Changeset 1550


Ignore:
Timestamp:
Mar 6, 2012, 12:40:28 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #365: Export bioplate information to a file that can be used by the Caliper machine

Export HiSense? setting in the "User comment" field. Can be moved to be part of the name if that is better, but then the importer also need to be updated since the sample names in the Caliper output files are affected.

Otherwise, the exporter should now be fully working.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/rnaqc_plate_export.jsp

    r1548 r1550  
    3737 
    3838<script language="JavaScript">
    39 var debug = true;
     39var debug = false;
    4040var rnaQcBioPlates = null
    4141
     
    136136          Select the bioplate to export sample names from.
    137137          <p>
    138           The list contain RNAQC bioplates which has not had quality score data imported yet
    139           (determined by absense of QCRunDate annotation).
     138          The list contain RNAQC bioplates without quality score data (determined by
     139          absence of QCRunDate annotation).
    140140          <p>
    141141          Tip! You can run the exporter for any bioplate as a regular plug-in by selecting
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/plugins/CaliperSampleNameExporter.java

    r1548 r1550  
    1111import java.util.Set;
    1212
     13import net.sf.basedb.core.AnnotationType;
    1314import net.sf.basedb.core.BaseException;
    1415import net.sf.basedb.core.BioMaterial;
     
    3435import net.sf.basedb.core.query.Hql;
    3536import net.sf.basedb.core.query.Orders;
     37import net.sf.basedb.reggie.Reggie;
    3638import net.sf.basedb.util.export.TableWriter;
    3739
     
    284286   
    285287    Iterator<BioWell> it = query.iterate(dc);
     288    AnnotationType qcHiSenseType = Reggie.findAnnotationType(dc, Item.EXTRACT, Reggie.ANNOTATION_QC_HISENSE, false);
    286289    while (it.hasNext())
    287290    {
     
    291294      {
    292295        bm = well.getBioMaterial();
    293         tw.tablePrintData(well.getCoordinate(), bm.getName(), "", "", "");
     296        String comment = "";
     297        if (qcHiSenseType != null)
     298        {
     299          if (Boolean.TRUE.equals(Reggie.getAnnotationValue(bm, qcHiSenseType)))
     300          {
     301            comment = "HiSense";
     302          }
     303        }
     304        tw.tablePrintData(well.getCoordinate(), bm.getName(), comment, "", "");
    294305        numExported++;
    295306      }
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