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 d2e243a164a0a4353af6d9de8f9f033fc8997cb0..95b77ef86f66eff04726a3742966f52848591f73 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
@@ -32,6 +32,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
/**
+ * Handler of {@link Parameter} objects of type 'abundance'.
+ *
* @author Franz-Josef Elmer
*/
class AbundanceHandler extends AbstractHandler
@@ -96,7 +98,9 @@ class AbundanceHandler extends AbstractHandler
sampleOrError.error = "an unidentified sample: " + parameterName;
} else if (list.size() > 1)
{
- sampleOrError.error = list.size() + " samples are found: " + parameterName;
+ sampleOrError.error =
+ "a not uniquely specified sample (" + list.size()
+ + " samples are found): " + parameterName;
} else
{
sampleOrError.sample = getOrCreateSample(experiment, list.get(0).getPermId());
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
new file mode 100644
index 0000000000000000000000000000000000000000..3a97d8de87c1381690bf3e9054d4c3ef3eb7bc1a
--- /dev/null
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandlerTest.java
@@ -0,0 +1,279 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.AssertJUnit;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+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.phosphonetx.dto.Experiment;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.Parameter;
+import ch.systemsx.cisd.openbis.generic.shared.basic.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;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class AbundanceHandlerTest extends AssertJUnit
+{
+ private static final GroupIdentifier GROUP_IDENTIFIER = new GroupIdentifier("MY-DB", "G1");
+ 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.toUpperCase());
+ 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
+ .toUpperCase(), GROUP_IDENTIFIER.getGroupCode(), null);
+
+ private Mockery context;
+
+ private IProtDAO dao;
+
+ private IEncapsulatedOpenBISService service;
+
+ private Experiment experiment;
+
+ private AbundanceHandler handler;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ context = new Mockery();
+ dao = context.mock(IProtDAO.class);
+ service = context.mock(IEncapsulatedOpenBISService.class);
+ experiment = new Experiment();
+ experiment.setPermID(EXPERIMENT_PERM_ID);
+ experiment.setId(EXPERIMENT_ID);
+ handler = new AbundanceHandler(service, dao, GROUP_IDENTIFIER, experiment);
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one do not known which test failed.
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testAddAbundanceValueWhichIsNotANumber()
+ {
+ prepareCreateSampleIdentifiedByCode();
+
+ try
+ {
+ handler.addAbundancesToDatabase(createParameter("blabla"), PROTEIN_ID, PROTEIN_NAME);
+ fail("UserFailureException expected");
+ } catch (UserFailureException e)
+ {
+ assertEquals("Abundance of sample '" + PARAMETER_NAME + "' of protein '" + PROTEIN_NAME
+ + "' is not a number: blabla", e.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testAddTwoAbundanceValuesForASampleIdentifiedByCode()
+ {
+ prepareCreateSampleIdentifiedByCode();
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, ABUNDANCE);
+ one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, 1.5);
+ }
+ });
+
+ handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID, PROTEIN_NAME);
+ handler.addAbundancesToDatabase(createParameter("1.5"), PROTEIN_ID, PROTEIN_NAME);
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testAddTwoAbundanceValuesForASampleIdentifiedByPropertyButNoSampleFound()
+ {
+ prepareCreateSampleIdentifiedByProperty(Arrays.<Sample>asList());
+
+ try
+ {
+ 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.toUpperCase(), e.getMessage());
+ }
+
+ try
+ {
+ 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.toUpperCase(), e.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testAddAbundanceValuesForASampleIdentifiedByPropertyButTwoSamplesFound()
+ {
+ Sample sample = new Sample();
+ sample.setPermId(SAMPLE_PERM_ID);
+ prepareCreateSampleIdentifiedByProperty(Arrays.<Sample>asList(sample, sample));
+
+ try
+ {
+ handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID, PROTEIN_NAME);
+ fail("UserFailureException expected");
+ } catch (UserFailureException e)
+ {
+ assertEquals("Protein '" + PROTEIN_NAME
+ + "' has an abundance value for a not uniquely specified sample "
+ + "(2 samples are found): " + PARAMETER_NAME.toUpperCase(), e.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testAddAbundanceValuesForASampleIdentifiedByProperty()
+ {
+ Sample sample = new Sample();
+ sample.setPermId(SAMPLE_PERM_ID);
+ prepareCreateSampleIdentifiedByProperty(Arrays.<Sample>asList(sample));
+ prepareCreateSample();
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).createAbundance(PROTEIN_ID, SAMPLE_ID, ABUNDANCE);
+ }
+ });
+
+ handler.addAbundancesToDatabase(createParameter(PARAMETER_VALUE), PROTEIN_ID, PROTEIN_NAME);
+
+ context.assertIsSatisfied();
+ }
+
+ private Parameter createParameter(String value)
+ {
+ Parameter parameter = new Parameter();
+ parameter.setName(PARAMETER_NAME);
+ parameter.setValue(value);
+ return parameter;
+ }
+
+ private void prepareCreateSampleIdentifiedByCode()
+ {
+ SamplePE samplePE = new SamplePE();
+ samplePE.setPermId(SAMPLE_PERM_ID);
+ prepareGetSample(samplePE);
+ prepareCreateSample();
+ }
+
+ private void prepareCreateSample()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dao).tryToGetSampleByPermID(SAMPLE_PERM_ID);
+ will(returnValue(null));
+
+ one(dao).createSample(EXPERIMENT_ID, SAMPLE_PERM_ID);
+ will(returnValue(SAMPLE_ID));
+ }
+ });
+ }
+
+ private void prepareCreateSampleIdentifiedByProperty(final List<Sample> samples)
+ {
+ prepareGetSample(null);
+ context.checking(new Expectations()
+ {
+ {
+ 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);
+
+ }
+ }));
+ will(returnValue(samples));
+ }
+ });
+ }
+
+ private void prepareGetSample(final SamplePE sample)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetSampleWithExperiment(
+ with(new BaseMatcher<SampleIdentifier>()
+ {
+
+ public boolean matches(Object item)
+ {
+ return SAMPLE_IDENTIFER.toString().equals(item.toString());
+ }
+
+ public void describeTo(Description description)
+ {
+ description.appendValue(SAMPLE_IDENTIFER);
+
+ }
+ }));
+ will(returnValue(sample));
+ }
+ });
+ }
+}