From f8758ae4aa8ccde56eb018653c51402cab2a006a Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 18 Oct 2011 07:01:57 +0000
Subject: [PATCH] bug in ProteinResultDataSetParentLinkingTask fixed.
SVN: 23339
---
...DataSetInfoExtractorForProteinResults.java | 62 ++++++++-----
...ProteinResultDataSetParentLinkingTask.java | 20 +---
.../phosphonetx/dto/ParentDataSetCodes.java | 51 ++++++++++
...SetInfoExtractorForProteinResultsTest.java | 92 +++++++++++++++++++
...einResultDataSetParentLinkingTaskTest.java | 35 ++++---
5 files changed, 205 insertions(+), 55 deletions(-)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ParentDataSetCodes.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
index b68ab4c4b2b..994cb92c143 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResults.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.io.File;
import java.util.ArrayList;
-import java.util.Arrays;
import java.util.List;
import java.util.Properties;
@@ -31,6 +30,7 @@ import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ParentDataSetCodes;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
@@ -96,14 +96,20 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
Properties properties =
loadSearchProperties(new File(incomingDataSetPath, experimentPropertiesFileName));
experiment.setProperties(Util.getAndCheckProperties(properties, experimentType));
- service.registerExperiment(experiment);
DataSetInformation info = new DataSetInformation();
info.setExperimentIdentifier(experimentIdentifier);
String parentDataSetCodesOrNull = getProperty(properties, PARENT_DATA_SET_CODES);
String baseExperimentIdentifier = getProperty(properties, EXPERIMENT_IDENTIFIER_KEY);
- List<String> parentDataSetCodes =
+ ParentDataSetCodes parentDataSetCodes =
getParentDataSetCodes(parentDataSetCodesOrNull, baseExperimentIdentifier, service);
- info.setParentDataSetCodes(parentDataSetCodes);
+ if (parentDataSetCodes.getErrorMessage() == null)
+ {
+ info.setParentDataSetCodes(parentDataSetCodes.getDataSetCodes());
+ } else
+ {
+ throw new UserFailureException(parentDataSetCodes.getErrorMessage());
+ }
+ service.registerExperiment(experiment);
return info;
}
@@ -111,35 +117,45 @@ public class DataSetInfoExtractorForProteinResults extends AbstractDataSetInfoEx
* Returns data set codes either from the first argument or if <code>null</code> from
* the data sets of the specified experiment.
*/
- static List<String> getParentDataSetCodes(String parentDataSetCodesOrNull,
+ static ParentDataSetCodes getParentDataSetCodes(String parentDataSetCodesOrNull,
String baseExperimentIdentifier, IEncapsulatedOpenBISService service)
{
- List<String> parentDataSetCodes = new ArrayList<String>();
+ List<ExternalData> parentDataSets = new ArrayList<ExternalData>();
+ StringBuilder builder = new StringBuilder();
if (parentDataSetCodesOrNull != null)
{
- parentDataSetCodes = Arrays.asList(StringUtils.split(parentDataSetCodesOrNull, ", "));
- } else
- {
- if (baseExperimentIdentifier != null)
+ for (String code : StringUtils.split(parentDataSetCodesOrNull, ", "))
{
- ExperimentIdentifier identifier =
- new ExperimentIdentifierFactory(baseExperimentIdentifier)
- .createIdentifier();
- Experiment baseExperiment = service.tryToGetExperiment(identifier);
- if (baseExperiment == null)
+ ExternalData dataSet = service.tryGetDataSet(code);
+ if (dataSet != null)
{
- throw new UserFailureException("Property " + EXPERIMENT_IDENTIFIER_KEY
- + " specifies an unknown experiment: " + baseExperimentIdentifier);
- }
- List<ExternalData> dataSets =
- service.listDataSetsByExperimentID(baseExperiment.getId());
- for (ExternalData dataSet : dataSets)
+ parentDataSets.add(dataSet);
+ } else
{
- parentDataSetCodes.add(dataSet.getCode());
+ builder.append(builder.length() == 0 ? "Unknown data sets: " : ", ");
+ builder.append(code);
}
}
+ } else if (baseExperimentIdentifier != null)
+ {
+ ExperimentIdentifier identifier =
+ new ExperimentIdentifierFactory(baseExperimentIdentifier).createIdentifier();
+ Experiment baseExperiment = service.tryToGetExperiment(identifier);
+ if (baseExperiment != null)
+ {
+ parentDataSets.addAll(service.listDataSetsByExperimentID(baseExperiment.getId()));
+ } else
+ {
+ builder.append("Unkown experiment ").append(baseExperimentIdentifier);
+ }
+ }
+ List<String> parentDataSetCodes = new ArrayList<String>();
+ for (ExternalData dataSet : parentDataSets)
+ {
+ parentDataSetCodes.add(dataSet.getCode());
}
- return parentDataSetCodes;
+ String errorMessage = builder.length() > 0 ? builder.toString() : null;
+ return new ParentDataSetCodes(parentDataSetCodes, errorMessage);
}
private String getProperty(Properties properties, String key)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTask.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTask.java
index 1c33685a076..b5e2450fdd9 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTask.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTask.java
@@ -22,7 +22,6 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;
-import java.util.regex.Pattern;
import org.apache.log4j.Logger;
@@ -54,8 +53,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
*/
public class ProteinResultDataSetParentLinkingTask implements IMaintenanceTask
{
- private static final Pattern DATA_SET_CODE_PATTERN = Pattern.compile("\\d{17}-\\d+");
-
private static final String PARENT_DATA_SET_CODES_KEY =
DataSetInfoExtractorForProteinResults.PARENT_DATA_SET_CODES.toUpperCase();
@@ -99,8 +96,9 @@ public class ProteinResultDataSetParentLinkingTask implements IMaintenanceTask
String parentDataSetCodes =
tryGetProperty(propertiesMap, PARENT_DATA_SET_CODES_KEY);
List<String> codes =
- filter(DataSetInfoExtractorForProteinResults.getParentDataSetCodes(
- parentDataSetCodes, baseExperimentIdentifier, service));
+ DataSetInfoExtractorForProteinResults.getParentDataSetCodes(
+ parentDataSetCodes, baseExperimentIdentifier, service)
+ .getDataSetCodes();
if (codes.isEmpty())
{
continue;
@@ -160,16 +158,4 @@ public class ProteinResultDataSetParentLinkingTask implements IMaintenanceTask
return property == null ? null : property.tryGetAsString();
}
- private List<String> filter(List<String> codes)
- {
- List<String> result = new ArrayList<String>();
- for (String code : codes)
- {
- if (DATA_SET_CODE_PATTERN.matcher(code).matches())
- {
- result.add(code);
- }
- }
- return result;
- }
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ParentDataSetCodes.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ParentDataSetCodes.java
new file mode 100644
index 00000000000..3305a4f05a9
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/dto/ParentDataSetCodes.java
@@ -0,0 +1,51 @@
+/*
+ * Copyright 2011 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.dto;
+
+import java.util.List;
+
+/**
+ * Data transfer object which contains a list of data set codes and an optional
+ * error message.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ParentDataSetCodes
+{
+ private final List<String> dataSetCodes;
+
+ private final String errorMessage;
+
+ public ParentDataSetCodes(List<String> dataSetCodes, String errorMessage)
+ {
+ super();
+ this.dataSetCodes = dataSetCodes;
+ this.errorMessage = errorMessage;
+ }
+
+ public List<String> getDataSetCodes()
+ {
+ return dataSetCodes;
+ }
+
+ public String getErrorMessage()
+ {
+ return errorMessage;
+ }
+
+
+}
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
index 0ffa9aae8dc..e9f10fe211f 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/DataSetInfoExtractorForProteinResultsTest.java
@@ -96,6 +96,10 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
String experimentType = "MY_EXPERIMENT";
properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
+ prepareGetDataSet("1");
+ prepareGetDataSet("2");
+ prepareGetDataSet("3");
+ prepareGetDataSet("4");
prepare(experimentType);
context.checking(new Expectations()
{
@@ -120,6 +124,10 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
DataSetInfoExtractorForProteinResults.DEFAULT_EXPERIMENT_PROPERTIES_FILE_NAME),
"answer=42\nblabla=blub\n" + PARENT_DATA_SET_CODES + "=1 2 3 4\n");
prepare(DEFAULT_EXPERIMENT_TYPE_CODE);
+ prepareGetDataSet("1");
+ prepareGetDataSet("2");
+ prepareGetDataSet("3");
+ prepareGetDataSet("4");
context.checking(new Expectations()
{
@@ -214,6 +222,70 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
context.assertIsSatisfied();
}
+ @Test
+ public void testWithUnkownBaseExperiment()
+ {
+ String propertiesFile = "my.properties";
+ FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ + EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n");
+ Properties properties = new Properties();
+ String experimentType = "MY_EXPERIMENT";
+ properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
+ properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
+ prepare(experimentType);
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryToGetExperiment(
+ new ExperimentIdentifier(new ProjectIdentifier("TEST", "PROJECT"),
+ "EXP1"));
+ will(returnValue(null));
+
+ }
+ });
+
+ IDataSetInfoExtractor extractor = createExtractor(properties);
+
+ try
+ {
+ extractor.getDataSetInformation(dataSet, service);
+ fail("UserFailureException expected.");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Unkown experiment /TEST/PROJECT/EXP1", ex.getMessage());
+ }
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testWithUnkownParentDataSets()
+ {
+ String propertiesFile = "my.properties";
+ FileUtilities.writeToFile(new File(dataSet, propertiesFile), "answer=42\nblabla=blub\n"
+ + EXPERIMENT_IDENTIFIER_KEY + "= /TEST/PROJECT/EXP1\n" + PARENT_DATA_SET_CODES_KEY
+ + " = ds1 ds2, ds3");
+ Properties properties = new Properties();
+ String experimentType = "MY_EXPERIMENT";
+ properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
+ properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
+ prepare(experimentType);
+ prepareGetDataSet("ds1");
+ prepareGetDataSet("ds2", null);
+ prepareGetDataSet("ds3", null);
+
+ IDataSetInfoExtractor extractor = createExtractor(properties);
+
+ try
+ {
+ extractor.getDataSetInformation(dataSet, service);
+ fail("UserFailureException expected.");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Unknown data sets: ds2, ds3", ex.getMessage());
+ }
+ context.assertIsSatisfied();
+ }
+
@Test
public void testWithParentDataSetsSeparatedBySpaces()
{
@@ -226,6 +298,8 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
prepare(experimentType);
+ prepareGetDataSet("ds1");
+ prepareGetDataSet("ds2");
context.checking(new Expectations()
{
{
@@ -253,6 +327,8 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
properties.setProperty(EXPERIMENT_TYPE_CODE_KEY, experimentType);
properties.setProperty(EXPERIMENT_PROPERTIES_FILE_NAME_KEY, propertiesFile);
prepare(experimentType);
+ prepareGetDataSet("ds1");
+ prepareGetDataSet("ds2");
context.checking(new Expectations()
{
{
@@ -290,6 +366,22 @@ public class DataSetInfoExtractorForProteinResultsTest extends AbstractFileSyste
});
}
+ private void prepareGetDataSet(final String dataSetCode)
+ {
+ prepareGetDataSet(dataSetCode, new DataSetBuilder().code(dataSetCode).getDataSet());
+ }
+
+ private void prepareGetDataSet(final String dataSetCode, final ExternalData data)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetDataSet(dataSetCode);
+ will(returnValue(data));
+ }
+ });
+ }
+
private IDataSetInfoExtractor createExtractor(Properties properties)
{
return new DataSetInfoExtractorForProteinResults(properties, service);
diff --git a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTaskTest.java b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTaskTest.java
index 53aff1de1eb..616c2309f51 100644
--- a/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTaskTest.java
+++ b/rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProteinResultDataSetParentLinkingTaskTest.java
@@ -85,25 +85,21 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
.getExperiment();
final Experiment e2 =
new ExperimentBuilder().id(2).identifier("/A/P2/E2")
- .property(PARENT_DATA_SET_CODES_KEY, "non-sense").getExperiment();
+ .property(PARENT_DATA_SET_CODES_KEY, "non-sense2").getExperiment();
final Experiment e3 =
- new ExperimentBuilder()
- .id(3)
- .identifier("/A/P2/E3")
- .property(PARENT_DATA_SET_CODES_KEY,
- "20100930111833087-297733, 20100511163311581-25265")
- .getExperiment();
+ new ExperimentBuilder().id(3).identifier("/A/P2/E3")
+ .property(PARENT_DATA_SET_CODES_KEY, "ds1, ds3").getExperiment();
final Experiment e4 =
new ExperimentBuilder().id(4).identifier("/S/P1/E4")
.property(BASE_EXPERIMENT_KEY, "/S/P1/E1").getExperiment();
final DataSet ds1 =
- new DataSetBuilder(1).code("20100930111811581-25265").fileFormat("A")
+ new DataSetBuilder(1).code("ds1").fileFormat("A")
.experiment(e1).modificationDate(new Date(11)).getDataSet();
final DataSet ds2 =
- new DataSetBuilder(2).code("20100930111811087-29765").fileFormat("B")
+ new DataSetBuilder(2).code("ds2").fileFormat("B")
.experiment(e4).modificationDate(new Date(22)).getDataSet();
final DataSet ds3 =
- new DataSetBuilder(3).code("20100530111833087-297733").fileFormat("C")
+ new DataSetBuilder(3).code("ds3").fileFormat("C")
.experiment(e3).modificationDate(new Date(33)).property("ALPHA", "3.1")
.getDataSet();
final RecordingMatcher<AtomicEntityOperationDetails> operationRecorder =
@@ -122,7 +118,16 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
one(service).tryToGetExperiment(ExperimentIdentifierFactory.parse("/S/P1/E1"));
will(returnValue(e1));
-
+
+ one(service).tryGetDataSet("non-sense2");
+ will(returnValue(null));
+
+ one(service).tryGetDataSet("ds1");
+ will(returnValue(ds1));
+
+ one(service).tryGetDataSet("ds3");
+ will(returnValue(ds3));
+
one(service).listDataSetsByExperimentID(e1.getId());
will(returnValue(Arrays.asList(ds1)));
@@ -139,10 +144,10 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
task.execute();
assertEquals("INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
- + "Parent data set links of data set 20100930111811087-29765 "
+ + "Parent data set links of data set ds2 "
+ "from experiment /S/P1/E4 will be updated.\n"
+ "INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
- + "Parent data set links of data set 20100530111833087-297733 "
+ + "Parent data set links of data set ds3 "
+ "from experiment /A/P2/E3 will be updated.\n"
+ "INFO OPERATION.ProteinResultDataSetParentLinkingTask - "
+ "Parent data set links for 2 data sets have been updated.",
@@ -155,7 +160,7 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
assertEquals("[]", dataSetUpdates.get(0).getProperties().toString());
assertEquals(e4.getIdentifier(), dataSetUpdates.get(0).getExperimentIdentifierOrNull()
.toString());
- assertEquals("[20100930111811581-25265]",
+ assertEquals("[ds1]",
Arrays.asList(dataSetUpdates.get(0).getModifiedParentDatasetCodesOrNull())
.toString());
assertEquals(3L, dataSetUpdates.get(1).getDatasetId().getId().longValue());
@@ -164,7 +169,7 @@ public class ProteinResultDataSetParentLinkingTaskTest extends AssertJUnit
assertEquals("[ALPHA: 3.1]", dataSetUpdates.get(1).getProperties().toString());
assertEquals(e3.getIdentifier(), dataSetUpdates.get(1).getExperimentIdentifierOrNull()
.toString());
- assertEquals("[20100930111833087-297733, 20100511163311581-25265]",
+ assertEquals("[ds1, ds3]",
Arrays.asList(dataSetUpdates.get(1).getModifiedParentDatasetCodesOrNull())
.toString());
assertEquals(2, dataSetUpdates.size());
--
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