Changeset 3106


Ignore:
Timestamp:
Feb 6, 2007, 3:11:19 PM (15 years ago)
Author:
Jari Häkkinen
Message:

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

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/www/plugins/org/tigr/microarray/mev/launch_mev.jsp

    r3102 r3106  
    2727
    2828<%@ page session="false"
     29  import="net.sf.basedb.core.Application"
     30  import="net.sf.basedb.core.BioAssaySet"
     31  import="net.sf.basedb.core.DbControl"
     32  import="net.sf.basedb.core.ExtendedProperties"
     33  import="net.sf.basedb.core.SessionControl"
     34  import="net.sf.basedb.plugins.BioAssaySetExporter"
     35  import="net.sf.basedb.util.Values"
    2936%>
    3037<%
    3138final String SessionID=request.getParameter("ID");
    32 final String bioassaysetId=request.getParameter("bioassayset_id");
     39final int bioassaysetId=Values.getInt(request.getParameter("bioassayset_id"));
    3340final String serverName=request.getServerName();
    3441final int serverPort=request.getServerPort();
    3542final String serverPath=request.getContextPath();
     43// MeV needs to know where the expression data starts in the exported
     44// file. Columns and row index in MeV starts at 0. Starting column is
     45// the sum of: number of extended reporter data (server specific
     46// number) + number of non extended reporter data (currently 4 is used
     47// in mevExport in bioassayset exporter) + the experimental factor
     48// column (that is 1).
     49final int column_idx=ExtendedProperties.getProperties("ReporterData").size()+5;
     50// The starting row is the sum of: The header line (1) + the number of
     51// experimental factor annotations for an experiemnt.
     52final SessionControl sc=Application.getSessionControl(SessionID,
     53                                                      request.getRemoteAddr());
     54DbControl dc=sc.newDbControl();
     55BioAssaySet bas=BioAssaySet.getById(dc, bioassaysetId);
     56BioAssaySetExporter base=new BioAssaySetExporter();
     57final int row_idx= 1 + base.getExperimentalFactors(dc,bas).size();
    3658%>
    3759
     
    97119  <application-desc main-class="org.tigr.microarray.mev.TMEV">
    98120    <argument>-download_url http://<%=serverName%>:<%=serverPort%><%=serverPath%>/plugins/org/tigr/microarray/mev/export?ID=<%=SessionID%>&bioassayset_id=<%=bioassaysetId%></argument>
    99     <argument>-row 1</argument>
    100     <argument>-column 20</argument>
     121    <argument>-row <%=row_idx%></argument>
     122    <argument>-column <%=column_idx%></argument>
    101123  </application-desc>
    102124</jnlp>
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