Changeset 5694


Ignore:
Timestamp:
Aug 12, 2011, 9:32:37 AM (10 years ago)
Author:
Nicklas Nordborg
Message:

References #1153: Handling short read transcript sequence data

Extended the Illumina test case to also create extracts to make sure that the raw bioassay -> extract linking is working as expected.

File:
1 edited

Legend:

Unmodified
Added
Removed
  • trunk/src/test/TestIlluminaImporter.java

    r5693 r5694  
    4444    TestReporter.test_import_from_file("data/test.illumina.reporters.txt", "Search_key,Target,ProbeId.*", ",(?=(?:[^\"]*\"[^\"]*\")*(?![^\"]*\"))", 1, 1);
    4545    int fileId = TestFile.test_create("data/test.illumina.rawdata.txt", false, false);
    46     int hyb1Id = TestPhysicalBioAssay.test_create(0, "Hyb #1677718123", 0, 1);
     46    int hyb1Id = TestPhysicalBioAssay.test_create(0, "Hyb #1677718123", 0, 12);
    4747    int scan1Id = TestDerivedBioAssay.test_create_root("1677718123", hyb1Id, SystemItems.getId(DerivedBioAssay.SCAN), 0, 0, 0);
    48     int hyb2Id = TestPhysicalBioAssay.test_create(0, "Hyb #1677718142", 0, 1);
     48    int hyb2Id = TestPhysicalBioAssay.test_create(0, "Hyb #1677718142", 0, 12);
    4949    int scan2Id = TestDerivedBioAssay.test_create_root("1677718142", hyb2Id, SystemItems.getId(DerivedBioAssay.SCAN), 0, 0, 0);
    5050    int protocolId = TestProtocol.test_create(SystemItems.getId(Protocol.FEATURE_EXTRACTION), null, false);
     
    5252    int experimentId = TestExperiment.test_create("illumina", false);
    5353   
     54    // Extracts
     55    int cy3 = TestTag.test_load("cy3");
     56    int labeledExtract = SystemItems.getId(Extract.LABELED);
     57    int[] extractIds = new int[12];
     58    for (int i = 0; i < 12; ++i)
     59    {
     60      extractIds[i] = TestExtract.test_create(0, "#" + (i+1), labeledExtract, cy3, false);
     61      TestPhysicalBioAssay.test_add_extract(hyb1Id, extractIds[i], i+1, null);
     62    }
     63   
    5464    // Create plugin configuration and job
    5565    int pluginDefinitionId  = TestPluginDefinition.test_get("net.sf.basedb.plugins.IlluminaRawDataImporter");
     
    7787    TestDerivedBioAssay.test_delete(scan1Id);
    7888    TestDerivedBioAssay.test_delete(scan2Id);
     89   
    7990    TestSoftware.test_delete(softwareId);
    8091    TestProtocol.test_delete(protocolId);
     
    8394    TestFile.test_delete(fileId);
    8495    TestReporter.test_delete();
     96    for (int i = 0; i < extractIds.length; ++i)
     97    {
     98      TestExtract.test_delete(extractIds[i]);
     99    }
    85100
    86101    write("++Testing Illumina rawdata import "+(ok ? "OK" : "Failed")+"\n");
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