diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java
index a6ec738733d517dd5151a5fb9d05a842de27aebe..fbc0955110fff79e2e6f5a37aec18bdecae0a093 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbstractSampleHandler.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
@@ -57,31 +58,49 @@ abstract class AbstractSampleHandler extends AbstractHandler
private final Map<String, SampleOrError> samplesOrErrors = new HashMap<String, SampleOrError>();
+ private final String delimiter;
+
+ private final boolean restrictedSampleResolving;
+
AbstractSampleHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
- ExperimentIdentifier experimentIdentifier, Experiment experiment)
+ ExperimentIdentifier experimentIdentifier, Experiment experiment, String delimiter,
+ boolean restrictedSampleResolving)
{
super(dao);
this.openbisService = openbisService;
this.experimentIdentifier = experimentIdentifier;
this.experiment = experiment;
+ this.delimiter = delimiter;
+ this.restrictedSampleResolving = restrictedSampleResolving;
String databaseInstanceCode = experimentIdentifier.getDatabaseInstanceCode();
space = new SpaceIdentifier(databaseInstanceCode, CommonConstants.MS_DATA_SPACE);
}
- protected SampleOrError getOrCreateSampleOrError(String sampleName)
+ protected SampleOrError getOrCreateSampleOrError(String sampleNameAndMore)
{
+ int indexOfDelimiter = sampleNameAndMore.indexOf(delimiter);
+ String sampleName;
+ if (indexOfDelimiter < 0)
+ {
+ sampleName = sampleNameAndMore;
+ } else
+ {
+ sampleName = sampleNameAndMore.substring(0, indexOfDelimiter);
+ }
SampleOrError sampleOrError = samplesOrErrors.get(sampleName);
if (sampleOrError == null)
{
// first we look for a sample in space MS_DATA
- SampleIdentifier sampleIdentifier = new SampleIdentifier(space, sampleName);
+ SampleIdentifier sampleIdentifier =
+ SampleIdentifierFactory.parse(sampleName, "/" + CommonConstants.MS_DATA_SPACE);
+ String sampleCode = sampleIdentifier.getSampleCode();
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
openbisService.tryGetSampleWithExperiment(sampleIdentifier);
sampleOrError = new SampleOrError();
if (sample != null)
{
sampleOrError.sample = getOrCreateSample(sample.getPermId());
- } else
+ } else if (restrictedSampleResolving == false)
{
// second we look for a sample in same space as search experiment with
// a property specified by 'sampleName'
@@ -102,10 +121,13 @@ abstract class AbstractSampleHandler extends AbstractHandler
sample = list.get(0);
sampleOrError.sample = getOrCreateSample(sample.getPermId());
}
+ } else
+ {
+ sampleOrError.error = "Couldn't resolve sample: " + sampleIdentifier;
}
if (sample != null)
{
- handleSample(sampleName, sample);
+ handleSample(sampleCode, sample);
}
samplesOrErrors.put(sampleName, sampleOrError);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java
index 1a6789b2ffdcc363d38df1a9fc93ece2c8f4def9..392589c0ca2412b6a246e7831ec97a04540ddba9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandler.java
@@ -37,9 +37,11 @@ class AbundanceHandler extends AbstractSampleHandler
private final SampleType sampleType;
AbundanceHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
- ExperimentIdentifier experimentIdentifier, Experiment experiment)
+ ExperimentIdentifier experimentIdentifier, Experiment experiment, String delimiter,
+ boolean restrictedSampleResolving)
{
- super(openbisService, dao, experimentIdentifier, experiment);
+ super(openbisService, dao, experimentIdentifier, experiment, delimiter,
+ restrictedSampleResolving);
sampleType = new SampleType();
sampleType.setCode(Constants.SEARCH_SAMPLE_TYPE);
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java
index 537565ff6afde633da0c950898f19ccd4fe74017..fdf2c118531586f1b799421453e64c7c86d8c7f2 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ModificationFractionHandler.java
@@ -32,9 +32,11 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
class ModificationFractionHandler extends AbstractSampleHandler
{
public ModificationFractionHandler(IEncapsulatedOpenBISService openbisService, IProtDAO dao,
- ExperimentIdentifier experimentIdentifier, Experiment experiment)
+ ExperimentIdentifier experimentIdentifier, Experiment experiment, String delimiter,
+ boolean restrictedSampleResolving)
{
- super(openbisService, dao, experimentIdentifier, experiment);
+ super(openbisService, dao, experimentIdentifier, experiment, delimiter,
+ restrictedSampleResolving);
}
@Override
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
index 6aaac2c90f209d18876ccfa50a055ea575e30f67..5d169ddbd01fae39056a2b5008807b5bcf150730 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploader.java
@@ -44,6 +44,10 @@ public class ProtXMLUploader implements IDataSetUploader
private static final String VALIDATING_XML = "validating-xml";
private static final String ASSUMING_EXTENDED_PROT_XML = "assuming-extended-prot-xml";
+
+ private static final String MS_INJECTION_SAMPLE_DELIMITER = "delimiter_for_sample_resolving";
+
+ private static final String RESTRICTED_SAMPLE_RESOLVING = "restricted_sample_resolving";
private static final String DATABASE_ENGINE = "database.engine";
@@ -80,6 +84,10 @@ public class ProtXMLUploader implements IDataSetUploader
private final boolean assumingExtendedProtXML;
+ private final String msInjectionSampleDelimiter;
+
+ private final boolean restrictedSampleResolving;
+
private ResultDataSetUploader currentResultDataSetUploader;
public ProtXMLUploader(Properties properties, IEncapsulatedOpenBISService openbisService)
@@ -87,6 +95,8 @@ public class ProtXMLUploader implements IDataSetUploader
dataSource = createDataSource(properties);
this.openbisService = openbisService;
assumingExtendedProtXML = PropertyUtils.getBoolean(properties, ASSUMING_EXTENDED_PROT_XML, false);
+ msInjectionSampleDelimiter = properties.getProperty(MS_INJECTION_SAMPLE_DELIMITER, "~");
+ restrictedSampleResolving = PropertyUtils.getBoolean(properties, RESTRICTED_SAMPLE_RESOLVING, true);
loader = new ProtXMLLoader(PropertyUtils.getBoolean(properties, VALIDATING_XML, false));
}
@@ -152,7 +162,8 @@ public class ProtXMLUploader implements IDataSetUploader
{
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
- return new ResultDataSetUploader(connection, openbisService, assumingExtendedProtXML);
+ return new ResultDataSetUploader(connection, openbisService, assumingExtendedProtXML,
+ msInjectionSampleDelimiter, restrictedSampleResolving);
}
private File getProtXMLFile(File dataSet)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploader.java
index 78d2cd6eec011c71462f572c4485a2a5ec32aaec..c12c66e204b8629c182aed92c38626bfb4fd91a8 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploader.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploader.java
@@ -75,18 +75,28 @@ class ResultDataSetUploader extends AbstractHandler
private final boolean assumingExtendedProtXML;
- ResultDataSetUploader(Connection connection, IEncapsulatedOpenBISService openbisService, boolean assumingExtendedProtXML)
+ private final String delimiter;
+
+ private final boolean restrictedSampleResolving;
+
+ ResultDataSetUploader(Connection connection, IEncapsulatedOpenBISService openbisService,
+ boolean assumingExtendedProtXML, String delimiter,
+ boolean restrictedSampleResolving)
{
- this(QueryTool.getQuery(connection, IProtDAO.class), connection, openbisService, assumingExtendedProtXML);
+ this(QueryTool.getQuery(connection, IProtDAO.class), connection, openbisService,
+ assumingExtendedProtXML, delimiter, restrictedSampleResolving);
}
ResultDataSetUploader(IProtDAO dao, Connection connection,
- IEncapsulatedOpenBISService openbisService, boolean assumingExtendedProtXML)
+ IEncapsulatedOpenBISService openbisService, boolean assumingExtendedProtXML,
+ String delimiter, boolean restrictedSampleResolving)
{
super(dao);
this.connection = connection;
this.openbisService = openbisService;
this.assumingExtendedProtXML = assumingExtendedProtXML;
+ this.delimiter = delimiter;
+ this.restrictedSampleResolving = restrictedSampleResolving;
this.errorMessages = new StringBuffer();
}
@@ -207,10 +217,11 @@ class ResultDataSetUploader extends AbstractHandler
long dataSetID = dataSet.getId();
Long databaseID = dataSet.getDatabaseID();
AbundanceHandler abundanceHandler =
- new AbundanceHandler(openbisService, dao, experimentIdentifier, experiment);
+ new AbundanceHandler(openbisService, dao, experimentIdentifier, experiment,
+ delimiter, restrictedSampleResolving);
ModificationFractionHandler modificationFractionHandler =
new ModificationFractionHandler(openbisService, dao, experimentIdentifier,
- experiment);
+ experiment, delimiter, restrictedSampleResolving);
ProbabilityToFDRCalculator calculator = createProbabilityToFDRMapping(dataSetID, summary);
List<ProteinGroup> proteinGroups = summary.getProteinGroups();
for (ProteinGroup proteinGroup : proteinGroups)
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandlerTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandlerTest.java
index 9930301d650ad4cba9c7da0d08ebcdb95f47db64..b9aa45dd89189b6646c2f49611b7530833c9c22d 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandlerTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/AbundanceHandlerTest.java
@@ -31,8 +31,6 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.AbundanceHandler;
-import ch.systemsx.cisd.openbis.etlserver.proteomics.IProtDAO;
import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Experiment;
import ch.systemsx.cisd.openbis.etlserver.proteomics.dto.Parameter;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
@@ -42,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.proteomics.shared.basic.CommonConstants;
@@ -107,7 +106,7 @@ public class AbundanceHandlerTest extends AssertJUnit
experiment = new Experiment();
experiment.setPermID(EXPERIMENT_PERM_ID);
experiment.setId(EXPERIMENT_ID);
- handler = new AbundanceHandler(service, dao, EXPERIMENT_IDENTIFIER, experiment);
+ handler = new AbundanceHandler(service, dao, EXPERIMENT_IDENTIFIER, experiment, "+", false);
}
@AfterMethod
@@ -153,6 +152,27 @@ public class AbundanceHandlerTest extends AssertJUnit
context.assertIsSatisfied();
}
+
+ @Test
+ public void testAddTwoAbundanceValuesForASampleIdentifiedByCodeAndSpace()
+ {
+ String sampleIdentifier = "/" + SPACE_CODE + "/" + PARAMETER_NAME;
+ prepareCreateSampleIdentifiedByIdentifier(sampleIdentifier);
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, ABUNDANCE);
+ one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, 1.5);
+ }
+ });
+
+ handler.addAbundancesToDatabase(createParameter(sampleIdentifier, PARAMETER_VALUE),
+ PROTEIN_ID, PROTEIN_NAME);
+ handler.addAbundancesToDatabase(createParameter(sampleIdentifier, "1.5"), PROTEIN_ID,
+ PROTEIN_NAME);
+
+ context.assertIsSatisfied();
+ }
@Test
public void testAddTwoAbundanceValuesForASampleIdentifiedByPropertyButNoSampleFound()
@@ -248,25 +268,40 @@ public class AbundanceHandlerTest extends AssertJUnit
}
});
- handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID, PROTEIN_NAME);
+ handler.addAbundancesToDatabase(
+ createParameter(PARAMETER_NAME + "+blabla.xml", PARAMETER_VALUE), PROTEIN_ID,
+ PROTEIN_NAME);
context.assertIsSatisfied();
}
private Parameter createParameter(String value)
+ {
+ return createParameter(PARAMETER_NAME, value);
+ }
+
+ Parameter createParameter(String parameterName, String value)
{
Parameter parameter = new Parameter();
- parameter.setName(PARAMETER_NAME);
+ parameter.setName(parameterName);
parameter.setValue(value);
return parameter;
}
private void prepareCreateSampleIdentifiedByCode()
+ {
+ prepareCreateSampleIdentifiedByIdentifier(PARAMETER_NAME);
+ }
+
+ void prepareCreateSampleIdentifiedByIdentifier(final String sampleIdentifier)
{
Sample sample = new Sample();
sample.setPermId(SAMPLE_PERM_ID);
- sample.setIdentifier(PARAMETER_NAME);
- prepareGetSample(sample);
+ sample.setIdentifier(sampleIdentifier);
+ prepareGetSample(
+ SampleIdentifierFactory
+ .parse(sampleIdentifier, "/" + CommonConstants.MS_DATA_SPACE).toString(),
+ sample);
prepareCreateSample();
context.checking(new Expectations()
{
@@ -283,7 +318,7 @@ public class AbundanceHandlerTest extends AssertJUnit
+ EXPERIMENT_CODE, newSample.getIdentifier());
assertEquals(EXPERIMENT_IDENTIFIER.toString(),
newSample.getExperimentIdentifier());
- assertEquals(PARAMETER_NAME, newSample.getParentIdentifier());
+ assertEquals(sampleIdentifier, newSample.getParentIdentifier());
return true;
}
return false;
@@ -314,7 +349,7 @@ public class AbundanceHandlerTest extends AssertJUnit
private void prepareCreateSampleIdentifiedByProperty(final List<Sample> samples)
{
- prepareGetSample(null);
+ prepareGetSample(SAMPLE_IDENTIFER.toString(), null);
context.checking(new Expectations()
{
{
@@ -337,7 +372,7 @@ public class AbundanceHandlerTest extends AssertJUnit
});
}
- private void prepareGetSample(final Sample sample)
+ private void prepareGetSample(final String expectedSampleIdentifier, final Sample sample)
{
context.checking(new Expectations()
{
@@ -348,12 +383,12 @@ public class AbundanceHandlerTest extends AssertJUnit
public boolean matches(Object item)
{
- return SAMPLE_IDENTIFER.toString().equals(item.toString());
+ return expectedSampleIdentifier.equals(item.toString());
}
public void describeTo(Description description)
{
- description.appendValue(SAMPLE_IDENTIFER);
+ description.appendValue(expectedSampleIdentifier);
}
}));
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
index ae14179b04c7f5499029465271465cf6dde15113..5c4912e98d1a80d73cb770967c2078ab97cd9b44 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ProtXMLUploaderTest.java
@@ -55,7 +55,7 @@ public class ProtXMLUploaderTest extends ProtXMLTestCase
@Override
protected ResultDataSetUploader createUploader()
{
- return new ResultDataSetUploader(null, null, null, true)
+ return new ResultDataSetUploader(null, null, null, true, "+", false)
{
@Override
void upload(DataSetInformation dataSetInfo, ProteinSummary summary)
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploaderTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploaderTest.java
index fe45fe551d8ac9782d3a2e12fb0292f61dd98caf..676dfd9930bd54ad00ac3c8445bba33a330137d1 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploaderTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/proteomics/ResultDataSetUploaderTest.java
@@ -145,7 +145,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
dao = context.mock(IProtDAO.class);
service = context.mock(IEncapsulatedOpenBISService.class);
- uploader = new ResultDataSetUploader(dao, connection, service, true);
+ uploader = new ResultDataSetUploader(dao, connection, service, true, "+", false);
}
@AfterMethod
@@ -310,7 +310,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
p1.setName(PROTEIN_NAME1);
p1.getParameters().add(createAbundance(CELL_LYSATE1, 2.5));
p1.getParameters().add(new Parameter());
- final GroupIdentifier groupIdentifier = new GroupIdentifier(DB_INSTANCE, CommonConstants.MS_DATA_SPACE);
+ final GroupIdentifier groupIdentifier = new GroupIdentifier((String) null, CommonConstants.MS_DATA_SPACE);
final SampleIdentifier sampleIdentifier =
new SampleIdentifier(groupIdentifier, CELL_LYSATE1);
final ListSamplesByPropertyCriteria criteria =
@@ -533,7 +533,7 @@ public class ResultDataSetUploaderTest extends AssertJUnit
{
{
one(service).tryGetSampleWithExperiment(
- new SampleIdentifier(new SpaceIdentifier(DB_INSTANCE,
+ new SampleIdentifier(new SpaceIdentifier((String) null,
CommonConstants.MS_DATA_SPACE), CELL_LYSATE1));
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();