diff --git a/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py b/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
index 412e67333d2aa62afdaee080edbee0bb920135f8..4f4df43954f3d02971a0957700dd7cdde6c9974c 100644
--- a/eu_basynthec/dist/etc/growth-profiles/data-set-handler.py
+++ b/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)
diff --git a/eu_basynthec/dist/etc/metabolomics/data-set-handler.py b/eu_basynthec/dist/etc/metabolomics/data-set-handler.py
index c4ac2a23f3f6d4bac218f6f91fc82895e36d7ff1..9cdbf69004f4efaa291af3b51d81335adacebc50 100644
--- a/eu_basynthec/dist/etc/metabolomics/data-set-handler.py
+++ b/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)
diff --git a/eu_basynthec/dist/etc/proteomics/data-set-handler.py b/eu_basynthec/dist/etc/proteomics/data-set-handler.py
index c6ac2b22ff496be2d621d6360a47456c43f8f3d6..4ab87d54b496d78b196f88b4945206769bd321ed 100644
--- a/eu_basynthec/dist/etc/proteomics/data-set-handler.py
+++ b/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)
diff --git a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py b/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
index bcd7a8617c5bd3754a33333e35c8fca1c1893926..d7d875f0585b23cf9e227339c72955aa05212a25 100644
--- a/eu_basynthec/dist/etc/transcriptomics/data-set-handler.py
+++ b/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)
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 82cce8477cd602ca14ae7d101b4bc37eacb4f57d..3a05bdbb6ca8516434bf2490712314846056633f 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/AbstractBaSynthecDataSetRegistratorTest.java
+++ b/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()));
}
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
index 6226926a6e2860db74851c65fd13ec903a61d975..a8a036d19b62128999be6273ce01bb1dd72a2b75 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/growthprofiles/OD600DataSetRegistratorTest.java
+++ b/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());
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java
index de439fc36b670676e9c91f0c92416cf94d9fedc0..641a9ed8277a5b4a25833863cbc93c2959746611 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/metabolomics/MetabolomicsDataSetRegistratorTest.java
+++ b/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());
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 d2c186a68215def31d0385803156ada39bb12e4e..3a71075823435d316ec85aa91a06612189d825c9 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
@@ -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());
diff --git a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java b/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
index 8c26bae12866af7611e8f9cfea607a3f1e6b58b1..d8da395faf3557e028848856698835209330dd3d 100644
--- a/eu_basynthec/sourceTest/java/eu/basynthec/cisd/dss/transcriptomics/TranscriptomicsDataSetRegistratorTest.java
+++ b/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();
}