LMS-2391 Fixed tests.

SVN: 22052

eu_basynthec/dist/etc/growth-profiles/data-set-handler.py

@@ -84,4 +84,6 @@ if dataset.getExperiment() is None:
 	exp = retrieve_experiment(tr, exp_id)
 	if exp is not None:
 		dataset.setExperiment(exp)
+		original_dataset.setExperiment(exp)
+		tsv_dataset.setExperiment(exp)
 

eu_basynthec/dist/etc/metabolomics/data-set-handler.py

@@ -71,5 +71,7 @@ if dataset.getExperiment() is None:
 	exp = retrieve_experiment(tr, exp_id)
 	if exp is not None:
 		dataset.setExperiment(exp)
+		original_dataset.setExperiment(exp)
+		tsv_dataset.setExperiment(exp)
 
 

eu_basynthec/dist/etc/proteomics/data-set-handler.py

@@ -72,5 +72,7 @@ if dataset.getExperiment() is None:
 	exp = retrieve_experiment(tr, exp_id)
 	if exp is not None:
 		dataset.setExperiment(exp)
+		original_dataset.setExperiment(exp)
+		tsv_dataset.setExperiment(exp)
 
 

eu_basynthec/dist/etc/transcriptomics/data-set-handler.py

@@ -113,5 +113,7 @@ if dataset.getExperiment() is None:
 	exp = retrieve_experiment(tr, exp_id)
 	if exp is not None:
 		dataset.setExperiment(exp)
+		original_dataset.setExperiment(exp)
+		tsv_dataset.setExperiment(exp)
 
 

eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java

@@ -51,6 +51,11 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
 
     private static final String EXPERIMENT_IDENTIFIER = "/TEST/TEST/TEST";
 
+    protected static final DataSetType TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE = new DataSetType(
+            "TSV_MULTISTRAIN_EXPORT");
+
+    protected static final DataSetType TSV_DATA_SET_TYPE = new DataSetType("TSV_EXPORT");
+
     /**
      *
      *
@@ -61,7 +66,7 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
     }
 
     protected RecordingMatcher<AtomicEntityOperationDetails> setUpDataSetRegistrationExpectations(
-            final DataSetType dataSetType)
+            final DataSetType dataSetType, final DataSetType tsvDataSetType)
     {
         ExperimentBuilder builder = new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER);
         final Experiment experiment = builder.getExperiment();
@@ -72,13 +77,39 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
                 {
                     one(openBisService).createDataSetCode();
                     will(returnValue(DATA_SET_CODE));
+
+                    String excelDataSetCode = DATA_SET_CODE + "-EXCEL";
+                    one(openBisService).createDataSetCode();
+                    will(returnValue(excelDataSetCode));
+
+                    String tsvDataSetCode = DATA_SET_CODE + "-TSV";
+                    one(openBisService).createDataSetCode();
+                    will(returnValue(tsvDataSetCode));
+
                     atLeast(1).of(openBisService).tryToGetExperiment(
                             new ExperimentIdentifierFactory(experiment.getIdentifier())
                                     .createIdentifier());
                     will(returnValue(experiment));
 
-                    one(dataSetValidator).assertValidDataSet(dataSetType,
-                            new File(new File(stagingDirectory, DATA_SET_CODE), "data"));
+                    allowing(openBisService).tryToGetExperiment(null);
+                    will(returnValue(null));
+
+                    one(dataSetValidator).assertValidDataSet(dataSetType, null);
+
+                    one(dataSetValidator).assertValidDataSet(new DataSetType("EXCEL_ORIGINAL"),
+                            new File(new File(stagingDirectory, excelDataSetCode), "xls"));
+
+                    if (tsvDataSetType == TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE)
+                    {
+                        one(dataSetValidator).assertValidDataSet(
+                                TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE,
+                                new File(new File(stagingDirectory, tsvDataSetCode), "tsv-multi"));
+                    } else
+                    {
+                        one(dataSetValidator).assertValidDataSet(TSV_DATA_SET_TYPE,
+                                new File(new File(stagingDirectory, tsvDataSetCode), "tsv"));
+                    }
+
                     one(openBisService).performEntityOperations(with(atomicatOperationDetails));
                     will(returnValue(new AtomicEntityOperationResult()));
                 }

eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java

@@ -44,15 +44,16 @@ public class OD600DataSetRegistratorTest extends AbstractBaSynthecDataSetRegistr
         createHandler(properties, false, true);
         createData("OD600-Example.xlsx");
 
-        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
-                setUpDataSetRegistrationExpectations(DATA_SET_TYPE);
+        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
+                setUpDataSetRegistrationExpectations(DATA_SET_TYPE,
+                        TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE);
 
         handler.handle(markerFile);
 
-        assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+        assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
 
         NewExternalData dataSet =
-                atomicatOperationDetails.recordedObject().getDataSetRegistrations().get(0);
+                atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
 
         assertEquals(DATA_SET_CODE, dataSet.getCode());
         assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());

eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java

@@ -44,15 +44,15 @@ public class MetabolomicsDataSetRegistratorTest extends AbstractBaSynthecDataSet
         createHandler(properties, false, true);
         createData("Proteomics-Example.xlsx");
 
-        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
-                setUpDataSetRegistrationExpectations(DATA_SET_TYPE);
+        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
+                setUpDataSetRegistrationExpectations(DATA_SET_TYPE, TSV_DATA_SET_TYPE);
 
         handler.handle(markerFile);
 
-        assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+        assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
 
         NewExternalData dataSet =
-                atomicatOperationDetails.recordedObject().getDataSetRegistrations().get(0);
+                atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
 
         assertEquals(DATA_SET_CODE, dataSet.getCode());
         assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());

eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java

@@ -44,15 +44,15 @@ public class ProteomicsDataSetRegistratorTest extends AbstractBaSynthecDataSetRe
         createHandler(properties, false, true);
         createData("Metabolomics-Example.xlsx");
 
-        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
-                setUpDataSetRegistrationExpectations(DATA_SET_TYPE);
+        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
+                setUpDataSetRegistrationExpectations(DATA_SET_TYPE, TSV_DATA_SET_TYPE);
 
         handler.handle(markerFile);
 
-        assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+        assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
 
         NewExternalData dataSet =
-                atomicatOperationDetails.recordedObject().getDataSetRegistrations().get(0);
+                atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
 
         assertEquals(DATA_SET_CODE, dataSet.getCode());
         assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());

eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java

@@ -46,15 +46,16 @@ public class TranscriptomicsDataSetRegistratorTest extends AbstractBaSynthecData
         createHandler(properties, false, true);
         createData("Transcriptomics-Example.xlsx");
 
-        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
-                setUpDataSetRegistrationExpectations(DATA_SET_TYPE);
+        final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
+                setUpDataSetRegistrationExpectations(DATA_SET_TYPE,
+                        TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE);
 
         handler.handle(markerFile);
 
-        assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+        assertEquals(3, atomicOperationDetails.recordedObject().getDataSetRegistrations().size());
 
         NewExternalData dataSet =
-                atomicatOperationDetails.recordedObject().getDataSetRegistrations().get(0);
+                atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
 
         assertEquals(DATA_SET_CODE, dataSet.getCode());
         assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());
@@ -67,10 +68,12 @@ public class TranscriptomicsDataSetRegistratorTest extends AbstractBaSynthecData
         assert null != strainProperty;
         assertEquals("MGP253,MGP776", strainProperty.getValue());
 
-        String location = dataSet.getLocation();
+        NewExternalData tsvDataSet =
+                atomicOperationDetails.recordedObject().getDataSetRegistrations().get(2);
+        String location = tsvDataSet.getLocation();
         File tsvFile =
                 new File(new File(workingDirectory, "/1/" + location),
-                        "tsv/Transcriptomics-Example.xlsx.tsv");
+                        "Transcriptomics-Example.xlsx.tsv");
         checkTsvContent(tsvFile);
         context.assertIsSatisfied();
     }