Changeset 1104 for extensions/net.sf.basedb.genepattern

Timestamp:

May 29, 2009, 2:53:33 PM (14 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:

• META-INF/MANIFEST.MF (added)
• META-INF/servlets.xml (added)
• README (modified) (3 diffs)
• build.xml (modified) (3 diffs)
• lib/compile/servlet-api.jar (added)
• lib/genepattern/axis-license.txt (added)
• lib/genepattern/axis.jar (added)
• lib/genepattern/commons-discovery-0.2.jar (added)
• lib/genepattern/commons-discovery-license.txt (added)
• lib/genepattern/jaxrpc-license.txt (added)
• lib/genepattern/jaxrpc.jar (added)
• resources/edit_server.jsp (modified) (2 diffs)
• resources/server_test.jsp (added)
• src/net/sf/basedb/genepattern/servlet (added)
• src/net/sf/basedb/genepattern/servlet/TestServer.java (added)

extensions/net.sf.basedb.genepattern/trunk/README

@@ -1 +1 @@
 == Requirements ==
 
- 1. BASE 2.12.0 or later.
+ 1. BASE 2.12.1 or later.
  
 == Introduction ==
@@ -18 +18 @@
  1. Download the gp-integration-*.tar.gz file.
  2. Unpack the downloaded file to a directory of your choice.
- 3. Copy the gp-integration.jar file to your BASE extensions directory: 
-    WEB-INF/extensions. 
+ 3. Copy the `gp-integration.jar` file and the `lib` directory, including sub-
+    directories and files, to your BASE extensions directory, `WEB-INF/extensions`.
  4. Run the 'Extensions -> Manual scan' command if you have disabled automatic
     installation. Otherwise, just wait a bit and the automatic installation will
@@ -30 +30 @@
  7. Done. 
 
- 
+
 == Known issues ==
 

extensions/net.sf.basedb.genepattern/trunk/build.xml

@@ -23 +23 @@
   <property name="javac.target" value="1.5" />
   <property name="javac.encoding" value="UTF-8" />
-  <property name="depend.jars" value="http://base2.thep.lu.se/base/jars/2.12.0" />
+  <property name="depend.jars" value="http://base2.thep.lu.se/base/jars/2.12.1" />
   <property name="genepattern.jars" value="http://genepattern.broad.mit.edu/gp/downloads" />
 
@@ -59 +59 @@
         prefix="${tar.prefix}"
         preserveLeadingSlashes="true"
-        includes="${jar.name},README,LICENSE*"
+        includes="${jar.name},README,LICENSE*,lib/genepattern/*"
+        excludes="lib/genepattern/GenePattern.jar,lib/genepattern/gp-modules.jar"
         >
       </tarfileset>
@@ -76 +77 @@
     <jar 
       jarfile="${jar.name}" 
+      manifest="${build}/META-INF/MANIFEST.MF"
       >
       <fileset dir="${build}" />

extensions/net.sf.basedb.genepattern/trunk/resources/edit_server.jsp

@@ -81 +81 @@
     if (validate()) document.forms['options'].submit();
   }
+  function testServer()
+  {
+    if (!validate()) return;
+    var frm = document.forms['options'];
+    var url = '<%=homeUrl%>/TestServer.servlet';
+    url += '?server=' + encodeURIComponent(frm.gpServer.value);
+    url += '&login=' + encodeURIComponent(frm.gpLogin.value);
+    url += '&password=' + encodeURIComponent(frm.gpPassword.value);
+    Main.openPopup(url, 'TestGPServer', 700, 500);
+  }
   </script>
 </base:head>
@@ -110 +120 @@
   <table align="center">
   <tr>
-    <td width="50%"><base:button onclick="saveSettings();" title="Save" /></td>
-    <td width="50%"><base:button onclick="window.close();" title="Cancel" /></td>
+    <td width="33%"><base:button onclick="testServer();" title="Test" 
+      image="<%=homeUrl + "/images/genepattern.gif" %>" 
+      onclick="testServer()" /></td>
+    <td width="33%"><base:button onclick="saveSettings();" title="Save" /></td>
+    <td width="33%"><base:button onclick="window.close();" title="Cancel" /></td>
   </tr>
   </table>