Changeset 3796

Timestamp:

Sep 27, 2007, 10:05:24 PM (16 years ago)

Author:

Nicklas Nordborg

Message:

Merged log:trunk#3775:3995 into filedb branch

Location:

branches/filedb

Files:

• build.xml (modified) (1 diff)
• doc/src/docbook/appendix/menuguide.xml (modified) (1 diff)
• doc/src/docbook/developerdoc/api_overview.xml (modified) (10 diffs)
• doc/src/docbook/developerdoc/documentation.xml (modified) (1 diff)
• doc/src/docbook/figures/uml/corelayer.datainfiles.png (modified) (previous)
• doc/src/docbook/figures/uml/datalayer.platforms.png (modified) (previous)
• doc/src/docbook/userdoc/index.xml (modified) (1 diff)
• doc/src/docbook/userdoc/overview.xml (copied) (copied from trunk/doc/src/docbook/userdoc/overview.xml)
• doc/src/docbook/userdoc/project_permission.xml (modified) (2 diffs)
• doc/src/docbook/userdoc/userdoc_overview.xml (deleted)
• doc/src/docbook/userdoc/webclient.xml (modified) (4 diffs)
• doc/src/uml/baseuml.mdzip (modified) (previous)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/InvalidPathException.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ItemContext.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Job.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/ParameterType.java (modified) (1 diff)
• src/core/net/sf/basedb/core/ParameterValuesImpl.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/Path.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PathParameterType.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PluginConfiguration.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (6 diffs)
• src/core/net/sf/basedb/util/overview/ExperimentOverview.java (modified) (12 diffs)
• src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java (modified) (3 diffs)
• src/test/TestAnnotation.java (modified) (3 diffs)
• src/test/TestPath.java (modified) (4 diffs)
• www/common/annotations/list_annotations.jsp (modified) (1 diff)
• www/views/reporters/index.jsp (modified) (3 diffs)

branches/filedb/build.xml

@@ -1078 +1078 @@
     <mkdir dir="${docbook.html.out}/userdoc/trashcan"/>
     <mkdir dir="${docbook.html.out}/userdoc/webclient"/>
+    <mkdir dir="${docbook.html.out}/userdoc/overview"/>
     <mkdir dir="${docbook.html.out}/faqs" />
     <mkdir dir="${docbook.html.out}/appendix" />

branches/filedb/doc/src/docbook/appendix/menuguide.xml

@@ -37 +37 @@
       <listitem>
         <simpara>
-          <link linkend="menuguide.tables.config">Config</link>
+          <link linkend="menuguide.tables.config">Configurations</link>
         </simpara>
       </listitem>

branches/filedb/doc/src/docbook/developerdoc/api_overview.xml

@@ -824 +824 @@
           The <classname>PlatformData</classname> holds information about a
           platform. A platform can have one or more <classname>PlatformVariant</classname>:s.
-          Both the platform and variant are identified by a system ID that
+          Both the platform and variant are identified by an external ID that
           is fixed and can't be changed. <emphasis>Affymetrix</emphasis>
           and <emphasis>Illumina</emphasis> are examples of platforms.
@@ -837 +837 @@
         <para>
           Each platform and it's variant can be connected to one or more
-          <classname>FileSetMemberTypeData</classname> items. This item 
+          <classname>DataFileTypeData</classname> items. This item 
           describes the kind of files that are used to hold data for
           the platform and/or variant. The file types are re-usable between
@@ -848 +848 @@
         <para>
           The file type is also identified
-          by a fixed, non-changable system ID. The <varname>itemType</varname>
+          by a fixed, non-changable external ID. The <varname>itemType</varname>
           property tells us what type of item the file holds data for (ie. 
           array design or raw bioassay). It also links to a <classname>FileType</classname>
@@ -857 +857 @@
           get another file.
         </para>
+        <para>
+          The <varname>required</varname> flag in <classname>PlatformFileTypeData</classname>
+          is used to signal that the file is a required file. This will, however, not be
+          enforeced by the core. It is intended to be used by client applications
+          for creating a better GUI and/or validation of an experiment.
+        </para>
 
       </sect3>
       
       <sect3 id="data_api.platforms.files">
-        <title>Files</title>
+        <title>Data files</title>
         
         <para>
           An item must implement the <interfacename>FileStoreEnabledData</interfacename>
           interface to be able to store data in files instead of in the database.
-          The interface creates a link to a <classname>FileSetData</classname> object.
-          In a file set it is only possible to store one file for each 
-          <classname>FileSetMemberTypeData</classname> item.
+          The interface creates a link to a <classname>FileSetData</classname> object,
+          which is can hold several <classname>FileSetMemberData</clasname> items.
+          Each member points to specific <classname>FileData</classname> item.
+          A file set can only store one file of each type.
         </para>
         
@@ -1030 +1037 @@
         <para>
           Given that we have a <interfacename>FileStoreEnabled</interfacename>
-          item we use the <methodname>FileSetMemberType.getQuery()</methodname>
+          item we use the <methodname>DataFileType.getQuery()</methodname>
           method to find which file types that can be used for that
           item. Internally, the <methodname>getQuery()</methodname>
@@ -1039 +1046 @@
           a platform or variant the query will only return file types
           that are associated with the given item type, but not with any specific 
-          platform. In any case, we get a list of <classname>FileSetMemberType</classname>
+          platform. In any case, we get a list of <classname>DataFileType</classname>
           items, each one representing a specific file type that 
           we should ask the user about. Examples:
@@ -1069 +1076 @@
 DbControl dc = ...
 FileStoreEnabled item = ...
-ItemQuery&lt;FileSetMemberType&gt; query =
-   FileSetMemberType.getQuery(item);
-List&lt;FileSetMemberType&gt; types = query.list(dc);
+ItemQuery&lt;DataFileType&gt; query =
+   DataFileType.getQuery(item);
+List&lt;DataFileType&gt; types = query.list(dc);
 // We now have a list of file types...
 // ... ask the user to select a file for each one of them
@@ -1099 +1106 @@
           and metadata extraction is automatically done by the core when a
           file is added to a file set. The process is partly pluggable
-          since each <classname>FileSetMemberType</classname> can name a class
+          since each <classname>DataFileType</classname> can name a class
           that should do the validation and/or metadata extraction. 
           Here is the general outline:
@@ -1106 +1113 @@
         <programlisting>
 FileStoreEnabled item = ...
-FileSetMemberType type = ...
+DataFileType type = ...
 File file = ...
 FileSetMember member = new FileSetMember(file, type);
 
-FileValidator validator = type.getValidator();
-MetadataReader metadata = type.getMetadataReader();
+DataFileValidator validator = type.getValidator();
+DataFileMetadataReader metadata = type.getMetadataReader();
 validator.setFile(member);
 validator.setItem(item);
@@ -1135 +1142 @@
         <para>
           All validators and meta data extractors should extend
-          the <classname>AbstractFileHandler</classname> class. The reason
-          is that we may want to add more methods to the <interfacename>FileHandler</interfacename>
-          interface in the future. The <classname>AbstractFileHandler</classname> will
+          the <classname>AbstractDataFileHandler</classname> class. The reason
+          is that we may want to add more methods to the <interfacename>DataFileHandler</interfacename>
+          interface in the future. The <classname>AbstractDataFileHandler</classname> will
           be used to provide default implementations for backwards compatibility.
         </para>

branches/filedb/doc/src/docbook/developerdoc/documentation.xml

@@ -982 +982 @@
             <tip>
               <para>
-              Change your BASE <link linkend="webclient.configuration.preferences"
-                >preferences</link> to a smaller font size or use
-              the zoom functionality in the web browser to make more information
-              fit in the same image width.
+                Change your BASE preferences, see
+                <xref linkend="webclient.configuration.preferences" />,
+                to a smaller font size or use the zoom functionality in the web
+                browser to make more information fit in the same image width.
               </para>
             </tip>

branches/filedb/doc/src/docbook/userdoc/index.xml

@@ -29 +29 @@
   <?dbhtml dir="userdoc"?>
   <title>User documentation</title>
-  <include file="userdoc_overview.xml"/>
+  <include file="overview.xml"/>
   <include file="webclient.xml"/>
   <include file="project_permission.xml"/>

branches/filedb/doc/src/docbook/userdoc/project_permission.xml

@@ -107 +107 @@
             <listitem>
               <para>
-              Permission to change the owner of an item. This is implemented
-              as a <link linkend="webclient.items.takeownership">Take ownership</link>
-              function in the web client, where you can take the ownership of  
-              items that you do not already own.
+                Permission to change the owner of an item. This is implemented as a
+                <synopsis>Take ownership</synopsis> function in the web client
+                (<xref linkend="webclient.items.takeownership" />), where you can 
+                take the ownership of items that you do not already own.
               </para>
             </listitem>
@@ -386 +386 @@
             <listitem>
               <para>
-              The easiest way and the one you will probably
-              use most of the time is to use the 
-              <link linkend="webclient.intro.menubar">menu bar</link> shortcut.
-              Look in the menu for the project icon (<guiicon><inlinemediaobject>
-              <imageobject><imagedata fileref="figures/project.gif" format="GIF" /></imageobject>
-              </inlinemediaobject></guiicon>). Next to it, the name of the active project
-              is displayed. If you see <guilabel>- none -</guilabel> here, it
-              means that no project is active. Click on the icon or project name 
-              to open a drop-down menu and select a project to set as the active
-              project. If another project is already active it will automatically
-              be unactivated.
+                The easiest way and the one you will probably use most of the time
+                is to use the menu bar shortcut. Look in the menu for the project
+                icon 
+                (<guiicon>
+                  <inlinemediaobject>
+                    <imageobject>
+                      <imagedata fileref="figures/project.gif" format="GIF" />
+                    </imageobject>
+                  </inlinemediaobject>
+                </guiicon>). 
+                Next to it, the name of the active project is displayed. If you see
+                <guilabel>- none -</guilabel>
+                here, it means that no project is active. Click on the icon or
+                project name to open a drop-down menu and select a project to set as
+                the active project. If another project is already active it will
+                automatically be inactivated.
               </para>
             </listitem>

branches/filedb/doc/src/docbook/userdoc/webclient.xml

@@ -1006 +1006 @@
             the same protocol is used the next time you create another extract.
             In fact, BASE will remember as many items as specified by
-            the <link linkend="webclient.configuration.preferences.appearance">
-            <guilabel>Recently used items</guilabel></link> setting (default is 4),
-            allowing you to quickly select one of those protocols.
+            the 
+            <guilabel>Recently used items</guilabel> setting (default is 4),
+            allowing you to quickly select one of those protocols. 
+            <xref linkend="webclient.configuration.preferences.appearance"/> 
+            contains more information about the setting.
             </para>
           </listitem>
@@ -1101 +1103 @@
           You can restore deleted items either from the trashcan,
           from the list view or from the single-item view. This section only covers the last two
-          cases. The trashcan has a <link linkend="trashcan">chapter of it's own</link>.
+          cases. The trashcan has a section of it's own(<xref linkend="trashcan"/>).
         </para>
 
@@ -1322 +1324 @@
       
       <para>
-        Use the <link linkend="webclient.intro.menubar">menu</link> to
-        open a page listing items. Most list pages can only
-        list one type of items. For example: use the 
-        <menuchoice><guimenu>View</guimenu><guimenuitem>Samples</guimenuitem></menuchoice>
-        menu to list samples and the 
-        <menuchoice><guimenu>View</guimenu><guimenuitem>Experiments</guimenuitem></menuchoice>
-        menu to list experiments. 
+        Use the menu to open a page listing items. Most list pages can only list one type of
+        items. For example: use the
+        <menuchoice>
+          <guimenu>View</guimenu>
+          <guimenuitem>Samples</guimenuitem>
+        </menuchoice>
+        menu to list samples and the
+        <menuchoice>
+          <guimenu>View</guimenu>
+          <guimenuitem>Experiments</guimenuitem>
+        </menuchoice>
+        menu to list experiments.
       </para>
-      
+
       <tip>
         An example of a list page that can list
@@ -1680 +1687 @@
               <listitem>
                 <para><guilabel>Other&hellip;</guilabel> - 
-                  Open the <link linkend="webclient.itemlist.columns">configure columns dialog box</link>.</para>
+                  Open the configure columns dialog box, described in 
+                  <xref linkend="webclient.itemlist.columns"/>.</para>
               </listitem>
             </itemizedlist>

branches/filedb/src/core/net/sf/basedb/core/Install.java

@@ -107 +107 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(42).intValue();
+  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(43).intValue();
   
   public static synchronized void createTables(boolean update, final ProgressReporter progress)

branches/filedb/src/core/net/sf/basedb/core/InvalidPathException.java

@@ -43 +43 @@
   public InvalidPathException(String path)
   {
-    super("Invalid path: " + path);
+    super(path);
   }
 

branches/filedb/src/core/net/sf/basedb/core/ItemContext.java

@@ -898 +898 @@
     // Tempoarary storage for all associations that must be left joined
     Set<String> leftJoins = autoLeftJoin ? new HashSet<String>() : null;
+    Set<String> sortedProperties = autoLeftJoin ? new HashSet<String>() : null;
     
     // Add sort order information
@@ -930 +931 @@
           if (dotIndex >= 0)
           {
-            leftJoins.add(sortProperty.substring(0, dotIndex));
+            String toJoin = sortProperty.substring(0, dotIndex);
+            leftJoins.add(toJoin);
+            sortedProperties.add(toJoin);
           }
         }
@@ -995 +998 @@
     {
       int i = 0;
+      // Use fetch joins for columns appearing in the ORDER BY clause
+      // if the query is distinct and the database requires it
+      boolean selectOrderBy = query.isDistinct() && 
+        HibernateUtil.getDbEngine().selectOrderByColumnsIfDistinct();
       for (String property : leftJoins)
       {
+        boolean fetch = selectOrderBy && sortedProperties.contains(property);
         if (property.startsWith("@")) property = property.substring(1);
         i++;
-        query.join(Hql.leftJoin(property, "alj"+i));
+        query.join(Hql.leftJoin(null, property, "alj"+i, null, fetch));
       }
     }

branches/filedb/src/core/net/sf/basedb/core/Job.java

@@ -997 +997 @@
     throws InvalidDataException, PermissionDeniedException, BaseException
   {
+    checkPermission(Permission.WRITE);
+    if (name == null) throw new InvalidUseOfNullException("name");
     if (getStatus() == Status.EXECUTING) 
     {
@@ -1002 +1004 @@
     }
     getData().setStatus(Status.WAITING.getValue());
-    setParameterValuesInternal(name, label, description, parameterType, Arrays.asList(value));
+    setParameterValuesInternal(name, label, description, parameterType, Arrays.asList(value), true);
   }
   
@@ -1046 +1048 @@
     throws InvalidDataException, PermissionDeniedException, BaseException
   {
+    checkPermission(Permission.WRITE);
+    if (name == null) throw new InvalidUseOfNullException("name");
     if (getStatus() == Status.EXECUTING) 
     {
@@ -1051 +1055 @@
     }
     getData().setStatus(Status.WAITING.getValue());
-    setParameterValuesInternal(name, label, description, parameterType, values);
+    setParameterValuesInternal(name, label, description, parameterType, values, true);
   }
   
@@ -1111 +1115 @@
     @param values A list containing the new values, null or empty to remove the 
       configuration values
+    @param validate If validation by {@link ParameterType#validate(String, List)}
+      is needed or not
     @throws PermissionDeniedException If the logged in user doesn't have
       write permission
@@ -1117 +1123 @@
     @throws BaseException If there is another error
   */
-  void setParameterValuesInternal(String name, String label, String description, ParameterType<?> parameterType, List<?> values)
+  void setParameterValuesInternal(String name, String label, String description, 
+    ParameterType<?> parameterType, List<?> values, boolean validate)
     throws InvalidDataException, PermissionDeniedException, BaseException
   {
-    checkPermission(Permission.WRITE);
-    if (name == null) throw new InvalidUseOfNullException("name");
     ParameterValueData old = null;
     if (values == null || values.size() == 0)
@@ -1130 +1135 @@
     {
       if (parameterType == null) throw new InvalidUseOfNullException("parameterType");
-      parameterType.validate(name, values);
+      if (validate) parameterType.validate(name, values);
       ParameterValueData<?> parameterValue = parameterType.newParameterValueData();
       parameterValue.setLabel(label);

branches/filedb/src/core/net/sf/basedb/core/ParameterType.java

@@ -218 +218 @@
       if (!items.contains(value))
       {
-        throw new InvalidDataException("The value '" + value + "' isn't in the list of allowed values.");
+        throw new InvalidDataException("The value '" + value + "' isn't in the list of allowed values for parameter '" + name + "'.");
       }
     }

branches/filedb/src/core/net/sf/basedb/core/ParameterValuesImpl.java

@@ -161 +161 @@
     if (writeProtected) 
     {
-      throw new PermissionDeniedException(Permission.WRITE, "Job parameter: "+name);
-    }
+      throw new PermissionDeniedException(Permission.WRITE, "Parameter: "+name);
+    }
+    if (name == null) throw new InvalidUseOfNullException("name");
+    if (type == null) throw new InvalidUseOfNullException("type[name=" + name + "]");
     if (value == null && type.getNotNull()) value = type.getDefaultValue();
+    type.validate(name, value);
     List<T> l = new ArrayList<T>(1);
     l.add(value);
@@ -176 +179 @@
     if (writeProtected) 
     {
-      throw new PermissionDeniedException(Permission.WRITE, "Job parameter: "+name);
-    }
+      throw new PermissionDeniedException(Permission.WRITE, "Parameter: "+name);
+    }
+    if (name == null) throw new InvalidUseOfNullException("name");
+    if (type == null) throw new InvalidUseOfNullException("type[name=" + name + "]");
     if ((values == null || values.size() == 0) && type.getNotNull() && type.getDefaultValue() != null)
     {
       values = Arrays.asList(type.getDefaultValue());
     }
+    type.validate(name, values);
     parameters.put(name, values);
     parameterTypes.put(name, type);
@@ -203 +209 @@
       if (pp == null)
       {
-        job.setParameterValuesInternal(name, null, null, parameterTypes.get(name), parameters.get(name));
+        job.setParameterValuesInternal(name, null, null,
+          parameterTypes.get(name), parameters.get(name), false);
       }
       else
       {
-        job.setParameterValuesInternal(name, pp.getLabel(), pp.getDescription(), parameterTypes.get(name), parameters.get(name));
+        job.setParameterValuesInternal(name, pp.getLabel(), pp.getDescription(), 
+          parameterTypes.get(name), parameters.get(name), false);
       }
     }
@@ -223 +231 @@
       if (pp == null)
       {
-        config.setParameterValues(name, null, null, parameterTypes.get(name), parameters.get(name));
+        config.setParameterValuesInternal(name, null, null, 
+          parameterTypes.get(name), parameters.get(name), false);
       }
       else
       {
-        config.setParameterValues(name, pp.getLabel(), pp.getDescription(), parameterTypes.get(name), parameters.get(name));
+        config.setParameterValuesInternal(name, pp.getLabel(), pp.getDescription(), 
+          parameterTypes.get(name), parameters.get(name), false);
       }
     }

branches/filedb/src/core/net/sf/basedb/core/Path.java

@@ -143 +143 @@
       }
       filename = parts[parts.length-1];
+      if (!Path.isValidName(filename)) 
+      {
+        throw new InvalidPathException("Path contains invalid characters ("+Path.INVALID_CHARACTERS+"): "+path);
+      }
       parts[parts.length-1] = "";
     }

branches/filedb/src/core/net/sf/basedb/core/PathParameterType.java

@@ -87 +87 @@
     Checks if the value is a valif {@link Path} value.
     @param value The value to test
-    @throws InvalidDataException If the value is not a string or too long
+    @throws InvalidDataException If the value is not a valid path
   */
   void validateValue(String name, String value)
     throws InvalidDataException
   {
-    new Path(value, pathType);
+    try
+    {
+      new Path(value, pathType);
+    }
+    catch (InvalidPathException ex)
+    {
+      throw new InvalidPathException("Path for parameter '"+ name + "' is invalid: " + ex.getMessage());
+    }
   }
   /**

branches/filedb/src/core/net/sf/basedb/core/PluginConfiguration.java

@@ -428 +428 @@
     checkPermission(Permission.WRITE);
     if (name == null) throw new InvalidUseOfNullException("name");
-    
+    setParameterValuesInternal(name, label, description, parameterType, values, true);
+  }
+
+  /**
+    Set the values of a configuration parameter.
+    @param name The name of the configuration parameter
+    @param label The label of the parameter (optional)
+    @param description A description of the parameter (optional)
+    @param parameterType The type of the parameter
+    @param values A list containing the new values, null or empty to remove the 
+      configuration values
+    @param validate If validation by {@link ParameterType#validate(String, List)}
+      is needed or not
+    @throws PermissionDeniedException If the logged in user doesn't have
+      write permission
+    @throws InvalidDataException If name is null or the new value doesn't
+      validate against the parameter type
+    @throws BaseException If there is another error
+  */
+  void setParameterValuesInternal(String name, String label, String description, 
+    ParameterType<?> parameterType, List<?> values, boolean validate)
+    throws InvalidDataException, PermissionDeniedException, BaseException
+  {
+
     VersionedParameter param = new VersionedParameter(name, getNewParameterVersion());
-    
     if (values == null || values.size() == 0)
     {
@@ -438 +460 @@
     {
       if (parameterType == null) throw new InvalidUseOfNullException("parameterType");
-      parameterType.validate(name, values);
+      if (validate) parameterType.validate(name, values);
       ParameterValueData<?> parameterValue = parameterType.newParameterValueData();
       parameterValue.setLabel(label);
@@ -446 +468 @@
     }
   }
-
+  
   /**
     Copy all parameter values from another plugin configuration. This method

branches/filedb/src/core/net/sf/basedb/core/Update.java

@@ -474 +474 @@
     <td>40</td>
     <td>
-      Change invalid property filter on 'guiContexts.itemType' to 
-      '$ctx.itemType'.
+      Used to "Change invalid property filter on 'guiContexts.itemType' to 
+      '$ctx.itemType'", but since the source problem never was fixed this is now
+      done in 43.
     </td>
   </tr>
@@ -499 +500 @@
       The update will query the database or check the CDF file to get
       the information.
+    </td>
+  </tr>
+  
+  <tr>
+    <td>43</td>
+    <td>
+      Change invalid property filter on 'guiContexts.itemType' to 
+      '$ctx.itemType'". Was originally fixed by 40, but since the source
+      problem never was fixed it must be done again.
     </td>
   </tr>
@@ -697 +707 @@
         schemaVersion = updateToSchemaVersion39(session);
       }
-      
-      if (schemaVersion < 40)
-      {
-        if (progress != null) progress.display((int)(39*progress_factor), "--Updating schema version: " + schemaVersion + " -> 40...");        
-        schemaVersion = updateToSchemaVersion40(session);
-      }
-      
+          
       if (schemaVersion < 41)
       {
@@ -714 +718 @@
         if (progress != null) progress.display((int)(41*progress_factor), "--Updating schema version: " + schemaVersion + " -> 42...");
         schemaVersion = updateToSchemaVersion42(session);
+      }
+      
+      if (schemaVersion < 43)
+      {
+        if (progress != null) progress.display((int)(42*progress_factor), "--Updating schema version: " + schemaVersion + " -> 43...");        
+        schemaVersion = updateToSchemaVersion43(session);
       }
 
@@ -1589 +1599 @@
       if (tx != null) HibernateUtil.rollback(tx); 
       log.error("updateToSchemaVersion39: FAILED", ex);
-      throw ex;
-    }
-    return schemaVersion;   
-  }
-
-  /**
-    Update property filter on 'guiContexts.itemType' to '$ctx.itemType'
-    @return The new schema version (=40)
-  */
-  private static int updateToSchemaVersion40(org.hibernate.Session session)
-  {
-    final int schemaVersion = 40;
-    org.hibernate.Transaction tx = null;
-    try
-    {
-      tx = HibernateUtil.newTransaction(session);
-  
-      // Change property values
-      org.hibernate.Query query = HibernateUtil.getPredefinedSQLQuery(session, 
-          "UPDATE_PROPERTY_FILTER");
-      /*
-        UPDATE PropertyFilters pf
-        SET pf.property = :newProperty
-        WHERE pf.property = :oldProperty
-       */
-      query.setString("oldProperty", "guiContexts.itemType");
-      query.setString("newProperty", "$ctx.itemType");
-      HibernateUtil.executeUpdate(query);
-
-      // Update the schema version number
-      setSchemaVersion(session, schemaVersion);
-  
-      // Commit the changes
-      HibernateUtil.commit(tx);
-      log.info("updateToSchemaVersion40: OK");
-    }
-    catch (BaseException ex)
-    {
-      if (tx != null) HibernateUtil.rollback(tx); 
-      log.error("updateToSchemaVersion40: FAILED", ex);
       throw ex;
     }
@@ -1718 +1688 @@
   }
   
-  
+  /**
+    Update property filter on 'guiContexts.itemType' to '$ctx.itemType'
+    @return The new schema version (=43)
+  */
+  private static int updateToSchemaVersion43(org.hibernate.Session session)
+  {
+    final int schemaVersion = 43;
+    org.hibernate.Transaction tx = null;
+    try
+    {
+      tx = HibernateUtil.newTransaction(session);
+  
+      // Change property values
+      org.hibernate.Query query = HibernateUtil.getPredefinedSQLQuery(session, 
+          "UPDATE_PROPERTY_FILTER");
+      /*
+        UPDATE PropertyFilters pf
+        SET pf.property = :newProperty
+        WHERE pf.property = :oldProperty
+       */
+      query.setString("oldProperty", "guiContexts.itemType");
+      query.setString("newProperty", "$ctx.itemType");
+      HibernateUtil.executeUpdate(query);
+  
+      // Update the schema version number
+      setSchemaVersion(session, schemaVersion);
+  
+      // Commit the changes
+      HibernateUtil.commit(tx);
+      log.info("updateToSchemaVersion40: OK");
+    }
+    catch (BaseException ex)
+    {
+      if (tx != null) HibernateUtil.rollback(tx); 
+      log.error("updateToSchemaVersion40: FAILED", ex);
+      throw ex;
+    }
+    return schemaVersion;   
+  }
+
   /**
     Adjust the existing items in the database to be compatible with the latest mappings.

branches/filedb/src/core/net/sf/basedb/util/overview/ExperimentOverview.java

@@ -283 +283 @@
     
     // Load 'Required for MIAME' annotation types (parameter='false' must also be set)
-    ItemQuery<AnnotationType> query = initQuery(AnnotationType.getQuery(null), "name");
+    ItemQuery<AnnotationType> query = initQuery(AnnotationType.getQuery(null), null, "name");
     query.restrict(
       Restrictions.eq(
@@ -556 +556 @@
     Node efNode = new Node("experimental.factors", "Experimental factors", rootNode);
     Experiment experiment = (Experiment)rootNode.getItem();
-    ItemQuery<AnnotationType> efQuery = initQuery(experiment.getExperimentalFactors(), "name");
+    ItemQuery<AnnotationType> efQuery = initQuery(experiment.getExperimentalFactors(), null, "name");
     for (AnnotationType ef : efQuery.list(dc))
     {
@@ -574 +574 @@
     Node rawBioAssaysNode = new Node("rawbioassays", "Raw bioassays", rootNode);
     Experiment experiment = (Experiment)rootNode.getItem();
-    ItemQuery<RawBioAssay> rbaQuery = initQuery(experiment.getRawBioAssays(), "name");
+    ItemQuery<RawBioAssay> rbaQuery = initQuery(experiment.getRawBioAssays(), null, "name");
     Set<BasicItem> arrayDesigns = new HashSet<BasicItem>();
     for (RawBioAssay rba : rbaQuery.list(dc))
@@ -801 +801 @@
     Node imagesNode = new Node("images", "Images", scanNode);
     Scan scan = (Scan)scanNode.getItem();
-    ItemQuery<Image> imageQuery = initQuery(scan.getImages(), "name");
+    ItemQuery<Image> imageQuery = initQuery(scan.getImages(), null, "name");
     for (Image image : imageQuery.list(dc))
     {
@@ -831 +831 @@
     Hybridization hyb = (Hybridization)hybNode.getItem();
     ItemQuery<LabeledExtract> leQuery = 
-      (ItemQuery<LabeledExtract>)initQuery(hyb.getCreationEvent().getSources(), "label.name");
+      (ItemQuery<LabeledExtract>)initQuery(hyb.getCreationEvent().getSources(), null, "label.name");
     int added = 0;
     int channels = experiment.getRawDataType().getChannels();
@@ -935 +935 @@
     
     ItemQuery<LabeledExtract> sourceQuery = 
-      initQuery((ItemQuery<LabeledExtract>)product.getCreationEvent().getSources(), "name");
+      initQuery((ItemQuery<LabeledExtract>)product.getCreationEvent().getSources(), null, "name");
     
     int added = 0;
@@ -1058 +1058 @@
     
     ItemQuery<Extract> sourceQuery = 
-      initQuery((ItemQuery<Extract>)product.getCreationEvent().getSources(), "name");
+      initQuery((ItemQuery<Extract>)product.getCreationEvent().getSources(), null, "name");
     
     int added = 0;
@@ -1162 +1162 @@
     
     ItemQuery<Sample> sourceQuery = 
-      initQuery((ItemQuery<Sample>)product.getCreationEvent().getSources(), "name");
+      initQuery((ItemQuery<Sample>)product.getCreationEvent().getSources(), null, "name");
     
     int added = 0;
@@ -1534 +1534 @@
     AnnotationSet as = annotatable != null && annotatable.isAnnotated() ? 
         annotatable.getAnnotationSet() : null;
-    ItemQuery<AnnotationType> parameterQuery = initQuery(protocol.getParameters(), "name");
+    ItemQuery<AnnotationType> parameterQuery = initQuery(protocol.getParameters(), null, "name");
     List<AnnotationType> parameters = parameterQuery.list(dc);
     Node parameterNode = null;
@@ -1582 +1582 @@
       annotationsNode = new Node("annotations", "Annotations", parentNode);
       AnnotationSet as = parent.getAnnotationSet();
-      ItemQuery<Annotation> annotationQuery = initQuery(as.getAnnotations(), "annotationType.name");
+      ItemQuery<Annotation> annotationQuery = initQuery(as.getAnnotations(), null, "annotationType.name");
     
       for (Annotation a : annotationQuery.list(dc))
@@ -1662 +1662 @@
       annotationTypes.clear();
       AnnotationSet as = parent.getAnnotationSet();
-      ItemQuery<Annotation> annotationQuery = initQuery(as.getAllInheritedAnnotations(), "annotationType.name");
+      ItemQuery<Annotation> annotationQuery = initQuery(as.getAllInheritedAnnotations(), "at", "name");
+      annotationQuery.join(Hql.innerJoin(null, "annotationType", "at", true));
       List<Annotation> inherited = annotationQuery.list(dc);
       if (inherited.size() > 0)
@@ -1727 +1728 @@
     Set include options and sorting order for a query.
   */
-  private <T extends BasicItem> ItemQuery<T> initQuery(ItemQuery<T> query, String sortProperty)
+  private <T extends BasicItem> ItemQuery<T> initQuery(ItemQuery<T> query, String sortAlias, String sortProperty)
   {
     query.include(Include.MINE, Include.IN_PROJECT, Include.SHARED, Include.OTHERS);
-    query.order(Orders.asc(Hql.property(sortProperty)));
+    query.order(Orders.asc(Hql.property(sortAlias, sortProperty)));
     return query;
   }

branches/filedb/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -1377 +1377 @@
         if (bas == null)
         {
-          bas = t.newProduct(null, "new", false);
+          bas = t.newProduct("new", "new", false);
         }
         spotBatcher = bas.getSpotBatcher();

branches/filedb/src/plugins/core/net/sf/basedb/plugins/PackedFileExporter.java

@@ -376 +376 @@
     // Prepare for compression
     String rootPath = rootDir.getPath().toString();
+    if (!rootPath.endsWith("/")) rootPath += "/";
     out.setMimeType(packer.getMimeType());
     out.setFilename(generateDefaultName(packer, rootDir, itemsToPack));
@@ -405 +406 @@
       
       // Remove rootPath from entryPath
-      entryPath = entryPath.substring(rootPath.length()+1);
+      entryPath = entryPath.substring(rootPath.length());
       
       // Update progress
@@ -657 +658 @@
   private String generateDefaultPath(FilePacker packer, Directory rootDir, Collection<Nameable> selectedItems)
   {
-    String defaultPath = rootDir == null ? "~/" : rootDir.getPath().toString() + "/";
+    String defaultPath = rootDir == null ? "~/" : rootDir.getPath().toString();
+    if (!defaultPath.endsWith("/")) defaultPath += "/";
     defaultPath +=  generateDefaultName(packer, rootDir, selectedItems);
     return defaultPath;

branches/filedb/src/test/TestAnnotation.java

@@ -26 +26 @@
 
 import net.sf.basedb.core.*;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Orders;
 
 import java.util.Date;
@@ -81 +83 @@
     // Test: list inherited annotations and annotation sets
     test_list_inherited_annotations(rawBioAssayId, 2);
+    test_list_allinherited_annotations(rawBioAssayId, 9);
     test_list_inherited_annotationsets(rawBioAssayId, 1);
     test_list_inheriting_annotationsets(arrayDesignId, 1);
@@ -342 +345 @@
     }
   }
+  
+  static void test_list_allinherited_annotations(int rawBioAssayId, int expectedResults)
+  {
+    if (rawBioAssayId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      RawBioAssay rba = RawBioAssay.getById(dc, rawBioAssayId);
+      ItemQuery<Annotation> query = rba.getAnnotationSet().getAllInheritedAnnotations();
+      query.join(Hql.innerJoin(null, "annotationType", "at", true));
+      query.order(Orders.asc(Hql.property("at", "name")));
+      List<Annotation> l = query.list(dc);
+      for (int i = 0; i<l.size(); i++)
+      {
+        write_item(i, l.get(i));
+      }
+      if (expectedResults >= 0 && expectedResults != l.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+l.size());
+      }
+      write("--List all inherited annotations OK ("+l.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List all inherited annotations FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
 
   static void test_list_inherited_annotationsets(int rawBioAssayId, int expectedResults)

branches/filedb/src/test/TestPath.java

@@ -42 +42 @@
   {
     write("++Testing path");
-    test_create("/filename", Path.Type.FILE);
-    test_create("/directory/filename", Path.Type.FILE);
-    test_create("/directory/subdirectory/filename", Path.Type.FILE);
-    test_create("~userlogin/filename", Path.Type.FILE);
-    test_create("~userlogin/directory/filename", Path.Type.FILE);
-    test_create("~userlogin/directory/subdirectory/filename", Path.Type.FILE);
-    test_create("~/filename", Path.Type.FILE);
-    test_create("~/directory/filename", Path.Type.FILE);
-    test_create("~/directory/subdirectory/filename", Path.Type.FILE);
+    test_create("/filename", Path.Type.FILE, false);
+    test_create("/directory/filename", Path.Type.FILE, false);
+    test_create("/directory/subdirectory/filename", Path.Type.FILE, false);
+    test_create("~userlogin/filename", Path.Type.FILE, false);
+    test_create("~userlogin/directory/filename", Path.Type.FILE, false);
+    test_create("~userlogin/directory/subdirectory/filename", Path.Type.FILE, false);
+    test_create("~/filename", Path.Type.FILE, false);
+    test_create("~/directory/filename", Path.Type.FILE, false);
+    test_create("~/directory/subdirectory/filename", Path.Type.FILE, false);
 
-    test_create("/", Path.Type.DIRECTORY);
-    test_create("/directory", Path.Type.DIRECTORY);
-    test_create("/directory/subdirectory", Path.Type.DIRECTORY);
-    test_create("/directory/subdirectory/subsub", Path.Type.DIRECTORY);
-    test_create("~userlogin", Path.Type.DIRECTORY);
-    test_create("~userlogin/directory", Path.Type.DIRECTORY);
-    test_create("~userlogin/directory/subdirectory", Path.Type.DIRECTORY);
-    test_create("~userlogin/directory/subdirectory/subsub", Path.Type.DIRECTORY);
-    test_create("~", Path.Type.DIRECTORY);
-    test_create("~/directory", Path.Type.DIRECTORY);
-    test_create("~/directory/subdirectory", Path.Type.DIRECTORY);
-    test_create("~/directory/subdirectory/subsub", Path.Type.DIRECTORY);
+    test_create("/", Path.Type.DIRECTORY, false);
+    test_create("/directory", Path.Type.DIRECTORY, false);
+    test_create("/directory/subdirectory", Path.Type.DIRECTORY, false);
+    test_create("/directory/subdirectory/subsub", Path.Type.DIRECTORY, false);
+    test_create("~userlogin", Path.Type.DIRECTORY, false);
+    test_create("~userlogin/directory", Path.Type.DIRECTORY, false);
+    test_create("~userlogin/directory/subdirectory", Path.Type.DIRECTORY, false);
+    test_create("~userlogin/directory/subdirectory/subsub", Path.Type.DIRECTORY, false);
+    test_create("~", Path.Type.DIRECTORY, false);
+    test_create("~/directory", Path.Type.DIRECTORY, false);
+    test_create("~/directory/subdirectory", Path.Type.DIRECTORY, false);
+    test_create("~/directory/subdirectory/subsub", Path.Type.DIRECTORY, false);
 
     test_valid_name("abc", true);
@@ -77 +77 @@
     test_valid_name("|abc", false);
     
+    test_create("/file<name>", Path.Type.FILE, true);
+    test_create("/dire<ctory>/filename", Path.Type.FILE, true);
+    test_create("/directory/file<name>", Path.Type.FILE, true);
+    test_create("/sub<dir>", Path.Type.DIRECTORY, true);
+    test_create("/directory/sub<dir>", Path.Type.DIRECTORY, true);
+    
     test_replace_invalid("abc", ".", "abc");
     test_replace_invalid("~abc", ".", ".abc");
@@ -85 +91 @@
   }
   
-  static void test_create(String path, Path.Type type)
+  static void test_create(String path, Path.Type type, boolean shouldFail)
   {
     try
@@ -95 +101 @@
         throw new Exception("Original path ("+path+") is different from path: "+pp);
       }
-      write("--Path " + p.getType() + ": '"+p+"' OK");
+      if (shouldFail)
+      {
+        write("--Path '"+path+"' FAILED");
+        new Throwable("Expected test to fail but it didn't.").printStackTrace();
+        ok = false;
+      }
+      else
+      {
+        write("--Path " + p.getType() + ": '"+p+"' OK");
+      }
     }
     catch (Throwable ex)
     {
-      write("--Path '"+path+"' FAILED");
-      ex.printStackTrace();
-      ok = false;
+      if (!shouldFail)
+      {
+        write("--Path '"+path+"' FAILED");
+        ex.printStackTrace();
+        ok = false;
+      }
+      else
+      {
+        write("--Path " + type + ": '"+path+"' OK");
+      }
     }
   }

branches/filedb/www/common/annotations/list_annotations.jsp

@@ -83 +83 @@
   {
     ItemQuery<Annotation> inheritedQuery = as.getAllInheritedAnnotations();
+    // Need FETCH JOIN because Postgres don't like the DISTINCT keyword
+    // if we sort on a non-selected column See ticket #731
+    inheritedQuery.join(Hql.innerJoin(null, "annotationType", "at", true));
     inheritedQuery.order(Orders.asc(Hql.property("annotationSet")));
-    inheritedQuery.order(Orders.asc(Hql.property("annotationType.name")));
+    inheritedQuery.order(Orders.asc(Hql.property("at", "name")));
     inheritedAnnotations = inheritedQuery.list(dc);
   }

branches/filedb/www/views/reporters/index.jsp

@@ -41 +41 @@
   import="net.sf.basedb.core.DataQuery"
   import="net.sf.basedb.core.PermissionDeniedException"
+  import="net.sf.basedb.core.BaseException"
   import="net.sf.basedb.util.RemovableUtil"
   import="net.sf.basedb.util.ShareableUtil"
@@ -175 +176 @@
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
     ReporterBatcher batcher = ReporterBatcher.getNew(dc);
-    batcher.delete(cc.getId());
-    batcher.close();
-    dc.commit();
-    redirect = listPage;
+    try
+    {
+      batcher.delete(cc.getId());
+      batcher.close();
+      dc.commit();    
+      redirect = listPage;
+    }
+    catch (BaseException bex)
+    {
+      message = "The reporter can not be deleted. " +
+        "Probably because it is used by other items";
+      redirect = viewPage + "&popmessage="+HTML.urlEncode(message);
+    }
   }
   else if ("DeleteItems".equals(cmd))
@@ -186 +196 @@
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
     ReporterBatcher batcher = ReporterBatcher.getNew(dc);
+    batcher.setBatchSize(1);
+    int notDeleted = 0;
     for (int reporterId : cc.getSelected())
     {
-      batcher.delete(reporterId);
-    }
-    batcher.close();
+      try
+      {
+        batcher.delete(reporterId);
+      }
+      catch (BaseException bex)
+      {
+        notDeleted++;
+      }     
+    }   
     dc.commit();
-    redirect = listPage;
+    message = notDeleted > 0 ? notDeleted + " reporters can not be deleted. " +
+        "Probably because they are used by other items" : null;
+    redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");
   }
   else if ("ExportItems".equals(cmd))