Changeset 5696


Ignore:
Timestamp:
Aug 12, 2011, 2:51:53 PM (12 years ago)
Author:
Nicklas Nordborg
Message:

References #1153: Handling short read transcript sequence data

Implemented DerivedBioAssayImporter that replaces the scan importer. Added support for linking to extracts in the raw bioassay importer.

Location:
trunk/src
Files:
1 added
18 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/core/net/sf/basedb/core/DerivedBioAssay.java

    r5695 r5696  
    324324  */
    325325  @Override
    326   @SubtypableRelatedItems({Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY, Item.SOFTWARE, Item.HARDWARE, Item.PROTOCOL})
     326  @SubtypableRelatedItems({Item.PHYSICALBIOASSAY, Item.DERIVEDBIOASSAY, Item.EXTRACT, Item.SOFTWARE, Item.HARDWARE, Item.PROTOCOL})
    327327  public ItemSubtype getItemSubtype()
    328328  {

  • trunk/src/core/net/sf/basedb/core/Install.java

    r5689 r5696  
    491491      createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.SCAN,
    492492        "Scan", "A hybridization that has been scanned to produce one or more images.",
    493         hybridization, scanner, scanningProtocol);
     493        hybridization, scanner, scanningProtocol, labeledExtract);
    494494      createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.SEQUENCED,
    495495        "Sequenced", "A flow cell that has been sequenced.",
    496         flowCell, sequencer, sequencingProtocol);
     496        flowCell, sequencer, sequencingProtocol, library);
    497497      createItemSubtype(Item.DERIVEDBIOASSAY, DerivedBioAssay.ASSEMBLY,
    498498        "Assembly", "A data set of sequences that has been aligned against a reference database",
    499         alignmentSoftware);
     499        alignmentSoftware, library);
    500500     
    501501      // Hardware

  • trunk/src/plugins/core/core-plugins.xml

    r5649 r5696  
    578578  </plugin-definition>
    579579 
     580  <!--
     581  Used for backwards compatibility with older server installations
    580582  <plugin-definition id="ScanImporter">
    581583    <about>
    … …  
    590592    </settings>
    591593  </plugin-definition>
    592 
     594  -->
     595 
     596  <plugin-definition id="DerivedBioAssayImporter">
     597    <about>
     598      <name>Derived bioassay importer</name>
     599      <description>
     600        Imports and updates derived bioassays in a batch.
     601      </description>
     602    </about>
     603    <plugin-class>net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter</plugin-class>
     604    <settings>
     605      <property name="everyone-use">1</property>
     606    </settings>
     607  </plugin-definition>
     608 
    593609  <plugin-definition id="RawBioAssayImporter">
    594610    <about>

  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java

    r5689 r5696  
    10261026    If a mapping for item subtype has been specified or if a single subtype was selected
    10271027    for item identification in this job, this method is will update the subtype on the item.
    1028     @param dc A DbControl used to lookup the permission template
     1028    @param dc A DbControl used to lookup the subtype
    10291029    @param item The item to update
    10301030    @param data Data from the file
    … …  
    10431043      item.setItemSubtype(selectedSubtype);
    10441044    }
     1045  }
     1046 
     1047  /**
     1048    Try to find subtype from the given file data. If a single subtype was selected
     1049    for item identification in this job, that subtype is used if no mapped subtype
     1050    can be found.
     1051    @param dc A DbControl used to lookup the subtype
     1052    @param mainItemType The main item type of the subtype
     1053    @param data Data from the file
     1054    @return A subtype of null if no subtype could be found
     1055    @since 3.0
     1056  */
     1057  protected ItemSubtype findItemSubtype(DbControl dc, Item mainItemType, FlatFileParser.Data data)
     1058  {
     1059    ItemSubtype subtype = null;
     1060    if (subtypeMapper != null)
     1061    {
     1062      String nameOrId = subtypeMapper.getValue(data);
     1063      subtype = findItemSubtype(dc, FallbackIdMethod.NAME_OR_SYSTEMID_OR_ID, mainItemType, nameOrId);
     1064    }
     1065    if (subtype == null) subtype = selectedSubtype;
     1066    return subtype;
    10451067  }
    10461068  // ---------------------------------------

  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/RawBioAssayImporter.java

    r5688 r5696  
    3030import net.sf.basedb.core.DbControl;
    3131import net.sf.basedb.core.DerivedBioAssay;
     32import net.sf.basedb.core.Extract;
    3233import net.sf.basedb.core.File;
    3334import net.sf.basedb.core.Item;
    … …  
    104105      );
    105106
    106   protected static final PluginParameter<String> scanColumnMapping = new PluginParameter<String>(
    107       "scanColumnMapping",
    108       "Scan",
    109       "Mapping that picks the name or ID of the scan from the data columns. " +
    110       "The plug-in will first try to find a scan with the given name. If none is found and " +
    111       "the value is numeric it will try to load by internal ID. " +
    112       "Example: \\Scan\\",
    113       optionalColumnMapping
    114       );
    115  
     107  protected static final PluginParameter<String> bioAssayColumnMapping = new PluginParameter<String>(
     108      "bioAssayColumnMapping",
     109      "Parent bioassay",
     110      "Mapping that picks the name or ID of the parent derived bioassay from the data columns. " +
     111      "The plug-in will first try to find a bioassay with the given name. If none is found and " +
     112      "the value is numeric it will try to load by internal ID. " +
     113      "Example: \\Parent bioassay\\",
     114      optionalColumnMapping
     115      );
     116
     117  protected static final PluginParameter<String> extractColumnMapping = new PluginParameter<String>(
     118      "extractColumnMapping",
     119      "Parent extract",
     120      "Mapping that picks the name or ID of the parent extract from the data columns. " +
     121      "The plug-in will first try to find an extract with the given name. If none is found and " +
     122      "the value is numeric it will try to load by internal ID. " +
     123      "Example: \\Parent extract\\\n\n" +
     124      "NOTE! This column may not be needed when creating new items if the parent bioassay " +
     125      "already contains a link to an extract (which will be copied)",
     126      optionalColumnMapping
     127      );
     128
    116129  protected static final PluginParameter<String> arrayDesignColumnMapping = new PluginParameter<String>(
    117130      "arrayDesignColumnMapping",
    … …  
    120133      "The plug-in will first try to find an array design with the given name. If none is found and " +
    121134      "the value is numeric it will try to load by internal ID. " +
    122       "Example: \\Array design\\",
    123       optionalColumnMapping
    124       );
    125  
    126   protected static final PluginParameter<String> arrayIndexColumnMapping =
    127     new PluginParameter<String>(
    128         "arrayIndexColumnMapping",
    129         "Array index",
    130         "Mapping that picks the (1-based) index of the array the raw bioassay " +
    131         "is linked to on the hybridization. The value should be between 1 and the " +
    132         "number of arrays on the hybridization and must be in the numeric format " +
    133         "specified by the 'Number format' parameter." +
    134         "Example: \\Array index\\",
    135         optionalColumnMapping
    136     );
     135      "Example: \\Array design\\\n\n" +
     136      "NOTE! This column may not be needed when creating new items if the parent bioassay " +
     137      "already contains a link to an array design (which will be copied)",
     138      optionalColumnMapping
     139      );
    137140 
    138141  protected static final PluginParameter<String> fileTypeColumnMapping =
    … …  
    180183  private Mapper nameMapper;
    181184  private Mapper descriptionMapper;
    182   private Mapper arrayIndexMapper;
    183185  private Mapper protocolMapper;
    184186  private Mapper softwareMapper;
    185187  private Mapper bioAssayMapper;
     188  private Mapper extractMapper;
    186189  private Mapper arrayDesignMapper;
    187190  private Mapper platformMapper;
    … …  
    235238    parameters.add(nameColumnMapping);
    236239    parameters.add(descriptionColumnMapping);
    237     parameters.add(arrayIndexColumnMapping);
    238240    parameters.add(platformColumnMapping);
    239241    parameters.add(variantColumnMapping);
    240242    parameters.add(rawDataTypeColumnMapping);
    241     parameters.add(scanColumnMapping);
     243    parameters.add(bioAssayColumnMapping);
     244    parameters.add(extractColumnMapping);
    242245    parameters.add(arrayDesignColumnMapping);
    243246    parameters.add(protocolColumnMapping);
    … …  
    264267    descriptionMapper = getMapper(ffp, (String)job.getValue("descriptionColumnMapping"),
    265268        cropStrings ? RawBioAssay.MAX_DESCRIPTION_LENGTH : null, null);
    266     arrayIndexMapper = getMapper(ffp, (String)job.getValue("arrayIndexColumnMapping"), null, null);
    267269    protocolMapper = getMapper(ffp, (String)job.getValue("protocolColumnMapping"), null, null);
    268270    softwareMapper = getMapper(ffp, (String)job.getValue("softwareColumnMapping"), null, null);
    269271    bioAssayMapper = getMapper(ffp, (String)job.getValue("bioAssayColumnMapping"), null, null);
     272    extractMapper = getMapper(ffp, (String)job.getValue("extractColumnMapping"), null, null);
    270273    arrayDesignMapper = getMapper(ffp, (String)job.getValue("arrayDesignColumnMapping"), null, null);
    271274    platformMapper = getMapper(ffp, (String)job.getValue("platformColumnMapping"), null, null);
    … …  
    329332    if (descriptionMapper != null) rba.setDescription(descriptionMapper.getValue(data));
    330333    ArrayDesign designFromBioAssay = null;
     334    Extract extractFromBioAssay = null;
    331335    if (bioAssayMapper != null)
    332336    {
    333337      String nameOrId = bioAssayMapper.getValue(data);
    334       DerivedBioAssay bioAssay = findDerivedBioAssay(dc, FallbackIdMethod.NAME_OR_ID, bioAssayMapper.getValue(data), null);
     338      DerivedBioAssay bioAssay = findDerivedBioAssay(dc, FallbackIdMethod.NAME_OR_ID, nameOrId, null);
    335339      if (nameOrId == null || bioAssay != null) rba.setParentBioAssay(bioAssay);
    336340      if (bioAssay != null)
    … …  
    342346        catch (PermissionDeniedException ex)
    343347        {}
     348        try
     349        {
     350          extractFromBioAssay = bioAssay.getExtract();
     351        }
     352        catch (PermissionDeniedException ex)
     353        {}
    344354      }
     355    }
     356   
     357    if (extractMapper != null)
     358    {
     359      String nameOrId = extractMapper.getValue(data);
     360      Extract extract = nameOrId == null ?
     361          extractFromBioAssay : findExtract(dc, FallbackIdMethod.NAME_OR_ID, nameOrId);
     362      if (nameOrId == null || extract != null) rba.setParentExtract(extract);
     363    }
     364    else if (extractFromBioAssay != null)
     365    {
     366      rba.setParentExtract(extractFromBioAssay);
    345367    }
    346368   

  • trunk/src/test/TestArrayBatch.java

    r5688 r5696  
    7272  }
    7373
    74   static void test_list(int expectedResults)
     74  static boolean test_list(int expectedResults)
    7575  {
    7676    DbControl dc = null;
    … …  
    9696      ex.printStackTrace();
    9797      ok = false;
    98     }
    99     finally
    100     {
    101       if (dc != null) dc.close();
    102     }
    103    
     98      return false;
     99    }
     100    finally
     101    {
     102      if (dc != null) dc.close();
     103    }
     104    return true;
    104105  }
    105106

  • trunk/src/test/TestArrayDesign.java

    r5688 r5696  
    194194
    195195
    196   static void test_list(int expectedResults)
     196  static boolean test_list(int expectedResults)
    197197  {
    198198    DbControl dc = null;
    … …  
    217217      ex.printStackTrace();
    218218      ok = false;
    219     }
    220     finally
    221     {
    222       if (dc != null) dc.close();
    223     }
     219      return false;
     220    }
     221    finally
     222    {
     223      if (dc != null) dc.close();
     224    }
     225    return true;
    224226  }
    225227

  • trunk/src/test/TestArraySlide.java

    r5688 r5696  
    131131  }
    132132
    133   static void test_list(int expectedResults)
     133  static boolean test_list(int expectedResults)
    134134  {
    135135    DbControl dc = null;
    … …  
    153153      ex.printStackTrace();
    154154      ok = false;
    155     }
    156     finally
    157     {
    158       if (dc != null) dc.close();
    159     }
     155      return false;
     156    }
     157    finally
     158    {
     159      if (dc != null) dc.close();
     160    }
     161    return true;
    160162  }
    161163

  • trunk/src/test/TestBioPlate.java

    r5688 r5696  
    168168  }
    169169
    170   static void test_list(int expectedResults)
     170  static boolean test_list(int expectedResults)
    171171  {
    172172    DbControl dc = null;
    … …  
    191191      ex.printStackTrace();
    192192      ok = false;
    193     }
    194     finally
    195     {
    196       if (dc != null) dc.close();
    197     }
     193      return false;
     194    }
     195    finally
     196    {
     197      if (dc != null) dc.close();
     198    }
     199    return ok;
    198200  }
    199201

  • trunk/src/test/TestBioSource.java

    r5688 r5696  
    114114  }
    115115
    116   static void test_list(int expectedResults)
     116  static boolean test_list(int expectedResults)
    117117  {
    118118    DbControl dc = null;
    … …  
    136136      ex.printStackTrace();
    137137      ok = false;
    138     }
    139     finally
    140     {
    141       if (dc != null) dc.close();
    142     }
     138      return false;
     139    }
     140    finally
     141    {
     142      if (dc != null) dc.close();
     143    }
     144    return true;
    143145  }
    144146

  • trunk/src/test/TestDerivedBioAssay.java

    r5688 r5696  
    202202  }
    203203
    204   static void test_list(int physicalBioAssayId, int expectedResults)
     204  static boolean test_list(int physicalBioAssayId, int expectedResults)
    205205  {
    206206    DbControl dc = null;
    … …  
    234234      ex.printStackTrace();
    235235      ok = false;
    236     }
    237     finally
    238     {
    239       if (dc != null) dc.close();
    240     }
     236      return false;
     237    }
     238    finally
     239    {
     240      if (dc != null) dc.close();
     241    }
     242    return true;
    241243  }
    242244

  • trunk/src/test/TestExtract.java

    r5688 r5696  
    211211  }
    212212
    213   static void test_list(int subtypeId, int expectedResults)
     213  static boolean test_list(int subtypeId, int expectedResults)
    214214  {
    215215    DbControl dc = null;
    … …  
    238238      ex.printStackTrace();
    239239      ok = false;
    240     }
    241     finally
    242     {
    243       if (dc != null) dc.close();
    244     }
     240      return false;
     241    }
     242    finally
     243    {
     244      if (dc != null) dc.close();
     245    }
     246    return true;
    245247  }
    246248

  • trunk/src/test/TestItemImporter.java

    r5689 r5696  
    2323import net.sf.basedb.core.BaseException;
    2424import net.sf.basedb.core.DbControl;
     25import net.sf.basedb.core.DerivedBioAssay;
    2526import net.sf.basedb.core.Extract;
    2627import net.sf.basedb.core.File;
    … …  
    7475    int printProtocolId = TestProtocol.test_create(SystemItems.getId(Protocol.PRINTING), "Printing", false);
    7576    int freezerId = TestHardware.test_create(SystemItems.getId(Hardware.FREEZER), "Freezer", false);
     77    int childScanId = TestItemSubtype.test_create(Item.DERIVEDBIOASSAY, "ChildScan", SystemItems.getId(DerivedBioAssay.SCAN));
    7678   
    7779    // Import bioplates
    … …  
    7981    int bioPlateImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.BioPlateImporter");
    8082    int bioPlateJobId = test_create_item_import_job(Item.BIOPLATE, bioPlateImporterId, bioPlateFileId);
    81     ok &= TestJob.test_execute(bioPlateJobId, false);
    82     TestBioPlate.test_list(2);
     83    ok = ok & TestJob.test_execute(bioPlateJobId, false);
     84    ok = ok & TestBioPlate.test_list(2);
    8385   
    8486    // Import biosources
    … …  
    8688    int bioSourceImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.BioSourceImporter");
    8789    int bioSourceJobId = test_create_item_import_job(Item.BIOSOURCE, bioSourceImporterId, bioSourceFileId);
    88     ok &= TestJob.test_execute(bioSourceJobId, false);
    89     TestBioSource.test_list(3);
     90    ok = ok & TestJob.test_execute(bioSourceJobId, false);
     91    ok = ok & TestBioSource.test_list(3);
    9092   
    9193    // Import samples
    … …  
    9395    int sampleImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.SampleImporter");
    9496    int sampleJobId = test_create_item_import_job(Item.SAMPLE, sampleImporterId, sampleFileId);
    95     ok &= TestJob.test_execute(sampleJobId, false);
    96     TestSample.test_list(4);
     97    ok = ok & TestJob.test_execute(sampleJobId, false);
     98    ok = ok & TestSample.test_list(4);
    9799
    98100    // Import extracts
    … …  
    100102    int extractImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ExtractImporter");
    101103    int extractJobId = test_create_item_import_job(Item.EXTRACT, extractImporterId, extractFileId);
    102     ok &= TestJob.test_execute(extractJobId, false);
    103     TestExtract.test_list(0, 4);
     104    ok = ok & TestJob.test_execute(extractJobId, false);
     105    ok = ok & TestExtract.test_list(0, 4);
    104106
    105107    // Import labeled extracts
    … …  
    107109    int labledExtractImporterId  = extractImporterId;
    108110    int labledExtractJobId = test_create_item_import_job(Item.EXTRACT, labledExtractImporterId, labledExtractFileId);
    109     ok &= TestJob.test_execute(labledExtractJobId, false);
    110     TestExtract.test_list(SystemItems.getId(Extract.LABELED), 7);
     111    ok = ok & TestJob.test_execute(labledExtractJobId, false);
     112    ok = ok & TestExtract.test_list(SystemItems.getId(Extract.LABELED), 7);
    111113   
    112114    // Import array designs
    … …  
    118120    int designImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArrayDesignImporter");
    119121    int designJobId = test_create_item_import_job(Item.ARRAYDESIGN, designImporterId, designFileId);
    120     ok &= TestJob.test_execute(designJobId, false);
    121     TestArrayDesign.test_list(3);
     122    ok = ok & TestJob.test_execute(designJobId, false);
     123    ok = ok & TestArrayDesign.test_list(3);
    122124   
    123125    // Import array batches
    … …  
    125127    int arrayBatchImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArrayBatchImporter");
    126128    int arrayBatchJobId = test_create_item_import_job(Item.ARRAYBATCH, arrayBatchImporterId, arrayBatchFileId);
    127     ok &= TestJob.test_execute(arrayBatchJobId, false);
    128     TestArrayBatch.test_list(3);
     129    ok = ok & TestJob.test_execute(arrayBatchJobId, false);
     130    ok = ok & TestArrayBatch.test_list(3);
    129131
    130132    // Import array slides
    … …  
    132134    int arraySlideImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ArraySlideImporter");
    133135    int arraySlideJobId = test_create_item_import_job(Item.ARRAYSLIDE, arraySlideImporterId, arraySlideFileId);
    134     ok &= TestJob.test_execute(arraySlideJobId, false);
    135     TestArraySlide.test_list(5);
     136    ok = ok & TestJob.test_execute(arraySlideJobId, false);
     137    ok = ok & TestArraySlide.test_list(5);
    136138   
    137139    // Import hybridizations
    … …  
    139141    int hybImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter");
    140142    int hybJobId = test_create_item_import_job(Item.PHYSICALBIOASSAY, hybImporterId, hybFileId);
    141     ok &= TestJob.test_execute(hybJobId, false);
    142     TestPhysicalBioAssay.test_list(3);
     143    ok = ok & TestJob.test_execute(hybJobId, false);
     144    ok = ok & TestPhysicalBioAssay.test_list(3);
    143145
    144146    // Import scans
     147    int samId = TestFile.test_create("data/test.assembly.sam", false, false);
     148    TestFile.test_rename(samId, "test.sam");
    145149    int scanFileId = TestFile.test_create("data/test.batchimport.scans.txt", false, false);
    146     int scanImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.ScanImporter");
     150    int scanImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter");
    147151    int scanJobId = test_create_item_import_job(Item.DERIVEDBIOASSAY, scanImporterId, scanFileId);
    148     ok &= TestJob.test_execute(scanJobId, false);
    149     TestDerivedBioAssay.test_list(0, 3);
     152    ok = ok & TestJob.test_execute(scanJobId, false);
     153    ok = ok & TestDerivedBioAssay.test_list(0, 4);
    150154 
    151155    // Import raw bioassays
    … …  
    157161    int rbaImporterId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.batchimport.RawBioAssayImporter");
    158162    int rbaJobId = test_create_item_import_job(Item.RAWBIOASSAY, rbaImporterId, rbaFileId);
    159     ok &= TestJob.test_execute(rbaJobId, false);
    160     TestRawBioAssay.test_list(4);
     163    ok = ok & TestJob.test_execute(rbaJobId, false);
     164    ok = ok & TestRawBioAssay.test_list(4);
    161165   
    162166    if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
    … …  
    173177    TestJob.test_delete(scanJobId);
    174178    TestFile.test_delete(scanFileId);
     179    TestFile.test_delete(samId);
    175180
    176181    // Delete hybridizations
    … …  
    236241    TestSoftware.test_delete(featureSoftwareId);
    237242    TestPlatform.test_delete_variant(variantId);
     243    TestItemSubtype.test_delete(childScanId);
    238244
    239245    write("++Testing item import using plugin "+(ok ? "OK" : "Failed")+"\n");
    … …  
    371377    if (itemType == Item.DERIVEDBIOASSAY)
    372378    {
    373       request.setParameterValue("hybridizationColumnMapping", "\\Hybridization\\");
     379      request.setParameterValue("dataDirectory", "/");
     380      request.setParameterValue("subtypeColumnMapping", "\\Subtype\\");
     381      request.setParameterValue("parentColumnMapping", "\\Parent\\");
     382      request.setParameterValue("extractColumnMapping", "\\Extract\\");
    374383      request.setParameterValue("protocolColumnMapping", "\\Protocol\\");
    375384      request.setParameterValue("hardwareColumnMapping", "\\Scanner\\");
     385      request.setParameterValue("fileTypeColumnMapping", "\\File type\\");
     386      request.setParameterValue("fileColumnMapping", "\\File\\");
    376387    }
    377388    if (itemType == Item.RAWBIOASSAY)
    378389    {
    379390      request.setParameterValue("dataDirectory", "/");
    380       request.setParameterValue("arrayIndexColumnMapping", "\\Array index\\");
    381391      request.setParameterValue("bioAssayColumnMapping", "\\Scan\\");
    382392      request.setParameterValue("protocolColumnMapping", "\\Protocol\\");

  • trunk/src/test/TestItemSubtype.java

    r5641 r5696  
    6161  }
    6262
    63   static int test_create(Item itemType, String name)
     63  static int test_create(Item itemType, String name, int... relatedSubtypes)
    6464  {
    6565    if (!TestUtil.hasPermission(Permission.CREATE, Item.ITEMSUBTYPE)) return 0;
    … …  
    7373      subtype.setName(name);
    7474      subtype.setDescription("Added at "+new Date());
     75      if (relatedSubtypes != null)
     76      {
     77        for (int i = 0; i < relatedSubtypes.length; ++i)
     78        {
     79          subtype.setRelatedSubtype(ItemSubtype.getById(dc, relatedSubtypes[i]));
     80        }
     81      }
    7582      dc.saveItem(subtype);
    7683      dc.commit();

  • trunk/src/test/TestPhysicalBioAssay.java

    r5688 r5696  
    154154  }
    155155
    156   static void test_list(int expectedResults)
     156  static boolean test_list(int expectedResults)
    157157  {
    158158    DbControl dc = null;
    … …  
    176176      ex.printStackTrace();
    177177      ok = false;
    178     }
    179     finally
    180     {
    181       if (dc != null) dc.close();
    182     }
     178      return false;
     179    }
     180    finally
     181    {
     182      if (dc != null) dc.close();
     183    }
     184    return true;
    183185  }
    184186

  • trunk/src/test/TestRawBioAssay.java

    r5689 r5696  
    199199  }
    200200
    201   static void test_list(int expectedResults)
     201  static boolean test_list(int expectedResults)
    202202  {
    203203    DbControl dc = null;
    … …  
    221221      ex.printStackTrace();
    222222      ok = false;
    223     }
    224     finally
    225     {
    226       if (dc != null) dc.close();
    227     }
     223      return false;
     224    }
     225    finally
     226    {
     227      if (dc != null) dc.close();
     228    }
     229    return true;
    228230  }
    229231

  • trunk/src/test/TestSample.java

    r5688 r5696  
    198198  }
    199199
    200   static void test_list(int expectedResults)
     200  static boolean test_list(int expectedResults)
    201201  {
    202202    DbControl dc = null;
    … …  
    220220      ex.printStackTrace();
    221221      ok = false;
    222     }
    223     finally
    224     {
    225       if (dc != null) dc.close();
    226     }
     222      return false;
     223    }
     224    finally
     225    {
     226      if (dc != null) dc.close();
     227    }
     228    return true;
    227229  }
    228230

  • trunk/src/test/data/test.batchimport.scans.txt

    r4426 r5696  
    1 Name  Description Hybridization Protocol  Scanner
    2 Scan 1  The first Hyb 1 Scanning  Scanner
    3 Scan 2  The second  Hyb 2 Scanning  Scanner
    4 Scan 3    Hyb all
     1Name  Subtype Description Parent  Extract Protocol  Scanner File type File
     2Scan 1  Scan  The first Hyb 1 Labeled 1.1 Scanning  Scanner assembly.sam  test.sam
     3Scan 2  Scan  The second  Hyb 2 Labeled 2.1 Scanning  Scanner
     4Scan 3  Scan    Hyb all
     5Child bioassay 1  ChildScan A child to Scan 1 Scan 1 
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