Changeset 1117 for extensions/net.sf.basedb.genepattern

Timestamp:

Jun 10, 2009, 1:13:21 PM (14 years ago)

Author:

Nicklas Nordborg

Message:

References #221: Configure GenePattern? server

Changed the AJAX calls to a new servlet. Now requires BASE 2.13 since that depends on new functionality in BASE.

Location:

extensions/net.sf.basedb.genepattern/trunk

Files:

• META-INF/servlets.xml (modified) (1 diff)
• README (modified) (2 diffs)
• build.xml (modified) (1 diff)
• resources/edit_server.jsp (modified) (4 diffs)
• src/net/sf/basedb/genepattern/GPServer.java (added)
• src/net/sf/basedb/genepattern/servlet/Ajax.java (added)
• src/net/sf/basedb/genepattern/servlet/TestServer.java (deleted)

extensions/net.sf.basedb.genepattern/trunk/META-INF/servlets.xml

@@ -2 +2 @@
 <servlets xmlns="http://base.thep.lu.se/servlets.xsd">
   <servlet>
-    <servlet-name>TestServer</servlet-name>
-    <servlet-class>net.sf.basedb.genepattern.servlet.TestServer</servlet-class>
-    <!-- 
-      Specify the name of a GenePattern module that should be used with
-      the "Test server" function in the GUI. This function tests that
-      the user has entered a correct url, login and password and requires
-      an existing module on the server.
-    -->
-    <init-param>
-      <param-name>moduleToCheck</param-name>
-      <param-value>ComparativeMarkerSelection</param-value>
-    </init-param>
+    <servlet-name>Ajax</servlet-name>
+    <servlet-class>net.sf.basedb.genepattern.servlet.Ajax</servlet-class>
   </servlet>
   <servlet>

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

@@ -1 +1 @@
 == Requirements ==
 
- 1. BASE 2.12.1 or later.
+ 1. BASE 2.13 or later.
  
 == Introduction ==
@@ -39 +39 @@
 To compile this package you also need:
  
- 1. Ant 1.7
+ 1. Ant 1.6
  2. Java 1.6
 

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/2.13.0" />
   <property name="genepattern.jars" value="http://genepattern.broad.mit.edu/gp/downloads" />
 

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

@@ -85 +85 @@
     if (!validate()) return;
     var frm = document.forms['options'];
-    var url = '<%=homeUrl%>/TestServer.servlet';
-    url += '?server=' + encodeURIComponent(frm.gpServer.value);
+    var url = '<%=homeUrl%>/Ajax.servlet?cmd=TestLogin';
+    url += '&server=' + encodeURIComponent(frm.gpServer.value);
     url += '&login=' + encodeURIComponent(frm.gpLogin.value);
     url += '&password=' + encodeURIComponent(frm.gpPassword.value);
@@ -94 +94 @@
     request.send(null);
     document.getElementById('testStatus').innerHTML = 'Testing';
-    document.getElementById('testReport').innerHTML = 'Please wait...';
+    document.getElementById('testReport').innerHTML = 'Please wait. . .';
+    setTimeout('testResult(null)', 15000);
+    setTimeout('showProgress()', 250);
+  }
+  function showProgress()
+  {
+    var progress = document.getElementById('testReport');
+    if (progress.innerHTML.indexOf('Please wait') == 0)
+    {
+      progress.innerHTML += ' .';
+      setTimeout('showProgress()', 250);
+    }
   }
 
   function testResult(request)
   {
+    if (document.getElementById('testReport').innerHTML.indexOf('Please wait') != 0) return;
     var frm = document.forms['options'];
-    var response = request.responseText; //.split('\n');
+    var responseText = request != null ? request.responseText : 'status:error\nstacktrace:No response from server';
+    var response = Ajax.parseResponse(responseText);
     var testStatus;
     var testReport;
-    if (response == 'ok')
+    if (response.isError())
+    {
+      testStatus = 'Test failed';
+      var stacktrace = response.getElements()[0]['stacktrace'];
+      testReport = '<div class="error stacktrace" style="width: 420px; height: 15em; overflow: auto;">' + stacktrace + '</div>';
+    }
+    else
     {
       testStatus = 'Test result';
       testReport = 'Test of <b>' + frm.gpServer.value + '</b> was successful';
     }
-    else
-    {
-      testStatus = 'Test failed';
-      testReport = '<div class="error stacktrace" style="width: 420px; height: 15em; overflow: auto;">' + response + '</div>';
-    }
     document.getElementById('testStatus').innerHTML = testStatus;
     document.getElementById('testReport').innerHTML = testReport;
   }
-  
   </script>
 </base:head>
@@ -126 +139 @@
   <h3 class="docked"><%=HTML.encodeTags(title)%></h3>
   <div class="boxedbottom">
-    <table class="form" cellspacing=0>
+    <table class="form" cellspacing="0" width="100%">
     <tr>
       <td class="prompt">Server URL</td>
-      <td colspan="2"><input class="text required" type="text" name="gpServer" size="50"
+      <td><input class="text required" type="text" name="gpServer" size="50"
           value="<%=HTML.encodeTags(server.getName())%>"></td>
     </tr>
     <tr>
       <td class="prompt">Login</td>
-      <td colspan="2"><input class="text required" type="text" name="gpLogin" size="50"
+      <td><input class="text required" type="text" name="gpLogin" size="50"
           value="<%=HTML.encodeTags(server.getSetting("server.login"))%>"></td>
     </tr>
@@ -142 +155 @@
           value="<%=HTML.encodeTags(server.getSetting("server.password"))%>">
       </td>
-      <td>
-        <table border=0 cellspacing=0 cellpadding=0 align="right"><tr><td>
-        <base:button onclick="testServer();" title="Test" 
-        image="<%=homeUrl + "/images/genepattern.gif" %>" 
-        onclick="testServer()" />
-        </td></tr></table>
-      </td>
     </tr>
     <tr>
       <td class="prompt" id="testStatus"></td>
-      <td colspan="2" id="testReport">
+      <td id="testReport">
       </td>
     </tr>
     </table>
   </div>
+  </form>
   <p>
   <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" %>" /></td>
+    <td width="33%"><base:button onclick="saveSettings();" title="Save" /></td>
+    <td width="33%"><base:button onclick="window.close();" title="Cancel" /></td>
   </tr>
   </table>