Changeset 5700


Ignore:
Timestamp:
Aug 17, 2011, 12:38:19 PM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1613: Extend the 'roles' test case with some sequence-related tests

Fixed batch importer tests. Beware that the tab-separated text files are a bit different than those used by BASE 2.17 and before.

Location:
trunk
Files:
4 edited

Legend:

Unmodified
Added
Removed
  • trunk/doc/test/roles/index.html

    r5699 r5700  
    172172      <ul>
    173173      <li><code>-b</code>: if the batch importers should be tested</li>
    174       <li><code>-w</code>: if the test program should wait for ENTER before emptying the database.</li>
    175174      </ul>
    176175    </li>
     
    13731372      </tr>
    13741373      <tr>
    1375         <td>Extracts</td>
     1374        <td>Extracts (including labeled extracts and libraries)</td>
    13761375        <td>extract_out.txt</td>
    13771376      </tr>
    13781377      <tr>
    1379         <td>Labeled extracts</td>
    1380         <td>labeledextract_out.txt</td>
    1381       </tr>
    1382       <tr>
    1383         <td>Hybridizations</td>
    1384         <td>hybridization_out.txt</td>
    1385       </tr>
    1386       <tr>
    1387         <td>Scans</td>
    1388         <td>scan_out.txt</td>
     1378        <td>Physical bioassays (hybridizations, flow cells)</td>
     1379        <td>physicalbioassay_out.txt</td>
     1380      </tr>
     1381      <tr>
     1382        <td>Derived bioassays (scans, assemblys)</td>
     1383        <td>derivedbioassay_out.txt</td>
    13891384      </tr>
    13901385      <tr>
     
    13931388      </tr>
    13941389      </table>
    1395       The files listed for biosource, samples and scans also contains annotations
     1390      The files listed for biosource, samples and derived bioassays also contain annotations
    13961391      for the items and these files should also be used with the annotation importer.
    13971392      The procedure is the same as for batch importers except that only <code>\Name\</code>
    13981393      is needed in the column mapping. The annotation column should be selected by default in
    1399       the second wizzard-step.       
     1394      the second wizard-step.
    14001395    </li>
    1401     <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizzard-page.</li>
     1396    <li>Start the import-job by clicking on the <code>Finish</code> button on the third wizard-page.</li>
    14021397    <li>Continue with <a href="#step3">the third step</a>.</li>     
    14031398  </ol>
  • trunk/src/core/net/sf/basedb/core/Project.java

    r5689 r5700  
    899899  {
    900900    ItemParameterValueData defaultItems = getData().getDefaultItems();
    901     if (defaultItems == null) return null;
     901    if (defaultItems == null) return Collections.emptyList();
    902902   
    903903    List<BasicData> result = new ArrayList<BasicData>();
  • trunk/src/test/net/sf/basedb/test/roles/PowerUserTest.java

    r5699 r5700  
    219219        importArrayDesigns(arrayDesignImporter, batchImportFile_ArrayDesign);
    220220        design = Util.findArrayDesign(dc, "Array design A");
    221         assert design != null : "Could not find expected Array design: 'Array design A'";
    222221        design.setPlateList(Util.findPlates(dc));               
     222        affyDesign = Util.findArrayDesign(dc, "Affymetrix A");
    223223      }
    224224      dc.commit();
  • trunk/src/test/net/sf/basedb/test/roles/UserTest.java

    r5699 r5700  
    100100      PluginDefinition sampleBatchImporter = null;
    101101      PluginDefinition extractBatchImporter = null;
    102       PluginDefinition labeledExtractBatchImporter = null;
    103       PluginDefinition hybridizationBatchImporter = null;
    104       PluginDefinition scanBatchImporter = null;
     102      PluginDefinition physicalBioAssayBatchImporter = null;
     103      PluginDefinition derivedBioAssayBatchImporter = null;
    105104      PluginDefinition rawBioAssayBatchImporter = null;
    106105      PluginDefinition annotationImporter = null;
     
    109108      File batchImportFile_Sample = null;
    110109      File batchImportFile_Extract = null;
    111       File batchImportFile_LabeledExtract = null;
    112       File batchImportFile_Hybridization = null;
    113       File batchImportFile_Scan = null;
     110      File batchImportFile_PhysicalBioAssay = null;
     111      File batchImportFile_DerivedBioAssay = null;
    114112      File batchImportFile_RawBioAssay = null;
    115113     
     
    128126        sampleBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.SampleImporter");
    129127        extractBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.ExtractImporter");
    130         labeledExtractBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.LabeledExtractImporter");
    131         hybridizationBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.HybridizationImporter");
    132         scanBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.ScanImporter");
     128        physicalBioAssayBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter");
     129        derivedBioAssayBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter");
    133130        rawBioAssayBatchImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.batchimport.RawBioAssayImporter");
    134131        annotationImporter = PluginDefinition.getByClassName(dc, "net.sf.basedb.plugins.AnnotationFlatFileImporter");
     
    137134        batchImportFile_Sample = FileUtil.uploadFile(dc, "/batchimport", "sample_out.txt", null);
    138135        batchImportFile_Extract = FileUtil.uploadFile(dc, "/batchimport", "extract_out.txt", null);
    139         batchImportFile_LabeledExtract = FileUtil.uploadFile(dc, "/batchimport", "labeledextract_out.txt", null);
    140         batchImportFile_Hybridization = FileUtil.uploadFile(dc, "/batchimport", "hybridization_out.txt", null);
    141         batchImportFile_Scan = FileUtil.uploadFile(dc, "/batchimport", "scan_out.txt", null);
     136        batchImportFile_PhysicalBioAssay = FileUtil.uploadFile(dc, "/batchimport", "physicalbioassay_out.txt", null);
     137        batchImportFile_DerivedBioAssay = FileUtil.uploadFile(dc, "/batchimport", "derivedbioassay_out.txt", null);
    142138        batchImportFile_RawBioAssay = FileUtil.uploadFile(dc, "/batchimport", "rawbioassay_out.txt", null);
    143139        dc.commit();
     
    308304       
    309305        importExtracts(extractBatchImporter, batchImportFile_Extract);
    310         importLabelExtracts(labeledExtractBatchImporter, batchImportFile_LabeledExtract);
    311306       
    312307        // Hybridizations, etc.
    313         importHybridizations(hybridizationBatchImporter, batchImportFile_Hybridization);     
    314         importScans(scanBatchImporter, batchImportFile_Scan);
    315         importAnnotations(annotationImporter, batchImportFile_Scan, Item.DERIVEDBIOASSAY, getScanColumnHeaders(), "\\t");
     308        importPhysicalBioAssays(physicalBioAssayBatchImporter, batchImportFile_PhysicalBioAssay);     
     309        importDerivedBioAssays(derivedBioAssayBatchImporter, batchImportFile_DerivedBioAssay);
     310        importAnnotations(annotationImporter, batchImportFile_DerivedBioAssay, Item.DERIVEDBIOASSAY, getDerivedBioAssayColumnHeaders(), "\\t");
    316311        importRawBioAssays(rawBioAssayBatchImporter, batchImportFile_RawBioAssay);
    317312        bioSource = Util.findBioSource(dc, "Biosource A");
     
    444439    Extract extract = Extract.getNew(dc);
    445440    extract.setName(name);
    446     extract.setOriginalQuantity(100.0f);
     441    extract.setOriginalQuantity(200.0f);
    447442    extract.getCreationEvent().setSource(sample).setUsedQuantity(50.0f);
    448443    extract.getCreationEvent().setProtocol(Util.findProtocol(dc, "Extraction A"));
     
    710705      job.setParameterValue("dataSplitterRegexp", new StringParameterType(), "\\t");
    711706      job.setParameterValue("dataHeaderRegexp", new StringParameterType(),
    712           "Name\\tPlatform\\tVariant\\tRaw data type\\tArray index\\tScan\\tSoftware\\tProtocol\\tArray design\\tDescription\\tFile type\\tFile");
     707          "Name\\tPlatform\\tVariant\\tRaw data type\\tParent\\tExtract\\tSoftware\\tProtocol\\tArray design\\tDescription\\tFile type\\tFile");
    713708     
    714709      job.setParameterValue("nameColumnMapping", new StringParameterType(), "\\Name\\");
     
    717712      job.setParameterValue("platformColumnMapping", new StringParameterType(), "\\Platform\\");
    718713      job.setParameterValue("variantColumnMapping", new StringParameterType(), "\\Variant\\");
    719       job.setParameterValue("arrayIndexColumnMapping", new StringParameterType(), "\\Array index\\");
    720       job.setParameterValue("scanColumnMapping", new StringParameterType(), "\\Scan\\");
     714      job.setParameterValue("bioAssayColumnMapping", new StringParameterType(), "\\Parent\\");
     715      job.setParameterValue("extractColumnMapping", new StringParameterType(), "\\Extract\\");
    721716      job.setParameterValue("softwareColumnMapping", new StringParameterType(), "\\Software\\");
    722717      job.setParameterValue("protocolColumnMapping", new StringParameterType(), "\\Protocol\\");
     
    735730  }
    736731 
    737   public static void importScans(PluginDefinition batchImporter, File file)
    738   {
    739     TestUtil.write("--Importing scans from file: " + file + "\n");
     732  public static void importDerivedBioAssays(PluginDefinition batchImporter, File file)
     733  {
     734    TestUtil.write("--Importing derived bioassays from file: " + file + "\n");
    740735    DbControl dc = null;
    741736    try
     
    745740      Job job = Job.getNew(dc, plugin, null, null);
    746741     
    747       job.setName("Batch import of scans to Project A");
     742      job.setName("Batch import of derived bioassays to Project A");
    748743      job.setParameterValue("file", new FileParameterType(), file);
    749744      job.setParameterValue("dataSplitterRegexp", new StringParameterType(), "\\t");
    750745      job.setParameterValue("dataHeaderRegexp", new StringParameterType(),
    751           "Name\\tHybridization\\tDescription\\tProtocol\\tScanner\\tPMT gain");
     746          "Name\\tSubtype\\tParent type\\tParent\\tExtract\\tDescription\\tProtocol\\tHardware\\tSoftware\\tPMT gain");
    752747     
    753748      job.setParameterValue("nameColumnMapping", new StringParameterType(), "\\Name\\");
     749      job.setParameterValue("subtypeColumnMapping", new StringParameterType(), "\\Subtype\\");
    754750      job.setParameterValue("descriptionColumnMapping", new StringParameterType(), "\\Description\\");
    755       job.setParameterValue("hybridizationColumnMapping", new StringParameterType(), "\\Hybridization\\");
    756       job.setParameterValue("hardwareColumnMapping", new StringParameterType(), "\\Scanner\\");     
     751      job.setParameterValue("parentTypeColumnMapping", new StringParameterType(), "\\Parent type\\");
     752      job.setParameterValue("parentColumnMapping", new StringParameterType(), "\\Parent\\");
     753      job.setParameterValue("extractColumnMapping", new StringParameterType(), "\\Extract\\");
     754      job.setParameterValue("hardwareColumnMapping", new StringParameterType(), "\\Hardware\\");     
     755      job.setParameterValue("softwareColumnMapping", new StringParameterType(), "\\Software\\");     
    757756      job.setParameterValue("protocolColumnMapping", new StringParameterType(), "\\Protocol\\");
    758757     
    759      
    760758      dc.saveItem(job);
    761759      dc.commit();
     
    768766  }
    769767 
    770   public static void importHybridizations(PluginDefinition batchImporter, File file)
    771   {
    772     TestUtil.write("--Importing hybridizations from file: " + file + "\n");
     768  public static void importPhysicalBioAssays(PluginDefinition batchImporter, File file)
     769  {
     770    TestUtil.write("--Importing physical bioassays from file: " + file + "\n");
    773771    DbControl dc = null;
    774772    try
     
    778776      Job job = Job.getNew(dc, plugin, null, null);
    779777     
    780       job.setName("Batch import of hybridizations to Project A");
     778      job.setName("Batch import of physical bioassays to Project A");
    781779      job.setParameterValue("file", new FileParameterType(), file);
    782780      job.setParameterValue("dataSplitterRegexp", new StringParameterType(), "\\t");
    783781      job.setParameterValue("dataHeaderRegexp", new StringParameterType(),
    784           "Name\\tArray slide\\tDescription\\tHardware\\tArrays/slide\\tProtocol\\tParent\\tParent used quantity\\tCreated");
     782          "Name\\tSubtype\\tArray slide\\tDescription\\tHardware\\tSize\\tProtocol\\tParent\\tParent used quantity\\tParent position\\tCreated");
    785783     
    786784      job.setParameterValue("nameColumnMapping", new StringParameterType(), "\\Name\\");
     785      job.setParameterValue("subtypeColumnMapping", new StringParameterType(), "\\Subtype\\");
    787786      job.setParameterValue("descriptionColumnMapping", new StringParameterType(), "\\Description\\");
    788787      job.setParameterValue("hardwareColumnMapping", new StringParameterType(), "\\Hardware\\");
    789788      job.setParameterValue("parentColumnMapping", new StringParameterType(), "\\Parent\\");
    790789      job.setParameterValue("usedQuantityColumnMapping", new StringParameterType(), "\\Parent used quantity\\");
     790      job.setParameterValue("extractPositionColumnMapping", new StringParameterType(), "\\Parent position\\");
    791791      job.setParameterValue("protocolColumnMapping", new StringParameterType(), "\\Protocol\\");
    792792      job.setParameterValue("arraySlideColumnMapping", new StringParameterType(), "\\Array slide\\");
    793       job.setParameterValue("numArraysColumnMapping", new StringParameterType(), "\\Arrays/slide\\");
     793      job.setParameterValue("sizeColumnMapping", new StringParameterType(), "\\Size\\");
    794794      job.setParameterValue("createdColumnMapping", new StringParameterType(), "\\Created\\");
    795795     
     
    804804  }
    805805
    806   public static void importLabelExtracts(PluginDefinition batchImporter, File file)
    807   {
    808     TestUtil.write("--Importing labeled extracts from file: " + file + "\n");
     806  public  static void importExtracts(PluginDefinition batchImporter,  File file)
     807  {
     808    TestUtil.write("--Importing extracts from file: " + file + "\n");
    809809    DbControl dc = null;
    810810    try
     
    814814      Job job = Job.getNew(dc, plugin, null, null);
    815815     
    816       job.setName("Batch import of labeled extracts to Project A");
     816      job.setName("Batch import of extracts to Project A");
    817817      job.setParameterValue("file", new FileParameterType(), file);
    818818      job.setParameterValue("dataSplitterRegexp", new StringParameterType(), "\\t");
    819819      job.setParameterValue("dataHeaderRegexp", new StringParameterType(),
    820           "Name\\tLabel\\tOriginal quantity\\tDescription\\tExternal id\\tProtocol\\tCreated\\tPooled\\tParent\\tParent used quantity\\tBioplate\\tBiowell row\\tBiowell column");
     820          "Name\\tSubtype\\tTag\\tOriginal quantity\\tDescription\\tExternal id\\tProtocol\\tCreated\\tParent type\\tParent\\tParent used quantity\\tBioplate\\tRow\\tColumn");
     821     
     822      job.setParameterValue("nameColumnMapping", new StringParameterType(), "\\Name\\");
     823      job.setParameterValue("subtypeColumnMapping", new StringParameterType(), "\\Subtype\\");
     824      job.setParameterValue("descriptionColumnMapping", new StringParameterType(), "\\Description\\");
     825      job.setParameterValue("externalIdColumnMapping", new StringParameterType(), "\\External id\\");
     826      job.setParameterValue("originalQuantityColumnMapping", new StringParameterType(), "\\Original quantity\\");
     827      job.setParameterValue("createdColumnMapping", new StringParameterType(), "\\Created\\");
     828      job.setParameterValue("parentTypeColumnMapping", new StringParameterType(), "\\Parent type\\");
     829      job.setParameterValue("parentColumnMapping", new StringParameterType(), "\\Parent\\");
     830      job.setParameterValue("tagColumnMapping", new StringParameterType(), "\\Tag\\");
     831      job.setParameterValue("usedQuantityColumnMapping", new StringParameterType(), "\\Parent used quantity\\");
     832      job.setParameterValue("protocolColumnMapping", new StringParameterType(), "\\Protocol\\");
     833      job.setParameterValue("bioPlateColumnMapping", new StringParameterType(), "\\Bioplate\\");
     834      job.setParameterValue("bioWellRowColumnMapping", new StringParameterType(), "\\Row\\");
     835      job.setParameterValue("bioWellColColumnMapping", new StringParameterType(), "\\Column\\");
     836     
     837      dc.saveItem(job);
     838      dc.commit();
     839      PluginUtil.executeJob(job);
     840    }
     841    finally
     842    {
     843      if (dc != null) dc.close();
     844    }
     845  }
     846
     847  public static void importSamples(PluginDefinition batchImporter, File file)
     848  {
     849    TestUtil.write("--Importing samples from file: " + file + "\n");
     850    DbControl dc = null;
     851    try
     852    {
     853      dc = TestUtil.getDbControl();
     854      PluginDefinition plugin = PluginDefinition.getById(dc, batchImporter.getId());
     855      Job job = Job.getNew(dc, plugin, null, null);
     856     
     857      job.setName("Batch import of samples to Project A");
     858      job.setParameterValue("file", new FileParameterType(), file);
     859      job.setParameterValue("dataSplitterRegexp", new StringParameterType(), "\\t");
     860      job.setParameterValue("dataHeaderRegexp", new StringParameterType(),
     861          "Name\\tOriginal quantity\\tDescription\\tExternal id\\tCreated\\tBiosource\\tProtocol\\tBioplate\\tRow\\tColumn\\tTime");
    821862     
    822863      job.setParameterValue("nameColumnMapping", new StringParameterType(), "\\Name\\");
     
    825866      job.setParameterValue("originalQuantityColumnMapping", new StringParameterType(), "\\Original quantity\\");
    826867      job.setParameterValue("createdColumnMapping", new StringParameterType(), "\\Created\\");
    827       job.setParameterValue("pooledColumnMapping", new StringParameterType(), "\\Pooled\\");
    828       job.setParameterValue("parentColumnMapping", new StringParameterType(), "\\Parent\\");
    829       job.setParameterValue("usedQuantityColumnMapping", new StringParameterType(), "\\Parent used quantity\\");
    830       job.setParameterValue("protocolColumnMapping", new StringParameterType(), "\\Protocol\\");
    831       job.setParameterValue("labelColumnMapping", new StringParameterType(), "\\Label\\");
    832       job.setParameterValue("bioPlateColumnMapping", new StringParameterType(), "\\Bioplate\\");
    833       job.setParameterValue("bioWellRowColumnMapping", new StringParameterType(), "\\Biowell row\\");
    834       job.setParameterValue("bioWellColColumnMapping", new StringParameterType(), "\\Biowell column\\");
    835      
    836       dc.saveItem(job);
    837       dc.commit();
    838       PluginUtil.executeJob(job);
    839     }
    840     finally
    841     {
    842       if (dc != null) dc.close();
    843     }   
    844   }
    845 
    846   public  static void importExtracts(PluginDefinition batchImporter,  File file)
    847   {
    848     TestUtil.write("--Importing extracts from file: " + file + "\n");
    849     DbControl dc = null;
    850     try
    851     {
    852       dc = TestUtil.getDbControl();
    853       PluginDefinition plugin = PluginDefinition.getById(dc, batchImporter.getId());
    854       Job job = Job.getNew(dc, plugin, null, null);
    855      
    856       job.setName("Batch import of extracts to Project A");
    857       job.setParameterValue("file", new FileParameterType(), file);
    858       job.setParameterValue("dataSplitterRegexp", new StringParameterType(), "\\t");
    859       job.setParameterValue("dataHeaderRegexp", new StringParameterType(),
    860           "Name\\tOriginal quantity\\tDescription\\tExternal id\\tProtocol\\tCreated\\tPooled\\tParent\\tParent used quantity\\tBioplate\\tBiowell row\\tBiowell column");
    861      
    862       job.setParameterValue("nameColumnMapping", new StringParameterType(), "\\Name\\");
    863       job.setParameterValue("descriptionColumnMapping", new StringParameterType(), "\\Description\\");
    864       job.setParameterValue("externalIdColumnMapping", new StringParameterType(), "\\External id\\");
    865       job.setParameterValue("originalQuantityColumnMapping", new StringParameterType(), "\\Original quantity\\");
    866       job.setParameterValue("createdColumnMapping", new StringParameterType(), "\\Created\\");
    867       job.setParameterValue("pooledColumnMapping", new StringParameterType(), "\\Pooled\\");
    868       job.setParameterValue("parentColumnMapping", new StringParameterType(), "\\Parent\\");
    869       job.setParameterValue("usedQuantityColumnMapping", new StringParameterType(), "\\Parent used quantity\\");
    870       job.setParameterValue("protocolColumnMapping", new StringParameterType(), "\\Protocol\\");
    871       job.setParameterValue("bioPlateColumnMapping", new StringParameterType(), "\\Bioplate\\");
    872       job.setParameterValue("bioWellRowColumnMapping", new StringParameterType(), "\\Biowell row\\");
    873       job.setParameterValue("bioWellColColumnMapping", new StringParameterType(), "\\Biowell column\\");
    874      
    875       dc.saveItem(job);
    876       dc.commit();
    877       PluginUtil.executeJob(job);
    878     }
    879     finally
    880     {
    881       if (dc != null) dc.close();
    882     }
    883   }
    884 
    885   public static void importSamples(PluginDefinition batchImporter, File file)
    886   {
    887     TestUtil.write("--Importing samples from file: " + file + "\n");
    888     DbControl dc = null;
    889     try
    890     {
    891       dc = TestUtil.getDbControl();
    892       PluginDefinition plugin = PluginDefinition.getById(dc, batchImporter.getId());
    893       Job job = Job.getNew(dc, plugin, null, null);
    894      
    895       job.setName("Batch import of samples to Project A");
    896       job.setParameterValue("file", new FileParameterType(), file);
    897       job.setParameterValue("dataSplitterRegexp", new StringParameterType(), "\\t");
    898       job.setParameterValue("dataHeaderRegexp", new StringParameterType(),
    899           "Name\\tOriginal quantity\\tDescription\\tExternal id\\tCreated\\tPooled\\tBiosource\\tProtocol\\tBioplate\\tBiowell row\\tBiowell column\\tTime");
    900      
    901       job.setParameterValue("nameColumnMapping", new StringParameterType(), "\\Name\\");
    902       job.setParameterValue("descriptionColumnMapping", new StringParameterType(), "\\Description\\");
    903       job.setParameterValue("externalIdColumnMapping", new StringParameterType(), "\\External id\\");
    904       job.setParameterValue("originalQuantityColumnMapping", new StringParameterType(), "\\Original quantity\\");
    905       job.setParameterValue("createdColumnMapping", new StringParameterType(), "\\Created\\");
    906       job.setParameterValue("pooledColumnMapping", new StringParameterType(), "\\Pooled\\");
    907868      job.setParameterValue("parentColumnMapping", new StringParameterType(), "\\Biosource\\");
    908869      job.setParameterValue("protocolColumnMapping", new StringParameterType(), "\\Protocol\\");
    909870      job.setParameterValue("bioPlateColumnMapping", new StringParameterType(), "\\Bioplate\\");
    910       job.setParameterValue("bioWellRowColumnMapping", new StringParameterType(), "\\Biowell row\\");
    911       job.setParameterValue("bioWellColColumnMapping", new StringParameterType(), "\\Biowell column\\");
     871      job.setParameterValue("bioWellRowColumnMapping", new StringParameterType(), "\\Row\\");
     872      job.setParameterValue("bioWellColColumnMapping", new StringParameterType(), "\\Column\\");
    912873     
    913874      dc.saveItem(job);
     
    1010971  private static String[] getSampleColumnHeaders()
    1011972  {
    1012     return new String[] {"Name", "Original quantity", "Description", "External id", "Created", "Pooled", "Biosource", "Protocol", "Bioplate", "Biowell row", "Biowell column", "Time"};
    1013   }
    1014  
    1015   private static String[] getScanColumnHeaders()
    1016   {
    1017     return new String[] {"Name", "Hybridization", "Description", "Protocol", "Scanner", "PMT gain"};
     973    return new String[] {"Name", "Original quantity", "Description", "External id", "Created", "Biosource", "Protocol", "Bioplate", "Row", "Column", "Time"};
     974  }
     975 
     976  private static String[] getDerivedBioAssayColumnHeaders()
     977  {
     978    return new String[] {"Name", "Subtype", "Parent type", "Parent", "Extract", "Description", "Protocol", "Hardware", "Software", "PMT gain"};
    1018979  }
    1019980
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