diff --git a/deep_sequencing_unit/.classpath b/deep_sequencing_unit/.classpath
index 5d146a2f5be0637210a81eebacb7a32ba8d74414..e3ed3cc42fc79c41dfd9903a3d39f330e08497e3 100644
--- a/deep_sequencing_unit/.classpath
+++ b/deep_sequencing_unit/.classpath
@@ -18,5 +18,7 @@
<classpathentry kind="lib" path="/libraries/jaxb/jaxb-api.jar" sourcepath="/libraries/jaxb/jaxb-api-src.zip"/>
<classpathentry kind="lib" path="/libraries/jaxb/jaxb-impl.jar" sourcepath="/libraries/jaxb/jaxb-impl.src.zip"/>
<classpathentry kind="lib" path="/libraries/jaxb/jsr173_1.0_api.jar"/>
+ <classpathentry kind="lib" path="/libraries/activation/activation.jar"/>
+ <classpathentry kind="lib" path="/libraries/restrictionchecker/restrictions.jar"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFT.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFT.java
index a31a7ed0764a9d4e0c0efefbcea557aa087484f4..ab5d32d186f15ffbbd3458d96a3e63b0caaa8fc3 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFT.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFT.java
@@ -30,6 +30,7 @@ import javax.mail.util.ByteArrayDataSource;
import org.apache.commons.io.FileUtils;
import org.apache.log4j.Logger;
+import ch.rinn.restrictions.Private;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.logging.LogCategory;
@@ -58,21 +59,23 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*/
public class DataSetToSOFT implements IProcessingPluginTask
{
- private static final String EXTERNAL_SAMPLE_NAME_PROPERTY = "EXTERNAL_SAMPLE_NAME";
+ @Private static final String EXTERNAL_SAMPLE_NAME_PROPERTY = "EXTERNAL_SAMPLE_NAME";
private static final String EMPTY = "<<<NEED_TO_BE_FILLED>>>";
- private static final Template SOFT_FILE_NAME_TEMPLATE = new Template(
+ @Private
+ static final Template SOFT_FILE_NAME_TEMPLATE = new Template(
"${flow-lane}_${external-sample-name}_SOFT.txt");
- private static final Template E_MAIL_SUBJECT_TEMPLATE = new Template(
- "SOFT file for ${external-sample-name}");
-
- private static final Template E_MAIL_CONTENT_TEMPLATE =
- new Template("Dear User\n\n"
- + "Enclosed you will find the SOFT file for ${external-sample-name}.\n"
- + "Flow lane: ${flow-lane}\nData Set: ${data-set}");
-
+ @Private
+ static final Template E_MAIL_SUBJECT_TEMPLATE = new Template(
+ "SOFT file for '${external-sample-name}'");
+
+ @Private
+ static final Template E_MAIL_CONTENT_TEMPLATE = new Template("Dear User\n\n"
+ + "Enclosed you will find the SOFT file for '${external-sample-name}'.\n"
+ + "Flow lane: ${flow-lane}\nData Set: ${data-set}");
+
private static final class SOFTBuilder
{
private final StringBuilder builder = new StringBuilder();
@@ -130,18 +133,26 @@ public class DataSetToSOFT implements IProcessingPluginTask
return null;
}
-
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, DataSetToSOFT.class);
private static final long serialVersionUID = 1L;
+
private final File storeRoot;
- private Map<String, String> translation;
+ private final Map<String, String> translation;
+
+ private IEncapsulatedOpenBISService service;
public DataSetToSOFT(Properties properties, File storeRoot)
+ {
+ this(properties, storeRoot, null);
+ }
+
+ DataSetToSOFT(Properties properties, File storeRoot, IEncapsulatedOpenBISService service)
{
this.storeRoot = storeRoot;
+ this.service = service;
translation = new HashMap<String, String>();
translation.put("GENOMIC_DNA", "genomic");
translation.put("FRAGMENTED_GENOMIC_DNA", "genomic");
@@ -160,7 +171,6 @@ public class DataSetToSOFT implements IProcessingPluginTask
DataSetProcessingContext context)
{
EMailAddress address = new EMailAddress(context.getUserEmailOrNull());
- IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
ProcessingStatus status = new ProcessingStatus();
for (DatasetDescription datasetDescription : datasets)
{
@@ -171,7 +181,7 @@ public class DataSetToSOFT implements IProcessingPluginTask
{
operationLog.info("Create SOFT file for data set " + dataSetCode);
}
- ExternalData srfDataSet = service.tryGetDataSet(dataSetCode);
+ ExternalData srfDataSet = getService().tryGetDataSet(dataSetCode);
Sample flowLaneSample = getFlowLaneSample(srfDataSet);
Sample flowCellSample = getFlowCellSample(flowLaneSample);
Sample sequencingSample = getSequencingSample(flowLaneSample);
@@ -194,7 +204,7 @@ public class DataSetToSOFT implements IProcessingPluginTask
softBuilder.addSampleProperty("biomaterial_provider", sequencingSample, "CONTACT_PERSON_NAME");
softBuilder.addSampleProperty("molecule", sequencingSample, "SEQUENCING_APPLICATION");
softBuilder.addSampleProperty("extract_protocol", sequencingSample, "SAMPLE_EXTRACT_PROTOCOL");
- softBuilder.addSampleProperty("data_processing", sequencingSample, "AMPLE_DATA_PROCESSING");
+ softBuilder.addSampleProperty("data_processing", sequencingSample, "SAMPLE_DATA_PROCESSING");
softBuilder.addSampleProperty("library_strategy", sequencingSample, "SEQUENCING_APPLICATION");
softBuilder.addSampleProperty("library_source", sequencingSample, "SAMPLE_KIND", translation);
softBuilder.addSampleProperty("library_selection", sequencingSample, "SAMPLE_KIND");
@@ -238,7 +248,8 @@ public class DataSetToSOFT implements IProcessingPluginTask
private String createSoftFileName(Sample sequencingSample, Sample flowLaneSample)
{
Template template = SOFT_FILE_NAME_TEMPLATE.createFreshCopy();
- bindExternalSampleName(template, sequencingSample);
+ String externalSampleName = tryToGetProperty(sequencingSample, EXTERNAL_SAMPLE_NAME_PROPERTY);
+ template.bind("external-sample-name", externalSampleName.replace(' ', '_'));
template.bind("flow-lane", flowLaneSample.getCode().replace(':', '-'));
return template.createText();
}
@@ -291,22 +302,19 @@ public class DataSetToSOFT implements IProcessingPluginTask
private Sample getFlowLaneSample(ExternalData dataSet)
{
- IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
SampleIdentifier identifier = SampleIdentifierFactory.parse(dataSet.getSampleIdentifier());
- return service.tryGetSampleWithExperiment(identifier);
+ return getService().tryGetSampleWithExperiment(identifier);
}
private Sample getFlowCellSample(Sample flowLaneSample)
{
- IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
SampleIdentifier identifier = SampleIdentifierFactory.parse(flowLaneSample.getContainer().getIdentifier());
- return service.tryGetSampleWithExperiment(identifier);
+ return getService().tryGetSampleWithExperiment(identifier);
}
private Sample getSequencingSample(Sample flowLaneSample)
{
- IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
- List<Sample> parents = service.listSamples(ListSampleCriteria.createForChild(new TechId(flowLaneSample.getId())));
+ List<Sample> parents = getService().listSamples(ListSampleCriteria.createForChild(new TechId(flowLaneSample.getId())));
return parents.get(0);
}
@@ -321,5 +329,13 @@ public class DataSetToSOFT implements IProcessingPluginTask
}
}
+ private IEncapsulatedOpenBISService getService()
+ {
+ if (service == null)
+ {
+ service = ServiceProvider.getOpenBISService();
+ }
+ return service;
+ }
}
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFTTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFTTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..0233f85afb1bc6acfecf1e608cf617ce62f569d6
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFTTest.java
@@ -0,0 +1,255 @@
+/*
+ * Copyright 2010 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.ethz.bsse.cisd.dsu.dss.plugins;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Properties;
+
+import javax.activation.DataHandler;
+import javax.activation.DataSource;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.log4j.Level;
+import org.hamcrest.core.IsNull;
+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.rinn.restrictions.Friend;
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.logging.BufferedAppender;
+import ch.systemsx.cisd.common.mail.EMailAddress;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.test.RecordingMatcher;
+import ch.systemsx.cisd.common.utilities.Template;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IProcessingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.ProcessingStatus;
+import ch.systemsx.cisd.openbis.dss.generic.shared.DataSetProcessingContext;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+@Friend(toClasses=DataSetToSOFT.class)
+public class DataSetToSOFTTest extends AbstractFileSystemTestCase
+{
+ private static final String USER_EMAIL = "user@ho.me";
+ private static final String SRF_FILE_NAME = "sample.srf";
+ private static final String SRF_FILE_CONTENT = "hello world!";
+ private static final String DATASET_CODE = "ds-1";
+ private static final String FLOW_LANE_SAMPLE_CODE = "flow-lane:1";
+
+ private BufferedAppender logRecorder;
+ private Mockery context;
+ private IEncapsulatedOpenBISService service;
+ private IMailClient mailClient;
+ private DataSetProcessingContext dataSetProcessingContext;
+ private IProcessingPluginTask processingPlugin;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ logRecorder = new BufferedAppender("%-5p %c - %m%n", Level.DEBUG);
+ context = new Mockery();
+ service = context.mock(IEncapsulatedOpenBISService.class);
+ mailClient = context.mock(IMailClient.class);
+ dataSetProcessingContext =
+ new DataSetProcessingContext(new HashMap<String, String>(), mailClient, USER_EMAIL);
+ File testFolder = new File(workingDirectory, "test");
+ testFolder.mkdirs();
+ File sampleSrfFile = new File(testFolder, SRF_FILE_NAME);
+ FileUtilities.writeToFile(sampleSrfFile, SRF_FILE_CONTENT);
+ processingPlugin = new DataSetToSOFT(new Properties(), workingDirectory, service);
+ }
+
+ @AfterMethod
+ public void afterMethod()
+ {
+ logRecorder.reset();
+ // 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 test() throws IOException
+ {
+ DatasetDescription datasetDescription = new DatasetDescription();
+ datasetDescription.setDatasetCode(DATASET_CODE);
+ datasetDescription.setDataSetLocation(".");
+ List<DatasetDescription> dataSets = Arrays.asList(datasetDescription);
+ final Sample flowLaneSample = sample(42, FLOW_LANE_SAMPLE_CODE);
+ flowLaneSample.setCode(FLOW_LANE_SAMPLE_CODE);
+ prepareGetDataSet(DATASET_CODE, flowLaneSample);
+ Sample flowCellSample = sample(43, "flow-cell");
+ addProperty(flowCellSample, "GENOME_ANALYZER", "my-analyzer");
+ final Sample sequencingSample = sample(44, "sequencing");
+ addProperty(sequencingSample, DataSetToSOFT.EXTERNAL_SAMPLE_NAME_PROPERTY, "my sample");
+ addProperty(sequencingSample, "SAMPLE_SOURCE_NAME", "source");
+ addProperty(sequencingSample, "NCBI_ORGANISM_TAXONOMY", "organism");
+ addProperty(sequencingSample, "CONTACT_PERSON_NAME", "person");
+ addProperty(sequencingSample, "SEQUENCING_APPLICATION", "application");
+ addProperty(sequencingSample, "SAMPLE_EXTRACT_PROTOCOL", "protocol");
+ addProperty(sequencingSample, "SAMPLE_DATA_PROCESSING", "processing");
+ addProperty(sequencingSample, "SAMPLE_KIND", "CHIP");
+ flowLaneSample.setContainer(flowCellSample);
+ prepareGetSample(flowLaneSample);
+ prepareGetSample(flowCellSample);
+ final RecordingMatcher<ListSampleCriteria> listSampleCriteriaMatcher = new RecordingMatcher<ListSampleCriteria>();
+ final RecordingMatcher<String> subjectMatcher = new RecordingMatcher<String>();
+ final RecordingMatcher<String> contentMatcher = new RecordingMatcher<String>();
+ final RecordingMatcher<String> fileNameMatcher = new RecordingMatcher<String>();
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher = new RecordingMatcher<EMailAddress[]>();
+ context.checking(new Expectations()
+ {
+ {
+ one(service).listSamples(with(listSampleCriteriaMatcher));
+ will(returnValue(Arrays.asList(sequencingSample)));
+
+ one(mailClient).sendEmailMessageWithAttachment(with(subjectMatcher),
+ with(contentMatcher), with(fileNameMatcher), with(attachmentMatcher),
+ with(new IsNull<EMailAddress>()), with(new IsNull<EMailAddress>()),
+ with(addressesMatcher));
+ }
+ });
+
+ ProcessingStatus status = processingPlugin.process(dataSets, dataSetProcessingContext);
+
+ assertEquals(0, status.getErrorStatuses().size());
+ assertEquals(flowLaneSample.getId(), listSampleCriteriaMatcher.getRecordedObjects().get(0).getChildSampleId().getId());
+ Template template = initTemplate(DataSetToSOFT.E_MAIL_SUBJECT_TEMPLATE);
+ assertEquals("[" + template.createText() + "]", subjectMatcher.getRecordedObjects().toString());
+ Template content = initTemplate(DataSetToSOFT.E_MAIL_CONTENT_TEMPLATE);
+ content.bind("flow-lane", flowLaneSample.getCode());
+ content.bind("data-set", DATASET_CODE);
+ assertEquals("[" + content.createText() + "]", contentMatcher.getRecordedObjects().toString());
+ Template fileNameTemplate = DataSetToSOFT.SOFT_FILE_NAME_TEMPLATE.createFreshCopy();
+ fileNameTemplate.bind("external-sample-name", "my_sample");
+ fileNameTemplate.bind("flow-lane", flowLaneSample.getCode().replace(':', '-'));
+ assertEquals("[" + fileNameTemplate.createText() + "]", fileNameMatcher.getRecordedObjects().toString());
+ List<EMailAddress[]> emailAddresses = addressesMatcher.getRecordedObjects();
+ assertEquals(USER_EMAIL, emailAddresses.get(0)[0].tryGetEmailAddress());
+ DataSource dataSource = attachmentMatcher.getRecordedObjects().get(0).getDataSource();
+ String attachmentContent = getContent(dataSource);
+ assertEquals("^SAMPLE = my sample\n"
+ + "!Sample_type = SRA\n"
+ + "!Sample_title = my sample\n"
+ + "!Sample_source_name = source\n"
+ + "!Sample_organism = organism\n"
+ + "!Sample_characteristics = <<<NEED_TO_BE_FILLED>>>\n"
+ + "!Sample_biomaterial_provider = person\n"
+ + "!Sample_molecule = application\n"
+ + "!Sample_extract_protocol = protocol\n"
+ + "!Sample_data_processing = processing\n"
+ + "!Sample_library_strategy = application\n"
+ + "!Sample_library_source = genomic\n"
+ + "!Sample_library_selection = CHIP\n"
+ + "!Sample_instrument_model = my-analyzer\n"
+ + "!Sample_raw_file_1 = sample.srf\n"
+ + "!Sample_raw_file_type_1 = srf\n"
+ + "!Sample_file_checksum_1 = fc3ff98e8c6a0d3087d515c0473f8677\n", attachmentContent);
+ context.assertIsSatisfied();
+ }
+
+ String getContent(DataSource dataSource) throws IOException
+ {
+ StringBuilder builder = new StringBuilder();
+ @SuppressWarnings("rawtypes")
+ List fileLines = IOUtils.readLines(dataSource.getInputStream());
+ for (Object object : fileLines)
+ {
+ builder.append(object).append('\n');
+ }
+ return builder.toString();
+ }
+
+ Template initTemplate(Template originalTemplate)
+ {
+ Template template = originalTemplate.createFreshCopy();
+ template.bind("external-sample-name", "my sample");
+ return template;
+ }
+
+ private void prepareGetDataSet(final String dataSetCode, final Sample flowLaneSample)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetDataSet(dataSetCode);
+ ExternalData dataSet = new ExternalData();
+ dataSet.setCode(dataSetCode);
+ dataSet.setSample(flowLaneSample);
+ will(returnValue(dataSet));
+ }
+ });
+ }
+
+ private void prepareGetSample(final Sample sample)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetSampleWithExperiment(SampleIdentifierFactory.parse(sample.getIdentifier()));
+ will(returnValue(sample));
+ }
+ });
+ }
+
+ private void addProperty(Sample sample, String propertyTypeCode, String value)
+ {
+ List<IEntityProperty> properties = sample.getProperties();
+ if (properties == null)
+ {
+ properties = new ArrayList<IEntityProperty>();
+ sample.setProperties(properties);
+ }
+ EntityProperty property = new EntityProperty();
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode(propertyTypeCode);
+ property.setPropertyType(propertyType);
+ property.setValue(value);
+ properties.add(property);
+ }
+
+ private Sample sample(long id, String identifier)
+ {
+ Sample sample = new Sample();
+ sample.setId(id);
+ sample.setIdentifier(identifier);
+ return sample;
+ }
+}
+