From c14bb492ded8e953bd908ae459f9b7823061ac0e Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 26 Aug 2009 14:39:50 +0000
Subject: [PATCH] SE-126 protXML file uploading: parameter name is either code
of a sample or value of property MZXML_FILENAME
SVN: 12296
---
.../phosphonetx/AbundanceHandler.java | 33 +++++++++++++++----
.../ResultDataSetUploaderTest.java | 31 +++++++++++++----
2 files changed, 50 insertions(+), 14 deletions(-)
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 aceab659958..c5ac2124a17 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
@@ -17,13 +17,16 @@
package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.util.HashMap;
+import java.util.List;
import java.util.Map;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Experiment;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Parameter;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -33,6 +36,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
*/
class AbundanceHandler extends AbstractHandler
{
+ @Private static final String MZXML_FILENAME = "MZXML_FILENAME";
+
private final IEncapsulatedOpenBISService openbisService;
private final GroupIdentifier groupIdentifier;
private final Experiment experiment;
@@ -69,18 +74,32 @@ class AbundanceHandler extends AbstractHandler
SampleIdentifier sampleIdentifier =
new SampleIdentifier(groupIdentifier, parameterName);
SamplePE samplePE = openbisService.tryGetSampleWithExperiment(sampleIdentifier);
- if (samplePE == null)
+ String permID;
+ if (samplePE != null)
{
- samplePE =
- openbisService.tryToGetSampleWithProperty("MZXML_FILENAME",
- groupIdentifier, parameterName);
- if (samplePE == null)
+ permID = samplePE.getPermId();
+ } else
+ {
+ List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample> list =
+ openbisService
+ .listSamplesByCriteria(new ListSamplesByPropertyCriteria(
+ MZXML_FILENAME, parameterName, groupIdentifier
+ .getGroupCode(), null));
+ if (list == null || list.size() == 0)
+ {
+ throw new UserFailureException("Protein '" + proteinName
+ + "' has an abundance value for an unidentified samples: "
+ + parameterName);
+ }
+ if (list.size() > 1)
{
throw new UserFailureException("Protein '" + proteinName
- + "' has an abundance value for a non-existing sample: " + sampleIdentifier);
+ + "' has an abundance value for which " + list.size()
+ + " samples are found: " + parameterName);
}
+ permID = list.get(0).getPermId();
}
- sample = getOrCreateSample(experiment, samplePE.getPermId());
+ sample = getOrCreateSample(experiment, permID);
samples.put(parameterName, sample);
}
return sample;
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
index a42b6b4b6f5..c53c2590e38 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetUploaderTest.java
@@ -23,6 +23,8 @@ import java.util.Arrays;
import java.util.Collections;
import java.util.List;
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
import org.jmock.Expectations;
import org.jmock.Mockery;
import org.testng.AssertJUnit;
@@ -57,6 +59,7 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Sequence;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -297,17 +300,31 @@ public class ResultDataSetUploaderTest extends AssertJUnit
p1.getParameters().add(createAbundance(CELL_LYSATE1, 2.5));
p1.getParameters().add(new Parameter());
final GroupIdentifier groupIdentifier = new GroupIdentifier(DB_INSTANCE, GROUP_CODE);
+ String upperCaseParameterName = CELL_LYSATE1.toUpperCase();
final SampleIdentifier sampleIdentifier =
- new SampleIdentifier(groupIdentifier, CELL_LYSATE1
- .toUpperCase());
+ new SampleIdentifier(groupIdentifier, upperCaseParameterName);
+ final ListSamplesByPropertyCriteria criteria =
+ new ListSamplesByPropertyCriteria(AbundanceHandler.MZXML_FILENAME,
+ upperCaseParameterName, GROUP_CODE, null);
context.checking(new Expectations()
{
{
one(service).tryGetSampleWithExperiment(sampleIdentifier);
will(returnValue(null));
-
- one(service).tryToGetSampleWithProperty("MZXML_FILENAME", groupIdentifier, CELL_LYSATE1
- .toUpperCase());
+
+ one(service).listSamplesByCriteria(
+ with(new BaseMatcher<ListSamplesByPropertyCriteria>()
+ {
+ public boolean matches(Object item)
+ {
+ return criteria.toString().equals(item.toString());
+ }
+
+ public void describeTo(Description description)
+ {
+ description.appendValue(criteria);
+ }
+ }));
}
});
p1.setPeptides(Collections.<Peptide> emptyList());
@@ -321,8 +338,8 @@ public class ResultDataSetUploaderTest extends AssertJUnit
} catch (UserFailureException ex)
{
AssertionUtil.assertContains("Protein '" + PROTEIN_NAME1
- + "' has an abundance value for a non-existing sample: " + sampleIdentifier, ex
- .getMessage());
+ + "' has an abundance value for an unidentified samples: "
+ + upperCaseParameterName, ex.getMessage());
}
context.assertIsSatisfied();
--
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