Changeset 3581

branches/webservices/build.xml

-                      r3533
+                      r3581
     name="dist"
     depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,webservices.aar,installprg.jar,
       jobagent.jar,migrate.jar,copy.config,copy.jar,doc,doc.dist"
+      jobagent.jar,migrate.jar,copy.config,copy.jar"
     description="Create everything needed for distribution"
+    >
 …
   <target
     name="package"
     depends="package.bin,package.src"
+    depends="package.bin"
     description="Generate tar.gz files for the binary and source distribution"
+    >

branches/webservices/config/dist/extended-properties.xml

-                      r2959
+                      r3581
     </property>
   </class>
+  <!-- Extended properties for Users -->
+  <class name="UserData">
+    <property
+      name="mobile"
+      title="Mobile"
+      description="The user's mobile number"
+      column="mobile"
+      type="string"
+      length="255"
+    />
+    <property
+      name="skype"
+      title="Skype"
+      description="The user's skype contact"
+      column="skype"
+      type="string"
+      length="255"
+    />
+  </class>
 </extended-properties>

branches/webservices/doc/admin/plugin_configuration/coreplugins.html

-                      r3133
+                      r3581
               </tr>
               <tr>
+                <td>Packed&nbsp;file&nbsp;exporter</td>
+                <td><i>Not needed</i></td>
+                <td>BASE 2.4</td>
+                <td>
+                  Exports files and directories as an archive-file.
+              </tr>
+              <tr class="evenrow">
                 <td>Plate&nbsp;mapping&nbsp;exporter</td>
                 <td><i>Not needed</i></td>
 …
                 <td>Exports plate mappings.</td>
               </tr>
               <tr class="evenrow">
+              <tr>
                 <td>Plugin&nbsp;configuration exporter</td>
                 <td><i>Not needed</i></td>
 …
                 <td>Exports plugin configurations to a XML-file.</td>
               </tr>
               <tr>
+              <tr class="evenrow">
                 <td>Table&nbsp;exporter</td>
                 <td><i>Not needed</i></td>
 …
               the changes at
               <a
               href=http://trac.thep.lu.se/tracs/BASE-hacks>http://trac.thep.lu.se/tracs/BASE-hacks</a>.</td>
+              href=http://trac.thep.lu.se/trac/BASE-hacks>http://trac.thep.lu.se/trac/BASE-hacks</a>.</td>
           </tr>
         </table>

branches/webservices/doc/src/docbook/developerdoc/plugin_developer.xml

-                      r3533
+                      r3581
     <sect2 id="plugin_developer.organize.eclipse">
       <title>With Eclipse</title>
+      <para>TODO</para>
+      <para>
+        If somebody is willing to add information to this
+        chapter please send us a note or some written text to put here.
+        Otherwise, this chapter will be removed.
+      </para>
     </sect2>
 …
         </itemizedlist>
         A plug-in is always required to implement the
+        A plug-in must always implement the
         <interfacename>Plugin</interfacename> interface.
         The <interfacename>InteractivePlugin</interfacename>
 …
         <para>
         A plug-in must also have public no-argument contructor. Otherwise, BASE will not
         be able to create instances of the class.
+        be able to create new instances of the plug-in class.
         </para>
       </important>
       <sect3 id="plugin_developer.api.interfaces.plugin">
+        <title>net.sf.basedb.core.plugin.Plugin</title>
+        <para>This interface defines seven methods and must be implemented by all plug-ins.</para>
+        <title>The net.sf.basedb.core.plugin.Plugin interface</title>
+        <para>
+          This interface defines the following methods and must be implemented
+          by all plug-ins.
+        </para>
         <variablelist>
           <varlistentry>
 …
    "Spot images creator",
    "Converts a full-size scanned image into smaller preview jpg " +
    "images for each individual spot.",
+     "images for each individual spot.",
    "2.0",
    "2006, Department of Theoretical Physics, Lund University",
 …
               <methodsynopsis language="java">
                 <modifier>public</modifier>
+                <type>Collection&lt;Permissions&gt;</type>
+                <methodname>getPermissions</methodname>
+                <void />
+              </methodsynopsis>
+            </term>
+            <listitem>
+              <para>
+                Return a collection of permissions that the plug-in needs
+                to be able to function as expected. This method may return null
+                or an empty collection. In this case the plug-in permission system
+                isn't used and the plug-in always get the same permissions as the
+                logged in user. If permissions are specified the plug-in should
+                list all permissions it require. Permissions that are not listed
+                are denied.
+              </para>
+              <note>
+                <para>
+                The final assignment of permissions to a plug-in is always
+                at the hands of a server administrator. He/she may decide to
+                disable the plug-in permission system or revoke some of the
+                requested permissions. The permissions returned by this method is
+                only a recommendation that the server administrator may or may not
+                accept. See <xref linkend="plugins.permissions" />
+                for more information about plug-in permissions.
+                </para>
+              </note>
+            </listitem>
+          </varlistentry>
+          <varlistentry>
+            <term>
+              <methodsynopsis language="java">
+                <modifier>public</modifier>
                 <void />
                 <methodname>init</methodname>
 …
             <listitem>
               <para>
                 Prepare the plug-in for execution (or configuration). If the plug-in needs
+                Prepare the plug-in for execution or configuration. If the plug-in needs
                 to do some initialization this is the place to do it. A typical
                 implementation however only stores the passed parameters in instance
+                variables for later use.
+                variables for later use. Since it is not possible what the user is going to
+                do at this stage, we recommend lazy initialisation of all other resources.
               </para>
               <para>
 …
                 a configuration this object is null.
                 The <varname>job</varname> object holds all parameters that are
                 stored together with a <classname>Jon</classname> object in the
+                stored together with a <classname>Job</classname> object in the
                 database. This object is null if the plug-in is started without a job.
               </para>
 …
               </para>
               <example id="net.sf.basedb.core.plugin.Plugin.init">
                 <title>The <classname>AbstractPlugin</classname> implementation of this Plugin.init()</title>
+                <title>The <classname>AbstractPlugin</classname> implementation of Plugin.init()</title>
 <programlisting>protected SessionControl sc = null;
 protected ParameterValues configuration = null;
 …
             <listitem>
               <para>
+                Runs the plug-in. The <varname>request</varname>
+                Run the plug-in.
+              </para>
+              <para>
+                The <varname>request</varname>
                 parameter is of historical interest only. It has no useful information
                 and can be ignored.
 …
                 failed. Not setting a response is considered a failure by the core. From
                 the run method it is only allowed to use the
                 <methodname>setDone()</methodname>
+                <methodname>Response.setDone()</methodname>
                 or the
                 <methodname>setError()</methodname>
+                <methodname>Response.setError()</methodname>
                 methods.
               </para>
               <note>
+              <important>
                 It is also considered bad practice to let exceptions escape
                 out from this method. Always use <code>try...catch</code>
                 to catch exceptions and use <code>response.setError()</code>
+                to catch exceptions and use <code>Response.setError()</code>
                 to reporter the error back to the core.
               </note>
+              </important>
               <example id="net.sf.basedb.core.plugin.Plugin.run">
 …
       <sect3 id="plugin_developer.api.interfaces.interactive">
         <title>net.sf.basedb.core.plugin.InteractivePlugin</title>
+        <title>The net.sf.basedb.core.plugin.InteractivePlugin interface</title>
         <para>
           If you want the plug-in to be able to interact with the user you must also implement
 …
           is one plug-in that does not interact with the user. Instead, the web client has
           special JSP pages that handles all the interaction, creates a job for it and sets
+          the parameters. This, kind of hardcoded, approach can be used for other plug-ins as
+          well, but then it usually requires modification of the client application as well.
+          the parameters. This, kind of hardcoded, approach can also be used for other
+          plug-ins, but then it usually requires modification of the client application
+          as well.
         </para>
         <para>
 …
                 The configure method works much like the <methodname>Plugin.run()</methodname>
                 method. It must return the result in the <classname>Response</classname> object,
                 and should not trow any exceptions.
+                and should not throw any exceptions.
               </para>
 …
     <sect2 id="plugin_developer.api.callsequence">
       <title>What happens when...</title>
+      <title>How the BASE core interacts with the plug-in when...</title>
       <para>
 …
           If the plug-in implements the <interfacename>InteractivePlugin</interfacename>
           interface the <methodname>InteractivePlugin.getGuiContexts()</methodname>
           method is called. This is the only time this method. The information it
+          method is called. This is the only time this method is called and the information it
           returns are copied and stored in the database.
           </para>
 …
         <listitem>
           <para>
           The plug-in has three different respones:
+          The plug-in can choose between three different respones:
           <itemizedlist>
 …
             <methodname>Response.setContinue()</methodname>: The parameters are correct
             but the plug-in wants more parameters. The process continues with
+            step <xref linkend="plugin_developer.api.callsequence.configure.requestinformation" />.
+            step <xref linkend="plugin_developer.api.callsequence.configure.requestinformation" />
+            but the <varname>command</varname> has the value that was passed to the
+            <methodname>setContinue()</methodname> method.
             </para>
           </listitem>
 …
           Use the <methodname>Response.setDone()</methodname>
           method to report success or the <methodname>Response.setError()</methodname>
           to reporter errors.
+          to report errors.
           </para>
         </listitem>
 …
         <para>
           This is an advanced option for plug-ins that require a different interface for
+          specifying plug-in parameters than the default list showing each parameter at a
+          time. This feature is used by setting the RequestInformation.getJspPage()
+          specifying plug-in parameters than the default list showing one parameter at a
+          time. This feature is used by setting the
+          <methodname>RequestInformation.getJspPage()</methodname>
           property when constructing the request information object. If this property has
           a non-null value, the web client will send the browser to the specified JSP page
 …
   <sect1 id="plugin_developer.import">
     <title>Import plug-ins</title>
     <para>
+      This documentation is only available in the old format.
+      See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/plugins/import/index.html"
+        >http://base.thep.lu.se/chrome/site/doc/development/plugins/import/index.html</ulink>
+      A plugin becoms an import plugin simply by returning
+      <constant>Plugin.MainType.IMPORT</constant>
+      from the <methodname>Plugin.getMainType()</methodname> method.
     </para>
     <sect2 id="plugin_developer.import.autodetect">
+      <title>Autodetecting importer</title>
+      <para></para>
+      <title>Autodetect file formats</title>
+      <para>
+        BASE has built-in functionality for autodetecting file formats.
+        Your plug-in can be part of that feature if it reads it data
+        from a single file. It must also implement the
+        <interfacename>AutoDetectingImporter</interfacename>
+        interface.
+      </para>
+      <sect3 id="plugin_developer.api.interfaces.autodetecting">
+        <title>The net.sf.basedb.core.plugin.AutoDetectingImporter interface</title>
+        <variablelist>
+        <varlistentry>
+          <term>
+            <methodsynopsis language="java">
+              <modifier>public</modifier>
+              <type>boolean</type>
+              <methodname>isImportable</methodname>
+              <methodparam>
+                <type>InputStream</type>
+                <parameter>in</parameter>
+              </methodparam>
+              <exceptionname>BaseException</exceptionname>
+            </methodsynopsis>
+          </term>
+          <listitem>
+            <para>
+              Check the input stream if it seems to contain data that can be imported by
+              the plugin. Usually it means scanning a few lines for some header
+              mathing a predefined string or a regexp.
+            </para>
+            <para>
+              The <classname>AbstractFlatFileImporter</classname> implements this method
+              by reading the headers from the input stream and checking if
+              it stopped at an unknown type of line or not:
+                <programlisting>
+public final boolean isImportable(InputStream in)
+   throws BaseException
+{
+   FlatFileParser ffp = getInitializedFlatFileParser();
+   ffp.setInputStream(in);
+   try
+   {
+      FlatFileParser.LineType result = ffp.parseHeaders();
+      return result != FlatFileParser.LineType.UNKNOWN;
+   }
+   catch (IOException ex)
+   {
+      throw new BaseException(ex);
+   }
+}
+</programlisting>
+            </para>
+            <para>
+              Note that the input stream doesn't have to be a text file.
+              It can be any type of file, for example a binary or an XML file.
+              In the case of an XML file you would need to validate the entiry
+              input stream in order to be a 100% sure that it is a valid
+              xml file, but we recommend that you only check the first few XML tags,
+              for example, the &lt;!DOCTYPE &gt; declaration and/or the root element
+              tag.
+            </para>
+          </listitem>
+        </varlistentry>
+        <varlistentry>
+          <term>
+            <methodsynopsis language="java">
+              <modifier>public</modifier>
+              <void/>
+              <methodname>doImport</methodname>
+              <methodparam>
+                <type>InputStream</type>
+                <parameter>in</parameter>
+              </methodparam>
+              <methodparam>
+                <type>ProgressReporter</type>
+                <parameter>progress</parameter>
+              </methodparam>
+              <exceptionname>BaseException</exceptionname>
+            </methodsynopsis>
+          </term>
+          <listitem>
+            <para>
+              Parse the input stream and import all data that is found.
+              This method is of course only called if the
+              <methodname>isImportable()</methodname> has returned true. Note
+              however that the input stream is reopened at the start of the
+              file. It may even be the case that the <methodname>isImportable()</methodname>
+              method is called on one instance of the plugin and the
+              <methodname>doImport()</methodname> method is called on another.
+              Thus, the <methodname>doImport()</methodname> can't rely on any state set
+              by the <methodname>isImportable()</methodname> method.
+            </para>
+          </listitem>
+        </varlistentry>
+        </variablelist>
+      </sect3>
+      <sect3 id="plugin_developer.import.autodetect.callsequence">
+        <title>Call sequence during autodetection</title>
+        <para>
+          The call sequence for autodetection resembles the call sequence for
+          checking if the plug-in can be used in a given context.
+        </para>
+        <orderedlist>
+        <listitem>
+          <para>
+          A new instance of the plug-in class is created. The plug-in must
+          have a public no-argument constructor.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+          The <methodname>Plugin.init()</methodname> method is called.
+          The <varname>job</varname> parameter is <constant>null</constant>.
+          The <varname>configuration</varname> parameter is <constant>null</constant>
+          if the plug-in does not have any configuration parameters.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+          If the plug-in is interactive the the <methodname>InteractivePlugin.isInContext()</methodname>
+          is called. If the context is a list context, the <varname>item</varname>
+          parameter is null, otherwise the current item is passed. The plug-in
+          should return <constant>null</constant> if it can be used under the
+          current circumstances, or a message explaining why not.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+          If the plug-in can be used the <methodname>AutoDetectingImporter.isImportable()</methodname>
+          method is called to check if the selected file is importable or not.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+          After this, <methodname>Plugin.done()</methodname> is called and
+          the plug-in instance is discarded. If there are
+          several configurations for a plug-in, this procedure is repeated
+          for each configuration. If the plug-in can be used without
+          a configuration the procedure is also repeated without
+          configuration parameters.
+          </para>
+        </listitem>
+        <listitem>
+          <para>
+          If a single plug-in was found the user is taken to the regular
+          job configuration wizard. A new plug-in instance is created for
+          this. If more than one plug-in was found the user is presented
+          with a list of the plug-ins. After selecting one of them the
+          regular job configuration wizard is used with a new plug-in instance.
+          </para>
+        </listitem>
+        </orderedlist>
+      </sect3>
     </sect2>
     <sect2 id="plugin_developer.import.abstractflatfileimporter">
       <title>The AbstractFlatFileImporter superclass</title>
+      <para></para>
+      <para>
+        The <classname>AbstractFlatFileImporter</classname> is a very useful abstract
+        class to use as a superclass for your own import plug-ins. It can be used
+        if your plug-in uses regular text files that can be parsed by an instance of the
+        <classname>net.sf.basedb.util.FlatFileParser</classname> class. This class parses a file
+        by checking each line against a few regular expressions. Depending on which regular
+        expression matches the line, it is classified as a header line, a section line,
+        a comment, a data line, a footer line or unknown. Header lines are inspected as a group,
+        but data lines individually, meaning that it consumes very little memory since only
+        a few lines at a time needs to be loaded.
+      </para>
+      <para>
+        The <classname>AbstractFlatFileImporter</classname> defines
+        <classname>PluginParameter</classname> objects
+        for each of the regular expressions and other parameters used by the parser. It also
+        implements the <methodname>Plugin.run()</methodname> method and does most of
+        the ground work for instantiating a <methodname>FlatFileParser</methodname> and
+        parsing the file. What you have to do in your plugin is to put together the
+        <classname>RequestInformation</classname> objects
+        for configuring the plugin and creating a job and implement the
+        <methodname>InteractivePlugin.configure()</methodname> method for validating and
+        storing the parameteters. You should also implement or override some methods
+        defined by <classname>AbstractFlatFileImporter</classname>.
+      </para>
+      <para>
+      Here is what you need to do:
+      </para>
+      <itemizedlist>
+      <listitem>
+        <para>
+        Implement the <methodname>Plugin.getAbout()</methodname> and
+        <methodname>Plugin.getMainType()</methodname> methods. See
+        <xref linkend="plugin_developer.api.interfaces.plugin" /> for more information.
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+        Implement the <interfacename>InteractivePlugin</interfacename> methods.
+        See <xref linkend="plugin_developer.api.interfaces.interactive" /> for more information. Note that the
+        <classname>AbstractFlatFileImporter</classname>
+        has defined many parameters for regular expressions used by the parser
+        already. You should just pick them and put in your <classname>RequestInformation</classname>
+        object.
+        </para>
+        <programlisting>
+// Parameter that maps the items name from a column
+private PluginParameter&lt;String&gt; nameColumnMapping;
+// Parameter that maps the items description from a column
+private PluginParameter&lt;String&gt; descriptionColumnMapping;
+private RequestInformation getConfigurePluginParameters(GuiContext context)
+{
+   if (configurePlugin == null)
+   {
+      // To store parameters for CONFIGURE_PLUGIN
+      List&lt;PluginParameter&lt;?&gt;&gt; parameters =
+         new ArrayList&lt;PluginParameter&lt;?&gt;&gt;();
+      // Parser regular expressions - from AbstractFlatFileParser
+      parameters.add(parserSection);
+      parameters.add(headerRegexpParameter);
+      parameters.add(dataHeaderRegexpParameter);
+      parameters.add(dataSplitterRegexpParameter);
+      parameters.add(ignoreRegexpParameter);
+      parameters.add(dataFooterRegexpParameter);
+      parameters.add(minDataColumnsParameter);
+      parameters.add(maxDataColumnsParameter);
+      // Column mappings
+      nameColumnMapping = new PluginParameter&lt;String&gt;(
+         "nameColumnMapping",
+         "Name",
+         "Mapping that picks the items name from the data columns",
+         new StringParameterType(255, null, true)
+      );
+      descriptionColumnMapping = new PluginParameter&lt;String&gt;(
+        "descriptionColumnMapping",
+        "Description",
+        "Mapping that picks the items description from the data columns",
+        new StringParameterType(255, null, false)
+      );
+      parameters.add(mappingSection);
+      parameters.add(nameColumnMapping);
+      parameters.add(descriptionColumnMapping);
+      configurePlugin = new RequestInformation
+      (
+         Request.COMMAND_CONFIGURE_PLUGIN,
+         "File parser settings",
+         "",
+         parameters
+      );
+   }
+   return configurePlugin;
+}
+</programlisting>
+      </listitem>
+      <listitem>
+        <para>
+        Implement/override some of the methods defined by
+        <classname>AbstractFlatFileParser</classname>. The most important
+        methods are listed below.
+        </para>
+      </listitem>
+      </itemizedlist>
+      <variablelist>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected</modifier>
+            <type>FlatFileParser</type>
+            <methodname>getInitializedFlatFileParser</methodname>
+            <exceptionname>BaseException</exceptionname>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+          The method is called to create a <classname>FlatFileParser</classname>
+          and set the regular expressions that should be used for parsing the file.
+          The default implementation assumes that your plug-in has used the built-in
+          <classname>PluginParameter</classname> objects and has stored the values
+          at the configuration level. You should override this method if you need to
+          initiailise the parser in a different way. See for example the
+          code for the <classname>PrintMapFlatFileImporter</classname> plug-in which
+          has a fixed format and doesn't use configurations.
+          </para>
+          <programlisting>
+@Override
+protected FlatFileParser getInitializedFlatFileParser()
+   throws BaseException
+{
+   FlatFileParser ffp = new FlatFileParser();
+   ffp.setSectionRegexp(Pattern.compile("\\[(.+)\\]"));
+   ffp.setHeaderRegexp(Pattern.compile("(.+)=,(.*)"));
+   ffp.setDataSplitterRegexp(Pattern.compile(","));
+   ffp.setDataFooterRegexp(Pattern.compile(""));
+   ffp.setMinDataColumns(12);
+   return ffp;
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected</modifier>
+            <void/>
+            <methodname>begin</methodname>
+            <methodparam>
+              <type>FlatFileParser</type>
+              <parameter>ffp</parameter>
+            </methodparam>
+            <exceptionname>BaseException</exceptionname>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+          This method is called just before the parsing of the file
+          begins. Override this method if you need to initialise some
+          internal state. This is, for example, a good place to open
+          a <classname>DbControl</classname> object, read parameters from the
+          job and configuration and put them into more useful variables. The default
+          implementation does nothing, but we recommend that
+          <methodname>super.begin()</methodname> is always called.
+          </para>
+          <programlisting>
+// Snippets from the RawDataFlatFileImporter class
+private DbControl dc;
+private RawDataBatcher batcher;
+private RawBioAssay rawBioAssay;
+private Map&lt;String, String&gt; columnMappings;
+private int numInserted;
+@Override
+protected void begin()
+   throws BaseException
+{
+   super.begin();
+   // Get DbControl
+   dc = sc.newDbControl();
+   rawBioAssay = (RawBioAssay)job.getValue(rawBioAssayParameter.getName());
+   // Reload raw bioassay using current DbControl
+   rawBioAssay = RawBioAssay.getById(dc, rawBioAssay.getId());
+   // Create a batcher for inserting spots
+   batcher = rawBioAssay.getRawDataBatcher();
+   // For progress reporting
+   numInserted = 0;
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected</modifier>
+            <void/>
+            <methodname>handleHeader</methodname>
+            <methodparam>
+              <type>FlatFileParser.Line</type>
+              <parameter>line</parameter>
+            </methodparam>
+            <exceptionname>BaseException</exceptionname>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+          This method is called once for every header line that is found in
+          the file. The <varname>line</varname> parameter contains information
+          about the header. The default implementation of this method does
+          nothing.
+          </para>
+          <programlisting>
+@Override
+protected void handleHeader(Line line)
+   throws BaseException
+{
+   super.handleHeader(line);
+   if (line.name() != null &amp;&amp; line.value() != null)
+   {
+      rawBioAssay.setHeader(line.name(), line.value());
+   }
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected</modifier>
+            <void/>
+            <methodname>handleSection</methodname>
+            <methodparam>
+              <type>FlatFileParser.Line</type>
+              <parameter>line</parameter>
+            </methodparam>
+            <exceptionname>BaseException</exceptionname>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+            This method is called once for each section that is found in the file.
+            The <varname>line</varname> parameter contains information
+            about the section. The default implementation of this method does
+            nothing.
+          </para>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected abstract</modifier>
+            <void/>
+            <methodname>beginData</methodname>
+            <exceptionname>BaseException</exceptionname>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+          This method is called after the headers has been parsed, but before
+          the first line of data. This is a good place to add code that
+          depends on information in the headers, for example, put
+          together column mappings.
+          </para>
+          <programlisting>
+private Mapper reporterMapper;
+private Mapper blockMapper;
+private Mapper columnMapper;
+private Mapper rowMapper;
+// ... more mappers
+@Override
+protected void beginData()
+{
+   boolean cropStrings = ("crop".equals(job.getValue("stringTooLongError")));
+   // Mapper that always return null; used if no mapping expression has been entered
+   Mapper nullMapper = new ConstantMapper((String)null);
+   // Column mappers
+   reporterMapper = getMapper(ffp, (String)configuration.getValue("reporterIdColumnMapping"),
+      cropStrings ? ReporterData.MAX_EXTERNAL_ID_LENGTH : null, nullMapper);
+   blockMapper = getMapper(ffp, (String)configuration.getValue("blockColumnMapping"), null, nullMapper);
+   columnMapper = getMapper(ffp, (String)configuration.getValue("columnColumnMapping"), null, nullMapper);
+   rowMapper = getMapper(ffp, (String)configuration.getValue("rowColumnMapping"), null, nullMapper);
+   // ... more mappers: metaGrid coordinate, X-Y coordinate, extended properties
+   // ...
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected abstract</modifier>
+            <void/>
+            <methodname>handleData</methodname>
+            <methodparam>
+              <type>FlatFileParser.Data</type>
+              <parameter>data</parameter>
+            </methodparam>
+            <exceptionname>BaseException</exceptionname>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+          This method is abstract and must be implemented by all subclasses.
+          It is called once for every data line in the the file.
+          </para>
+          <programlisting>
+// Snippets from the RawDataFlatFileImporter class
+@Override
+protected void handleData(Data data)
+   throws BaseException
+{
+   // Create new RawData object
+   RawData raw = batcher.newRawData();
+   // External ID for the reporter
+   String externalId = reporterMapper.getValue(data);
+   // Block, row and column numbers
+   raw.setBlock(blockMapper.getInt(data));
+   raw.setColumn(columnMapper.getInt(data));
+   raw.setRow(rowMapper.getInt(data));
+   // ... more: metaGrid coordinate, X-Y coordinate, extended properties
+   // Insert raw data to the database
+   batcher.insert(raw, externalId);
+   numInserted++;
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected</modifier>
+            <void/>
+            <methodname>end</methodname>
+            <methodparam>
+              <type>boolean</type>
+              <parameter>success</parameter>
+            </methodparam>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+            Called when the parsing has ended, either because the end of
+            file was reached or because an error has occurred. The subclass
+            should close any open resources, ie. the <classname>DbControl</classname>
+            object. The <varname>success</varname> parameter is <constant>true</constant>
+            if the parsing was successful, <constant>false</constant> otherwise.
+            The default implementation does nothing.
+          </para>
+          <programlisting>
+@Override
+protected void end(boolean success)
+   throws BaseException
+{
+   try
+   {
+      // Commit if the parsing was successful
+      if (success)
+      {
+         batcher.close();
+         dc.commit();
+      }
+   }
+   catch (BaseException ex)
+   {
+      // Well, now we got an exception
+      success = false;
+      throw ex;
+   }
+   finally
+   {
+      // Always close... and call super.end()
+      if (dc != null) dc.close();
+      super.end(success);
+   }
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      <varlistentry>
+        <term>
+          <methodsynopsis language="java">
+            <modifier>protected</modifier>
+            <type>String</type>
+            <methodname>getSuccessMessage</methodname>
+            <void/>
+          </methodsynopsis>
+        </term>
+        <listitem>
+          <para>
+          This is the last method that is called, and it is only called if
+          everything went suceessfully. This method allows a subclass to generate
+          a short message that is sent back to the database as a final progress
+          report. The default implementation returns null, which means that no
+          message will be generated.
+          </para>
+          <programlisting>
+@Override
+protected String getSuccessMessage()
+{
+   return numInserted + " spots inserted";
+}
+</programlisting>
+        </listitem>
+      </varlistentry>
+      </variablelist>
+      <para>
+        The <classname>AbstractFlatFileImporter</classname> has a lot of
+        other methods that you may use and/or override in your own plug-in.
+        Check the javadoc for more information.
+      </para>
     </sect2>
   </sect1>
 …
         <listitem>
           <para>
+          Set the total size of the exported data (if known).
+          Set the total size of the exported data. Don't call this method if the
+          total size is not known.
           </para>
         </listitem>
 …
         The plug-in must call <methodname>Response.setDownloadImmediately()</methodname>
         instead of <methodname>Response.setDone()</methodname> in <methodname>Plugin.configure()</methodname>
         to to end the job configuration wizard. This requests that the core starts
+        to end the job configuration wizard. This requests that the core starts
         an immediate download.
         </para>
 …
         <para>
         If immediate download is not granted and the job is added to the job queue
+        the regular job execution sequence is used. That is, the
+        <methodname>Plugin.run()</methodname> method is called.
+        the regular job execution sequence is used.
         </para>
       </listitem>
 …
         class. It has the same parameters as the <methodname>ImmediateDownloadExporter.doExport()</methodname>
         method and they have the same meaning. The only difference is that the
         <varname>out</varname> stream can be linked to a file and not just to the
         immediate download.
+        <varname>out</varname> stream can be linked to a file in the BASE filesystem
+        and not just to the HTTP response stream.
         </para>
       </listitem>
 …
       <methodname>Plugin.getMainType()</methodname> method. The information returned from
       <methodname>InteractivePlugin.getGuiContexts()</methodname>
+      must include: [<constant>Item.BIOASSAYSET</constant>, <constant>Type.ITEM</constant>] since
+      this is the only place where the web client looks for analysis plug-ins.
+      must include: [<constant>Item.BIOASSAYSET</constant>, <constant>Type.ITEM</constant>]
+      since this is the main place where the web client looks for analysis plug-ins. If
+      the plug-in can work on a subset of the bioassays it may also include
+      [<constant>Item.BIOASSAY</constant>, <constant>Type.LIST</constant>]
+      among the contexts. This will make it possible for a user to select
+      bioassays from the list and then invoke the plug-in.
     </para>
+<programlisting>private static final Set&lt;GuiContext&gt; guiContexts =
+<programlisting>
+private static final Set&lt;GuiContext&gt; guiContexts =
    Collections.singleton(new GuiContext(Item.BIOASSAYSET, GuiContext.Type.ITEM));
 …
 }</programlisting>
+    <para>
+    If the plugin depends on a specific raw data type or on the number of
+    channels, it should check that the current bioassayset is of the
+    correct type in the <methodname>InteractivePlugin.isInContext()</methodname>
+    method. It is also a good idea to check if the current user has permission
+    to use the current experiment. This permission is needed to create new bioassaysets or
+    other data belonging to the experiment.
+    </para>
+    <programlisting>
+public boolean isInContext(GuiContext context, Object item)
+{
+   if (item == null)
+   {
+      message = "The object is null";
+   }
+   else if (!(item instanceof BioAssaySet))
+   {
+      message = "The object is not a BioAssaySet: " + item;
+   }
+   else
+   {
+      BioAssaySet bas = (BioAssaySet)item;
+      int channels = bas.getRawDataType().getChannels();
+      if (channels != 2)
+      {
+         message = "This plug-in requires 2-channel data, not " + channels + "-channel.";
+      }
+      else
+      {
+         Experiment e = bas.getExperiment();
+         e.checkPermission(Permission.USE);
+      }
+   }
+}
+</programlisting>
+    <para>
+    The plugin should always include a parameter asking for the current
+    bioassay set when the <methodname>InteractivePlugin.getRequestInformation()</methodname>
+    is called with <literal>command = Request.COMMAND_CONFIGURE_JOB</literal>.
+    </para>
+    <programlisting>
+private static final RequestInformation configurePlugin;
+private RequestInformation configureJob;
+private PluginParameter&lt;BioAssaySet&gt; bioAssaySetParameter;
+public RequestInformation getRequestInformation(GuiContext context, String command)
+   throws BaseException
+{
+   RequestInformation requestInformation = null;
+   if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
+   {
+      requestInformation = getConfigurePlugin(context);
+   }
+   else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+   {
+      requestInformation = getConfigureJob(context);
+   }
+   return requestInformation;
+}
+private RequestInformation getConfigureJob(GuiContext context)
+{
+   if (configureJob == null)
+   {
+      bioAssaySetParameter; = new PluginParameter&lt;BioAssaySet&gt;(
+         "bioAssaySet",
+         "Bioassay set",
+         "The bioassay set used as the source for this analysis plugin",
+         new ItemParameterType&lt;BioAssaySet&gt;(BioAssaySet.class, null, true, 1, null)
+      );
+      List&lt;PluginParameter&lt;?&gt;&gt; parameters = new ArrayList&lt;PluginParameter&lt;?&gt;&gt;();
+      parameters.add(bioAssaySetParameter);
+      // Add more plug-in-specific parameters here...
+      configureJob = new RequestInformation(
+         Request.COMMAND_CONFIGURE_JOB,
+         "Configure job",
+         "Set parameter for plug-in execution",
+         parameters
+      );
+   }
+   return configureJob;
+}
+</programlisting>
+    <para>
+    Of course, the <methodname>InteractivePlugin.configure()</methodname> method needs
+    to validate and store the bioassay set parameter as well:
+    </para>
+    <programlisting>
+public void configure(GuiContext context, Request request, Response response)
+{
+   String command = request.getCommand();
+   try
+   {
+      if (command.equals(Request.COMMAND_CONFIGURE_PLUGIN))
+      {
+         // Validate and store configuration parameters
+         response.setDone("Plugin configuration complete");
+      }
+      else if (command.equals(Request.COMMAND_CONFIGURE_JOB))
+      {
+         List&lt;Throwable&gt; errors =
+            validateRequestParameters(configureJob.getParameters(), request);
+         if (errors != null)
+         {
+            response.setError(errors.size() +
+               " invalid parameter(s) were found in the request", errors);
+            return;
+         }
+         storeValue(job, request, bioAssaySetParameter);
+         // Store other plugin-specific parameters
+         response.setDone("Job configuration complete", Job.ExecutionTime.SHORT);
+      }
+   }
+   catch (Throwable ex)
+   {
+      // Never throw exception, always set response!
+      response.setError(ex.getMessage(), Arrays.asList(ex));
+   }
+}
+</programlisting>
+    <para>
+    Now, the typical <methodname>Plugin.run()</methodname> method loads the specfied bioassay set
+    and it's spot data. It may do some filtering and recalculation of the spot
+    intensity value(s). In most cases it will store the result as a child bioassay
+    set with one bioassay for each bioassay in the parent bioassay set.
+    Here is an example, which just copies the intensity values, while
+    removing those with a negative value in either channel.
+    </para>
+    <programlisting>
+public void run(Request request, Response response, ProgressReporter progress)
+{
+   DbControl dc = sc.newDbControl();
+   try
+   {
+      BioAssaySet source = (BioAssaySet)job.getParameter("bioAssaySet");
+      // Reload with current DbControl
+      source = BioAssaySet.getById(dc, source.getId());
+      int channels = source.getRawDataType().getChannels();
+      // Create transformation and new bioassay set
+      Job j = Job.getById(dc, job.getId());
+      Transformation t = source.newTransformation(j);
+      t.setName("Copy spot intensities &gt;= 0");
+      dc.saveItem(t);
+      BioAssaySet result = t.newProduct(null, "new", true);
+      result.setName("After: Copying spot intensities");
+      dc.saveItem(result);
+      // Get query for source data
+      DynamicSpotQuery query = source.getSpotData();
+      // Do not return spots with intensities &lt; 0
+      for (int ch = 1; ch &lt;= channels; ++ch)
+      {
+         query.restrict(
+            Restrictions.gteq(
+               Dynamic.column(VirtualColumn.channel(ch)),
+               Expressions.integer(0)
+            )
+         );
+      }
+      // Create batcher and copy data
+      SpotBatcher batcher = result.getSpotBatcher();
+      int spotsCopied = batcher.insert(query);
+      batcher.close();
+      // Commit and return
+      dc.commit();
+      response.setDone("Copied " + spotsCopied + " spots.");
+   }
+   catch (Throwable t)
+   {
+      response.setError(t.getMessage(), Arrays.asList(t));
+   }
+   finally
+   {
+      if (dc != null) dc.close();
+   }
+}
+</programlisting>
+    <para>
+    See <xref linkend="api_overview.dynamic_and_batch_api" />
+    for more examples of using the analysis API.
+    </para>
+    <sect2 id="plugin_developer.analyse.abstractanalysis">
+      <title>The AbstractAnalysisPlugin class</title>
       <para>
+        More documentation is available in the old format.
+        See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/plugins/analysis/index.html"
+          >http://base.thep.lu.se/chrome/site/doc/development/plugins/analysis/index.html</ulink>
+        This class is an abstract base class. It is a useful
+        class for most analysis plug-ins to inherit from. It's main
+        purpose is to define <classname>PluginParameter</classname>
+        objects that are commonly used in analysis plug-ins. This includes:
       </para>
+      <itemizedlist>
+      <listitem>
+        <para>
+        The source bioassay set:
+          <methodname>getSourceBioAssaySetParameter()</methodname>,
+          <methodname>getCurrentBioAssaySet()</methodname>,
+          <methodname>getSourceBioAssaySet()</methodname>
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+        The name and description of the child bioassay set that
+        is going to be created by the plug-in:
+        <methodname>getChildNameParameter()</methodname>,
+        <methodname>getChildDescriptionParameter()</methodname>
+        </para>
+      </listitem>
+      <listitem>
+        <para>
+        The name and description of the transformation that
+        represents the execution of the plug-in:
+        <methodname>getTransformationNameParameter()</methodname>,
+        <methodname>getTransformationName()</methodname>
+        </para>
+      </listitem>
+      </itemizedlist>
+    </sect2>
   </sect1>
 …
               <para>
               <exceptionname>UnknownLoginException</exceptionname>:
               This exception should be thrown if the login is not know to the
+              This exception should be thrown if the login is not known to the
               external authentication system.
               </para>
 …
               The <varname>dir</varname> parameter is the root directory where
               the unpacked files should be placed. If the compressed file
               contains subdirectory the plug-in must create those subdirectories
+              contains subdirectories the plug-in must create those subdirectories
               unless they already exists.
               </para>
 …
               progress back to the calling code. The plug-in should count
               the number of bytes read from the <varname>in</varname>
+              stream.
+              stream. If it is not possible by other means the stream can
+              be wrapped by a <classname>net.sf.basedb.util.InputStreamTracker</classname>
+              object which has a <methodname>getNumRead()</methodname> method.
               </para>
             </listitem>

branches/webservices/doc/src/docbook/overviewdoc/resources.xml

r3533	r3581
117	117	or requesting a new feature. Perhaps someone has registered the issue as a ticket
118	118	already. This list can also be used to see how the BASE 2 development is proceeding
119		and when some particular request is planed to be fixed.
	119	and when some particular request is planned to be fixed.
120	120	</para>
121	121

branches/webservices/doc/src/docbook/userdoc/file_system.xml

-                      r3533
+                      r3581
                   These settings are only active if you select
                   a compressed file format that BASE knows how to
+                  unpack. Currently, BASE ships with support for zip-files,
+                  unpack. BASE ships with support for some of the most common
+                  compressed file formats, such as zip and tar,
                   but this can be extended by the use of plug-ins.
                   <nohelp>See <xref linkend="plugin_developer.other.unpacker"

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

-                      r3533
+                      r3581
         </helptext>
+      </sect2>
+      <sect2 id="webclient.configuration.other">
+        <title>Other information</title>
+        <para>
+          Use the
+          <menuchoice>
+            <guimenu>File</guimenu>
+            <guimenuitem>Other information&hellip;</guimenuitem>
+          </menuchoice>
+          menu to bring up the other information dialog.
+        </para>
+        <helptext external_id="userpreferences.other" title="Other information">
+          <para>
+            This dialog has three tabs,
+            <guilabel>Contact information</guilabel>
+            ,
+            <guilabel>Password</guilabel>
+            and
+            <guilabel>Other information</guilabel>
+            (selected) .
+          </para>
+          <para>
+            The look of the
+            <guilabel>Other information</guilabel>
+            tab can differe abit between different servers, depending on what settings
+            the server is installed with. There are three inputs in a fresh BASE2
+            installation but it is only the
+            <guilabel>Description</guilabel>
+            textarea that is static, the others can be removed or more fields can be
+            added (managed by the server administrator). The three fields, included in a
+            the BASE2 installation, are
+            <variablelist>
+              <varlistentry>
+                <term>
+                  <guilabel>Mobile</guilabel>
+                </term>
+                <listitem>
+                  <para>Your mobile number(Optional).</para>
+                </listitem>
+              </varlistentry>
+              <varlistentry>
+                <term>
+                  <guilabel>Skype</guilabel>
+                </term>
+                <listitem>
+                  <para>Your skype contact information(Optional).</para>
+                </listitem>
+              </varlistentry>
+              <varlistentry>
+                <term>
+                  <guilabel>Description</guilabel>
+                </term>
+                <listitem>
+                  <para>
+                    Text area where you can put useful information that couldn't
+                    be stored anywhere else(Optional).
+                  </para>
+                </listitem>
+              </varlistentry>
+            </variablelist>
+          </para>
+          <para>Press &gbSave; to save the changes or &gbCancel; to abort.</para>
+          <seeother>
+            <other external_id="userpreferences.contact">Contact information</other>
+            <other external_id="userpreferences.password">Change password</other>
+          </seeother>
+        </helptext>
       </sect2>

branches/webservices/src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java

-                      r2993
+                      r3581
     Formatter<Number> intFormatter = FormatterFactory.getIntFormatter(sc);
     columns.add(new TableColumn("POSITION", "POSITION", null, Type.INT,
+      "Position", "Spot position", "always", true, true, true, false, intFormatter));
+      "Position", "Spot position", "always", true, true, true,
+      Formula.AverageMethod.NONE, intFormatter));
     for (int channel = 1; channel <= channels; ++channel)
+    {
       TableColumn tc = new TableColumn("ch"+channel, "%"+channel, "ch("+channel+")",
         Type.FLOAT, "Ch "+channel, "Channel " + channel + " intensity");
       tc.setFormatter(numberFormatter);
+        Type.FLOAT, "Ch "+channel, "Channel " + channel + " intensity", "auto", true, true, true,
+        Formula.AverageMethod.ARITHMETIC_MEAN, numberFormatter);
       columns.add(tc);
+    }
 …
       Formatter<Number> intFormatter = FormatterFactory.getIntFormatter(sc);
       columns.add(new TableColumn(idPrefix + "position", propertyPrefix+"position", "raw('position')",
+        Type.INT, titlePrefix+"Position", "Raw spot position", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Position", "Raw spot position", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "block", propertyPrefix+"block", "raw('block')",
+        Type.INT, titlePrefix+"Block", "Block number", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Block", "Block number", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "metaGridX", propertyPrefix+"metaGridX", "raw('metaGridX')",
+        Type.INT, titlePrefix+"Meta grid X", "Meta X coordinate", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Meta grid X", "Meta X coordinate", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "metaGridY", propertyPrefix+"metaGridY", "raw('metaGridY')",
+        Type.INT, titlePrefix+"Meta grid Y", "Meta Y coordinate", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Meta grid Y", "Meta Y coordinate", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "row", propertyPrefix+"row", "raw('row')", Type.INT,
+        titlePrefix+"Row", "Row number", "auto", true, true, true, false, intFormatter));
+        titlePrefix+"Row", "Row number", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "column", propertyPrefix+"column", "raw('column')",
+        Type.INT, titlePrefix+"Column", "Column number", "auto", true, true, true, false, intFormatter));
+        Type.INT, titlePrefix+"Column", "Column number", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "x", propertyPrefix+"x", "raw('x')", Type.INT,
+        titlePrefix+"X", "X coordinate", "auto", true, true, true, false, intFormatter));
+        titlePrefix+"X", "X coordinate", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       columns.add(new TableColumn(idPrefix + "y", propertyPrefix+"y", "raw('y')", Type.INT,
+        titlePrefix+"Y", "Y coordinate", "auto", true, true, true, false, intFormatter));
+        titlePrefix+"Y", "Y coordinate", "auto", true, true, true,
+        Formula.AverageMethod.NONE, intFormatter));
       List<RawDataProperty> rdpList = rawDataType.getProperties();
 …
         TableColumn tc = new TableColumn(idPrefix+rdpName, propertyPrefix+rdpName, "raw('"+rdpName+"')", rdp.getType(),
           titlePrefix + rdp.getTitle(), rdp.getDescription(), "auto", true, true, true,
           rdp.isAveragable(), FormatterFactory.getExtendedPropertyFormatter(sc, rdp));
+          rdp.getAverageMethod(), FormatterFactory.getExtendedPropertyFormatter(sc, rdp));
         columns.add(tc);
+      }
 …
     Formatter<Date> dateFormatter = FormatterFactory.getDateFormatter(sc);
     columns.add(new TableColumn(idPrefix + "name", propertyPrefix+"name", "rep('name')",
+      Type.STRING, titlePrefix + "Name", "Reporter name", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "Name", "Reporter name", "auto", true, true, true,
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "externalId", propertyPrefix+"externalId", "rep('externalId')",
+      Type.STRING, titlePrefix + "ID", "Reporter ID", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "ID", "Reporter ID", "auto", true, true, true,
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "symbol", propertyPrefix+"symbol", "rep('symbol')",
+      Type.STRING, titlePrefix + "Gene symbol", "Gene symbol", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "Gene symbol", "Gene symbol", "auto", true, true, true,
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "description", propertyPrefix+"description", "rep('description')",
+      Type.STRING, titlePrefix + "Description", "Reporter description", "auto", true, true, true, false, stringFormatter));
+      Type.STRING, titlePrefix + "Description", "Reporter description", "auto", true, true, true,
+      Formula.AverageMethod.NONE, stringFormatter));
     columns.add(new TableColumn(idPrefix + "lastUpdate", propertyPrefix+"lastUpdate", "rep('lastUpdate')",
+      Type.DATE, titlePrefix + "Last update", "Last updateded", "auto", true, true, true, false, dateFormatter));
+      Type.DATE, titlePrefix + "Last update", "Last updateded", "auto", true, true, true,
+      Formula.AverageMethod.NONE, dateFormatter));
     List<ExtendedProperty> extended = ExtendedProperties.getProperties("ReporterData");
 …
         String name = ep.getName();
         TableColumn tc = new TableColumn(idPrefix + name, propertyPrefix + name, "rep('"+name+"')",
           ep.getType(), titlePrefix + ep.getTitle(), ep.getDescription());
         tc.setFormatter(FormatterFactory.getExtendedPropertyFormatter(sc, ep));
+          ep.getType(), titlePrefix + ep.getTitle(), ep.getDescription(), "auto", true, true, true,
+          ep.getAverageMethod(), FormatterFactory.getExtendedPropertyFormatter(sc, ep));
         columns.add(tc);
+      }
 …
+    {
       ExtraValue ev = result.next();
-      ExtraValueType evt = ev.getExtraValueType();
       int id = ev.getId();
+      TableColumn tc = new TableColumn(idPrefix+id, propertyPrefix + id, "xtra('" + evt.getExternalId() + "')", ev.getValueType(),
+        titlePrefix+evt.getName(), evt.getDescription());
+      Formatter<?> formatter = FormatterFactory.getTypeFormatter(sc, evt.getValueType());
+      if (evt.getValueType().isNumerical())
+      {
+        // Numerical types *should* return a numberic formatter which is required by the color formatter
+      ExtraValueType evt = null;
+      TableColumn tc = null;
+      try
+      {
+        evt = ev.getExtraValueType();
+        tc = new TableColumn(idPrefix+id, propertyPrefix + id, "xtra('" + evt.getExternalId() + "')",
+            ev.getValueType(), titlePrefix+evt.getName(), evt.getDescription(),
+            "auto", true, true, true, evt.getAverageMethod(), null);
+      }
+      catch (Throwable t)
+      {
+        tc = new TableColumn(idPrefix+id, propertyPrefix + id, "xtra('" + id + "')",
+            ev.getValueType(), titlePrefix+ev.getValueType(), "",
+            "auto", true, true, true, null, null);
+      }
+      Formatter<?> formatter = FormatterFactory.getTypeFormatter(sc, ev.getValueType());
+      if (ev.getValueType().isNumerical() && evt != null)
+      {
+        // Numerical types *should* return a numeric formatter which is required by the color formatter
         formatter = FormatterFactory.getColorFormatter(sc, evt.getColoring(),
           (Formatter<Number>)formatter);
 …
+      {
         TableColumn tc = new TableColumn(idPrefix+f.getId(), "="+jepExpression, jepExpression, Type.FLOAT,
+            titlePrefix + f.getName(), f.getDescription());
+            titlePrefix + f.getName(), f.getDescription(), "auto", true, true, true,
+            f.getAverageMethod(), null);
         tc.setFormatter(FormatterFactory.getColorFormatter(sc, f.getColoring(), numberFormatter));
         columns.add(tc);
 …
     List<String> selectedIds = new ArrayList<String>(columns.size());
     List<String> selectedProperties = new ArrayList<String>(columns.size());
+    List<TableColumn> selectedColumns = new ArrayList<TableColumn>(columns.size());
     String visibleColumns = cc.getSetting("columns");
 …
           selectedProperties.add(tc.getProperty());
           selectedIds.add(tc.getId());
+          selectedColumns.add(tc);
+        }
+      }
+    }
     return new SelectedInfo(selectedProperties, selectedIds);
+    return new SelectedInfo(selectedProperties, selectedIds, selectedColumns);
+  }
 …
     public final List<String> selectedProperties;
     public final List<String> selectedIds;
+    public final List<TableColumn> selectedColumns;
     private SelectedInfo(List<String> properties, List<String> ids)
+    private SelectedInfo(List<String> properties, List<String> ids, List<TableColumn> columns)
+    {
       this.selectedIds = ids;
       this.selectedProperties = properties;
+      this.selectedColumns = columns;
+    }
+  }

branches/webservices/src/clients/web/net/sf/basedb/clients/web/ExperimentExplorer.java

-                      r3533
+                      r3581
 import net.sf.basedb.util.Values;
 import net.sf.basedb.clients.web.formatter.FormatterFactory;
+import net.sf.basedb.clients.web.taglib.table.TableColumn;
 import net.sf.basedb.core.AnnotationType;
 import net.sf.basedb.core.BaseException;
 …
     @return A query
   */
   public DynamicSpotQuery getSpotQuery(DbControl dc, ReporterData reporter, int positionIndex, List<String> selectionList)
+  public DynamicSpotQuery getSpotQuery(DbControl dc, ReporterData reporter, int positionIndex, List<TableColumn> selectionList)
+  {
     BioAssaySet bioAssaySet = getBioAssaySet(dc);
 …
     // Set additional selected columns
     int i = 0;
     for (String selectProperty : selectionList)
+    for (TableColumn tc : selectionList)
+    {
       // Skip channel intensities since they are already selected
       if (!selectProperty.startsWith("%"))
+      if (!tc.getProperty().startsWith("%"))
+      {
         Expression select = ItemContext.getDynamicExpression(dc, selectProperty);
+        Expression select = ItemContext.getDynamicExpression(dc, tc.getProperty());
         if (select != null)
+        {
 …
           if (positionIndex == SPOT_AVG)
+          {
             select = Aggregations.mean(select);
+            select = tc.getAverageMethod().getAverageExpression(select);
+          }
           spotQuery.select(Selects.expression(select, "e" + i));
 …
         if (positionIndex == SPOT_AVG)
+        {
+          sortby = Aggregations.mean(sortby);
+          // Find TableColumn to know which average method to use
+          boolean found = false;
+          for (TableColumn tc : selectionList)
+          {
+            if (sortProperty.equals(tc.getProperty()))
+            {
+              sortby = tc.getAverageMethod().getAverageExpression(sortby);
+              found = true;
+              break;
+            }
+          }
+          if (!found) sortby = null;
+        }
         if (sortby != null)

branches/webservices/src/clients/web/net/sf/basedb/clients/web/PermissionUtil.java

-                      r2916
+                      r3581
+  }
+  public static String translatePermissionsToString(Set<Permission> permissions)
+  {
+    StringBuilder permissionString = new StringBuilder();
+    permissionString.append(permissions.contains(Permission.READ) ? "R" : "");
+    permissionString.append(permissions.contains(Permission.USE) ? "U" : "");
+    permissionString.append(permissions.contains(Permission.WRITE) ? "W" : "");
+    permissionString.append(permissions.contains(Permission.DELETE) ? "D" : "");
+    permissionString.append(permissions.contains(Permission.SET_OWNER) ? "O" : "");
+    permissionString.append(permissions.contains(Permission.SET_PERMISSION) ? "P" : "");
+    return permissionString.toString();
+  }
+}

branches/webservices/src/clients/web/net/sf/basedb/clients/web/taglib/table/ColumnDef.java

r2942	r3581
604	604	for (int i = 0; i < enumeration.size(); ++i)
605	605	{
606		String selected = filterValue.equals(enumeration.getKey(i)) ? " selected" : "";
	606	String selected = filterValue.equals(enumeration.getKey(i).trim()) ? " selected" : "";
607	607	sb.append("<option value=\"").append(enumeration.getKey(i)).append("\"").append(selected);
608	608	sb.append(">").append(enumeration.getValue(i)).append("\n");

branches/webservices/src/clients/web/net/sf/basedb/clients/web/taglib/table/TableColumn.java

-                      r3433
+                      r3581
 package net.sf.basedb.clients.web.taglib.table;
+import net.sf.basedb.core.Formula;
 import net.sf.basedb.core.Type;
 import net.sf.basedb.util.formatter.Formatter;
 …
   private final boolean exportable;
   private final String show;
   private final boolean averagable;
+  private final Formula.AverageMethod averageMethod;
   private Formatter<?> formatter;
+  /**
+    Create TableColumn.
+    @param id
+    @param property
+    @param jepExpression
+    @param datatype
+    @param title
+    @param description
+    @deprecated
+   */
   public TableColumn(String id, String property, String jepExpression, Type datatype, String title, String description)
+  {
+    this(id, property, jepExpression, datatype, title, description, "auto", true, true, true, datatype.isNumerical(), null);
+    this(id, property, jepExpression, datatype, title, description, "auto", true, true, true,
+      datatype.isNumerical() ? Formula.AverageMethod.ARITHMETIC_MEAN : null, null);
+  }
   public TableColumn(String id, String property, String jepExpression, Type datatype, String title, String description, String show,
     boolean sortable, boolean filterable, boolean exportable, boolean averagable, Formatter<?> formatter)
+    boolean sortable, boolean filterable, boolean exportable, Formula.AverageMethod averageMethod, Formatter<?> formatter)
+  {
     this.id = id;
 …
     this.filterable = filterable;
     this.exportable = exportable;
     this.averagable = datatype.isNumerical() && averagable;
+    this.averageMethod = averageMethod;
     this.formatter = formatter;
+  }
 …
   public boolean isAveragable()
+  {
     return averagable;
+    return averageMethod != null && averageMethod != Formula.AverageMethod.NONE;
+  }
+  /**
+    @since 2.4
+  */
+  public Formula.AverageMethod getAverageMethod()
+  {
+    return averageMethod;
+  }
   /**
      @since 2.0.2

branches/webservices/src/core/common-queries.xml

-                      r3533
+                      r3581
     <sql>
       UPDATE FormulaData f
       SET f.averageMethod = 1
+      SET f.averageMethod = 2
       WHERE f.averageMethod IS NULL
     </sql>
     <description>
       A HQL query that sets the averageMethod to a for all
+      A HQL query that sets the averageMethod to arithmetic mean for all
       formulas with a null value.
     </description>
 …
     <sql>
       UPDATE ExtraValueTypeData evt
       SET evt.averageMethod = 1
+      SET evt.averageMethod = 2
       WHERE evt.averageMethod IS NULL
     </sql>
     <description>
       A HQL query that sets the averageMethod to a for all
+      A HQL query that sets the averageMethod to arithmetic mean for all
       extra value types with a null value.
     </description>

branches/webservices/src/core/net/sf/basedb/core/AnnotationBetweenRestriction.java

-                      r2304
+                      r3581
     Create a new annotation restriction.
+    @deprecated Use {@link #AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean)}
+      instead with alias=null
+  */
+  public AnnotationBetweenRestriction(AnnotationType annotationType, Object lowValue, Object highValue, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    this(null, annotationType, lowValue, highValue, includeInheriting);
+  }
+  /**
+    Create a new annotation restriction.
+    @param alias The alias of a joined item where the annotations are
+      located or null to use the root entity of the query
     @param annotationType The annotation type to use in the query
     @param lowValue The low value to use in the query, it must be of the
 …
     @throws InvalidDataException If any of the parameters are null
       or not follow the rules above.
+    @since 2.4
   */
   public AnnotationBetweenRestriction(AnnotationType annotationType, Object lowValue, Object highValue, boolean includeInheriting)
+  public AnnotationBetweenRestriction(String alias, AnnotationType annotationType, Object lowValue, Object highValue, boolean includeInheriting)
     throws InvalidDataException
+  {
     super(annotationType, includeInheriting);
+    super(alias, annotationType, includeInheriting);
     if (lowValue == null) throw new InvalidUseOfNullException("lowValue");
     if (highValue == null) throw new InvalidUseOfNullException("highValue");
 …
     this.highValue = highValue;
+  }
   /*

branches/webservices/src/core/net/sf/basedb/core/AnnotationInRestriction.java

-                      r2304
+                      r3581
     Create a new annotation restriction.
+    @deprecated Use {@link #AnnotationInRestriction(String, AnnotationType, boolean, Object[])}
+      instead with alias=null
+  */
+  public AnnotationInRestriction(AnnotationType annotationType, boolean includeInheriting, Object... values)
+    throws InvalidDataException
+  {
+    this(null, annotationType, includeInheriting, values);
+  }
+  /**
+    Create a new annotation restriction.
     @param annotationType The annotation type to use in the query
     @param includeInheriting If items inherting the annotation should be returned
 …
     @throws InvalidDataException If any of the parameters are null
       or the array is empty or not follow the rules above.
+    @since 2.4
   */
   public AnnotationInRestriction(AnnotationType annotationType, boolean includeInheriting, Object... values)
+  public AnnotationInRestriction(String alias, AnnotationType annotationType, boolean includeInheriting, Object... values)
     throws InvalidDataException
+  {
     super(annotationType, includeInheriting);
+    super(alias, annotationType, includeInheriting);
     if (values == null || values.length == 0) throw new InvalidUseOfNullException("values");
     for (int i = 0; i < values.length; ++i)
 …
     this.values = Arrays.asList(values);
+  }
   /*
     From the AnnotationRestriction class

branches/webservices/src/core/net/sf/basedb/core/AnnotationRestriction.java

-                      r2667
+                      r3581
   final int annotationTypeId;
   final boolean includeInheriting;
+  final String alias;
   /**
 …
     @param annotationType The annotation type to use in the query
   */
   AnnotationRestriction(AnnotationType annotationType, boolean includeInheriting)
+  AnnotationRestriction(String alias, AnnotationType annotationType, boolean includeInheriting)
     throws InvalidDataException
+  {
 …
     this.valueType = annotationType.getValueType();
     this.includeInheriting = includeInheriting;
+    this.alias = alias;
+  }
 …
     @param valueType The type of values for annotations
   */
   AnnotationRestriction(int annotationTypeId, Type valueType, boolean includeInheriting)
+  AnnotationRestriction(String alias, int annotationTypeId, Type valueType, boolean includeInheriting)
     throws InvalidDataException
+  {
 …
     this.valueType = valueType;
     this.includeInheriting = includeInheriting;
+    this.alias = alias;
+  }
 …
       annotationSetIds = annotationSets.toString();
+    }
+    String hql = query.getRootAlias()+".annotationSet IN ("+annotationSetIds+")";
+    String hql = (alias == null ? query.getRootAlias() : alias) +
+      ".annotationSet IN ("+annotationSetIds+")";
     return hql;
+  }

branches/webservices/src/core/net/sf/basedb/core/AnnotationSimpleRestriction.java

-                      r2610
+                      r3581
   /**
     Create a new annotation restriction using a simple expression:
+    <code>annotation operator value</code>.
+    <code>annotation operator value</code>. The restriction is applied to
+    the root element of the query.
+    @deprecated Use {@link #AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean)}
+      instead with alias=null
+  */
+  public AnnotationSimpleRestriction(AnnotationType annotationType, Operator operator, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    this(null, annotationType, operator, value, includeInheriting);
+  }
+  /**
+    Create a new annotation restriction using a simple expression:
+    <code>annotation operator value</code>.
+    @param alias The alias of a joined item where the annotations are
+      located or null to use the root entity of the query
     @param annotationType The annotation type to use in the query
     @param operator The operator, it must be one of the expression
 …
     @throws InvalidDataException If any of the parameters are null
       or not follow the rules above.
+    @since 2.4
   */
   public AnnotationSimpleRestriction(AnnotationType annotationType, Operator operator, Object value, boolean includeInheriting)
+  public AnnotationSimpleRestriction(String alias, AnnotationType annotationType, Operator operator, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
     super(annotationType, includeInheriting);
+    super(alias, annotationType, includeInheriting);
     if (operator == null) throw new InvalidUseOfNullException("operator");
     if (value == null) throw new InvalidUseOfNullException("value");
 …
+  }
   /**
+    Creates a new annotation restriction for a specific <code>valueType
+    Creates a new annotation restriction for a specific <code>valueType</code>.
+    The restriction is applied to the root element of the query.
+    @deprecated Use {@link #AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean)}
+      instead with alias=null
+  */
+  public AnnotationSimpleRestriction(int annotationTypeId, Type valueType, Operator operator, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    this(null, annotationTypeId, valueType, operator, value, includeInheriting);
+  }
+  /**
+    Creates a new annotation restriction for a specific <code>valueType</code>.
+    @param alias The alias of a joined item where the annotations are
+      located or null to use the root entity of the query
       @param annotationTypeId the id of the annotation type to use in the query
     @param valueType the type of values for annotations
 …
       @throws InvalidDataException If any of the parameters are null
       or not follow the rules above
+    @since 2.4
   */
   public AnnotationSimpleRestriction(int annotationTypeId, Type valueType, Operator operator, Object value, boolean includeInheriting)
+  public AnnotationSimpleRestriction(String alias, int annotationTypeId, Type valueType, Operator operator, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
     super(annotationTypeId, valueType, includeInheriting);
+    super(alias, annotationTypeId, valueType, includeInheriting);
     if (operator == null) throw new InvalidUseOfNullException("operator");
     if (value == null) throw new InvalidUseOfNullException("value");

branches/webservices/src/core/net/sf/basedb/core/ExtendedProperties.java

-                      r2747
+                      r3581
       if (type == Type.STRING && length > 255) type = Type.TEXT;
       boolean nullable = XMLUtil.getBooleanAttribute(property, "null", true);
       boolean insertable = XMLUtil.getBooleanAttribute(property, "insert", true);;
       boolean updateable = XMLUtil.getBooleanAttribute(property, "update", true);;
+      boolean insertable = XMLUtil.getBooleanAttribute(property, "insert", true);
+      boolean updateable = XMLUtil.getBooleanAttribute(property, "update", true);
       boolean averagable = XMLUtil.getBooleanAttribute(property, "averagable", type.isNumerical());
+      String avgMethod = property.getAttributeValue("averagemethod");
+      Formula.AverageMethod averageMethod = null;
+      if (avgMethod != null)
+      {
+        averageMethod = Formula.AverageMethod.valueOf(avgMethod.toUpperCase());
+      }
+      else if (averagable)
+      {
+        averageMethod = Formula.AverageMethod.ARITHMETIC_MEAN;
+      }
+      else
+      {
+        averageMethod = Formula.AverageMethod.NONE;
+      }
       List<Element> links = (List<Element>)property.getChildren("link");
 …
+        }
+      }
       properties.add(new ExtendedProperty(name, title, description, column, type, length, nullable, insertable, updateable, averagable, epLinks));
+      properties.add(new ExtendedProperty(name, title, description, column, type, length, nullable, insertable, updateable, averageMethod, epLinks));
+    }
     return properties;

branches/webservices/src/core/net/sf/basedb/core/ExtendedProperty.java

-                      r3533
+                      r3581
   private final boolean insertable;
   private final boolean updateable;
   private final boolean isAveragable;
+  private final Formula.AverageMethod averageMethod;
   private final List<ExtendedPropertyLinker> linkers;
 …
   ExtendedProperty(String name, String title, String description, String column,
     Type type, int length, boolean nullable, boolean insertable, boolean updateable,
     boolean isAveragable, List<ExtendedPropertyLinker> linkers)
+    Formula.AverageMethod averageMethod, List<ExtendedPropertyLinker> linkers)
+  {
     this.name = name;
 …
     this.insertable = insertable;
     this.updateable = updateable;
     this.isAveragable = type.isNumerical() && isAveragable;
+    this.averageMethod = averageMethod;
     this.linkers = linkers;
+  }
 …
     values. By default all numerical values are averagable.
     @return TRUE if it makes sense to take the average, FALSE otherwise
+    @see #getAverageMethod()
   */
   public boolean isAveragable()
+  {
+    return isAveragable;
+    return averageMethod != null && averageMethod != Formula.AverageMethod.NONE;
+  }
+  /**
+    Which method to use when calculating the average of a set of values.
+    Prior to 2.4 only arithmetic mean was supported.
+    @return The average method to use
+    @since 2.4
+  */
+  public Formula.AverageMethod getAverageMethod()
+  {
+    return averageMethod;
+  }

branches/webservices/src/core/net/sf/basedb/core/ExtraValueType.java

-                      r3533
+                      r3581
     ev.setExternalId(externalId);
     ev.setValueType(valueType);
     ev.setAverageMethod(AverageMethod.ARITHMETIC_MEAN);
+    ev.setAverageMethod(valueType.isNumerical() ? AverageMethod.ARITHMETIC_MEAN : AverageMethod.NONE);
     return ev;
+  }
 …
     Get the average method for this extra value type.
     @return A {@link AverageMethod} object
+    @since 2.4
    */
   public Formula.AverageMethod getAverageMethod()
 …
       write permission
     @throws InvalidDataException If the averageMethod is null
+    @since 2.4
   */
   public void setAverageMethod(Formula.AverageMethod averageMethod)

branches/webservices/src/core/net/sf/basedb/core/Formula.java

-                      r3533
+                      r3581
     Get the average method for this formula.
     @return A {@link AverageMethod} object
+   */
+    @since 2.4
+  */
   public Formula.AverageMethod getAverageMethod()
+  {
 …
       write permission
     @throws InvalidDataException If the averageMethod is null
+    @since 2.4
   */
   public void setAverageMethod(Formula.AverageMethod averageMethod)
 …
     The average method used for the values of this formula. The average
     is only useful with a {@link Type#COLUMN_EXPRESSION}.
+   */
+    @version 2.4
+  */
   public enum AverageMethod
+  {
+    NONE(0, "None"),
+    GEOMETRIC_MEAN(1, "Geometric mean"),
+    ARITHMETIC_MEAN(2, "Arithmetic mean"),
+    MIN(3, "Min"),
+    MAX(4, "Max");
+    NONE(0, "None")
+    {
+      public Expression getAverageExpression(Expression e)
+      {
+        return null;
+      }
+    },
+    GEOMETRIC_MEAN(1, "Geometric mean")
+    {
+      public Expression getAverageExpression(Expression e)
+      {
+        return Aggregations.geometricMean(e);
+      }
+    },
+    ARITHMETIC_MEAN(2, "Arithmetic mean")
+    {
+      public Expression getAverageExpression(Expression e)
+      {
+        return Aggregations.mean(e);
+      }
+    },
+    MIN(3, "Min")
+    {
+      public Expression getAverageExpression(Expression e)
+      {
+        return Aggregations.min(e);
+      }
+    },
+    MAX(4, "Max")
+    {
+      public Expression getAverageExpression(Expression e)
+      {
+        return Aggregations.max(e);
+      }
+    };
     /**
 …
+    }
+    public Expression getAverageExpression(Expression e)
+    {
+      Expression avg;
+      switch (this)
+      {
+        case GEOMETRIC_MEAN :
+          avg = Aggregations.geometricMean(e);
+          break;
+        case ARITHMETIC_MEAN :
+          avg = Aggregations.mean(e);
+          break;
+        case MIN :
+          avg = Aggregations.min(e);
+          break;
+        case MAX:
+          avg = Aggregations.max(e);
+          break;
+        case NONE:
+        default:
+          avg = Expressions.string("");
+          break;
+      }
+      return avg;
+    }
+    /**
+     * Get the integer value that is used when storing a
+     * <code>Formula.AverageMethod</code> in the database.
+     *
+     * @return The integer value of this type
+     */
+    /**
+      Given an expression, create an expression that takes the correct
+      average of it.
+      @param e The expression, null is not allowed
+      @return The average expression, or null if it is not possible
+        to create an average expression
+    */
+    public abstract Expression getAverageExpression(Expression e);
+    /**
+      Get the integer value that is used when storing a
+      <code>Formula.AverageMethod</code> in the database.
+      @return The integer value of this type
+    */
     public int getValue()
+    {
 …
       is typically used to create a root bioassay set from raw data.
     */
     INTENSITY_EXPRESSION(1, "Intensity expression", false)
+    INTENSITY_EXPRESSION(1, "Intensity expression", false, false)
+    {
       /**
 …
       bioassay set into a child bioassay set.
     */
     INTENSITY_TRANSFORMATION(2, "Intensity transformation", false)
+    INTENSITY_TRANSFORMATION(2, "Intensity transformation", false, false)
+    {
       /**
 …
       The formula can also be used to calculate extra values for a bioassay set.
     */
     COLUMN_EXPRESSION(3, "Column expression", true)
+    COLUMN_EXPRESSION(3, "Column expression", true, true)
+    {
       /**
 …
       to create a filtered bioassay set.
     */
     COLUMN_RESTRICTION(4, "Column restriction", false)
+    COLUMN_RESTRICTION(4, "Column restriction", false, false)
+    {
       /**
 …
     private final String displayValue;
     private final boolean canUseColoring;
+    private Type(int value, String displayValue, boolean canUseColoring)
+    private final boolean supportsAverage;
+    private Type(int value, String displayValue, boolean canUseColoring, boolean supportsAverage)
+    {
       this.value = value;
       this.displayValue = displayValue;
       this.canUseColoring = canUseColoring;
+      this.supportsAverage = supportsAverage;
+    }
 …
+    {
       return canUseColoring;
+    }
+    /**
+      If a formula of this type can be used in an average expression or not.
+      This is only possible for formulas which create one value.
+      @since 2.4
+    */
+    public boolean supportsAverage()
+    {
+      return supportsAverage;
+    }

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

-                      r3533
+                      r3581
     method.
   */
   public static final int NEW_SCHEMA_VERSION = Integer.valueOf(36).intValue();
+  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(37).intValue();
   public static synchronized void createTables(boolean update, final ProgressReporter progress)
 …
       createPluginDefinition("net.sf.basedb.plugins.PluginConfigurationImporter", null, null, true, null, false);
       createPluginDefinition("net.sf.basedb.plugins.CdfFileReporterImporter", null, null, true, null, false);
+      createPluginDefinition("net.sf.basedb.plugins.PackedFileExporter", null, keyEveryoneUse, true, null, true);
       // Plugin configurations

branches/webservices/src/core/net/sf/basedb/core/PropertyFilter.java

-                      r3533
+                      r3581
     Create a restriction from the filter. There are a few special cases:
     <p>
+    If the property starts with a $ it is interpreted as a <code>alias.property</code>
+    value, ignoring the root alias of the query. The alias is removed from the
+    property before proceeding.
+    <p>
     If the property starts with a # it is a filter on annotations. The rest of
     the property is the ID of the annotation type, and we use a
     {@link AnnotationSimpleRestriction} object for the restriction.
-    <p>
-    If the property starts with a $ it is interpreted as a <code>alias.property</code>
-    value, ignoring the root alias of the query.
     <p>
     If the property starts with a @ the property is a collection of values and
 …
     Restriction restriction = null;
     String property = getProperty();
+    String alias = null;
+    if (property != null && property.startsWith("$"))
+    {
+      // Property is alias.property or alias only
+      int dotIndex = property.indexOf(".");
+      if (dotIndex == -1)
+      {
+        // Alias only
+        alias = property.substring(1);
+        property = null;
+      }
+      else if (property != null)
+      {
+        // Alias.property
+        alias = property.substring(1, dotIndex);
+        property = property.substring(dotIndex+1);
+      }
+    }
     if (property != null && property.startsWith("#"))
 …
       // Property is id of annotation type: #id
       int annotationTypeId = (Integer)Type.INT.parseString(property.substring(1));
       restriction = new AnnotationSimpleRestriction(annotationTypeId, getValueType(),
+      restriction = new AnnotationSimpleRestriction(alias, annotationTypeId, getValueType(),
         getOperator(), getValueAsObject(), false);
+    }
 …
       Expression parameter = getValue() == null ? null :
         Expressions.parameter(parameterName, getValueAsObject(), getValueType());
+      String alias = null;
+      if (property != null && property.startsWith("$"))
+      {
+        // Property is alias.property or alias only
+        int dotIndex = property.indexOf(".");
+        if (dotIndex == -1)
+        {
+          // Alias only
+          alias = property.substring(1);
+          property = null;
+        }
+        else if (property != null)
+        {
+          // Alias.property
+          alias = property.substring(1, dotIndex);
+          property = property.substring(dotIndex+1);
+        }
+      }
       if (property != null && property.startsWith("@"))
+      {

branches/webservices/src/core/net/sf/basedb/core/RawDataProperty.java

-                      r2535
+                      r3581
   */
   RawDataProperty(String name, String title, String description, String column,
     Type type, int length, boolean nullable, boolean averagable, int channel)
+    Type type, int length, boolean nullable, Formula.AverageMethod averageMethod, int channel)
+  {
     super(name, title, description, column, type, length, nullable, true, false, averagable, null);
+    super(name, title, description, column, type, length, nullable, true, false, averageMethod, null);
     this.channel = channel;
+  }

branches/webservices/src/core/net/sf/basedb/core/RawDataTypes.java

-                      r2535
+                      r3581
       boolean nullable = XMLUtil.getBooleanAttribute(property, "null", true);
       boolean averagable = XMLUtil.getBooleanAttribute(property, "averagable", type.isNumerical());
+      String avgMethod = property.getAttributeValue("averagemethod");
+      Formula.AverageMethod averageMethod = null;
+      if (avgMethod != null)
+      {
+        averageMethod = Formula.AverageMethod.valueOf(avgMethod.toUpperCase());
+      }
+      else if (averagable)
+      {
+        averageMethod = Formula.AverageMethod.ARITHMETIC_MEAN;
+      }
+      else
+      {
+        averageMethod = Formula.AverageMethod.NONE;
+      }
       int channel = XMLUtil.getIntAttribute(property, "channel", 0);
       properties.add(new RawDataProperty(name, title, description, column, type, length, nullable, averagable, channel));
+      properties.add(new RawDataProperty(name, title, description, column, type, length, nullable, averageMethod, channel));
+    }
     return properties;

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

-                      r3533
+                      r3581
     </td>
   </tr>
+  <tr>
+    <td>37</td>
+    <td>
+      <ul>
+        <li>Implement {@link net.sf.basedb.core.data.ExtendableData} to {@link net.sf.basedb.core.data.UserData}</li>
+      </ul>
+      Only the schemaVersion number is increased in this class, the real update work is done when the database is re-build.
+    </td>
+  </tr>
   </table>
 …
+      }
       /*
       if (schemaVersion < 37)
+      {
         if (progress != null) progress.display((int)(36*progress_factor), "--Updating schema version: " + schemaVersion + " -> 37...");
         schemaVersion = setSchemaVersionInTransaction(session, 37);
+      }
+      /*
+      if (schemaVersion < 38)
+      {
+        if (progress != null) progress.display((int)(37*progress_factor), "--Updating schema version: " + schemaVersion + " -> 38...");
+        schemaVersion = setSchemaVersionInTransaction(session, 38);
         - or -
         schemaVersion = updateToSchemaVersion37(session);
+        schemaVersion = updateToSchemaVersion38(session);
+      }
       ... etc...
 …
         if (schemaVersion < 36)
+        {
           // Set averageMethod to 1 for all formulas with a null value
+          // Set averageMethod to arithmetic mean (=2) for all formulas with a null value
           org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session,
             "SET_AVERAGE_METHOD_ON_FORMULAS");
           /*
             UPDATE FormulaData f
             SET f.averageMethod = 1
+            SET f.averageMethod = 2
             WHERE f.averageMethod IS NULL
           */
           HibernateUtil.executeUpdate(query);
           // Set averageMethod to 1 for all extravaluetypes with a null value
+          // Set averageMethod to arithmetic mean (=2) for all extravaluetypes with a null value
           query = HibernateUtil.getPredefinedQuery(session,
             "SET_AVERAGE_METHOD_ON_EXTRAVALUETYPES");
           /*
             UPDATE ExtraValueTypeData evt
             SET evt.averageMethod = 1
+            SET evt.averageMethod = 2
             WHERE evt.averageMethod IS NULL
           */

branches/webservices/src/core/net/sf/basedb/core/User.java

-                      r3533
+                      r3581
     checkPermission(Permission.RESTRICTED_WRITE);
     getData().setUrl(StringUtil.setNullableString(url, "url", MAX_URL_LENGTH));
+  }
+  /**
+    Gets an extended property with a certain name
+    @param name The name of the property
+    @return An Object or
+      null if no extended property exists with the name
+    @since 2.4
+  */
+  public Object getExtended(String name)
+  {
+    return getData().getExtended(name);
+  }
+  /**
+    Sets an extended property
+    @param name The name to call the extended property by
+    @param value The value the extended property should have
+    @throws PermissionDeniedException If the logged in user doesn't
+      have @link {Permission#WRITE} permission for the user.
+    @since 2.4
+  */
+  public void setExtended(String name, Object value)
+  {
+    checkPermission(Permission.RESTRICTED_WRITE);
+    getData().setExtended(name, value);
+  }

branches/webservices/src/core/net/sf/basedb/core/data/ExtendableData.java

-                      r2601
+                      r3581
          update="true"
          insert="true"
          averagable="false"
+         averagemethod="geometric_mean"
          description="An extra property for all reporters"
       /&gt;
 …
     <td>averagable</td>
     <td>
+      <b>This attribute has been deprecated and is replaced by <code>averagemethod</code>!</b>
+      <br>
       If it makes sense to take the average of multiple values for this
       property. By default all numerical columns are averagable. For non-numerical
+      columns, this attribute is ignored.
+      columns, this attribute is ignored. The default method is to calculate the
+      arithmetic mean.
       <ul>
       <li>true
 …
       </ul>
       See {@link net.sf.basedb.core.ExtendedProperty#isAveragable()}.
+    </td>
+  </tr>
+  <tr valign="top">
+    <td>averagemethod</td>
+    <td>
+      The method to use when calculating the average of a set of values.
+      This attribute replaces the <code>averagable</code> attribute.
+      The following values can be used:
+      <ul>
+      <li>none: do not use this property when calculating averages
+      <li>arithmetic_mean: calculate the arithmetic mean
+      <li>geometric_mean: calculate the geometric mean
+      <li>min: use the minimum value among the values in the set
+      <li>max: use the maximum value among the values in the set
+      </ul>
+      If no value is given to this attribute the default is to use arithmetic
+      mean for all numerical value types.
+      See {@link net.sf.basedb.core.ExtendedProperty#getAverageMethod()}.
     </td>
   </tr>

branches/webservices/src/core/net/sf/basedb/core/data/ExtraValueTypeData.java

-                      r3533
+                      r3581
     The average method for thid formula:
     <ul>
+    <li>0 = none, {@link net.sf.basedb.core.Formula.AverageMethod#NONE}; no average is defined for this formula
+    <li>1 = geometric mean, {@link net.sf.basedb.core.Formula.AverageMethod#GEOMETRIC_MEAN}; this formula uses geometric mean
+    <li>2 = arithmetic mean, {@link net.sf.basedb.core.Formula.AverageMethod#ARITHMETIC_MEAN}; this formula uses arithmetic mean
+    <li>3 = min, {@link net.sf.basedb.core.Formula.AverageMethod#MIN}; this formula uses the min value as a "mean"
+    <li>4 = max, {@link net.sf.basedb.core.Formula.AverageMethod#MAX}; this formula uses the max value as a "mean"
+    <li>0 = none, {@link net.sf.basedb.core.Formula.AverageMethod#NONE};
+      no average is defined for this formula
+    <li>1 = geometric mean, {@link net.sf.basedb.core.Formula.AverageMethod#GEOMETRIC_MEAN};
+      this formula uses geometric mean
+    <li>2 = arithmetic mean, {@link net.sf.basedb.core.Formula.AverageMethod#ARITHMETIC_MEAN};
+      this formula uses arithmetic mean
+    <li>3 = min, {@link net.sf.basedb.core.Formula.AverageMethod#MIN};
+      this formula uses the min value as a "mean"
+    <li>4 = max, {@link net.sf.basedb.core.Formula.AverageMethod#MAX};
+      this formula uses the max value as a "mean"
     </ul>
     @hibernate.property column="`average_method`" type="int" not-null="true"
+    @since 2.4
   */
   public int getAverageMethod()

branches/webservices/src/core/net/sf/basedb/core/data/FormulaData.java

-                      r3533
+                      r3581
     The average method for thid formula:
     <ul>
+    <li>0 = none, {@link net.sf.basedb.core.Formula.AverageMethod#NONE}; no average is defined for this formula
+    <li>1 = geometric mean, {@link net.sf.basedb.core.Formula.AverageMethod#GEOMETRIC_MEAN}; this formula uses geometric mean
+    <li>2 = arithmetic mean, {@link net.sf.basedb.core.Formula.AverageMethod#ARITHMETIC_MEAN}; this formula uses arithmetic mean
+    <li>3 = min, {@link net.sf.basedb.core.Formula.AverageMethod#MIN}; this formula uses the min value as a "mean"
+    <li>4 = max, {@link net.sf.basedb.core.Formula.AverageMethod#MAX}; this formula uses the max value as a "mean"
+    <li>0 = none, {@link net.sf.basedb.core.Formula.AverageMethod#NONE};
+      no average is defined for this formula
+    <li>1 = geometric mean, {@link net.sf.basedb.core.Formula.AverageMethod#GEOMETRIC_MEAN};
+      this formula uses geometric mean
+    <li>2 = arithmetic mean, {@link net.sf.basedb.core.Formula.AverageMethod#ARITHMETIC_MEAN};
+      this formula uses arithmetic mean
+    <li>3 = min, {@link net.sf.basedb.core.Formula.AverageMethod#MIN};
+      this formula uses the min value as a "mean"
+    <li>4 = max, {@link net.sf.basedb.core.Formula.AverageMethod#MAX};
+      this formula uses the max value as a "mean"
     </ul>
     @hibernate.property column="`average_method`" type="int" not-null="true"
+    @since 2.4
   */
   public int getAverageMethod()

branches/webservices/src/core/net/sf/basedb/core/data/UserData.java

-                      r2962
+                      r3581
 public class UserData
   extends BasicData
   implements NameableData, RemovableData, SystemData
+  implements NameableData, RemovableData, SystemData, ExtendableData
+{
 …
+  {
     this.systemId = systemId;
+  }
+  // -------------------------------------------
+  /*
+    From the ExtendableData interface
+    -------------------------------------------
+  */
+  private Map<String, Object> extendedProperties;
+  /**
+    @since 2.4
+  */
+  public Object getExtended(String name)
+  {
+    return extendedProperties == null ? null : extendedProperties.get(name);
+  }
+  /**
+    @since 2.4
+  */
+  public void setExtended(String name, Object value)
+  {
+    if (extendedProperties == null) extendedProperties = new HashMap<String, Object>();
+    extendedProperties.put(name, value);
+  }
   // -------------------------------------------

branches/webservices/src/core/net/sf/basedb/core/dtd/extended-properties.dtd

r2535	r3581
43	43	update (true\|false) "true"
44	44	averagable (true\|false) #IMPLIED
	45	averagemethod (none\|arithmetic_mean\|geometric_mean\|min\|max) #IMPLIED
45	46	>
46	47

branches/webservices/src/core/net/sf/basedb/core/dtd/raw-data-types.dtd

r2535	r3581
46	46	null (true\|false) "true"
47	47	averagable (true\|false) #IMPLIED
	48	averagemethod (none\|arithmetic_mean\|geometric_mean\|min\|max) #IMPLIED
48	49	channel CDATA #IMPLIED
49	50	>

branches/webservices/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java

-                      r3533
+                      r3581
 package net.sf.basedb.core.plugin;
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
+import net.sf.basedb.core.BioAssay;
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
 …
   /**
+    GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]
+    @since 2.4
+  */
+  protected static final GuiContext CONTEXT_BIOASSAYSET =
+    new GuiContext(Item.BIOASSAYSET, GuiContext.Type.ITEM);
+  /**
+    GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]
+    @since 2.4
+  */
+  protected static final GuiContext CONTEXT_BIOASSAYS =
+    new GuiContext(Item.BIOASSAY, GuiContext.Type.LIST);
+  /**
     The default gui contexts where it makes sense to use an analysis plugin.
     Override for the {@link InteractivePlugin#getGuiContexts()} method to
+    specify other contexts. This set can't be modified.
+    specify other contexts. This set can't be modified. This set only
+    includes the {@link #CONTEXT_BIOASSAYSET}.
   */
   protected static final Set<GuiContext> defaultGuiContexts =
+    Collections.unmodifiableSet(new HashSet<GuiContext>(
+        Arrays.asList(
+          new GuiContext(Item.BIOASSAYSET, GuiContext.Type.ITEM),
+          new GuiContext(Item.BIOASSAY, GuiContext.Type.LIST)
+        )
+      ));
+    Collections.singleton(CONTEXT_BIOASSAYSET);
   /**
 …
   */
   private PluginParameter<BioAssaySet> sourceParameter = null;
+  /**
+    The bioAssays subset parameter.
+    To use when working on subset of bioassays in a bioAssaySet
+    @see #getSourceBioAssaysSubSetParameter(String, String, List<BioAssay>)
+   */
+  private PluginParameter<BioAssay> sourceSubSetParameter = null;
   /**
 …
+  }
   /**
+    Check that the item is a bioassayset.
+    Check that the item is a bioassayset and that the logged in user has
+    permission to use the current experiment.
     @return null if the item is a bioassayset, an error message otherwise
     @throws PermissionDeniedException If the logged in user dosent have
       permission to use the Experiment.
+    @throws PermissionDeniedException If the logged in user dosen't have
+      permission to use the Experiment
   */
   public String isInContext(GuiContext context, Object item)
+  {
     String message = null;
+    if (defaultGuiContexts.contains(context))
+    Experiment e = null;
+    if (context.equals(CONTEXT_BIOASSAYSET))
+    {
       if (item == null)
 …
+      {
         BioAssaySet bas = (BioAssaySet)item;
+        Experiment e = bas.getExperiment();
+        e.checkPermission(Permission.USE);
+      }
+    }
+        e = bas.getExperiment();
+      }
+    }
+    else
+    {
+      DbControl dc = sc.newDbControl();
+      try
+      {
+        e = getCurrentExperiment(dc);
+      }
+      finally
+      {
+        if (dc != null) dc.close();
+      }
+    }
+    if (e != null) e.checkPermission(Permission.USE);
     return message;
+  }
 …
+    }
     return sourceParameter;
+  }
+  protected static final String SOURCE_BIOASSAYS = "source_subset";
+  /**
+    Gets a plugin parameter that asks for a subset of bioassays to use as data source
+    for the plugin.
+      @param label The parameter's label. Uses a default value if null.
+   * @param description Description of the parameter. Uses a default value if null.
+    @return A plugin parameter
+    @since 2.4
+  */
+  protected PluginParameter<BioAssay> getSourceBioAssaysParameter(String label, String description)
+  {
+    if (sourceSubSetParameter == null)
+    {
+      if (label == null) label = "Source bioassays";
+      if (description == null) description = "Select the bioassays that should be filtered. " +
+          "If no bioassay is selected all will be filtered.";
+      sourceSubSetParameter = new PluginParameter<BioAssay>
+        (
+          SOURCE_BIOASSAYS, label, description,
+          new ItemParameterType<BioAssay>(BioAssay.class, null, false, 0, null)
+        );
+    }
+    return sourceSubSetParameter;
+  }
 …
   /**
+    Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.
+      @param dc The DbControl to access the database with
+      @return A list with bioassays or null.
+      @since 2.4
+   */
+  @SuppressWarnings("unchecked")
+  protected List<BioAssay> getSourceBioAssays(DbControl dc)
+  {
+    List<BioAssay> bioAssaySubset = (List<BioAssay>)job.getValues(SOURCE_BIOASSAYS);
+    if (bioAssaySubset != null)
+    {
+      for (BioAssay ba : bioAssaySubset)
+      {
+        dc.reattachItem(ba);
+      }
+    }
+    return bioAssaySubset;
+  }
+  /**
     Generate a name for the transformation based on the plugin and it's
     configuration. The name is created by taking the name of the plugin from the

branches/webservices/src/core/net/sf/basedb/core/query/Aggregations.java

-                      r3533
+                      r3581
     Calculates the geometric mean of all values for an expression: new expression =
     EXP(AVG(LN(e))). Note that this method can handle values less then or equal with
 due although the mathematical definition of geometric mean doesn't alow it.
+although the mathematical definition of geometric mean doesn't allow it.
     This is caused by the way that sql handle null values in aggregated operations.
     The geometric mean of the numbers [2, -5, 8] is therefor 4 (because ln(-5) is
 …
     @return The new Expression
     @throws InvalidDataException If the expression is null
+    @since 2.4
   */
   public static Expression geometricMean(Expression e)

branches/webservices/src/core/net/sf/basedb/core/query/Annotations.java

-                      r2304
+                      r3581
   /**
     Create a restriction that searches for annotations
+    equal to a given value.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    equal to a given value on the root entity of a query.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @deprecated Use {@link #eq(String, AnnotationType, Object, boolean)} instead with alias=null
   */
   public static Restriction eq(AnnotationType annotationType, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(annotationType, Operator.EQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    not equal to a given value.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    return eq(null, annotationType, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    equal to a given value on the root or a joined entity of a
+    query.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction eq(String alias, AnnotationType annotationType, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(null, annotationType, Operator.EQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    not equal to a given value on the root entity of a query.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @deprecated Use {@link #neq(String, AnnotationType, Object, boolean)} instead with alias=null
   */
   public static Restriction neq(AnnotationType annotationType, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(annotationType, Operator.NEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    less than a given value.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    return neq(null, annotationType, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    not equal to a given value on the root or a joined entity of a
+    query.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction neq(String alias, AnnotationType annotationType, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(alias, annotationType, Operator.NEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    less than a given value on the root entity of a query.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @deprecated Use {@link #lt(String, AnnotationType, Object, boolean)} instead with alias=null
   */
   public static Restriction lt(AnnotationType annotationType, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(annotationType, Operator.LT, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    less than or equal to a given value.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    return lt(null, annotationType, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    less than a given value on the root or a joined entity of a
+    query.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction lt(String alias, AnnotationType annotationType, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(alias, annotationType, Operator.LT, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    less than or equal to a given value on the root entity of a query.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @deprecated Use {@link #lteq(String, AnnotationType, Object, boolean)} instead with alias=null
   */
   public static Restriction lteq(AnnotationType annotationType, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(annotationType, Operator.LTEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    greater than a given value.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    return lteq(null, annotationType, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    less than or equal to a given value on the root or a joined entity of a
+    query.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction lteq(String alias, AnnotationType annotationType, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(alias, annotationType, Operator.LTEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    greater than a given value on the root entity of a query.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @deprecated Use {@link #gt(String, AnnotationType, Object, boolean)} instead with alias=null
   */
   public static Restriction gt(AnnotationType annotationType, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(annotationType, Operator.GTEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    greater than or equal to a given value.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    return gt(null, annotationType, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    greater than a given value on the root or a joined entity of a
+    query.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction gt(String alias, AnnotationType annotationType, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(alias, annotationType, Operator.GTEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    greater than or equal to a given value on the root entity of a query.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @deprecated Use {@link #gteq(String, AnnotationType, Object, boolean)} instead with alias=null
   */
   public static Restriction gteq(AnnotationType annotationType, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(annotationType, Operator.GTEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    matching a given value.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    return gteq(null, annotationType, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    greater than or equal to a given value on the root or a joined entity of a
+    query.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction gteq(String alias, AnnotationType annotationType, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(alias, annotationType, Operator.GTEQ, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    matching a given value on the root entity of a query.
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @deprecated Use {@link #like(String, AnnotationType, Object, boolean)} instead with alias=null
   */
   public static Restriction like(AnnotationType annotationType, Object value, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(annotationType, Operator.LIKE, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    between two given values. If the end values are included or excluded
+    return like(null, annotationType, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    matching a given value on the root or a joined entity of a
+    query.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param value The value to search for
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction like(String alias, AnnotationType annotationType, Object value, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationSimpleRestriction(alias, annotationType, Operator.LIKE, value, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    between two given values on the root entity of a query.
+    If the end values are included or excluded
     depends on the database.
     @param annotationType The annotation type to search
     @param lowValue The lower bound
 …
     @param includeInheriting If items inherting the annotation should be returned
       by the query or not
+    @deprecated Use {@link #between(String, AnnotationType, Object, Object, boolean)}
+      instead with alias=null
   */
   public static Restriction between(AnnotationType annotationType, Object lowValue, Object highValue, boolean includeInheriting)
     throws InvalidDataException
+  {
+    return new AnnotationBetweenRestriction(annotationType, lowValue, highValue, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    return between(null, annotationType, lowValue, highValue, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations
+    between two given values on the root or a joined entity of a
+    query. If the end values are included or excluded
+    depends on the database.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param lowValue The lower bound
+    @param highValue The higher bound
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @since 2.4
+  */
+  public static Restriction between(String alias, AnnotationType annotationType, Object lowValue, Object highValue, boolean includeInheriting)
+    throws InvalidDataException
+  {
+    return new AnnotationBetweenRestriction(alias, annotationType, lowValue, highValue, includeInheriting);
+  }
+  /**
+    Create a restriction that searches for annotations on the root entity of a query
     equal to any value in a list of given values.
     @param annotationType The annotation type to search
 …
       by the query or not
     @param values An array of values
+    @deprecated Use {@link #in(String, AnnotationType, boolean, Object[])}
+      instead with alias=null
   */
   public static Restriction in(AnnotationType annotationType, boolean includeInheriting, Object... values)
     throws InvalidDataException
+  {
+    return new AnnotationInRestriction(annotationType, includeInheriting, values);
+  }
+    return in(null, annotationType, includeInheriting, values);
+  }
+  /**
+    Create a restriction that searches for annotations
+    on the root or a joined entity
+    equal to any value in a list of given values.
+    @param alias The alias of the joined entity or null to use the root element
+    @param annotationType The annotation type to search
+    @param includeInheriting If items inherting the annotation should be returned
+      by the query or not
+    @param values An array of values
+    @since 2.4
+  */
+  public static Restriction in(String alias, AnnotationType annotationType, boolean includeInheriting, Object... values)
+    throws InvalidDataException
+  {
+    return new AnnotationInRestriction(alias, annotationType, includeInheriting, values);
+  }
+}

branches/webservices/src/core/net/sf/basedb/core/query/GeometricMeanExpression.java

r3533	r3581
34	34
35	35	@author Johan Enell
36		@version 2.0
	36	@version 2.4
37	37	@see Aggregations#geometricMean(Expression)
38	38	@base.modified $Date$

branches/webservices/src/core/net/sf/basedb/util/AutoDetectFileFormat.java

-                      r2648
+                      r3581
     Map<PluginDefinition, List<PluginConfiguration>> plugins =
       new LinkedHashMap<PluginDefinition, List<PluginConfiguration>>();
     List<PluginDefinition> pluginDefs = null;
     if (pluginDef == null)
 …
     for (PluginDefinition plugin : pluginDefs)
+    {
-      ItemQuery<PluginConfiguration> configQuery = plugin.getPluginConfigurations();
-      configQuery.order(Orders.asc(Hql.property("name")));
-      configQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
       List<PluginConfiguration> configs = new LinkedList<PluginConfiguration>();
       for (PluginConfiguration config : configQuery.list(dc))
+      if (!plugin.requiresConfiguration())
+      {
+        AutoDetectingImporter importer = plugin.newInstance(AutoDetectingImporter.class,
+          null, sc, config, null);
+        if (currentItem == null || ((InteractivePlugin)importer).isInContext(context, currentItem) == null)
+        if (checkImportable(sc, plugin, null, file, context, currentItem))
+        {
+          InputStream in = file.getDownloadStream(0);
+          if (importer.isImportable(in))
+          configs.add(null);
+        }
+      }
+      if (plugin.supportsConfigurations())
+      {
+        ItemQuery<PluginConfiguration> configQuery = plugin.getPluginConfigurations();
+        configQuery.order(Orders.asc(Hql.property("name")));
+        configQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
+        for (PluginConfiguration config : configQuery.list(dc))
+        {
+          if (checkImportable(sc, plugin, config, file, context, currentItem))
+          {
             configs.add(config);
+          }
+        }
+      }
+      if (configs.size() > 0) plugins.put(plugin, configs);
+    }
+    return plugins;
+  }
+  private static boolean checkImportable(SessionControl sc, PluginDefinition plugin,
+    PluginConfiguration config, File file, GuiContext context, Object currentItem)
+  {
+    AutoDetectingImporter importer = null;
+    boolean canBeUsed = false;
+    try
+    {
+      importer = plugin.newInstance(AutoDetectingImporter.class, null, sc, config, null);
+      boolean isInContext = true;
+      if (plugin.isInteractive())
+      {
+        try
+        {
+          InteractivePlugin ip = (InteractivePlugin)importer;
+          isInContext = ip.isInContext(context, currentItem) == null;
+        }
+        catch (Throwable t)
+        {
+          isInContext = false;
+        }
+      }
+      if (isInContext)
+      {
+        InputStream in = file.getDownloadStream(0);
+        try
+        {
+          canBeUsed = importer.isImportable(in);
+        }
+        catch (Throwable t)
+        {
+          canBeUsed = false;
+        }
+        finally
+        {
           try
+          {
             in.close();
+          }
           catch (Exception ex)
+          catch (Throwable t)
           {}
+        }
+      }
+      if (configs.size() > 0)
+      {
+        plugins.put(plugin, configs);
+      }
+      else
+      {
+        AutoDetectingImporter importer = plugin.newInstance(AutoDetectingImporter.class,
+          null, sc, null, null);
+        if (currentItem == null || ((InteractivePlugin)importer).isInContext(context, currentItem) == null)
+        {
+          InputStream in = file.getDownloadStream(0);
+          if (importer.isImportable(in))
+          {
+            plugins.put(plugin, null);
+          }
+          try
+          {
+            in.close();
+          }
+          catch (Exception ex)
+          {}
+        }
+      }
+      }
+    }
+    return plugins;
+    finally
+    {
+      if (importer != null) importer.done();
+    }
+    return canBeUsed;
+  }
+}

branches/webservices/src/core/net/sf/basedb/util/ContextUtil.java

-                      r3533
+                      r3581
   @author Nicklas
   @version 2.4
   @base.modified $Date: $
+  @base.modified $Date$
 */
 public class ContextUtil
 …
       if (!plugin.requiresConfiguration())
+      {
         results.add(new ContextResult(sc, plugin, null, context, currentItem));
+      }
       if (pluginQuery != null && plugin.supportsConfigurations())
+          results.add(new ContextResult(sc, plugin, null, context, currentItem));
+      }
+      if (configQuery != null && plugin.supportsConfigurations())
+      {
         configQuery.setParameter("plugin", plugin.getId(), Type.INT);

branches/webservices/src/core/net/sf/basedb/util/ShareableUtil.java

-                      r2389
+                      r3581
 package net.sf.basedb.util;
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.Group;
 import net.sf.basedb.core.Item;
+import net.sf.basedb.core.ItemResultIterator;
+import net.sf.basedb.core.MultiPermissions;
+import net.sf.basedb.core.Nameable;
 import net.sf.basedb.core.Permission;
 import net.sf.basedb.core.PermissionDeniedException;
+import net.sf.basedb.core.Project;
 import net.sf.basedb.core.SharedItem;
+import net.sf.basedb.core.MultiPermissions;
+import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.User;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
-import java.util.HashSet;
 /**
 …
     return new MultiPermissions(ss);
+  }
+  /**
+    Gets a list with the projects, groups and users(in that order) that
+    an item is shared to.
+      @param item The item that is shared
+      @return A <code>List</code> with items implementing {@link net.sf.basedb.core.Nameable}
+      @since 2.4
+  */
+  public static List<Nameable> getSharedTo(DbControl dc, SharedItem item)
+  {
+    List<Nameable> sharees = new ArrayList<Nameable>();
+    if (item.isShared())
+    {
+      MultiPermissions mp = new MultiPermissions(Collections.singleton(item));
+      ItemResultIterator<Project> projects = mp.getProjects().iterate(dc);
+      ItemResultIterator<Group> groups = mp.getGroups().iterate(dc);
+      ItemResultIterator<User> users = mp.getUsers().iterate(dc);
+      while (projects.hasNext())
+      {
+        sharees.add(projects.next());
+      }
+      while (groups.hasNext())
+      {
+        sharees.add(groups.next());
+      }
+      while (users.hasNext())
+      {
+        sharees.add(users.next());
+      }
+    }
+    return sharees;
+  }
+}

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

-                      r3533
+                      r3581
 import java.net.URL;
 import java.sql.SQLException;
+import java.util.AbstractSet;
 import java.util.ArrayList;
 import java.util.Arrays;
 …
 import java.util.Map;
 import java.util.Set;
+import java.util.TreeMap;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 …
       Boolean mergeReporters = (Boolean) configuration.getValue(geneAveragesParameter.getName());
       Map<String, String> parameters = new HashMap<String, String>();
+      ListMap<String, String> parameters = new ListMap<String, String>();
       for (PluginParameter<?> pp : getJobParametersFromXML(String.valueOf(configuration.getValue(jobParametersParameter.getName()))))
+      {
 …
     try
+    {
-      List<PluginParameter<?>> p = new ArrayList<PluginParameter<?>>();
       String doctype = "<!DOCTYPE jobparameters SYSTEM \"base1-plugin-configuration-file.dtd\">";
       Document doc = XMLUtil.getValidatedXml(doctype+xml, dtdFile);
 …
+        }
       });
+      TreeMap<Integer, PluginParameter<?>> positionParameter = new TreeMap<Integer, PluginParameter<?>>();
       while (it.hasNext())
+      {
         Element e = it.next();
         JobParameter jp = new JobParameter(e);
+        p.add(jp.getPluginParameter());
+      }
+      return p;
+        if (positionParameter.containsKey(jp.getPosition()))
+        {
+          throw new BaseException("Duplicate parameter at position "+jp.getPosition());
+        }
+        positionParameter.put(jp.getPosition(), jp.getPluginParameter());
+      }
+      return new ArrayList<PluginParameter<?>>(positionParameter.values());
+    }
     catch (JDOMException e1)
 …
     ffp.setHeaderRegexp(Pattern.compile("(.*?)\\t(.*)"));
     ffp.setDataHeaderRegexp(Pattern.compile("%"));
+    ffp.setDataFooterRegexp(Pattern.compile("^$"));
     ffp.setDataSplitterRegexp(Pattern.compile("\\t"));
+    ffp.setUseNullIfEmpty(false);
     ffp.setInputStream(stream, Config.getCharset());
 …
                 // int2 = 10^a / 2^(0.5*m)
                 // int1 = int2  2^m
+                // int1 = int2 * 2^m
                 intensities[1] = new Float(Math.pow(10, a) / Math.pow(2, 0.5 * m));
                 intensities[0] = new Float(intensities[1] * Math.pow(2, m));
+                intensities[0] = new Float(intensities[1] * Math.pow(2, m));
+              }
 …
+    }
+  }
+  private class ListMap<K, V> extends java.util.AbstractMap<K, V>
+  {
+    private List<K> keys = new ArrayList<K>();
+    private List<V> values = new ArrayList<V>();
+    @Override
+    public Set<java.util.Map.Entry<K, V>> entrySet()
+    {
+      throw new UnsupportedOperationException();
+    }
+    @Override
+    public V put(K key, V value)
+    {
+      V ret = null;
+      int index = keys.indexOf(key);
+      if (index == -1)
+      {
+        keys.add(key);
+        values.add(value);
+      }
+      else
+      {
+        keys.set(index, key);
+        ret = values.set(index, value);
+      }
+      return ret;
+    }
+    @Override
+    public V get(Object key)
+    {
+      if (key == null) throw new NullPointerException();
+      int index = keys.indexOf(key);
+      V ret = null;
+      if (index != -1)
+      {
+        ret = values.get(index);
+      }
+      return ret;
+    }
+    @Override
+    public boolean isEmpty()
+    {
+      return keys.isEmpty();
+    }
+    @Override
+    public Set<K> keySet()
+    {
+      return new AbstractSet<K>()
+      {
+        @Override
+        public Iterator<K> iterator()
+        {
+          return Collections.unmodifiableList(keys).iterator();
+        }
+        @Override
+        public int size()
+        {
+          return keys.size();
+        }
+      };
+    }
+  }
   private enum Base1JobParameterType

branches/webservices/src/plugins/core/net/sf/basedb/plugins/BioAssaySetExporter.java

-                      r3533
+                      r3581
+  }
   private void exportBaseFileSectionAssays(PrintWriter out, DbControl dc, BioAssaySet bas)
+  {
 …
+    }
     out.println("columns\tid\tname" + annotationString);
     out.println("annotationColumns" + annotationString);
+    out.println("annotationColumns" + (annotationString.length() == 0 ? "\t" : annotationString));
     out.println("%");
     for (BioAssay ba : bas.getBioAssays().list(dc))
 …
+  }
   private void exportBaseFileSectionHead(PrintWriter out, Map<String, String> parameters)
+  {
     out.println("BASEfile");
     if (!parameters.isEmpty())
+    {
       Set<String> keys = new HashSet<String>(parameters.keySet());
       if (keys.remove("section"))
+      List<String> keys = new ArrayList<String>(parameters.keySet());
+      if ("section".equals(keys.get(0)))
+      {
         out.println("section\t"+parameters.get("section"));
+        keys = keys.subList(1, keys.size());
+      }
+      else
+      {
+        out.println("section\tsettings");
+      }
+      if (keys.contains("section"))
+      {
+        throw new BaseException("The parameters can't have a parameter 'section' in the middle of the list.");
+      }
       for (String key : keys)
 …
+    }
     out.println();
     out.println("count\t" + bas.getNumReporters()); //TODO: count number of column/position
+    out.println("count\t" + query.count(dc)); //TODO: count number of column/position
     out.println("%");
 …
     Integer prevPos = null;
     HashMap<Short, String> spotValues = new HashMap<Short, String>();
-    String reporter = null;
     while (iterator.hasNext())
+    {
 …
       Integer currentPos = r.getInt(posIndex);
+      if (prevPos != null && !currentPos.equals(prevPos))
+      {
+      if (!currentPos.equals(prevPos))
+      {
+        // Print spot fields
+        if (!spotValues.isEmpty())
+        {
+          String separator = "";
+          for (Short col : columnNo)
+          {
+            String spot = spotValues.get(col);
+            if (spot != null)
+            {
+              out.print(separator);
+              out.print(spot);
+            }
+            else
+            {
+              out.print(tabs);
+            }
+            separator = "\t";
+          }
+          out.println();
+          spotValues.clear();
+        }
         //Print reporter fields
-        out.print(reporter);
-        //Print spot fields
-        String separator = "";
-        for (Short col : columnNo)
+        {
-          String spot = spotValues.get(col);
-          if (spot != null)
+          {
-            out.print(separator);
-            out.print(spot);
+          }
-          else
+          {
-            out.print(tabs);
+          }
-          separator = "\t";
+        }
-        out.println();
-        reporter = null;
-        spotValues = new HashMap<Short, String>();
+      }
-      if (reporter == null)
+      {
-        reporter = "";
         for (int i = 0; i < reporterIndex.size(); ++i)
+        {
           String field = r.getString(reporterIndex.get(i));
+          reporter += field == null ? "" : field;
+          reporter += "\t";
+          out.print((field == null ? "" : field) + "\t");
+        }
+      }
 …
+      }
       spotValues.put(r.getShort(colIndex), spot);
+      prevPos = r.getInt(posIndex);
+      prevPos = currentPos;
+    }
+    // Print the last spot fields
+    if (!spotValues.isEmpty())
+    {
+      String separator = "";
+      for (Short col : columnNo)
+      {
+        String spot = spotValues.get(col);
+        if (spot != null)
+        {
+          out.print(separator);
+          out.print(spot);
+        }
+        else
+        {
+          out.print(tabs);
+        }
+        separator = "\t";
+      }
+      out.println();
+      spotValues.clear();
+    }
+  }
 …
     List<QueryItem> items = new ArrayList<QueryItem>();
     items.add(new QueryItem("rep.id", "Reporter (internal id)", "reporter", "rep('id')"));
+    items.add(new QueryItem("rep.position", "Position", "position", "pos()"));
     items.add(new QueryItem("rep.name", "Reporter Name", "name", "rep('name')"));
     items.add(new QueryItem("rep.externalId", "Reporter ID", "externalId", "rep('externalId')"));
 …
+  {
     List<QueryItem> items = new ArrayList<QueryItem>();
-    items.add(new QueryItem("position", "Position", "position", "pos()"));
     int channels = bas.getRawDataType().getChannels();
     for (int channel = 1; channel <= channels; ++channel)
 …
+  @Override
   public Plugin.MainType getMainType()
+  {
 …
   private DbControl dc;
   private BioAssaySet bas;
+  @Override
   protected void begin(DbControl dc)
+  {
 …
+  }
+  @Override
   @SuppressWarnings("unchecked")
   protected void performExport(ExportOutputStream out, ProgressReporter progress)
 …
+  }
+  @Override
   protected void end(boolean success)
+  {
     this.dc = null;
+  }
+  @Override
   protected String getSuccessMessage()
+  {
     return "Bioassay set '" + bas.getName() + "' exported successfully";
+  }
   @Override

branches/webservices/src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java

-                      r3533
+                      r3581
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashSet;
 …
   private static final Set<Permissions> permissions = new HashSet<Permissions>();
+  private static final Set<GuiContext> guiContexts = Collections.unmodifiableSet(
+    new HashSet<GuiContext>(Arrays.asList(CONTEXT_BIOASSAYSET, CONTEXT_BIOASSAYS))
+  );
   private RequestInformation configureJob;
 …
     -------------------------------------------
   */
+  @Override
+  public Set<GuiContext> getGuiContexts()
+  {
+    return guiContexts;
+  }
   public RequestInformation getRequestInformation(GuiContext context, String command)
     throws BaseException

branches/webservices/src/test/TestFlatFileParser.java

-                      r2992
+                      r3581
 import net.sf.basedb.util.parser.FlatFileParser;
 import net.sf.basedb.util.parser.Mapper;
+import net.sf.basedb.util.parser.FlatFileParser.Line;
 /*
 …
+    }
+  }
+  public static void testHeaderLine(Line line, String name, String value) throws Exception
+  {
+    if (!line.type().equals(FlatFileParser.LineType.HEADER))
+      throw new Exception("Line is no header: "+line.toString());
+    if (!line.name().equals(name))
+      throw new Exception("Cant find name '"+name+"' in line '"+line.line()+"'");
+    if (!line.value().equals(value))
+      throw new Exception("Cant find value '"+value+"' in line '"+line.line()+"'");
+  }
+  public static void testLine(Line line, String name) throws Exception
+  {
+    if (!line.line().equals(name))
+      throw new Exception("Line '"+line.line()+"' doesnt match '"+name+"'");
+  }
+  public static void testSection(Line line, String name) throws Exception
+  {
+    if (!line.type().equals(FlatFileParser.LineType.SECTION))
+      throw new Exception("Line is no section: "+line.toString());
+    if (!line.name().equals(name))
+      throw new Exception("Cant find sectionname '"+name+"' in line '"+line.line()+"'");
+  }
+}

branches/webservices/www/admin/annotationtypecategories/list_categories.jsp

-                      r3194
+                      r3581
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.core.plugin.Plugin"
   import="net.sf.basedb.util.Enumeration"
+  import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.ModeInfo"
 …
   import="net.sf.basedb.util.Values"
   import="net.sf.basedb.clients.web.PermissionUtil"
+  import="java.util.Iterator"
   import="java.util.List"
   import="java.util.Map"
 …
         id="permission"
         title="Permission"
+      />
+      <tbl:columndef
+        id="sharedTo"
+        title="Shared to"
       />
       <tbl:toolbar
 …
                   %>
                 </tbl:cell>
+                <tbl:cell column="sharedTo">
+                  <%
+                  Iterator<Nameable> sharees = ShareableUtil.getSharedTo(dc, item).iterator();
+                  while(sharees.hasNext())
+                  {
+                    Nameable n = sharees.next();
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, n, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(n.getName()));
+                    }
+                    out.write(sharees.hasNext() ? ", " : "");
+                  }
+                  %>
+                </tbl:cell>
               </tbl:row>
               <%

branches/webservices/www/admin/annotationtypecategories/view_category.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.SessionControl"
   import="net.sf.basedb.core.DbControl"
+  import="net.sf.basedb.core.Group"
   import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
   import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.AnnotationTypeCategory"
 …
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PermissionDeniedException"
 …
   import="net.sf.basedb.core.plugin.GuiContext"
   import="net.sf.basedb.core.plugin.Plugin"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.core.User"
   import="net.sf.basedb.clients.web.Base"
+  import="net.sf.basedb.clients.web.PermissionUtil"
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="java.util.Collections"
   import="java.util.Map"
+  import="java.util.Set"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 …
             visible="<%=annotationTypeCategory.isRemoved()%>"> This item has been flagged for deletion<br></base:icon>
           <base:icon image="shared.gif"
             visible="<%=annotationTypeCategory.isShared()%>"> This item is shared to other user, groups and/or projects</base:icon>
+            visible="<%=annotationTypeCategory.isShared()%>"> This item is shared to other users, groups and/or projects</base:icon>
         </div>
         <%
 …
         </tbl:table>
         <%
+      }
+      // Tables with users/groups/projects that this item is shared to
+      MultiPermissions mp = new MultiPermissions(Collections.singleton(annotationTypeCategory));
+      ItemResultIterator<User> users = mp.getUsers().iterate(dc);
+      ItemResultIterator<Group> groups = mp.getGroups().iterate(dc);
+      ItemResultIterator<Project> projects = mp.getProjects().iterate(dc);
+      if (users.hasNext() || groups.hasNext() || projects.hasNext())
+      {
+        %>
+        <h4 class="docked">Shared to</h4>
+        <tbl:table
+          id="itemsSharedTo"
+          clazz="itemlist"
+          columns="all"
+        >
+          <tbl:columndef
+            id="itemType"
+            title="Item type"
+          />
+          <tbl:columndef
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef
+            id="permissions"
+            title="Permissions"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            while(projects.hasNext())
+            {
+              Project project = projects.next();
+              Set<Permission> permissions = mp.getPermissions(project).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=project.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, project, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while(groups.hasNext())
+            {
+              Group group = groups.next();
+              Set<Permission> permissions = mp.getPermissions(group).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=group.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, group, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while (users.hasNext())
+            {
+              User user = users.next();
+              Set<Permission> permissions = mp.getPermissions(user).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=user.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, user, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      else
+      {
+        %>
+        <h4>Shared to</h4>
+        This annotation type category is not shared
+        (or, you don't have permission to view the ones it is shared to).
+        <%
+      }
       %>

branches/webservices/www/admin/annotationtypes/list_annotationtypes.jsp

-                      r3533
+                      r3581
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.core.plugin.Plugin"
   import="net.sf.basedb.util.Enumeration"
+  import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.PermissionUtil"
 …
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="java.util.Iterator"
   import="java.util.List"
   import="java.util.Map"
 …
         id="permission"
         title="Permission"
+      />
+      <tbl:columndef
+        id="sharedTo"
+        title="Shared to"
       />
       <tbl:toolbar
 …
                   %>
                 </tbl:cell>
+                <tbl:cell column="sharedTo">
+                  <%
+                  Iterator<Nameable> sharees = ShareableUtil.getSharedTo(dc, item).iterator();
+                  while(sharees.hasNext())
+                  {
+                    Nameable n = sharees.next();
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, n, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(n.getName()));
+                    }
+                    out.write(sharees.hasNext() ? ", " : "");
+                  }
+                  %>
+                </tbl:cell>
               </tbl:row>
               <%

branches/webservices/www/admin/annotationtypes/view_annotationtype.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
+  import="net.sf.basedb.core.ItemResultIterator"
+  import="net.sf.basedb.core.MultiPermissions"
+  import="net.sf.basedb.core.Group"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
   import="java.util.Map"
+  import="java.util.Collections"
   import="java.util.Date"
+  import="java.util.Set"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 …
             visible="<%=annotationType.isRemoved()%>"> This item has been flagged for deletion<br></base:icon>
           <base:icon image="shared.gif"
             visible="<%=annotationType.isShared()%>"> This item is shared to other user, groups and/or projects</base:icon>
+            visible="<%=annotationType.isShared()%>"> This item is shared to other users, groups and/or projects</base:icon>
         </div>
         <%
 …
         <%
+      }
+      // Tables with users/groups/projects that this item is shared to
+      MultiPermissions mp = new MultiPermissions(Collections.singleton(annotationType));
+      ItemResultIterator<User> users = mp.getUsers().iterate(dc);
+      ItemResultIterator<Group> groups = mp.getGroups().iterate(dc);
+      ItemResultIterator<Project> projects = mp.getProjects().iterate(dc);
+      if (users.hasNext() || groups.hasNext() || projects.hasNext())
+      {
+        %>
+        <h4 class="docked">Shared to</h4>
+        <tbl:table
+          id="itemsSharedTo"
+          clazz="itemlist"
+          columns="all"
+        >
+          <tbl:columndef
+            id="itemType"
+            title="Item type"
+          />
+          <tbl:columndef
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef
+            id="permissions"
+            title="Permissions"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            while(projects.hasNext())
+            {
+              Project project = projects.next();
+              Set<Permission> permissions = mp.getPermissions(project).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=project.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, project, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while(groups.hasNext())
+            {
+              Group group = groups.next();
+              Set<Permission> permissions = mp.getPermissions(group).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=group.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, group, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while (users.hasNext())
+            {
+              User user = users.next();
+              Set<Permission> permissions = mp.getPermissions(user).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=user.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, user, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      else
+      {
+        %>
+        <h4>Shared to</h4>
+        This annotation type is not shared
+        (or, you don't have permission to view the ones it is shared to).
+        <%
+      }
       %>

branches/webservices/www/admin/clients/list_clients.jsp

-                      r3194
+                      r3581
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.core.plugin.Plugin"
   import="net.sf.basedb.util.Enumeration"
+  import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.PermissionUtil"
 …
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="java.util.Iterator"
   import="java.util.List"
   import="java.util.Map"
 …
         id="permission"
         title="Permission"
+      />
+      <tbl:columndef
+        id="sharedTo"
+        title="Shared to"
       />
       <tbl:toolbar
 …
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
                 <tbl:cell column="permission"><%=PermissionUtil.getShortPermissions(item)%></tbl:cell>
+                <tbl:cell column="sharedTo">
+                  <%
+                  Iterator<Nameable> sharees = ShareableUtil.getSharedTo(dc, item).iterator();
+                  while(sharees.hasNext())
+                  {
+                    Nameable n = sharees.next();
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, n, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(n.getName()));
+                    }
+                    out.write(sharees.hasNext() ? ", " : "");
+                  }
+                  %>
+                </tbl:cell>
               </tbl:row>
               <%

branches/webservices/www/admin/clients/view_client.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.DbControl"
   import="net.sf.basedb.core.SystemItems"
+  import="net.sf.basedb.core.Group"
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.Client"
   import="net.sf.basedb.core.User"
+  import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.PluginDefinition"
   import="net.sf.basedb.core.plugin.GuiContext"
   import="net.sf.basedb.core.plugin.Plugin"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.PermissionUtil"
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="java.util.Collections"
   import="java.util.Map"
+  import="java.util.Set"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 …
   %>
   <base:page title="<%=title%>">
   <base:head scripts="tabcontrol.js" styles="toolbar.css,headertabcontrol.css,path.css">
+  <base:head scripts="table.js,tabcontrol.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css">
     <script language="JavaScript">
     function editItem()
 …
             visible="<%=client.isRemoved()%>"> This item has been flagged for deletion<br></base:icon>
           <base:icon image="shared.gif"
             visible="<%=client.isShared()%>"> This item is shared to other user, groups and/or projects</base:icon>
+            visible="<%=client.isShared()%>"> This item is shared to other users, groups and/or projects</base:icon>
         </div>
         <%
+      }
       %>
       <table class="form" cellspacing=0>
+      <table class="form" cellspacing="0">
       <tr>
         <td class="prompt">Name</td>
 …
       </tr>
       </table>
+      <%
+      // Tables with users/groups/projects that this item is shared to
+      MultiPermissions mp = new MultiPermissions(Collections.singleton(client));
+      ItemResultIterator<User> users = mp.getUsers().iterate(dc);
+      ItemResultIterator<Group> groups = mp.getGroups().iterate(dc);
+      ItemResultIterator<Project> projects = mp.getProjects().iterate(dc);
+      if (users.hasNext() || groups.hasNext() || projects.hasNext())
+      {
+        %>
+        <h4 class="docked">Shared to</h4>
+        <tbl:table
+          id="itemsSharedTo"
+          clazz="itemlist"
+          columns="all"
+        >
+          <tbl:columndef
+            id="itemType"
+            title="Item type"
+          />
+          <tbl:columndef
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef
+            id="permissions"
+            title="Permissions"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            while(projects.hasNext())
+            {
+              Project project = projects.next();
+              Set<Permission> permissions = mp.getPermissions(project).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=project.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, project, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while(groups.hasNext())
+            {
+              Group group = groups.next();
+              Set<Permission> permissions = mp.getPermissions(group).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=group.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, group, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while (users.hasNext())
+            {
+              User user = users.next();
+              Set<Permission> permissions = mp.getPermissions(user).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=user.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, user, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      else
+      {
+        %>
+        <h4>Shared to</h4>
+        This client is not shared
+        (or, you don't have permission to view the ones it is shared to).
+        <%
+      }
+      %>
     </div>

branches/webservices/www/admin/extravaluetypes/edit_extravaluetype.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.ExtraValueType"
+  import="net.sf.basedb.core.Formula"
   import="net.sf.basedb.core.Coloring"
   import="net.sf.basedb.core.PermissionDeniedException"
 …
   ExtraValueType extraValueType = null;
   Coloring coloring = null;
+  Formula.AverageMethod currentAverageMethod = null;
   if (itemId == 0)
 …
     title = "Create extra value type";
     cc.removeObject("item");
+    currentAverageMethod = Formula.AverageMethod.fromValue(Values.getInt(cc.getPropertyValue("averageMethod"),
+      Formula.AverageMethod.ARITHMETIC_MEAN.getValue()));
     coloring = new Coloring();
     coloring.setUsingColors(Values.getBoolean(cc.getPropertyValue("coloring.usingColors")));
 …
+  {
     extraValueType = ExtraValueType.getById(dc, itemId);
+    currentAverageMethod = extraValueType.getAverageMethod();
     coloring = extraValueType.getColoring();
     cc.setObject("item", extraValueType);
 …
     <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
     <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*200)+"px;"%>"
+    <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*240)+"px;"%>"
       position="bottom" remember="<%=extraValueType != null%>">
     <t:tab id="info" title="Extra value type" validate="validateExtraValueType()"
 …
+          }
           %>
+        </td>
+      </tr>
+      <tr>
+        <td class="prompt">Avg. method</td>
+        <td>
+          <select name="averageMethod" class="required">
+          <%
+          for (Formula.AverageMethod method : Formula.AverageMethod.values())
+          {
+            String selected = method == currentAverageMethod ? "selected" : "";
+            %>
+            <option value="<%=method.name()%>" <%=selected%>><%=HTML.encodeTags(method.toString())%>
+            <%
+          }
+          %>
+          </select>
         </td>
       </tr>

branches/webservices/www/admin/extravaluetypes/index.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.ExtraValueType"
+  import="net.sf.basedb.core.Formula"
   import="net.sf.basedb.core.Coloring"
   import="net.sf.basedb.core.ItemQuery"
 …
     extraValueType.setDescription(Values.getStringOrNull(request.getParameter("description")));
     extraValueType.setExternalId(externalId);
+    extraValueType.setAverageMethod(Formula.AverageMethod.valueOf(request.getParameter("averageMethod")));
     Coloring coloring = extraValueType.getColoring();
     coloring.setUsingColors(Values.getBoolean(request.getParameter("use_colors")));

branches/webservices/www/admin/extravaluetypes/list_extravaluetypes.jsp

-                      r3194
+                      r3581
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ExtraValueType"
+  import="net.sf.basedb.core.Formula"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.Include"
 …
   private static final Enumeration<String, String> valueTypes = new Enumeration<String, String>();
+  private static final Enumeration<String, String> avgMethods = new Enumeration<String, String>();
   static
+  {
 …
     valueTypes.add(Integer.toString(Type.FLOAT.getValue()), Type.FLOAT.toString());
     valueTypes.add(Integer.toString(Type.STRING.getValue()), Type.STRING.toString());
+    for (Formula.AverageMethod m : Formula.AverageMethod.values())
+    {
+      avgMethods.add(Integer.toString(m.getValue()), HTML.encodeTags(m.toString()));
+    }
+  }
 …
         title="Value type"
         enumeration="<%=valueTypes%>"
+        sortable="true"
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef
+        id="averageMethod"
+        property="averageMethod"
+        datatype="int"
+        enumeration="<%=avgMethods%>"
+        title="Avg. method"
         sortable="true"
         filterable="true"
 …
                 <tbl:cell column="externalId"><%=HTML.encodeTags(item.getExternalId())%></tbl:cell>
                 <tbl:cell column="valueType"><%=item.getValueType()%></tbl:cell>
+                <tbl:cell column="averageMethod"><%=item.getAverageMethod().toString()%></tbl:cell>
                 <tbl:cell column="useColors"><%=item.getColoring().isUsingColors() ? "yes" : "no"%></tbl:cell>
                 <tbl:cell column="logarithmic"><%=item.getColoring().isLogarithmic() ? "yes" : "no"%></tbl:cell>

branches/webservices/www/admin/extravaluetypes/view_extravaluetype.jsp

-                      r2978
+                      r3581
       </tr>
       <tr>
+        <td class="prompt">Avg. method</td>
+        <td><%=extraValueType.getAverageMethod().toString()%></td>
+      </tr>
+      <tr>
         <td class="prompt">Use coloring</td>
         <td>

branches/webservices/www/admin/hardware/list_hardware.jsp

-                      r3194
+                      r3581
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.core.plugin.Plugin"
   import="net.sf.basedb.util.Enumeration"
+  import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.PermissionUtil"
 …
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="java.util.Iterator"
   import="java.util.List"
   import="java.util.Map"
 …
         id="permission"
         title="Permission"
+      />
+      <tbl:columndef
+        id="sharedTo"
+        title="Shared to"
       />
       <tbl:toolbar
 …
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
                 <tbl:cell column="permission"><%=PermissionUtil.getShortPermissions(item)%></tbl:cell>
+                <tbl:cell column="sharedTo">
+                  <%
+                  Iterator<Nameable> sharees = ShareableUtil.getSharedTo(dc, item).iterator();
+                  while(sharees.hasNext())
+                  {
+                    Nameable n = sharees.next();
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, n, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(n.getName()));
+                    }
+                    out.write(sharees.hasNext() ? ", " : "");
+                  }
+                  %>
+                </tbl:cell>
               </tbl:row>
               <%

branches/webservices/www/admin/hardware/view_hardware.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.DbControl"
   import="net.sf.basedb.core.SystemItems"
+  import="net.sf.basedb.core.Group"
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.Hardware"
   import="net.sf.basedb.core.HardwareType"
   import="net.sf.basedb.core.User"
+  import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.PluginDefinition"
   import="net.sf.basedb.core.plugin.GuiContext"
   import="net.sf.basedb.core.plugin.Plugin"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.PermissionUtil"
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="java.util.Collections"
   import="java.util.Map"
+  import="java.util.Set"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 …
   %>
   <base:page title="<%=title%>">
   <base:head scripts="tabcontrol.js" styles="toolbar.css,headertabcontrol.css,path.css">
+  <base:head scripts="table,js,tabcontrol.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css">
     <script language="JavaScript">
     function editItem()
 …
             visible="<%=hardware.isRemoved()%>"> This item has been flagged for deletion<br></base:icon>
           <base:icon image="shared.gif"
             visible="<%=hardware.isShared()%>"> This item is shared to other user, groups and/or projects</base:icon>
+            visible="<%=hardware.isShared()%>"> This item is shared to other users, groups and/or projects</base:icon>
         </div>
         <%
 …
       </tr>
       </table>
+      <%
+      // Tables with users/groups/projects that this item is shared to
+      MultiPermissions mp = new MultiPermissions(Collections.singleton(hardware));
+      ItemResultIterator<User> users = mp.getUsers().iterate(dc);
+      ItemResultIterator<Group> groups = mp.getGroups().iterate(dc);
+      ItemResultIterator<Project> projects = mp.getProjects().iterate(dc);
+      if (users.hasNext() || groups.hasNext() || projects.hasNext())
+      {
+        %>
+        <h4 class="docked">Shared to</h4>
+        <tbl:table
+          id="itemsSharedTo"
+          clazz="itemlist"
+          columns="all"
+        >
+          <tbl:columndef
+            id="itemType"
+            title="Item type"
+          />
+          <tbl:columndef
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef
+            id="permissions"
+            title="Permissions"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            while(projects.hasNext())
+            {
+              Project project = projects.next();
+              Set<Permission> permissions = mp.getPermissions(project).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=project.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, project, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while(groups.hasNext())
+            {
+              Group group = groups.next();
+              Set<Permission> permissions = mp.getPermissions(group).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=group.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, group, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while (users.hasNext())
+            {
+              User user = users.next();
+              Set<Permission> permissions = mp.getPermissions(user).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=user.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, user, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      else
+      {
+        %>
+        <h4>Shared to</h4>
+        This hardware is not shared
+        (or, you don't have permission to view the ones it is shared to).
+        <%
+      }
+      %>
     </div>
       </t:tab>

branches/webservices/www/admin/jobagents/list_agents.jsp

-                      r3194
+                      r3581
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.core.plugin.Plugin"
   import="net.sf.basedb.util.Enumeration"
+  import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.PermissionUtil"
 …
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.Values"
+  import="java.util.Iterator"
   import="java.util.List"
   import="java.util.Map"
 …
         id="permission"
         title="Permission"
+      />
+      <tbl:columndef
+        id="sharedTo"
+        title="Shared to"
       />
       <tbl:toolbar
 …
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
                 <tbl:cell column="permission"><%=PermissionUtil.getShortPermissions(item)%></tbl:cell>
+                <tbl:cell column="sharedTo">
+                  <%
+                  Iterator<Nameable> sharees = ShareableUtil.getSharedTo(dc, item).iterator();
+                  while(sharees.hasNext())
+                  {
+                    Nameable n = sharees.next();
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, n, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(n.getName()));
+                    }
+                    out.write(sharees.hasNext() ? ", " : "");
+                  }
+                  %>
+                </tbl:cell>
               </tbl:row>
               <%

branches/webservices/www/admin/jobagents/view_agent.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
+  import="net.sf.basedb.core.ItemResultIterator"
+  import="net.sf.basedb.core.MultiPermissions"
+  import="net.sf.basedb.core.Group"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
 …
   import="java.util.Set"
   import="java.util.Date"
+  import="java.util.Collections"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 …
         <%
+      }
+      // Tables with users/groups/projects that this item is shared to
+      MultiPermissions mp = new MultiPermissions(Collections.singleton(agent));
+      ItemResultIterator<User> users = mp.getUsers().iterate(dc);
+      ItemResultIterator<Group> groups = mp.getGroups().iterate(dc);
+      ItemResultIterator<Project> projects = mp.getProjects().iterate(dc);
+      if (users.hasNext() || groups.hasNext() || projects.hasNext())
+      {
+        %>
+        <h4 class="docked">Shared to</h4>
+        <tbl:table
+          id="itemsSharedTo"
+          clazz="itemlist"
+          columns="all"
+        >
+          <tbl:columndef
+            id="itemType"
+            title="Item type"
+          />
+          <tbl:columndef
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef
+            id="permissions"
+            title="Permissions"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            while(projects.hasNext())
+            {
+              Project project = projects.next();
+              Set<Permission> permissions = mp.getPermissions(project).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=project.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, project, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while(groups.hasNext())
+            {
+              Group group = groups.next();
+              Set<Permission> permissions = mp.getPermissions(group).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=group.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, group, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while (users.hasNext())
+            {
+              User user = users.next();
+              Set<Permission> permissions = mp.getPermissions(user).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=user.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, user, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      else
+      {
+        %>
+        <h4>Shared to</h4>
+        This job agent is not shared
+        (or, you don't have permission to view the ones it is shared to).
+        <%
+      }
       %>

branches/webservices/www/admin/pluginconfigurations/list_configurations.jsp

-                      r3533
+                      r3581
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.util.Enumeration"
   import="net.sf.basedb.util.JarClassLoader"
+  import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.util.ToStringComparator"
   import="net.sf.basedb.clients.web.Base"
 …
   import="net.sf.basedb.util.Values"
   import="net.sf.basedb.clients.web.util.NameablePluginAdaptor"
+  import="java.util.Iterator"
   import="java.util.List"
   import="java.util.Map"
 …
         id="permission"
         title="Permission"
+      />
+      <tbl:columndef
+        id="sharedTo"
+        title="Shared to"
       />
       <tbl:toolbar
 …
                 </tbl:cell>
                 <tbl:cell column="permission"><%=PermissionUtil.getShortPermissions(item)%></tbl:cell>
+                <tbl:cell column="sharedTo">
+                  <%
+                  Iterator<Nameable> sharees = ShareableUtil.getSharedTo(dc, item).iterator();
+                  while(sharees.hasNext())
+                  {
+                    Nameable n = sharees.next();
+                    if (mode.hasPropertyLink())
+                    {
+                      out.write(Base.getLinkedName(ID, n, false, mode.hasEditLink()));
+                    }
+                    else
+                    {
+                      out.write(HTML.encodeTags(n.getName()));
+                    }
+                    out.write(sharees.hasNext() ? ", " : "");
+                  }
+                  %>
+                </tbl:cell>
               </tbl:row>
               <%

branches/webservices/www/admin/pluginconfigurations/view_configuration.jsp

-                      r2978
+                      r3581
   import="net.sf.basedb.core.DbControl"
   import="net.sf.basedb.core.SystemItems"
+  import="net.sf.basedb.core.Group"
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.core.BasicItem"
   import="net.sf.basedb.core.File"
+  import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.PermissionDeniedException"
 …
   import="net.sf.basedb.core.plugin.GuiContext"
   import="net.sf.basedb.core.plugin.Plugin"
+  import="net.sf.basedb.core.Project"
   import="net.sf.basedb.util.JarClassLoader"
   import="net.sf.basedb.util.ToStringComparator"
 …
   <base:page title="<%=title%>">
   <base:head scripts="tabcontrol.js" styles="toolbar.css,headertabcontrol.css,path.css">
+  <base:head scripts="table.js,tabcontrol.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css">
     <script language="JavaScript">
     function editItem()
 …
             visible="<%=configuration.isRemoved()%>"> This item has been flagged for deletion<br></base:icon>
           <base:icon image="shared.gif"
             visible="<%=configuration.isShared()%>"> This item is shared to other user, groups and/or projects</base:icon>
+            visible="<%=configuration.isShared()%>"> This item is shared to other users, groups and/or projects</base:icon>
         </div>
         <%
+      }
       %>
       <table class="form" cellspacing=0>
+      <table class="form" cellspacing="0">
       <tr>
         <td class="prompt">Name</td>
 …
       </tr>
       </table>
+      <%
+      // Tables with users/groups/projects that this item is shared to
+      MultiPermissions mp = new MultiPermissions(Collections.singleton(configuration));
+      ItemResultIterator<User> users = mp.getUsers().iterate(dc);
+      ItemResultIterator<Group> groups = mp.getGroups().iterate(dc);
+      ItemResultIterator<Project> projects = mp.getProjects().iterate(dc);
+      if (users.hasNext() || groups.hasNext() || projects.hasNext())
+      {
+        %>
+        <h4 class="docked">Shared to</h4>
+        <tbl:table
+          id="itemsSharedTo"
+          clazz="itemlist"
+          columns="all"
+        >
+          <tbl:columndef
+            id="itemType"
+            title="Item type"
+          />
+          <tbl:columndef
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef
+            id="permissions"
+            title="Permissions"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            while(projects.hasNext())
+            {
+              Project project = projects.next();
+              Set<Permission> permissions = mp.getPermissions(project).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=project.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, project, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while(groups.hasNext())
+            {
+              Group group = groups.next();
+              Set<Permission> permissions = mp.getPermissions(group).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=group.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, group, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            while (users.hasNext())
+            {
+              User user = users.next();
+              Set<Permission> permissions = mp.getPermissions(user).values().iterator().next();
+              %>
+              <tbl:row>
+                <tbl:cell column="itemType"><%=user.getType()%></tbl:cell>
+                <tbl:cell column="name"><%=Base.getLinkedName(ID, user, false, true)%></tbl:cell>
+                <tbl:cell column="permissions">
+                  <%=PermissionUtil.translatePermissionsToString(permissions)%>
+                </tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
+            </tbl:rows>
+          </tbl:data>
+        </tbl:table>
+        <%
+      }
+      else
+      {
+        %>
+        <h4>Shared to</h4>
+        This configuration is not shared
+        (or, you don't have permission to view the ones it is shared to).
+        <%
+      }
+      %>
     </div>
 …
       <t:tab id="parameters" title="Configuration parameters" >
       <div class="boxed">
       <table class="form" cellspacing=0>
+      <table class="form" cellspacing="0">
       <%
       if (plugin != null)

branches/webservices/www/admin/plugindefinitions/list_plugins.jsp

-                      r3533
+                      r3581
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.PluginDefinition"
 …
   import="net.sf.basedb.util.Enumeration"
   import="net.sf.basedb.util.JarClassLoader"
+  import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.util.ToStringComparator"
   import="net.sf.basedb.clients.web.Base"

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