Changeset 4298


Ignore:
Timestamp:
May 13, 2008, 11:26:29 AM (15 years ago)
Author:
Nicklas Nordborg
Message:

Merged pre-2.7-release to the trunk.

Location:
trunk
Files:
14 edited

Legend:

Unmodified
Added
Removed

  • trunk/build.xml

    r4286 r4298  
    188188  <target
    189189    name="dist"
    190     depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,webservices.jar,webservices.wsdl,
     190    depends="clean,dist.init,core.jar,coreplugins.jar,web.jar,xjspcompiler,webservices.jar,webservices.wsdl,
    191191      installprg.jar,jobagent.jar,migrate.jar,copy.config,copy.jar,doc,doc.dist"
    192192    description="Create everything needed for distribution"

  • trunk/doc/3rd-party-components.txt

    r4248 r4298  
    165165License   : LGPL (lgpl.txt)
    166166Jar files : jfreechart-1.0.3.jar jcommon-1.0.6.jar
    167 
    168 
    169 MultiExperiment Viewer
    170 ----------------------
    171 MeV is a versatile microarray data analysis tool, incorporating
    172 sophisticated algorithms for clustering, visualization,
    173 classification, statistical analysis and biological theme discovery.
    174 
    175 More info : http://www.tm4.org/
    176 Version   : Modified version based on official v4.0 release
    177 License   : The Artisic License (http://www.tm4.org/artistic_license.pdf)
    178 Jar files : <base>/www/plugins/org/tigr/microarray/mev/*.jar
    179 
    180 Note: Most of the jar files above are other 3rd-party components used
    181 by MeV. BASE doesn't use these components directly. For access to the
    182 modifed source go to http://trac.thep.lu.se/tracs/BASE-hacks
    183167
    184168

  • trunk/doc/development/build.html

    r3675 r4298  
    8787  </p>
    8888  <pre class="code">
    89 svn checkout http://lev.thep.lu.se/repository/base/trunk/ base
     89svn checkout http://base.thep.lu.se/svn/trunk/ base
    9090</pre>
    9191
    … …  
    243243  <dt>ant doc</dt>
    244244  <dd>
    245     Generate documentation for local use.
    246   </dd>
    247  
    248   <dt>ant docbook</dt>
    249   <dd>
    250     Temporary target for generating the docbook-based user documentation.
    251     In the future this will be included in the 'ant doc' target. Note!
    252     Docbook will work with pure Java but performance is a lot better if
    253     <a href="http://xmlsoft.org/XSLT/">XSLTPROC</a> is installed. The
    254     documentation is generated in the directory 'doc/docbook'.
     245    Generate documentation for local use. This generates all documentation
     246    and may take a long time.
     247  </dd>
     248 
     249  <dt>ant doc.javadoc</dt>
     250  <dd>
     251    Generate Javadoc documentation only. The
     252    documentation is generated in the 'doc/api' directory.
     253  </dd>
     254
     255  <dt>ant doc.docbook.html</dt>
     256  <dd>
     257    Generate user- and administrator documentation from docbook in
     258    HTML format. Docbook will work with pure Java but performance is a
     259    lot better if <a href="http://xmlsoft.org/XSLT/">XSLTPROC</a> is
     260    installed. The documentation is generated in the 'doc/html' directory.
    255261  </dd>
    256262  </dl>

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

    r4232 r4298  
    5151    to a pristine (empty) BASE 2 server with one exception; The
    5252    migration can be restarted if it fails during the RawBioAssaysData
    53     transfer, for all other failure points the migration has to be
     53    transfer. For all other failure points the migration has to be
    5454    restarted with an empty database. Migration from several BASE 1
    5555    installations to one BASE 2 server is not supported.
    … …  
    5858  <para>
    5959    The instructions here assume
    60     that <ulink url="http://tomcat.apache.org/">tomcat</ulink> is used
     60    that <ulink url="http://tomcat.apache.org/">Apache Tomcat 6</ulink> is used
    6161    on the server side. Other servlet engines may work but we only
    62     test tomcat.
     62    test with Tomcat.
    6363  </para>
    6464
    … …  
    7373        you must also make sure that you are running Tomcat 6 or higher.
    7474        Earlier BASE versions only required Tomcat 5.5. If you are not
    75         already running Tomcat 6 you need to upgrade.     
     75        already running Tomcat 6 you need to upgrade. Other serlvet
     76        engines may work if they implement the Servlet 2.5 and JSP
     77        2.1 specifications.
    7678      </para>
    7779    </important>
    … …  
    127129    <variablelist>
    128130      <varlistentry>
    129         <term>Shut down the tomcat server</term>
     131        <term>Shut down the Tomcat server</term>
    130132        <listitem>
    131133          <para>
    … …  
    223225            Local settings in the raw data
    224226            tables, <filename>&lt;base-dir&gt;/www/WEB-INF/classes/raw-data-types.xml</filename>,
    225             may need to be transferred.
     227            may need to be transferred. This also includes all files in
     228            the <filename>&lt;base-dir&gt;/www/WEB-INF/classes/raw-data-types</filename> and
     229            <filename>&lt;base-dir&gt;/www/WEB-INF/classes/extended-properties</filename>
     230            directories.
    226231          </para>
    227232        </listitem>
    … …  
    241246<programlisting>
    242247sh ./updatedb.sh [base_root_login] <emphasis>base_root_password</emphasis>
    243 sh ./updateindexes.sh <emphasis>base_root_password</emphasis>
     248sh ./updateindexes.sh
    244249</programlisting>
    245250            where <emphasis>base_root_login</emphasis> is the login
    … …  
    252257
    253258      <varlistentry>
    254         <term>Remove tomcat cache</term>
    255         <listitem>
    256           <para>
    257             As tomcat user, remove cached files and directories. Do
     259        <term>Remove Tomcat cache</term>
     260        <listitem>
     261          <para>
     262            As Tomcat user, remove cached files and directories. Do
    258263            something like
    259 <programlisting>cd /usr/share/apache-tomcat-6.0.14/
     264<programlisting>cd /usr/share/apache-tomcat-6.0/
    260265rm -rf work/Catalina</programlisting>
    261266          </para>
    … …  
    264269
    265270      <varlistentry>
    266         <term>Start tomcat</term>
    267         <listitem>
    268           <para>
    269             Start the tomcat server: <command>sudo
     271        <term>Start Tomcat</term>
     272        <listitem>
     273          <para>
     274            Start the Tomcat server: <command>sudo
    270275              /etc/init.d/tomcat6.0 start</command>
    271276          </para>
    … …  
    642647        <listitem>
    643648          <para>
    644             Download and install Java SDK 1.6, available from
    645             <ulink url="http://java.sun.com/" />. Earlier versions
    646             may work (eq. 1.5), but are not supported.
     649            Download and install Java SDK 1.6 (aka Java 6), available from
     650            <ulink url="http://java.sun.com/" />.
    647651          </para>
    648652        </listitem>
    … …  
    653657        <listitem>
    654658          <para>
    655             Download and install tomcat 6.0.14 or later, available
     659            Download and install Apache Tomcat 6.0.14 or later, available
    656660            from <ulink
    657661            url="http://tomcat.apache.org" />
    658             <important>
    659               You MUST make sure that Tomcat uses the SERVER mode of
    660               the Java run time engine
    661               (see <ulink
    662               url="http://lev.thep.lu.se/trac/base/ticket/99">ticket:99</ulink>).
    663             </important>
    664             On Linux you do this by setting the environment variable:
    665             <code>CATALINA_OPTS</code> to <code>-server</code>. It is
    666             also a good idea to specify the maximum allowed memory to
    667             use: <code>-server -Xmx500m</code> sets it to 500
    668             megabytes. Basically add the next line close to the top of
     662
     663            It is a good idea to specify the maximum allowed memory
     664            that Tomcat can use. The default setting is usually not
     665            large enough. To do this you have to set Java startup options
     666            in the <code>CATALINA_OPTS</code> environment variable.
     667           
     668            Basically add the next line close to the top of
    669669            the <filename>catalina.sh</filename> script that comes
    670             with tomcat
     670            with Tomcat
    671671            (directory <filename
    672672            class="directory">bin</filename>):
    673 <programlisting>CATALINA_OPTS="-server -Xmx500m"</programlisting>
     673<programlisting>CATALINA_OPTS="-Xmx500m"</programlisting>
    674674          </para>
    675675          <para>
    … …  
    881881            An area for file storage must be setup. Create an empty
    882882            directory in a proper location in your file system, and
    883             set the owner to be the same as the one that the tomcat
     883            set the owner to be the same as the one that the Tomcat
    884884            server will be running as. Remember this location for
    885885            later use.
    … …  
    964964
    965965      <varlistentry>
    966         <term>BASE and tomcat</term>
     966        <term>BASE and Tomcat</term>
    967967        <listitem>
    968968          <para>
    969969            Either move the <filename
    970970            class="directory">&lt;base-dir&gt;/www</filename> directory
    971             to the tomcat <filename class="directory">webapps</filename>
    972             directory or create a symbolic link from the tomcat
     971            to the Tomcat <filename class="directory">webapps</filename>
     972            directory or create a symbolic link from the Tomcat
    973973            <filename class="directory">webapps</filename> directory to
    974974            the <filename class="directory">&lt;base-dir&gt;/www</filename>
    … …  
    976976<programlisting>cd /path/to/tomcat/webapps
    977977ln -s /path_to_base/www base2</programlisting>
    978             Start/restart tomcat, and try http://hostname:8080/base2
     978            Start/restart Tomcat, and try http://hostname:8080/base2
    979979            (change <emphasis>hostname</emphasis> to your hostname) in
    980             your favourite browser. BASE log-in page should appear
     980            your favourite browser. The BASE log-in page should appear
    981981            after a few seconds.
    982982          </para>
    … …  
    985985
    986986      <varlistentry>
    987         <term>BASE, apache, and apache/tomcat connector</term>
     987        <term>BASE, Apache, and Apache/Tomcat connector</term>
    988988        <listitem>
    989989          <para>
    … …  
    991991          </para>
    992992          <para>
    993             If you want run the tomcat server through the apache web
    994             server, you need to install the apache version 2 web
     993            If you want run the Tomcat server through the Apache web
     994            server, you need to install the Apache version 2 web
    995995            server, available
    996996            from <ulink
    … …  
    10071007            <itemizedlist>
    10081008              <listitem>
    1009                 Get that tomcat server running in stand-alone
     1009                Get that Tomcat server running in stand-alone
    10101010                mode.
    10111011              </listitem>
    10121012              <listitem>
    1013                 Get the apache 2 server running.
     1013                Get the Apache 2 server running.
    10141014              </listitem>
    10151015              <listitem>
    … …  
    10211021                Create a <filename>workers.properties</filename> file
    10221022                in the
    1023                 tomcat <filename class="directory">base</filename>
     1023                Tomcat <filename class="directory">base</filename>
    10241024                directory (commonly copied from a template).
    10251025              </listitem>
    … …  
    10411041allow from all
    10421042&lt;/Directory&gt;
    1043 # The following lines mounts all base2 jsp files to tomcat
     1043# The following lines mounts all base2 jsp files to Tomcat
    10441044JkMount /base2 ajp13
    10451045JkMount /base2/* ajp13
    … …  
    10511051              </listitem>
    10521052            </itemizedlist>
    1053             You must restart the apache and the tomcat server after above steps.
     1053            You must restart the Apache and the Tomcat server after above steps.
    10541054          </para>
    10551055        </listitem>
    … …  
    13251325    <para>
    13261326      Migration can be restarted in one specific case only; If the
    1327       migration fails during the RawBioAssaysData transfer simply
     1327      migration fails during the RawBioAssayData transfer simply
    13281328      restart the migration and the script will ask you to verify that
    13291329      a restart should be attempted. For all other failure points the
    … …  
    13401340            behaviour), you must have file system access to BASE 1.2
    13411341            files, <emphasis>i.e.,</emphasis> the <filename
    1342             class="directory">/ 1.2/data</filename>
     1342            class="directory">/BASE 1.2/data</filename>
    13431343            directory containing directories
    13441344            <filename class="directory">rawdata</filename>,
    … …  
    14021402            Run migration utility:
    14031403<programlisting>cd /path_to_base/dist/bin
    1404 ./migrate_from_1.2.sh</programlisting>
    1405           </para>
    1406           <para>
    1407             If the migration fails during the RawBioAssaysData
     1404./migrate_from_1.2.sh disclaimer_understood</programlisting>
     1405          </para>
     1406          <para>
     1407            If the migration fails during the RawBioAssayData
    14081408            transfer you can restart the migration at the point of
    14091409            failure. Simply restart the migration and the script will

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

    r4151 r4298  
    3434    classification, statistical analysis and biological theme
    3535    discovery, <ulink
    36     url='http://www.tm4.org'>http://www.tm4.org</ulink>. We use a
    37     modified version of MeV and provide information about the changes
    38     at
    39     the <ulink url='http://dev.thep.lu.se/basehacks'>BASE-hacks
    40     web site</ulink>.
     36    url="http://www.tm4.org">http://www.tm4.org</ulink>. Before BASE 2.7
     37    it was shipped with the main BASE distribution, but is now distributed
     38    as an extension. Visit the
     39    <ulink url="http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev">BASE plug-ins site</ulink>
     40    for more information and download.
    4141  </para>
    4242</sect1>

  • trunk/doc/test/roles/index.html

    r4246 r4298  
    15991599  <li>
    16001600    Use the auto-detect feature to upload and import raw data for each
    1601     Genepix raw bioassay. Select the <code>skip</code> option for the "Feature mismatch"
    1602     parameter since the file contains rows with bogus reporter ID:s.
     1601    Genepix raw bioassay. Select the <code>smart</code> option for the "Feature mismatch"
     1602    parameter and <code>null</code> for "Invalid numeric value".
    16031603   
    16041604    <table class="listing" cellspacing="0" cellpadding="2" border="0">
    … …  
    16381638 
    16391639  <li>
    1640     Create a experiments:
     1640    Create experiments:
    16411641    <table class="listing" cellspacing="0" cellpadding="2" border="0">
    16421642    <tr>
    … …  
    17501750    <tr>
    17511751      <td>Filtered bioassay set</td>
    1752       <td>All intensities &gt; 0</td>
     1752      <td>-</td>
    17531753      <td>ch(1) &gt; 0 &amp;&amp; ch(2) &gt; 0 &amp;&amp; rep('id') != null</td>
    17541754    </tr>

  • trunk/lib/docbook/custom-styles/docbook/plain/css/docbook.css

    r3415 r4298  
    214214/* ADMONITIONS ------------------------------------------------------ {{{ */
    215215
    216 div.note, div.important, div.example, div.informalexample, div.tip, div.warning {
     216div.note, div.important, div.example, div.informalexample, div.tip, div.warning, div.caution {
    217217    margin:         1em;
    218218    padding:        0.5em;
    … …  
    221221}
    222222
    223 div.important th, div.note th, div.tip th, div.warning th {
     223div.important th, div.note th, div.tip th, div.warning th, div.caution th {
    224224    text-align:     left;
    225225    border-bottom:  solid 1px gray;

  • trunk/src/clients/web/net/sf/basedb/clients/web/taglib/tab/TabControl.java

    r4093 r4298  
    418418 
    419419      sb.append("</table>\n");
    420       sb.append("<script language=\"JavaScript\">\n");
     420      sb.append("<script language=\"JavaScript\" defer=\"defer\">\n");
    421421      sb.append("var switchFunction = TabControl.setActiveTab;\n");
    422422      sb.append("if (typeof ").append(getSwitch()).append(" != 'undefined') switchFunction = ").append(getSwitch()).append(";\n");

  • trunk/src/clients/web/net/sf/basedb/clients/web/taglib/table/Table.java

    r4143 r4298  
    594594    sb.append(hiddenForm);
    595595    sb.append("</form>");
    596     sb.append("\n<script language=\"JavaScript\">\n");
     596    sb.append("\n<script language=\"JavaScript\" defer=\"defer\">\n");
    597597    sb.append(script);
    598598    sb.append("\n</script>\n");

  • trunk/src/test/net/sf/basedb/test/TestUtil.java

    r4249 r4298  
    2424package net.sf.basedb.test;
    2525
     26import java.io.File;
     27import java.io.FileNotFoundException;
    2628import java.io.FileWriter;
    2729import java.io.Writer;
    … …  
    6466    Start the testing. Starts BASE and creates a SessionControl.
    6567  */
    66   public static void begin(boolean logMemoryUsage)
     68  public static void begin(boolean logMemoryUsage, boolean checkTestdata)
    6769  {
    6870    if (Application.isRunning()) return;
    … …  
    7072    try
    7173    {
     74      if (checkTestdata)
     75      {
     76        File testdata = new File("../..", "testdata");
     77        if (!testdata.exists() && !testdata.isDirectory())
     78        {
     79          throw new FileNotFoundException("Could not find 'testdata' directory. " +
     80            "It must be located in the project root.");
     81        }
     82      }
    7283      write("++Starting BASE...");
    7384      if (logMemoryUsage)
    … …  
    114125  public static SessionControl getSessionControl()
    115126  {
    116     if (sc == null) begin(false);
     127    if (sc == null) begin(false, true);
    117128    return sc;
    118129  }

  • trunk/src/test/net/sf/basedb/test/merge/Run.java

    r2815 r4298  
    5050    if (ok && (all || cmds.contains("setup")))
    5151    {
    52       TestUtil.begin(logMemoryUsage);
     52      TestUtil.begin(logMemoryUsage, false);
    5353      ok = MergeTest.run();
    5454      tests++;

  • trunk/src/test/net/sf/basedb/test/performance/Run.java

    r3675 r4298  
    5454
    5555    int tests = 0;
    56     TestUtil.begin(false);
     56    TestUtil.begin(false, true);
    5757    boolean ok = PrepareTest.run(user, password);
    5858    if (ok && (all || cmds.contains("raw")))

  • trunk/src/test/net/sf/basedb/test/roles/Run.java

    r2568 r4298  
    5050    if (ok && (all || cmds.contains("root")))
    5151    {
    52       TestUtil.begin(logMemoryUsage);
     52      TestUtil.begin(logMemoryUsage, true);
    5353      ok = RootTest.run();
    5454      tests++;
    … …  
    5656    if (ok && (all || cmds.contains("admin")))
    5757    {
    58       TestUtil.begin(logMemoryUsage);
     58      TestUtil.begin(logMemoryUsage, true);
    5959      ok = AdminTest.run();
    6060      tests++;
    … …  
    6262    if (ok && (all || cmds.contains("power")))
    6363    {
    64       TestUtil.begin(logMemoryUsage);
     64      TestUtil.begin(logMemoryUsage, true);
    6565      ok = PowerUserTest.run();
    6666      tests++;
    … …  
    6868    if (ok && (all || cmds.contains("user")))
    6969    {
    70       TestUtil.begin(logMemoryUsage);
     70      TestUtil.begin(logMemoryUsage, true);
    7171      ok = UserTest.run();
    7272      tests++;
    … …  
    7474    if (ok && (all || cmds.contains("guest")))
    7575    {
    76       TestUtil.begin(logMemoryUsage);
     76      TestUtil.begin(logMemoryUsage, true);
    7777      ok = GuestTest.run();
    7878      tests++;

  • trunk/www/include/menu.jsp

    r4262 r4298  
    961961    ActionIterator<MenuItemAction> it = invoker.iterate();
    962962    Map<String, List<MenuItemAction>> menus = new HashMap<String, List<MenuItemAction>>();
     963    menus.put("extensions", new LinkedList<MenuItemAction>());
    963964    while (it.hasNext())
    964965    {
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