Changeset 1104


Ignore:
Timestamp:
May 29, 2009, 2:53:33 PM (12 years ago)
Author:
Nicklas Nordborg
Message:

References #224: Add a "Test" button on the GenePattern? 'edit server' page

The "Test" button is now in place. The installation may still be a bit messy since the GenePattern? jar files has to be manually installed. We need a way to figure out what to do about that. Another problem is that the default configuration of a GenePattern? server allows a user to login with any username. Non-existing accounts are automatically created and given server admin permissions! It is possible to lock this down, but there is no web interface for adminitration of GenePattern? user accounts. There is some documentation about this: http://www.broad.mit.edu/cancer/software/genepattern/tutorial/gp_web_client.html#_Securing_the_Server

Location:
extensions/net.sf.basedb.genepattern/trunk
Files:
12 added
3 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.genepattern/trunk/README

    r1090 r1104  
    11== Requirements ==
    22
    3  1. BASE 2.12.0 or later.
     3 1. BASE 2.12.1 or later.
    44 
    55== Introduction ==
     
    1818 1. Download the gp-integration-*.tar.gz file.
    1919 2. Unpack the downloaded file to a directory of your choice.
    20  3. Copy the gp-integration.jar file to your BASE extensions directory:
    21     WEB-INF/extensions.
     20 3. Copy the `gp-integration.jar` file and the `lib` directory, including sub-
     21    directories and files, to your BASE extensions directory, `WEB-INF/extensions`.
    2222 4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
    2323    installation. Otherwise, just wait a bit and the automatic installation will
     
    3030 7. Done.
    3131
    32  
     32
    3333== Known issues ==
    3434
  • extensions/net.sf.basedb.genepattern/trunk/build.xml

    r1103 r1104  
    2323  <property name="javac.target" value="1.5" />
    2424  <property name="javac.encoding" value="UTF-8" />
    25   <property name="depend.jars" value="http://base2.thep.lu.se/base/jars/2.12.0" />
     25  <property name="depend.jars" value="http://base2.thep.lu.se/base/jars/2.12.1" />
    2626  <property name="genepattern.jars" value="http://genepattern.broad.mit.edu/gp/downloads" />
    2727
     
    5959        prefix="${tar.prefix}"
    6060        preserveLeadingSlashes="true"
    61         includes="${jar.name},README,LICENSE*"
     61        includes="${jar.name},README,LICENSE*,lib/genepattern/*"
     62        excludes="lib/genepattern/GenePattern.jar,lib/genepattern/gp-modules.jar"
    6263        >
    6364      </tarfileset>
     
    7677    <jar
    7778      jarfile="${jar.name}"
     79      manifest="${build}/META-INF/MANIFEST.MF"
    7880      >
    7981      <fileset dir="${build}" />
  • extensions/net.sf.basedb.genepattern/trunk/resources/edit_server.jsp

    r1102 r1104  
    8181    if (validate()) document.forms['options'].submit();
    8282  }
     83  function testServer()
     84  {
     85    if (!validate()) return;
     86    var frm = document.forms['options'];
     87    var url = '<%=homeUrl%>/TestServer.servlet';
     88    url += '?server=' + encodeURIComponent(frm.gpServer.value);
     89    url += '&login=' + encodeURIComponent(frm.gpLogin.value);
     90    url += '&password=' + encodeURIComponent(frm.gpPassword.value);
     91    Main.openPopup(url, 'TestGPServer', 700, 500);
     92  }
    8393  </script>
    8494</base:head>
     
    110120  <table align="center">
    111121  <tr>
    112     <td width="50%"><base:button onclick="saveSettings();" title="Save" /></td>
    113     <td width="50%"><base:button onclick="window.close();" title="Cancel" /></td>
     122    <td width="33%"><base:button onclick="testServer();" title="Test"
     123      image="<%=homeUrl + "/images/genepattern.gif" %>"
     124      onclick="testServer()" /></td>
     125    <td width="33%"><base:button onclick="saveSettings();" title="Save" /></td>
     126    <td width="33%"><base:button onclick="window.close();" title="Cancel" /></td>
    114127  </tr>
    115128  </table>
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