Changeset 3106

Timestamp:

Feb 6, 2007, 3:11:19 PM (17 years ago)

Author:

Jari Häkkinen

Message:

Addresses #10 and #352. Removed hard coded indexes for datamatrix retrieval.

File:

• trunk/www/plugins/org/tigr/microarray/mev/launch_mev.jsp (modified) (2 diffs)

trunk/www/plugins/org/tigr/microarray/mev/launch_mev.jsp

@@ -27 +27 @@
 
 <%@ page session="false"
+  import="net.sf.basedb.core.Application"
+  import="net.sf.basedb.core.BioAssaySet"
+  import="net.sf.basedb.core.DbControl"
+  import="net.sf.basedb.core.ExtendedProperties"
+  import="net.sf.basedb.core.SessionControl"
+  import="net.sf.basedb.plugins.BioAssaySetExporter"
+  import="net.sf.basedb.util.Values"
 %>
 <%
 final String SessionID=request.getParameter("ID");
-final String bioassaysetId=request.getParameter("bioassayset_id");
+final int bioassaysetId=Values.getInt(request.getParameter("bioassayset_id"));
 final String serverName=request.getServerName();
 final int serverPort=request.getServerPort();
 final String serverPath=request.getContextPath();
+// MeV needs to know where the expression data starts in the exported
+// file. Columns and row index in MeV starts at 0. Starting column is
+// the sum of: number of extended reporter data (server specific
+// number) + number of non extended reporter data (currently 4 is used
+// in mevExport in bioassayset exporter) + the experimental factor
+// column (that is 1).
+final int column_idx=ExtendedProperties.getProperties("ReporterData").size()+5;
+// The starting row is the sum of: The header line (1) + the number of
+// experimental factor annotations for an experiemnt.
+final SessionControl sc=Application.getSessionControl(SessionID,
+                                                      request.getRemoteAddr());
+DbControl dc=sc.newDbControl();
+BioAssaySet bas=BioAssaySet.getById(dc, bioassaysetId);
+BioAssaySetExporter base=new BioAssaySetExporter();
+final int row_idx= 1 + base.getExperimentalFactors(dc,bas).size();
 %>
 
@@ -97 +119 @@
   <application-desc main-class="org.tigr.microarray.mev.TMEV">
     <argument>-download_url http://<%=serverName%>:<%=serverPort%><%=serverPath%>/plugins/org/tigr/microarray/mev/export?ID=<%=SessionID%>&bioassayset_id=<%=bioassaysetId%></argument>
-    <argument>-row 1</argument>
-    <argument>-column 20</argument>
+    <argument>-row <%=row_idx%></argument>
+    <argument>-column <%=column_idx%></argument>
   </application-desc>
 </jnlp>