diff --git a/datastore_server/resource/test-data/JythonBasedAggregationServiceReportingPluginTest/script.py b/datastore_server/resource/test-data/JythonBasedAggregationServiceReportingPluginTest/script.py
new file mode 100644
index 0000000000000000000000000000000000000000..5420b4e0c640482320fdc1bf1dc5751633974554
--- /dev/null
+++ b/datastore_server/resource/test-data/JythonBasedAggregationServiceReportingPluginTest/script.py
@@ -0,0 +1,40 @@
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchSubCriteria
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClause
+from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClauseAttribute
+
+EXPERIMENT = "Experiment"
+CODE = "Data Set Code"
+NUMBER_OF_FILES = "Number of Files"
+NUMBER_OF_PROTEINS = "Number of Proteins"
+
+def countFiles(node):
+ sum = 1
+ if node.isDirectory():
+ for child in node.getChildNodes():
+ sum = sum + countFiles(child)
+ return sum
+
+def getNumberOfProteins(dataSetCode):
+ result = queryService.select("protein-db", "select count(*) as count from proteins where data_set = ?{1}", [dataSetCode])
+ return result[0].get("count")
+
+def aggregate(parameters, tableBuilder):
+ experimentCode = parameters.get('experiment-code')
+ searchCriteria = SearchCriteria()
+ subCriteria = SearchCriteria()
+ subCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, experimentCode))
+ searchCriteria.addSubCriteria(SearchSubCriteria.createExperimentCriteria(subCriteria))
+ dataSets = searchService.searchForDataSets(searchCriteria)
+ tableBuilder.addHeader(EXPERIMENT)
+ tableBuilder.addHeader(CODE)
+ tableBuilder.addHeader(NUMBER_OF_FILES)
+ tableBuilder.addHeader(NUMBER_OF_PROTEINS)
+ for dataSet in dataSets:
+ dataSetCode = dataSet.getDataSetCode()
+ content = contentProvider.getContent(dataSetCode)
+ row = tableBuilder.addRow()
+ row.setCell(EXPERIMENT, dataSet.experiment.experimentIdentifier)
+ row.setCell(CODE, dataSetCode)
+ row.setCell(NUMBER_OF_FILES, countFiles(content.rootNode))
+ row.setCell(NUMBER_OF_PROTEINS, getNumberOfProteins(dataSetCode))
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
index f2069906e55115a3b2d8718a710fd2b8961c33cd..17d480069e9e96f8f4dccd0d92790b7232b6e06b 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/PluginScriptRunnerFactory.java
@@ -161,12 +161,12 @@ public class PluginScriptRunnerFactory implements IPluginScriptRunnerFactory
return evaluator;
}
- private static ISearchService createSearchService()
+ protected ISearchService createSearchService()
{
return ServiceProvider.getSearchService();
}
- private static IDataSourceQueryService createDataSourceQueryService()
+ protected IDataSourceQueryService createDataSourceQueryService()
{
return ServiceProvider.getDataSourceQueryService();
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/Utils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/Utils.java
index a41f45632b54457abd5b41d832dfb88cf828c306..3d3f3588b7649dcd9cade9f5c74451783787785a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/Utils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/Utils.java
@@ -18,7 +18,6 @@ package ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython;
import org.apache.log4j.Logger;
-import ch.systemsx.cisd.common.evaluator.EvaluatorException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.utilities.ExceptionUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
@@ -39,16 +38,6 @@ class Utils
ISimpleTableModelBuilderAdaptor builder = SimpleTableModelBuilderAdaptor.create();
tableModelCreator.create(builder);
return (TableModel) builder.getTableModel();
- } catch (EvaluatorException ex)
- {
- if (null != ex.getCause())
- {
- notifyLog.error(createErrorMessage(scriptPath), ex.getCause());
- } else
- {
- notifyLog.error(createErrorMessage(scriptPath), ex);
- }
- throw createUserFailureException(ex);
} catch (RuntimeException ex)
{
notifyLog.error(createErrorMessage(scriptPath), ex);
@@ -64,7 +53,7 @@ class Utils
private static UserFailureException createUserFailureException(RuntimeException ex)
{
return new UserFailureException("Chosen plugin failed to create a report: "
- + ExceptionUtils.getEndOfChain(ex));
+ + ExceptionUtils.getEndOfChain(ex), ex);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java
index 19ab7023898edca899f54ff456d910e53840076a..1480bc984aa9950d0053c11dffb77ff18c363138 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/standard/AbstractAggregationServiceReportingPlugin.java
@@ -49,13 +49,19 @@ public abstract class AbstractAggregationServiceReportingPlugin extends Abstract
public TableModel createReport(List<DatasetDescription> datasets, DataSetProcessingContext context)
{
- throw new IllegalArgumentException(
- "The method createReport is not supported by AGGREGATION_TABLE_MODEL tasks");
+ throw createException();
}
public LinkModel createLink(DatasetDescription dataset)
{
- throw new IllegalArgumentException(
- "The method createLink is not supported by AGGREGATION_TABLE_MODEL tasks");
+ throw createException();
}
+
+ private IllegalArgumentException createException()
+ {
+ return new IllegalArgumentException(
+ "The method createReport is not supported by " + getReportingPluginType()
+ + " tasks");
+ }
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java
index a52649970aa87c221f7712f772a1fcce36ac21c5..327600f3857c9856061b537226293fad4d433ed5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java
@@ -113,7 +113,6 @@ public abstract class AbstractPluginTaskFactory<T>
servletPropertiesManager.addServletProperties(label, props);
}
String pluginKey = sectionProperties.getKey();
- String[] datasetCodes = extractDatasetCodes(pluginProperties);
this.className = PropertyUtils.getMandatoryProperty(pluginProperties, CLASS_PROPERTY_NAME);
this.instanceParameters = extractInstanceParameters(pluginProperties);
@@ -124,11 +123,15 @@ public abstract class AbstractPluginTaskFactory<T>
{
ReportingPluginType type =
((IReportingPluginTask) pluginInstance).getReportingPluginType();
+ String[] datasetCodes =
+ type == ReportingPluginType.AGGREGATION_TABLE_MODEL ? new String[0]
+ : extractDatasetCodes(pluginProperties);
this.description =
DatastoreServiceDescription.reporting(pluginKey, label, datasetCodes,
datastoreCode, type);
} else
{
+ String[] datasetCodes = extractDatasetCodes(pluginProperties);
this.description =
DatastoreServiceDescription.processing(pluginKey, label, datasetCodes,
datastoreCode);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedAggregationServiceReportingPluginTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedAggregationServiceReportingPluginTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..492ab1853fb9b83d2426bf1a44f60ac66d18e943
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/jython/JythonBasedAggregationServiceReportingPluginTest.java
@@ -0,0 +1,224 @@
+/*
+ * Copyright 2012 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.dss.generic.server.plugins.jython;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Map;
+import java.util.Properties;
+
+import net.lemnik.eodsql.DataSet;
+
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContent;
+import ch.systemsx.cisd.common.io.hierarchical_content.api.IHierarchicalContentNode;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSourceQueryService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISearchService;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.DataSetBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class JythonBasedAggregationServiceReportingPluginTest extends AbstractFileSystemTestCase
+{
+ private Mockery context;
+ private ISearchService searchService;
+ private IDataSourceQueryService queryService;
+ private File store;
+ private File scriptFolder;
+ private DataSetProcessingContext processingContext;
+ private IMailClient mailClient;
+ private IHierarchicalContentProvider contentProvider;
+ private IHierarchicalContent content;
+ private IHierarchicalContentNode rootNode;
+ private DataSet<?> dbDataSet;
+
+ @BeforeMethod
+ public void setUpTest()
+ {
+ context = new Mockery();
+ searchService = context.mock(ISearchService.class);
+ queryService = context.mock(IDataSourceQueryService.class);
+ mailClient = context.mock(IMailClient.class);
+ contentProvider = context.mock(IHierarchicalContentProvider.class);
+ content = context.mock(IHierarchicalContent.class);
+ rootNode = context.mock(IHierarchicalContentNode.class);
+ dbDataSet = context.mock(DataSet.class);
+ processingContext =
+ new DataSetProcessingContext(contentProvider, null, new HashMap<String, String>(),
+ mailClient, "test-user");
+ store = new File(workingDirectory, "store");
+ store.mkdirs();
+ scriptFolder = new File("resource/test-data/" + getClass().getSimpleName());
+ }
+
+ @AfterMethod
+ public void afterTest()
+ {
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testHappyCase()
+ {
+ final RecordingMatcher<SearchCriteria> searchCriteriaRecorder =
+ new RecordingMatcher<SearchCriteria>();
+ context.checking(new Expectations()
+ {
+ {
+ one(searchService).searchForDataSets(with(searchCriteriaRecorder));
+ will(returnValue(Arrays.asList(new DataSetImmutable(new DataSetBuilder()
+ .code("ds1")
+ .experiment(
+ new ExperimentBuilder().identifier("/A/B/ABC").getExperiment())
+ .getDataSet(), null))));
+
+ one(contentProvider).asContent("ds1");
+ will(returnValue(content));
+
+ one(content).getRootNode();
+ will(returnValue(rootNode));
+
+ one(rootNode).isDirectory();
+ will(returnValue(false));
+
+ one(content).close();
+
+ one(queryService).select("protein-db",
+ "select count(*) as count from proteins where data_set = ?{1}", "ds1");
+ will(returnValue(dbDataSet));
+
+ one(dbDataSet).size();
+ will(returnValue(1));
+
+ one(dbDataSet).get(0);
+ will(returnValue(new ParametersBuilder().parameter("count", 42L).getParameters()));
+ }
+ });
+ Map<String, Object> parameters =
+ new ParametersBuilder().parameter("experiment-code", "ABC").getParameters();
+
+ IReportingPluginTask plugin = createPlugin("script.py");
+ TableModel tableModel = plugin.createAggregationReport(parameters, processingContext);
+
+ assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],"
+ + "[SearchSubCriteria[EXPERIMENT,SearchCriteria[MATCH_ALL_CLAUSES,"
+ + "[SearchCriteria.AttributeMatchClause[ATTRIBUTE,CODE,ABC,EQUALS]],[]]]]]",
+ searchCriteriaRecorder.recordedObject().toString());
+ assertEquals("[Experiment, Data Set Code, Number of Files, Number of Proteins]", tableModel
+ .getHeader().toString());
+ assertEquals("[/A/B/ABC, ds1, 1, 42]", tableModel.getRows().get(0).getValues().toString());
+ assertEquals(1, tableModel.getRows().size());
+ context.assertIsSatisfied();
+ }
+
+
+ @Test
+ public void testSearchServiceThrowsException()
+ {
+ final RecordingMatcher<SearchCriteria> searchCriteriaRecorder =
+ new RecordingMatcher<SearchCriteria>();
+ context.checking(new Expectations()
+ {
+ {
+ one(searchService).searchForDataSets(with(searchCriteriaRecorder));
+ will(throwException(new IllegalArgumentException("Invalid")));
+ }
+ });
+ Map<String, Object> parameters =
+ new ParametersBuilder().getParameters();
+
+ IReportingPluginTask plugin = createPlugin("script.py");
+ try
+ {
+ plugin.createAggregationReport(parameters, processingContext);
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Chosen plugin failed to create a report: "
+ + "java.lang.IllegalArgumentException: Invalid", ex.getMessage());
+ String message = ex.getCause().getMessage();
+ String prefix =
+ "Error occured in line 28 of the script when evaluating 'aggregate({}, ";
+ assertEquals("Message '" + message + "' doesn't starts with '" + prefix + "'.", true,
+ message.startsWith(prefix));
+ }
+
+ assertEquals("SearchCriteria[MATCH_ALL_CLAUSES,[],"
+ + "[SearchSubCriteria[EXPERIMENT,SearchCriteria[MATCH_ALL_CLAUSES,"
+ + "[SearchCriteria.AttributeMatchClause[ATTRIBUTE,CODE,<null>,EQUALS]],[]]]]]",
+ searchCriteriaRecorder.recordedObject().toString());
+ context.assertIsSatisfied();
+ }
+
+ private static final class ParametersBuilder
+ {
+ private final Map<String, Object> parameters = new HashMap<String, Object>();
+
+ public ParametersBuilder parameter(String name, Object value)
+ {
+ parameters.put(name, value);
+ return this;
+ }
+
+ public Map<String, Object> getParameters()
+ {
+ return parameters;
+ }
+ }
+
+ private IReportingPluginTask createPlugin(String scriptFile)
+ {
+ return new JythonBasedAggregationServiceReportingPlugin(new Properties(), store,
+ new PluginScriptRunnerFactory(new File(scriptFolder, scriptFile).getPath())
+ {
+ private static final long serialVersionUID = 1L;
+
+ @Override
+ protected ISearchService createSearchService()
+ {
+ return searchService;
+ }
+
+ @Override
+ protected IDataSourceQueryService createDataSourceQueryService()
+ {
+ return queryService;
+ }
+ });
+ }
+
+}