From 8bb87dee4938523e125cf9fa1fb5e2b8eb55119f Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 7 Jul 2011 14:27:35 +0000
Subject: [PATCH] LMS-2391 Fixed tests.
SVN: 22052
---
.../etc/growth-profiles/data-set-handler.py | 2 +
.../dist/etc/metabolomics/data-set-handler.py | 2 +
.../dist/etc/proteomics/data-set-handler.py | 2 +
.../etc/transcriptomics/data-set-handler.py | 2 +
...stractBaSynthecDataSetRegistratorTest.java | 37 +++++++++++++++++--
.../OD600DataSetRegistratorTest.java | 9 +++--
.../MetabolomicsDataSetRegistratorTest.java | 8 ++--
.../ProteomicsDataSetRegistratorTest.java | 8 ++--
...TranscriptomicsDataSetRegistratorTest.java | 15 +++++---
9 files changed, 64 insertions(+), 21 deletions(-)
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 412e67333d2..4f4df43954f 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 c4ac2a23f3f..9cdbf69004f 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 c6ac2b22ff4..4ab87d54b49 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 bcd7a8617c5..d7d875f0585 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 82cce8477cd..3a05bdbb6ca 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 6226926a6e2..a8a036d19b6 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 de439fc36b6..641a9ed8277 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 d2c186a6821..3a710758234 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 8c26bae1286..d8da395faf3 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();
}
--
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