SP-31 BIS-28 : Improvements to the metabolomics2 data set handler

SVN: 25292

eu_basynthec/dist/etc/metabolomics2/data-set-handler.py

@@ -169,7 +169,7 @@ store_original_data(tr, original_dataset, "xls")
 
 tsv_dataset = tr.createNewDataSet("TSV_MULTISTRAIN_EXPORT")
 set_data_type(tsv_dataset)
-convert_data_to_tsv(tr, tsv_dataset, "tsv")
+convert_data_to_tsv(tr, tsv_dataset, "tsv-multi")
 
 # Make the original contain these
 contained_codes = [original_dataset.getDataSetCode(), tsv_dataset.getDataSetCode()]

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

@@ -47,13 +47,11 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
 {
 
     private static final String TEST_EXPERIMENT_IDENTIFIER = "/TEST/TEST/TEST";
-    
+
     protected static final String STRAIN_NAMES_PROP = "STRAIN_NAMES";
 
     protected static final String VALUE_UNIT_PROP = "VALUE_UNIT";
 
-    protected static final String DATA_SET_CODE = "data-set-code";
-
     protected static final DataSetType TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE = new DataSetType(
             "TSV_MULTISTRAIN_EXPORT");
 
@@ -70,6 +68,13 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
 
     protected RecordingMatcher<AtomicEntityOperationDetails> setUpDataSetRegistrationExpectations(
             final DataSetType dataSetType, final DataSetType tsvDataSetType)
+    {
+        return setUpDataSetRegistrationExpectations(dataSetType, tsvDataSetType, true);
+    }
+
+    protected RecordingMatcher<AtomicEntityOperationDetails> setUpDataSetRegistrationExpectations(
+            final DataSetType dataSetType, final DataSetType tsvDataSetType,
+            final boolean requireSingleStrainTsvExport)
     {
         ExperimentBuilder builder = new ExperimentBuilder().identifier(TEST_EXPERIMENT_IDENTIFIER);
         final Experiment experiment = builder.getExperiment();
@@ -95,8 +100,11 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
                     }
 
                     String tsvDataSetCode = DATA_SET_CODE + "-TSV";
-                    one(openBisService).createDataSetCode();
-                    will(returnValue(tsvDataSetCode));
+                    if (requireSingleStrainTsvExport)
+                    {
+                        one(openBisService).createDataSetCode();
+                        will(returnValue(tsvDataSetCode));
+                    }
 
                     atLeast(1).of(openBisService).tryToGetExperiment(
                             new ExperimentIdentifierFactory(experiment.getIdentifier())
@@ -119,15 +127,18 @@ public abstract class AbstractBaSynthecDataSetRegistratorTest extends
                                         + "-TSV-MULTISTRAIN"), "tsv-multi"));
                     }
 
-                    one(dataSetValidator).assertValidDataSet(TSV_DATA_SET_TYPE,
-                            new File(new File(stagingDirectory, tsvDataSetCode), "tsv"));
+                    if (requireSingleStrainTsvExport)
+                    {
+                        one(dataSetValidator).assertValidDataSet(TSV_DATA_SET_TYPE,
+                                new File(new File(stagingDirectory, tsvDataSetCode), "tsv"));
+                    }
 
                     one(openBisService).performEntityOperations(with(atomicatOperationDetails));
 
                     will(returnValue(new AtomicEntityOperationResult()));
 
                     allowing(openBisService).setStorageConfirmed(with(any(String.class)));
-                    
+
                 }
             });
         return atomicatOperationDetails;

eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.java

@@ -34,8 +34,8 @@ import eu.basynthec.cisd.dss.AbstractBaSynthecDataSetRegistratorTest;
  */
 public class MetabolomicsDataSetRegistrator2Test extends AbstractBaSynthecDataSetRegistratorTest
 {
-    private static final DataSetType METABOLITE_INTENSITIES_GROUPED = new DataSetType(
-            "METABOLITE_INTENSITIES_GROUPED");
+    private static final DataSetType METABOLITE_INTENSITIES = new DataSetType(
+            "METABOLITE_INTENSITIES");
 
     @Test
     public void testSimpleTransaction() throws IOException
@@ -46,7 +46,8 @@ public class MetabolomicsDataSetRegistrator2Test extends AbstractBaSynthecDataSe
         createData("Metabolomics-Example.xlsx");
 
         final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicOperationDetails =
-                setUpDataSetRegistrationExpectations(METABOLITE_INTENSITIES_GROUPED, TSV_DATA_SET_TYPE);
+                setUpDataSetRegistrationExpectations(METABOLITE_INTENSITIES,
+                        TSV_MULTISTRAIN_EXPORT_DATA_SET_TYPE, false);
 
         handler.handle(markerFile);
 
@@ -61,7 +62,7 @@ public class MetabolomicsDataSetRegistrator2Test extends AbstractBaSynthecDataSe
                 atomicOperationDetails.recordedObject().getDataSetRegistrations().get(0);
 
         assertEquals(DATA_SET_CODE, dataSet.getCode());
-        assertEquals(METABOLITE_INTENSITIES_GROUPED, dataSet.getDataSetType());
+        assertEquals(METABOLITE_INTENSITIES, dataSet.getDataSetType());
 
         HashMap<String, NewProperty> propertyMap =
                 getDataSetPropertiesMap(dataSet.getDataSetProperties());

eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.java

@@ -60,7 +60,6 @@ public class MetabolomicsValidator2Test extends AssertJUnit
                 ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
         List<ValidationError> errors =
                 scriptRunner.validate(new File("sourceTest/examples/Metabolomics-BadData.xlsx"));
-        System.out.println(errors);
         assertEquals("The bad data should have thirteen errors", 13, errors.size());
     }
 
@@ -71,7 +70,8 @@ public class MetabolomicsValidator2Test extends AssertJUnit
         ValidationScriptRunner scriptRunner =
                 ValidationScriptRunner.createValidatorFromScriptPaths(VALIDATION_SCRIPT_PATH);
         List<ValidationError> errors =
-                scriptRunner.validate(new File("sourceTest/examples/Metabolomics-GarbageData.xlsx"));
+                scriptRunner
+                        .validate(new File("sourceTest/examples/Metabolomics-GarbageData.xlsx"));
         assertEquals("The garbage data should have eight errors", 8, errors.size());
     }
 }

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

@@ -35,7 +35,8 @@ import eu.basynthec.cisd.dss.AbstractBaSynthecDataSetRegistratorTest;
 public class ProteomicsDataSetRegistratorTest extends AbstractBaSynthecDataSetRegistratorTest
 {
 
-    private static final DataSetType PROTEIN_QUANTIFICATIONS = new DataSetType("PROTEIN_QUANTIFICATIONS");
+    private static final DataSetType PROTEIN_QUANTIFICATIONS = new DataSetType(
+            "PROTEIN_QUANTIFICATIONS");
 
     @Test
     public void testSimpleTransaction() throws IOException