diff --git a/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py b/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
index 30a4a053675e4c1eb26ad832398042e05859b980..01d1a47bd7c233b8b058540c1b9db5891d4ebf8a 100644
--- a/eu_basynthec/dist/etc/metabolomics2/data-set-handler.py
+++ b/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()]
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
index d2712597435afc1ae46ddc84f9bfd012ccb7f8aa..ef568c27981430d7fbf41be9ea6adfdae346a925 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
+++ b/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;
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.java
index 6af4202177f5a3c98a9088b7ebd460313d0a0913..f864068bc516fed046a26268869ffc1eb7ec7ee7 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistrator2Test.java
+++ b/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());
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.java
index c5a93910e19970521b48136a3e4cd713af5e6abb..050f9618bf834fba93c337d0b2d6147b0a7f20f7 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsValidator2Test.java
+++ b/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());
}
}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java
index db27cbc2a09abeb30358528285ecee1d2fbef6c0..70cdb7f09df54e075685225b23c978f4b7ceb8d9 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/proteomics/ProteomicsDataSetRegistratorTest.java
+++ b/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