Changeset 1156

Timestamp:

Sep 14, 2009, 1:44:09 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

References #241: Add MeV Analysis file as a file type for bioassay sets

The MeV analysis file type is now supported by the launch functionality. There is still no automatic installation. This must be done manually. Eg. create a data file type with external id=mev.anl; name=MeV analysis file; extension=anl; generic file type=Spot data; Item type=Bioassay set.

Also, MeV is not able to open the file yet. We need the wrapper for that.

Location:

extensions/net.sf.basedb.mev/trunk

Files:

• resources/launch_mev.jsp (modified) (3 diffs)
• resources/mev_jnlp.jsp (modified) (1 diff)
• src/net/sf/basedb/mev/Mev.java (modified) (1 diff)

extensions/net.sf.basedb.mev/trunk/resources/launch_mev.jsp

@@ -75 +75 @@
   File tdmsFile = FileStoreUtil.getDataFile(dc, bas, "mev.tdms");
   File cghFile = FileStoreUtil.getDataFile(dc, bas, "mev.cgh");
+  File anlFile = FileStoreUtil.getDataFile(dc, bas, "mev.anl");
   boolean allowCreateFile = bas.hasPermission(Permission.WRITE)
     && sc.hasPermission(Permission.CREATE, Item.FILE);
@@ -155 +156 @@
   <table class="form">
   <tr>
+    <td class="prompt" colspan="2">MeV analysis file</td>
+  </tr>
+  <tr>
+    <td><base:button title="Start MeV" 
+      onclick="launchMev('mev.anl')" 
+      image="<%=anlFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>" 
+      disabled="<%=anlFile == null%>"/></td>
+    <td>
+    <%
+    if (anlFile == null)
+    {
+      %>
+      There is currently no MeV analysis file associated with the bioassay set.
+      <%
+    }
+    else
+    {
+      %>
+      Start MeV with the current analysis file:<br>
+      <%=HTML.encodeTags(anlFile.getName())%> <%=Base.getFileLinks(ID, anlFile, root) %>
+      <%
+    }
+    %>
+    </td>
+  </tr>
+  <tr>
     <td class="prompt" colspan="2">TDMS - Tab-delimited multiple sample</td>
   </tr>
@@ -208 +235 @@
     <td><base:button title="Start MeV" 
       onclick="launchMev('mev.cgh')" 
-      image="<%=tdmsFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>" 
+      image="<%=cghFile == null ? homeUrl + "/images/tm4_disabled.png" : homeUrl + "/images/tm4.png" %>" 
       disabled="<%=cghFile == null%>"/></td>
     <td>

extensions/net.sf.basedb.mev/trunk/resources/mev_jnlp.jsp

@@ -46 +46 @@
 final int bioAssaySetId = Values.getInt(request.getParameter("bioassayset_id"));
 final String fileType = Values.getString(request.getParameter("filetype"));
-final String mevFileType = "mev.cgh".equals(fileType) ? "cgh" : "tdms";
+final String mevFileType = fileType.substring(4);
 final String scheme = request.getScheme();
 final String serverName = request.getServerName();

extensions/net.sf.basedb.mev/trunk/src/net/sf/basedb/mev/Mev.java

@@ -44 +44 @@
   public static final String CGH_FILE = "mev.cgh";
   
+  /**
+    The external ID for the file type representing
+    a MeV Analysis file.
+    @see DataFileType#getByExternalId(net.sf.basedb.core.DbControl, String)
+    @since 1.5
+  */
+  public static final String ANALYSIS_FILE = "mev.anl";
+  
 }