Changeset 2101


Ignore:
Timestamp:
Oct 25, 2013, 8:15:42 AM (9 years ago)
Author:
Nicklas Nordborg
Message:

References #471: Add library preparation information to the 'Case summary' feature

Added comment fields to mRNA, cDNA, library and pooled library. Changed name of date-related properties to reflect the actual date used.

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

Legend:

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

    r2100 r2101  
    634634      addColumn('mrna.storageBox', asBioPlateLocation(r.bioWell)+asFileLink(r.platePdf, 'pdffile.png'));
    635635      addColumn('mrna.result', (r.result && r.result != 'Successful') ? asFailInfo(r.result, 'error.png') : null);
    636       addColumn('mrna.extractionDate', formatDate(r.extractionDate));
     636      addColumn('mrna.cleanupDate', formatDate(r.cleanupDate));
    637637      addColumn('mrna.usedQuantity', formatQuantity(r.usedQuantity, null, ' µg'));
     638      addColumn('mrna.comment', truncate(r.comment, truncateAt));
    638639    }
    639640  }
     
    663664      addColumn('cdna.storageBox', asBioPlateLocation(r.bioWell));
    664665      addColumn('cdna.result', (r.result && r.result != 'Successful') ? asFailInfo(r.result, 'error.png') : null);
    665       addColumn('cdna.extractionDate', formatDate(r.extractionDate));
     666      addColumn('cdna.synthesisDate', formatDate(r.synthesisDate));
     667      addColumn('cdna.comment', truncate(r.comment, truncateAt));
    666668    }
    667669  }
     
    691693      addColumn('lib.storageBox', asBioPlateLocation(r.bioWell));
    692694      addColumn('lib.result', (r.result && r.result != 'Successful') ? asFailInfo(r.result, 'error.png') : null);
    693       addColumn('lib.extractionDate', formatDate(r.extractionDate));
     695      addColumn('lib.cleanupDate', formatDate(r.cleanupDate));
    694696      addColumn('lib.remainingQuantity', formatQuantity(r.remainingQuantity, 0.001, ' ng'));
    695697      addColumn('lib.originalQuantity', formatQuantity(r.originalQuantity, 0.001, ' ng'));
     
    698700      addColumn('lib.ca_molarity', formatQuantity(r.ca_molarity, null, ' nM'));
    699701      addColumn('lib.qubitconc', formatQuantity(r.qubitconc, null, ' ng/µl'));
     702      addColumn('lib.comment', truncate(r.comment, truncateAt));
    700703    }
    701704  }
     
    723726      addColumn('pooledlib.name', makeLink('EXTRACT', r));
    724727      addColumn('pooledlib.registrationDate', formatDate(r.registrationDate));
    725       addColumn('pooledlib.extractionDate', formatDate(r.extractionDate));
     728      addColumn('pooledlib.poolDate', formatDate(r.poolDate));
    726729      addColumn('pooledlib.remainingQuantity', formatQuantity(r.remainingQuantity, 0.001, ' ng'));
    727730      addColumn('pooledlib.originalQuantity', formatQuantity(r.originalQuantity, 0.001, ' ng'));
    728       addColumn('pooledlib.poolmolarity', formatQuantity(r.poolmolarity, null, ' nM'));
    729       addColumn('pooledlib.poolconc', formatQuantity(r.poolconc, null, ' ng/µl'));
     731      addColumn('pooledlib.poolMolarity', formatQuantity(r.poolMolarity, null, ' nM'));
     732      addColumn('pooledlib.poolConc', formatQuantity(r.poolConc, null, ' ng/µl'));
     733      addColumn('pooledlib.comment', truncate(r.comment, truncateAt));
    730734    }
    731735  }
     
    13271331              <th>Plate result</th>
    13281332            </tr>
    1329             <tr id="mrna.extractionDate">
     1333            <tr id="mrna.cleanupDate">
    13301334              <th>Cleanup date</th>
    13311335            </tr>
    13321336            <tr id="mrna.usedQuantity">
    13331337              <th>Used quantity</th>
     1338            </tr>
     1339            <tr id="mrna.comment" class="comment dynamic-column">
     1340              <th>Comment</th>
    13341341            </tr>
    13351342          </tbody>
     
    13561363              <th>Plate result</th>
    13571364            </tr>
    1358             <tr id="cdna.extractionDate">
     1365            <tr id="cdna.synthesisDate">
    13591366              <th>Synthesis date</th>
     1367            </tr>
     1368            <tr id="cdna.comment" class="comment dynamic-column">
     1369              <th>Comment</th>
    13601370            </tr>
    13611371          </tbody>
     
    13821392              <th>Plate result</th>
    13831393            </tr>
    1384             <tr id="lib.extractionDate">
     1394            <tr id="lib.cleanupDate">
    13851395              <th>Cleanup date</th>
    13861396            </tr>
     
    14021412            <tr id="lib.qubitconc">
    14031413              <th>QubitConc</th>
     1414            </tr>
     1415            <tr id="lib.comment" class="comment dynamic-column">
     1416              <th>Comment</th>
    14041417            </tr>
    14051418          </tbody>
     
    14201433              <th>Registration date</th>
    14211434            </tr>
    1422             <tr id="pooledlib.extractionDate">
     1435            <tr id="pooledlib.poolDate">
    14231436              <th>Pool date</th>
    14241437            </tr>
     
    14291442              <th>Original quantity</th>
    14301443            </tr>
    1431             <tr id="pooledlib.poolmolarity">
     1444            <tr id="pooledlib.poolMolarity">
    14321445              <th>PoolMolarity</th>
    14331446            </tr>
    1434             <tr id="pooledlib.poolconc">
     1447            <tr id="pooledlib.poolConc">
    14351448              <th>PoolConc</th>
     1449            </tr>
     1450            <tr id="pooledlib.comment" class="comment dynamic-column">
     1451              <th>Comment</th>
    14361452            </tr>
    14371453          </tbody>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/CaseSummaryServlet.java

    r2100 r2101  
    646646    mrna.setAnnotation("editable", e.hasPermission(Permission.WRITE)); 
    647647    mrna.setAnnotation("usedQuantity", created.getUsedQuantity((Extract)e.getParent()));
     648    mrna.setAnnotation("comment", e.getDescription());
     649   
    648650    // Get BioPlate CleanupDate annotation
    649651    BioPlate plate = mrna.getItem().getBioWell().getPlate();
    650652    Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
    651     mrna.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
     653    mrna.setAnnotation("cleanupDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
    652654    // Get BioPlate PlateProcessResult annotation
    653655    String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
     
    662664    cdna.setAnnotation("registrationDate", Reggie.CONVERTER_DATE_TO_STRING.convert(e.getEntryDate()));
    663665    cdna.setAnnotation("editable", e.hasPermission(Permission.WRITE)); 
     666    cdna.setAnnotation("comment", e.getDescription());
    664667    // Get BioPlate SynthesisDate annotation
    665668    BioPlate plate = cdna.getItem().getBioWell().getPlate();
    666669    Date synthesisDate = (Date) Annotationtype.SYNTHESIS_DATE.getAnnotationValue(dc, plate);
    667     cdna.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(synthesisDate));
     670    cdna.setAnnotation("synthesisDate", Reggie.CONVERTER_DATE_TO_STRING.convert(synthesisDate));
    668671    // Get BioPlate PlateProcessResult annotation
    669672    String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
     
    681684    BioPlate plate = lib.getItem().getBioWell().getPlate();
    682685    Date cleanupDate = (Date) Annotationtype.CLEANUP_DATE.getAnnotationValue(dc, plate);
    683     lib.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
     686    lib.setAnnotation("cleanupDate", Reggie.CONVERTER_DATE_TO_STRING.convert(cleanupDate));
    684687    lib.setAnnotation("originalQuantity", e.getOriginalQuantity());
    685688    lib.setAnnotation("remainingQuantity", e.getRemainingQuantity());
     
    687690    lib.loadAnnotations(dc, "ca_molarity", Annotationtype.CA_MOLARITY, null);
    688691    lib.loadAnnotations(dc, "qubitconc", Annotationtype.QUBIT_CONC, null);
     692    lib.setAnnotation("comment", e.getDescription());
    689693    // Get BioPlate PlateProcessResult annotation
    690694    String result = (String) Annotationtype.PLATE_PROCESS_RESULT.getAnnotationValue(dc, plate);
     
    699703    lib.setAnnotation("registrationDate", Reggie.CONVERTER_DATE_TO_STRING.convert(e.getEntryDate()));
    700704    lib.setAnnotation("editable", e.hasPermission(Permission.WRITE));
    701     lib.setAnnotation("extractionDate", Reggie.CONVERTER_DATE_TO_STRING.convert(created.getEventDate()));
     705    lib.setAnnotation("poolDate", Reggie.CONVERTER_DATE_TO_STRING.convert(created.getEventDate()));
    702706    lib.setAnnotation("originalQuantity", e.getOriginalQuantity());
    703707    lib.setAnnotation("remainingQuantity", e.getRemainingQuantity());
    704     lib.loadAnnotations(dc, "poolmolarity", Annotationtype.POOL_MOLARITY, null);
    705     lib.loadAnnotations(dc, "poolconc", Annotationtype.POOL_CONC, null);
     708    lib.loadAnnotations(dc, "poolMolarity", Annotationtype.POOL_MOLARITY, null);
     709    lib.loadAnnotations(dc, "poolConc", Annotationtype.POOL_CONC, null);
     710    lib.setAnnotation("comment", e.getDescription());
    706711  }
    707712}
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