diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
index cdea22d4981122f394cda50676ba38d22bd4206c..89e0906ad2517d4ff74a8bf88af4a700ef12f8e4 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
@@ -53,9 +53,9 @@ class AbundanceHandler extends AbstractHandler
private final IEncapsulatedOpenBISService openbisService;
private final ExperimentIdentifier experimentIdentifier;
-
+
private final SpaceIdentifier msData;
-
+
private final Experiment experiment;
private final Map<String, SampleOrError> samplesOrErrors = new HashMap<String, SampleOrError>();
@@ -69,7 +69,9 @@ class AbundanceHandler extends AbstractHandler
this.openbisService = openbisService;
this.experimentIdentifier = experimentIdentifier;
this.experiment = experiment;
- msData = new SpaceIdentifier(experimentIdentifier.getDatabaseInstanceCode(), Constants.MS_DATA_SPACE);
+ msData =
+ new SpaceIdentifier(experimentIdentifier.getDatabaseInstanceCode(),
+ Constants.MS_DATA_SPACE);
sampleType = new SampleType();
sampleType.setCode(Constants.SEARCH_SAMPLE_TYPE);
}
@@ -88,14 +90,14 @@ class AbundanceHandler extends AbstractHandler
}
}
+ @SuppressWarnings("deprecation")
private Sample getOrCreateSample(String parameterName, String proteinName)
{
SampleOrError sampleOrError = samplesOrErrors.get(parameterName);
if (sampleOrError == null)
{
// first we look for a sample in space MS_DATA
- SampleIdentifier sampleIdentifier =
- new SampleIdentifier(msData, parameterName);
+ SampleIdentifier sampleIdentifier = new SampleIdentifier(msData, parameterName);
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
openbisService.tryGetSampleWithExperiment(sampleIdentifier);
sampleOrError = new SampleOrError();
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java
index c9c9bf9e536e2a76d61bd15f0d0456f01ce9c6e9..fb0d37445432fcf315832accbbac84540775f980 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java
@@ -43,29 +43,44 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class AbundanceHandlerTest extends AssertJUnit
{
private static final String SPACE_CODE = "G1";
- private static final SpaceIdentifier SPACE_IDENTIFIER = new SpaceIdentifier((String) null, SPACE_CODE);
+
+ private static final SpaceIdentifier SPACE_IDENTIFIER = new SpaceIdentifier((String) null,
+ SPACE_CODE);
+
private static final String EXPERIMENT_CODE = "E1";
- private static final GroupIdentifier GROUP_IDENTIFIER = new GroupIdentifier((String) null, Constants.MS_DATA_SPACE);
+
+ private static final GroupIdentifier GROUP_IDENTIFIER = new GroupIdentifier((String) null,
+ Constants.MS_DATA_SPACE);
+
private static final String PARAMETER_VALUE = "1234.5";
+
private static final double ABUNDANCE = 1234.5;
+
private static final String PARAMETER_NAME = "abc12";
- private static final SampleIdentifier SAMPLE_IDENTIFER =
- new SampleIdentifier(GROUP_IDENTIFIER, PARAMETER_NAME);
- private static final ExperimentIdentifier EXPERIMENT_IDENTIFIER =
- new ExperimentIdentifier(new ProjectIdentifier(SPACE_CODE, "P1"), EXPERIMENT_CODE);
+
+ private static final SampleIdentifier SAMPLE_IDENTIFER = new SampleIdentifier(GROUP_IDENTIFIER,
+ PARAMETER_NAME);
+
+ private static final ExperimentIdentifier EXPERIMENT_IDENTIFIER = new ExperimentIdentifier(
+ new ProjectIdentifier(SPACE_CODE, "P1"), EXPERIMENT_CODE);
+
private static final String SAMPLE_PERM_ID = "s12-34";
+
private static final String EXPERIMENT_PERM_ID = "e12345-42";
+
private static final long EXPERIMENT_ID = 42;
+
private static final long SAMPLE_ID = 43;
+
private static final long PROTEIN_ID = 4711;
+
private static final String PROTEIN_NAME = "my protein";
+
private static final ListSamplesByPropertyCriteria CRITERIA =
new ListSamplesByPropertyCriteria(AbundanceHandler.MZXML_FILENAME, PARAMETER_NAME,
SPACE_CODE, null);
@@ -135,32 +150,34 @@ public class AbundanceHandlerTest extends AssertJUnit
context.assertIsSatisfied();
}
-
+
@Test
public void testAddTwoAbundanceValuesForASampleIdentifiedByPropertyButNoSampleFound()
{
- prepareCreateSampleIdentifiedByProperty(Arrays.<Sample>asList());
+ prepareCreateSampleIdentifiedByProperty(Arrays.<Sample> asList());
try
{
- handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID, PROTEIN_NAME);
+ handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID,
+ PROTEIN_NAME);
fail("UserFailureException expected");
} catch (UserFailureException e)
{
assertEquals("Protein '" + PROTEIN_NAME
- + "' has an abundance value for an unidentified sample: " + PARAMETER_NAME, e
- .getMessage());
+ + "' has an abundance value for an unidentified sample: " + PARAMETER_NAME,
+ e.getMessage());
}
-
+
try
{
- handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID, PROTEIN_NAME);
+ handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID,
+ PROTEIN_NAME);
fail("UserFailureException expected");
} catch (UserFailureException e)
{
assertEquals("Protein '" + PROTEIN_NAME
- + "' has an abundance value for an unidentified sample: " + PARAMETER_NAME, e
- .getMessage());
+ + "' has an abundance value for an unidentified sample: " + PARAMETER_NAME,
+ e.getMessage());
}
context.assertIsSatisfied();
@@ -187,14 +204,14 @@ public class AbundanceHandlerTest extends AssertJUnit
context.assertIsSatisfied();
}
-
+
@Test
public void testAddAbundanceValuesForASampleIdentifiedByProperty()
{
final Sample sample = new Sample();
sample.setPermId(SAMPLE_PERM_ID);
sample.setIdentifier("blabla");
- prepareCreateSampleIdentifiedByProperty(Arrays.<Sample>asList(sample));
+ prepareCreateSampleIdentifiedByProperty(Arrays.<Sample> asList(sample));
prepareCreateSample();
context.checking(new Expectations()
{
@@ -203,6 +220,7 @@ public class AbundanceHandlerTest extends AssertJUnit
one(service).registerSample(with(new BaseMatcher<NewSample>()
{
+ @SuppressWarnings("deprecation")
public boolean matches(Object item)
{
if (item instanceof NewSample)
@@ -210,10 +228,10 @@ public class AbundanceHandlerTest extends AssertJUnit
NewSample newSample = (NewSample) item;
assertEquals(SPACE_IDENTIFIER + "/" + PARAMETER_NAME + "_"
+ EXPERIMENT_CODE, newSample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER.toString(), newSample
- .getExperimentIdentifier());
- assertEquals(sample.getIdentifier(), newSample
- .getParentIdentifier());
+ assertEquals(EXPERIMENT_IDENTIFIER.toString(),
+ newSample.getExperimentIdentifier());
+ assertEquals(sample.getIdentifier(),
+ newSample.getParentIdentifier());
return true;
}
return false;
@@ -252,7 +270,7 @@ public class AbundanceHandlerTest extends AssertJUnit
{
one(service).registerSample(with(new BaseMatcher<NewSample>()
{
-
+ @SuppressWarnings("deprecation")
public boolean matches(Object item)
{
if (item instanceof NewSample)
@@ -260,8 +278,8 @@ public class AbundanceHandlerTest extends AssertJUnit
NewSample newSample = (NewSample) item;
assertEquals(SPACE_IDENTIFIER + "/" + PARAMETER_NAME + "_"
+ EXPERIMENT_CODE, newSample.getIdentifier());
- assertEquals(EXPERIMENT_IDENTIFIER.toString(), newSample
- .getExperimentIdentifier());
+ assertEquals(EXPERIMENT_IDENTIFIER.toString(),
+ newSample.getExperimentIdentifier());
assertEquals(PARAMETER_NAME, newSample.getParentIdentifier());
return true;
}
@@ -290,7 +308,7 @@ public class AbundanceHandlerTest extends AssertJUnit
}
});
}
-
+
private void prepareCreateSampleIdentifiedByProperty(final List<Sample> samples)
{
prepareGetSample(null);
@@ -315,7 +333,7 @@ public class AbundanceHandlerTest extends AssertJUnit
}
});
}
-
+
private void prepareGetSample(final Sample sample)
{
context.checking(new Expectations()