edit
+          <varlistentry id="installation_upgrade.jobagent.client.properties">
+            <term>Edit
             the <filename>jobagent.properties</filename> file</term>
             <listitem>
@@ -744 +744 @@
       </varlistentry>
 
-      <varlistentry>
-        <term id="installation_upgrade.installation.database">BASE (database engine)</term>
+      <varlistentry id="installation_upgrade.installation.database">
+        <term>BASE (database engine)</term>
         <listitem>
           <para>
@@ -841 +841 @@
       </varlistentry>
 
-      <varlistentry>
-        <term id="installation_upgrade.installation.configuration">BASE (configuration)</term>
+      <varlistentry id="installation_upgrade.installation.configuration">
+        <term>BASE (configuration)</term>
         <listitem>
           <para>

trunk/doc/src/docbook/overviewdoc/resources.xml

@@ -222 +222 @@
     <title>Demo server</title>
     <para>
-      There is a demo server available for anyone to use and to
-      explore BASE without having to install anything. Follow the link
-      from BASE web site to the demo server or go directly to
+      There is a demo server up running for anyone who wants to explore BASE 2 without having
+      to install it. Follow the link on BASE 2's home page to the demo server or go directly
+      to
       <ulink url="http://base2.thep.lu.se/demo/">
         http://base2.thep.lu.se/demo/
@@ -285 +285 @@
     </important>
   </sect1>
+
+  <sect1 id="resources.basehacks">
+    <title>BASE-hacks</title>
+    <para>
+      There is a trac/subversion server keeping track of changes made
+      to third party projects that are changed to make them work with
+      BASE. Open source project usually have a requirement that
+      changes are made public. On
+      the <ulink
+      url='http://trac.thep.lu.se/trac/basehacks'>BASE-hacks web
+      site</ulink> you will find a list of modified packages and
+      information about the changes performed.
+    </para>
+  </sect1>
+
 </chapter>

trunk/doc/src/docbook/userdoc/analyse_mev.xml

@@ -29 +29 @@
 <sect1 id="experiments_analysis.mev">
   <title>Analysing data with Multiexperiment Viewer (MeV)</title>
-  <para>TODO</para>
+  <para>
+    MeV is a versatile microarray data analysis tool, incorporating
+    sophisticated algorithms for clustering, visualization,
+    classification, statistical analysis and biological theme
+    discovery, <ulink
+    url='http://www.tm4.org'>http://www.tm4.org</ulink>. We use a
+    modified version of MeV and provide information about the changes
+    at
+    the <ulink url='http://trac.thep.lu.se/trac/basehacks'>BASE-hacks
+    web site</ulink>.
+  </para>
 </sect1>

trunk/src/clients/migrate/net/sf/basedb/clients/migrate/QuotaTransfer.java

@@ -97 +97 @@
       quotas.put(totalQuota, quota);
     }
-    else
+    else if (quota.isInDatabase())
     {
       quota = Quota.getById(dc, quota.getId());

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -511 +511 @@
             if (value != null)
             {
+              boolean hasWildcard = value.indexOf('%') >= 0;
               Type valueType = Type.valueOf(name.substring(7, colonIndex));
   
@@ -517 +518 @@
               filter.setValueType(valueType);
               
-              Operator op = Operator.EQ;
+              Operator op = hasWildcard ? Operator.LIKE : Operator.EQ;
               if (value.startsWith("<>") || value.startsWith("!="))
               {
-                op = Operator.NEQ;
+                op = hasWildcard ? Operator.NOTLIKE : Operator.NEQ;
                 value = value.substring(2);
               }
@@ -545 +546 @@
               else if (value.startsWith("="))
               {
-                op = Operator.EQ;
+                op = hasWildcard ? Operator.LIKE : Operator.EQ;
                 value = value.substring(1);
-              }
-              else if (value.indexOf('%') >= 0)
-              {
-                op = Operator.LIKE;
               }
               if ("".equals(value)) value = null;
@@ -669 +666 @@
         {}
       }
-      if (op == Operator.EQ && (value == null || (value != null && value.indexOf('%') >= 0)))
+      if (op == Operator.EQ && value == null)
       {
         result = "=";
       }
-      else if (op == Operator.NEQ)
+      else if (op == Operator.NEQ || op == Operator.NOTLIKE)
       {
         result = "<>";

trunk/src/clients/web/net/sf/basedb/clients/web/plugins/SimpleExport.java

@@ -227 +227 @@
     String whichItems = (String)job.getValue(WHICH_ITEMS);
     String format = (String)job.getValue(FORMAT);
-    List<Integer> selectedItems = (List<Integer>)job.getValues("item");
     List<String> columns = (List<String>)job.getValues(WHICH_PROPERTIES);
     
@@ -265 +264 @@
     QueryWrapper queryWrapper = null;
     ResultIterator result = null;
+    Set<Integer>selectedItems = cc.getSelected();
     
     // The query wrapper allows us to get results from the query in a simplier way

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

@@ -75 +75 @@
   
   /**
-    Constructor that initiate everything.
-
-    @param dc The <code>DbControl</code> to get database access
+    Constructor for a batcher.
     @throws BaseException If there is an error
   */
-  AbstractBatcher(DbControl dc)
-  {
-    assert dc != null : "dc == null";
-    this.dc = new WeakReference<DbControl>(dc);
-    this.sc = dc.getSessionControl();
+  AbstractBatcher()
+  {
     this.batchSize = Config.getInt("db.batch-size", 50);
-    dc.addBatcher(this);
   }
 
@@ -133 +127 @@
   {
     sc.updateLastAccess();
+  }
+  
+  /**
+    Set the DbControl that is controlling this batcher. This
+    method MUST be called by all subclasses after successful construction
+    of a batcher. This method also registers the batcher with the DbControl
+    using {@link DbControl#addBatcher(Batcher)}
+    @since 2.4.2
+  */
+  protected final void setDbControl(DbControl dc)
+  {
+    assert dc != null : "dc == null";
+    this.dc = new WeakReference<DbControl>(dc);
+    this.sc = dc.getSessionControl();
+    dc.addBatcher(this);
   }
   

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

@@ -131 +131 @@
     Constructor that initiate everything.
 
-    @param dc DbControl to get database access
     @param dataClass The class of the data objects that are accepted by this batcher
     @param entityName The entity name of the data as known by Hibernate, use null
@@ -137 +136 @@
     @throws BaseException If there is an error
   */
-  BasicBatcher(DbControl dc, Class<D> dataClass, String entityName)
-    throws BaseException
-  {
-    super(dc);
+  BasicBatcher(org.hibernate.Session session, Class<D> dataClass, String entityName)
+    throws BaseException
+  {
+    super();
     assert dataClass != null : "dataClass == null";
     
@@ -159 +158 @@
     try
     {
-      java.sql.Connection c = HibernateUtil.getConnection(dc.getHibernateSession());
+      java.sql.Connection c = HibernateUtil.getConnection(session);
       insertStatement = c.prepareStatement(insertSql);
       updateStatement = c.prepareStatement(updateSql);

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

@@ -269 +269 @@
           batcher.close();
         }
-        catch (BaseException ex)
+        catch (Throwable ex)
         {
           log.warn("Exception during rollback in batcher.close()", ex);
@@ -281 +281 @@
       if (hStatelessSession != null) HibernateUtil.close(hStatelessSession);
     }
-    catch (BaseException ex)
+    catch (Throwable ex)
     {
       log.warn("Exception during rollback in Hibernate", ex);

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

@@ -91 +91 @@
     throws BaseException
   {
-    super(dc, FeatureData.class, null);
+    super(dc.getHibernateSession(), FeatureData.class, null);
     this.arrayDesign = arrayDesign;
     this.arrayDesignData = arrayDesign.getData();
     this.isAffy = arrayDesign.isAffyChip();
+    setDbControl(dc);
   }
 

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

@@ -142 +142 @@
   FilterBatcher(DbControl dc, BioAssaySet bioAssaySet)
   {
-    super(dc);
+    super();
     this.bioAssaySet = bioAssaySet;
     this.bytesPerRow = VirtualTable.FILTER.getBytesPerRow(bioAssaySet.getRawDataType());
+    setDbControl(dc);
   }
 

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

@@ -106 +106 @@
   MappingBatcher(DbControl dc, DataCube dataCube)
   {
-    super(dc);
+    super();
     this.dataCube = dataCube;
     this.noRawMapping = dataCube.isInDatabase();
     this.bytesPerRow = VirtualTable.RAWPARENTS.getBytesPerRow(dataCube.getRawDataType());
+    setDbControl(dc);
   }
 

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

@@ -126 +126 @@
       return Restrictions.like(lvalue, rvalue);
     }
+  },
+  
+  NOTLIKE(11, "NOT LIKE", "NOT LIKE", true)
+  {
+    public Restriction getRestriction(Expression lvalue, Expression rvalue)
+      throws InvalidDataException
+    {
+      return Restrictions.not(Restrictions.like(lvalue, rvalue));
+    }
   };
 

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

@@ -467 +467 @@
 
     int newVersion = getNewParameterVersion();
+    int copyFromVersion = copyFrom.getParameterVersion();
     try
     {
       for (Map.Entry<VersionedParameter, ParameterValueData<?>> fromEntry : from.entrySet())
       {
-        VersionedParameter toName = new VersionedParameter(fromEntry.getKey().getName(), newVersion);
-        ParameterValueData<?> fromParameter = fromEntry.getValue();
-        Class<? extends ParameterValueData> dataClass = fromParameter.getClass();
-        if (org.hibernate.proxy.HibernateProxy.class.isAssignableFrom(dataClass))
+        VersionedParameter fromName = fromEntry.getKey();
+        if (copyFromVersion == fromName.getVersion())
         {
-          // The 'fromParameter' is a proxy, we need the real data class
-          dataClass = 
-            (Class<? extends ParameterValueData>)org.hibernate.Hibernate.getClass(fromParameter);
+          VersionedParameter toName = new VersionedParameter(fromName.getName(), newVersion);
+          ParameterValueData<?> fromParameter = fromEntry.getValue();
+          Class<? extends ParameterValueData> dataClass = fromParameter.getClass();
+          if (org.hibernate.proxy.HibernateProxy.class.isAssignableFrom(dataClass))
+          {
+            // The 'fromParameter' is a proxy, we need the real data class
+            dataClass = 
+              (Class<? extends ParameterValueData>)org.hibernate.Hibernate.getClass(fromParameter);
+          }
+          ParameterValueData<?> toParameter = dataClass.newInstance();
+          toParameter.setLabel(fromParameter.getLabel());
+          toParameter.setDescription(fromParameter.getDescription());
+          toParameter.replaceValues(fromParameter.getValues());
+          to.put(toName, toParameter);
         }
-        ParameterValueData<?> toParameter = dataClass.newInstance();
-        toParameter.setLabel(fromParameter.getLabel());
-        toParameter.setDescription(fromParameter.getDescription());
-        toParameter.replaceValues(fromParameter.getValues());
-        to.put(toName, toParameter);
       }
     }

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

@@ -106 +106 @@
   PositionBatcher(DbControl dc, DataCube dataCube)
   {
-    super(dc);
+    super();
     this.dataCube = dataCube;
     this.bytesPerRow = VirtualTable.POSITION.getBytesPerRow(dataCube.getRawDataType());
+    setDbControl(dc);
   }
 

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

@@ -154 +154 @@
   PositionExtraValueBatcher(DbControl dc, ExtraValue extraValue)
   {
-    super(dc);
+    super();
     this.extraValue = extraValue;
     this.bytesPerRow = extraValue.getVirtualTable().getBytesPerRow(extraValue.getRawDataType());
     this.valueType = extraValue.getExtraValueType().getValueType();
     this.sqlType = valueType.getSQLType();
+    setDbControl(dc);
   }
 

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

@@ -291 +291 @@
   {
     super.onBeforeCommit(action);
-    if (action == Transactional.Action.DELETE && getSpots() > 0)
-    {
-      RawDataBatcher rdb = RawDataBatcher.getNew(getDbControl(), this);
-      rdb.deleteAll();
+    if (action == Transactional.Action.DELETE)
+    {
+      if (getRawDataType().isStoredInDb() && getSpots() > 0)
+      {
+        RawDataBatcher rdb = RawDataBatcher.getNew(getDbControl(), this);
+        rdb.deleteAll();
+      }
     }
   }

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

@@ -161 +161 @@
     throws BaseException
   {
-    super(dc, RawData.class, rawBioAssay.getRawDataType().getEntityName());
+    super(dc.getHibernateSession(), RawData.class, rawBioAssay.getRawDataType().getEntityName());
     this.rawBioAssay = rawBioAssay;
     this.rawBioAssayData = rawBioAssay.getData();
@@ -205 +205 @@
       this.preloaded = null;
     }
+    setDbControl(dc);
   }
 

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

@@ -77 +77 @@
     throws BaseException
   {
-    super(dc, ReporterData.class, null);
+    super(dc.getHibernateSession(), ReporterData.class, null);
     extendedProperties = ExtendedProperties.getProperties("ReporterData");
     batchedExternalIds = HibernateUtil.getDbEngine().caseInsensitiveComparison() ?
       new TreeSet<String>(String.CASE_INSENSITIVE_ORDER) : new HashSet<String>();
+    setDbControl(dc);
   }
 

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

@@ -141 +141 @@
   SpotBatcher(DbControl dc, BioAssaySet bioAssaySet)
   {
-    super(dc);
+    super();
     this.bioAssaySet = bioAssaySet;
     this.numChannels = bioAssaySet.getRawDataType().getChannels();
     this.bytesPerRow = VirtualTable.SPOT.getBytesPerRow(bioAssaySet.getRawDataType());
+    setDbControl(dc);
   }
 

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

@@ -144 +144 @@
   SpotExtraValueBatcher(DbControl dc, ExtraValue extraValue)
   {
-    super(dc);
+    super();
     this.extraValue = extraValue;
     this.bytesPerRow = extraValue.getVirtualTable().getBytesPerRow(extraValue.getRawDataType());
     this.valueType = extraValue.getExtraValueType().getValueType();
     this.sqlType = valueType.getSQLType();
+    setDbControl(dc);
   }
 

trunk/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -44 +44 @@
 import net.sf.basedb.core.Include;
 import net.sf.basedb.core.IntegerParameterType;
-import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemNotFoundException;
@@ -56 +55 @@
 import net.sf.basedb.core.PositionBatcher;
 import net.sf.basedb.core.ProgressReporter;
+import net.sf.basedb.core.Reporter;
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.SpotBatcher;
@@ -63 +63 @@
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.User;
+import net.sf.basedb.core.data.ReporterData;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
@@ -109 +110 @@
 import java.util.Set;
 import java.util.TreeMap;
-import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
@@ -138 +138 @@
  
   /**
-    The plug-ing permissions.
+    The plug-in permissions.
   */
   private static final Set<Permissions> permissions = new HashSet<Permissions>();
@@ -207 +207 @@
   
   /**
-    The reporter fields that should be exported as a tab separeated string
+    The reporter fields that should be exported as a tab separated string
     of column headers.
   */
@@ -214 +214 @@
   /**
     The spot fields that should be exported as a tab separated string of 
-    column headres.
+    column headers.
   */
   private PluginParameter<String> usedFieldsParameter;
@@ -265 +265 @@
   private int pluginDirectoryId = -1;
 
-  /* From InteractivePlugin iterface*/
+  /* From InteractivePlugin interface*/
 
   /**
@@ -273 +273 @@
     @param context The context from where the plugin is invoked.
     @param item The item that should be checked if it is in context.
-    @return null if the the item is in context, otherwise an error messge.
+    @return null if the the item is in context, otherwise an error message.
     @see net.sf.basedb.core.plugin.AbstractAnalysisPlugin#isInContext(net.sf.basedb.core.plugin.GuiContext, java.lang.Object)
   */
@@ -407 +407 @@
         storeValue(configuration, request, usedFieldsParameter);
         storeValue(configuration, request, jobParametersParameter);
-        // test the xml in the jobParameters parameres
+        // test the xml in the jobParameters parameters
         try
         {
@@ -448 +448 @@
   
   /**
-    Copies the content from a File to a directory on the filesystem.
+    Copies the content from a File to a directory on the file system.
     
     @param f The file to be copied.
@@ -483 +483 @@
         // Load existing...
         jobDirectory = Directory.getByPath(dc, path);
-        // ...and remove files and subdirectories in it
+        // ...and remove files and sub directories in it
         emptyDir(dc, path);
       }
@@ -503 +503 @@
   
   /**
-    Deletes all files and subdirectories under dir.
+    Deletes all files and sub directories under dir.
     
     @param dir
-    @return Returnes true if all deletions were succssful
+    @return true if all deletions were successful
   */
   private boolean deleteDir(java.io.File dir)
@@ -527 +527 @@
   
   /**
-    Deletes all files and subdirectories under dir. The directory given
+    Deletes all files and sub directories under dir. The directory given
     itself is not deleted.
     
     @param dc
     @param dir
-    @return Returnes true if all deletions were succssful
+    @return true if all deletions were successful
   */
   private boolean emptyDir(DbControl dc, Path dir)
@@ -567 +567 @@
       permissions.add(new Permissions(Item.PLUGINCONFIGURATION, EnumSet.of(Permission.WRITE), null));
       permissions.add(new Permissions(Item.RAWBIOASSAY, null, EnumSet.of(Permission.READ)));
-      permissions.add(new Permissions(Item.EXTRAVALUETYPE, null, EnumSet.of(Permission.READ)));
+      permissions.add(new Permissions(Item.REPORTER, null, EnumSet.of(Permission.READ)));
+      permissions.add(new Permissions(Item.EXTRAVALUETYPE, null, EnumSet.of(Permission.CREATE, Permission.USE)));
       permissions.add(new Permissions(Item.USER, null, EnumSet.of(Permission.READ)));
       permissions.add(new Permissions(Item.JOB, null, EnumSet.of(Permission.READ)));
@@ -605 +606 @@
     {
       DbControl dc = null;
+      File stdin = null;
+      File stdout = null;
+      Transformation trans = null;
       try
       {
@@ -611 +615 @@
         getConfigureJobParameters();
   
-        Transformation trans = null;
-        File stdin = null;
         
         //Export
@@ -653 +655 @@
           int exitValue = p.waitFor();
 
+          progress.display(50, "Reading from error stream.");
           for(int i = 0; errorStream.isAlive(); ++i)
           {
@@ -681 +684 @@
         {
           //Copy files
-          dc.deleteItem(stdin);
+          progress.display(60, "Copying files to server.");
           importFiles(dc, trans);
           if (!deleteDir(getExecDirectory()))
@@ -687 +690 @@
             response.setError("Could not remove execution directory: "+getExecDirectory().getAbsolutePath(), null);
           }
-        }
-              
+          stdout = File.getFile(dc, getPluginDirectory(dc), "stdout.txt", true);
+        }
+        
         //Import data
         try
         {
           progress.display(70, "Importing data from plugin.");
-          importData(dc, trans);
+          importData(dc, stdout, trans);
           response.setDone(msg);
         }
@@ -700 +704 @@
           response.setError(ex.getMessage(), Arrays.asList(ex));
           return;
+        }
+      }
+      finally
+      {
+        if (dc != null)
+        {
+          dc.commit();
+          dc.close();
+        }
+      }
+      
+      //Clean up
+      try
+      {
+        dc = sc.newDbControl();
+        if (!Values.getBoolean(String.valueOf(configuration.getValue(leaveStdinParameter.getName()))))
+        {
+          if (stdin != null)
+          {
+            stdin = File.getById(dc, stdin.getId());
+            if (trans != null)
+            {
+              trans = Transformation.getById(dc, trans.getId());
+              AnyToAny ata = AnyToAny.getByName(dc, trans, stdin.getPath().toString());
+              dc.deleteItem(ata);
+            }
+            dc.deleteItem(stdin);
+          }
+        }
+        if (!Values.getBoolean(String.valueOf(configuration.getValue(leaveStdoutParameter.getName()))))
+        {
+          if (stdout != null)
+          {
+            stdout = File.getById(dc, stdout.getId());
+            if (trans != null)
+            {
+              trans = Transformation.getById(dc, trans.getId());
+              AnyToAny ata = AnyToAny.getByName(dc, trans, stdout.getPath().toString());
+              dc.deleteItem(ata);
+            }
+            dc.deleteItem(stdout);
+          }
         }
       }
@@ -801 +847 @@
     Map<String, String> names = new HashMap<String, String>();
     
-    names.put("reporter", "rep.id");
-    names.put("reporterId", "rep.externalId");
-    
     ItemQuery<Formula> queryFormula = Formula.getQuery(Formula.Type.COLUMN_EXPRESSION, 
       bas.getRawDataType());
@@ -812 +855 @@
       names.put(f.getName(), "frm."+f.getId());
     }
+    
+    names.put("lastUpdate", "rep.lastUpdate");
+    names.put("geneName", "rep.name");
+    names.put("position", "rep.position");
+    names.put("reporter", "rep.id");
+    names.put("reporterId", "rep.externalId");
+    names.put("geneSymbol", "rep.symbol");
+    
+    names.put("rawPosition", "raw.position");
+    names.put("block", "raw.block");
+    names.put("numCol", "raw.col");
+    names.put("numRow", "raw.row");
+    names.put("x", "raw.x");
+    names.put("y", "raw.y");
     
     for (ExtraValue ev : bas.getExtraValues().list(dc))
@@ -1119 +1176 @@
   
   /**
-    Get the exec directory as a java.io.File. The exec directory is a sudirectory in 
+    Get the exec directory as a java.io.File. The exec directory is a sub directory in 
     "java.io.tmpdir".
     
@@ -1245 +1302 @@
     
     @return The id of the transformation the data is connected to.
-    @throws IOException if there is any error reading from stdou.txt
-  */
-  private int importData(DbControl dc, Transformation t)
+    @throws IOException if there is any error reading from stdout.txt
+  */
+  private int importData(DbControl dc, File stdout, Transformation t)
     throws IOException
   {
     BioAssaySet bas = null;
     SpotBatcher spotBatcher = null;
-    PositionBatcher posBatcher = null;
 
     HashMap<String, BioAssay> idMap = new HashMap<String, BioAssay>();
-    HashMap<Integer, Integer> posMap = new HashMap<Integer, Integer>();
+    HashMap<Integer, ReporterData> posRepMap = new HashMap<Integer, ReporterData>();
     HashMap<String, ExtraValueType> evtMap = new HashMap<String, ExtraValueType>();
 
-    File stdout = File.getFile(dc, getPluginDirectory(dc), "stdout.txt", true);
     FlatFileParser ffp = getInitializedFlatFileParser(stdout.getDownloadStream(0));
     
@@ -1325 +1380 @@
         }
         spotBatcher = bas.getSpotBatcher();
-//        posBatcher = bas.getPositionBatcher();
 
         for (String assayId : assays)
@@ -1453 +1507 @@
               spotBatcher.insert(ba.getDataCubeColumnNo(), position, intensities);
               
-//              if (posMap.containsKey(position))
-//              {
-//                if (!posMap.get(position).equals(reporter))
-//                  throw new BaseException("Invalid data. Position, "+position+", occures twice with different reporter data.");
-//                
-//              }
-//              else
-//              {
-//                posMap.put(position, reporter);
-//                posBatcher.insert(position, Reporter.getById(dc, reporter));
-//              }
+              if (posRepMap.containsKey(position))
+              {
+                if (!reporter.equals(posRepMap.get(position).getId()))
+                  throw new BaseException("Invalid data. Position, "+position+", occurs twice with different reporter data.");
+              }
+              else
+              {
+                posRepMap.put(position, Reporter.getById(dc, reporter));
+              }
+              
               for (int i = 0; i < evBatcher.size(); i++)
               {
@@ -1482 +1535 @@
       }
     }
+
+    //Batch reporters
+    if (bas != null)
+    {
+      PositionBatcher posBatcher = bas.getPositionBatcher();
+      for (Integer position : posRepMap.keySet())
+      {
+        posBatcher.insert(position, posRepMap.get(position));
+      }
+    }
+    
     // save bas
     if (bas != null)
@@ -1562 +1626 @@
   
   /**
-    This thread read everything from one input streat ant writes everything to an output stream.
+    This thread read everything from one input stream ant writes everything to an output stream.
     
     @author Johan Enell
@@ -1580 +1644 @@
 
     /**
-      Creates a steam handler connected to the specifiv streams.
+      Creates a steam handler connected to the specific streams.
       
       @param is The stream to read from.

trunk/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

@@ -858 +858 @@
       ExtraValueType evt = ev.getExtraValueType();
       items.add(new QueryItem("xtra."+evt.getExternalId(), "[Extra] "+evt.getName(), 
-        evt.getName(), "xtra('" + evt.getExternalId() + "')", evt.getAverageMethod()));
+        "_xc_"+evt.getName(), "xtra('" + evt.getExternalId() + "')", evt.getAverageMethod()));
     }
     Collections.sort(items, new QueryItemTitleComparator());
@@ -895 +895 @@
   {
     List<QueryItem> items = new ArrayList<QueryItem>();
-    items.add(new QueryItem("raw.position", "[Raw] Position", "position", "raw('position')", Formula.AverageMethod.NONE));
+    items.add(new QueryItem("raw.position", "[Raw] Position", "rawPosition", "raw('position')", Formula.AverageMethod.NONE));
     items.add(new QueryItem("raw.block", "[Raw] Array block", "block", "raw('block')", Formula.AverageMethod.NONE));
     items.add(new QueryItem("raw.metaGridX", "[Raw] Meta grid X", "metaGridX", "raw('metaGridX')", Formula.AverageMethod.NONE));
@@ -918 +918 @@
     items.add(new QueryItem("rep.position", "Position", "position", "pos()", Formula.AverageMethod.NONE));
     items.add(new QueryItem("rep.name", "Reporter Name", "name", "rep('name')", Formula.AverageMethod.MAX));
-    items.add(new QueryItem("rep.externalId", "Reporter ID", "externalId", "rep('externalId')", Formula.AverageMethod.MAX));
+    items.add(new QueryItem("rep.externalId", "Reporter ID", "reporterId", "rep('externalId')", Formula.AverageMethod.MAX));
     items.add(new QueryItem("rep.symbol", "Gene symbol", "symbol", "rep('symbol')", Formula.AverageMethod.MAX));
     items.add(new QueryItem("rep.description", "Description", "description", "rep('description')", Formula.AverageMethod.MAX));

trunk/src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java

@@ -123 +123 @@
   }
   /**
-    Request use access to Experiment:s and read access to Job:s.
+    Request use access to Experiment:s and read access to Job:s and ReporterLists.
   */
   public Collection<Permissions> getPermissions()
@@ -131 +131 @@
       permissions.add(new Permissions(Item.EXPERIMENT, null, EnumSet.of(Permission.USE)));
       permissions.add(new Permissions(Item.JOB, null, EnumSet.of(Permission.READ)));
+      permissions.add(new Permissions(Item.REPORTERLIST, null, EnumSet.of(Permission.READ)));
     }
     return permissions;

trunk/www/admin/jobagents/view_agent.jsp

@@ -341 +341 @@
           {
             PluginDefinition plugin = null;
+            NameablePluginAdaptor nameableProxy = null;
             boolean readPlugin = true;
             try
             {
               plugin = settings.getPluginDefinition();
+              nameableProxy = new NameablePluginAdaptor(plugin);
             }
             catch (PermissionDeniedException ex)
@@ -354 +356 @@
             %>
             <tbl:row>
-              <tbl:cell column="plugin"><%=Base.getLinkedName(ID, new NameablePluginAdaptor(plugin), !readPlugin, true)%></tbl:cell>
+              <tbl:cell column="plugin"><%=Base.getLinkedName(ID, nameableProxy, !readPlugin, true)%></tbl:cell>
               <tbl:cell column="jarPath"><%=jarPath == null ? "<i>- internal -</i>" : HTML.encodeTags(jarPath)%></tbl:cell>
               <tbl:cell column="trusted"><%=settings.isEffectivelyTrusted()%></tbl:cell>

trunk/www/admin/pluginconfigurations/list_configurations.jsp

@@ -429 +429 @@
               PluginConfiguration item = configurations.next();
               PluginDefinition plugin = null;
+              Nameable nameableProxy = null;
               contexts.clear();
               try
               {
                 plugin = item.getPluginDefinition();
+                nameableProxy = new NameablePluginAdaptor(plugin);
                 contexts.addAll(plugin.getGuiContexts());
               }
@@ -490 +492 @@
                 <tbl:cell column="pluginType"><%=plugin == null ? "<i>- denied -</i>" : plugin.getMainType().toString()%></tbl:cell>
                 <tbl:cell column="contexts"><%=plugin == null ? "<i>- denied -</i>" : (contexts.isEmpty() ? "<i>- none -</i>" : Values.getString(contexts, ", ", true))%></tbl:cell>
-                <tbl:cell column="pluginDefinition"><%=mode.hasPropertyLink() ? Base.getLinkedName(ID, new NameablePluginAdaptor(plugin), plugin == null, mode.hasEditLink()): Base.getEncodedName(new NameablePluginAdaptor(plugin), plugin == null)%></a></tbl:cell>
+                <tbl:cell column="pluginDefinition"><%=mode.hasPropertyLink() ? Base.getLinkedName(ID, nameableProxy, plugin == null, mode.hasEditLink()): Base.getEncodedName(nameableProxy, plugin == null)%></a></tbl:cell>
                 <tbl:cell column="owner"
                   ><base:propertyvalue 

trunk/www/admin/pluginconfigurations/view_configuration.jsp

@@ -97 +97 @@
   final Set<GuiContext> contexts = new TreeSet<GuiContext>(new ToStringComparator<GuiContext>(false));
   PluginDefinition plugin = null;
+  Nameable nameableProxy = null;
   boolean readPlugin = true;
   boolean configurable = false;
@@ -102 +103 @@
   {
     plugin = configuration.getPluginDefinition();
+    nameableProxy = new NameablePluginAdaptor(plugin);
     contexts.addAll(plugin.getGuiContexts());
     configurable = plugin.isInteractive() && plugin.supportsConfigurations();
@@ -265 +267 @@
         <td class="prompt">Plugin</td>
         <td>
-          <%=Base.getLinkedName(ID, new NameablePluginAdaptor(plugin), plugin == null, true)%>
+          <%=Base.getLinkedName(ID, nameableProxy, plugin == null, true)%>
         </td>
       </tr>

trunk/www/common/import/no_fileformat.jsp

@@ -71 +71 @@
   "mainType", Operator.EQ, String.valueOf(Plugin.MainType.IMPORT.getValue()), Type.INT));
 pluginContext.setPropertyFilter(new PropertyFilter(
-  "guiContexts.itemType", Operator.EQ, String.valueOf(itemType.getValue()), Type.INT));
+  "$ctx.itemType", Operator.EQ, String.valueOf(itemType.getValue()), Type.INT));
 try
 {

trunk/www/exception/exception.jsp

@@ -204 +204 @@
     StackTraceElement[] st = ex.getStackTrace();
     out.println("<pre>");
+    out.println(exceptionClassName);
     int i = 0;
     for (i=0; i < st.length && i < 8; i++)
     {
       out.print("...at ");
-      out.println(st[i].toString().replaceAll("net.sf.basedb.core.", ""));
+      out.println(HTML.encodeTags(st[i].toString().replaceAll("net.sf.basedb.core.", "")));
     }
     out.println("</pre>");
@@ -219 +220 @@
         {
           out.print("...at ");
-          out.println(st[j].toString().replaceAll("net.sf.basedb.core.", ""));
+          out.println(HTML.encodeTags(st[j].toString().replaceAll("net.sf.basedb.core.", "")));
         }
         ex = ex.getCause();

trunk/www/lims/arraydesigns/features/index.jsp

@@ -35 +35 @@
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PermissionDeniedException"
+  import="net.sf.basedb.core.ArrayDesign"
+  import="net.sf.basedb.core.data.FeatureData"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.WebException"
@@ -89 +91 @@
     forward = viewPage;
   }
+  else if ("ExportItems".equals(cmd))
+  {
+    // Run an export plugin in a list context
+    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    dc = sc.newDbControl();   
+    final ArrayDesign arrayDesign = ArrayDesign.getById(dc, arrayDesignId);
+    final DataQuery<FeatureData> query = arrayDesign.getFeatures();
+    cc.configureQuery(query, true);
+    cc.setQuery(query);
+    redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+features+of+array+design";
+  }
   else
   {