From 23d1feb95a64d345b31529e07d08ac83ad2588ae Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 7 Dec 2010 08:05:35 +0000
Subject: [PATCH] LMS-1880 first version of plugin DataSetToSOFT
SVN: 19023
---
.../cisd/dsu/dss/plugins/DataSetToSOFT.java | 325 ++++++++++++++++++
1 file changed, 325 insertions(+)
create mode 100644 deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFT.java
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
new file mode 100644
index 00000000000..a31a7ed0764
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/plugins/DataSetToSOFT.java
@@ -0,0 +1,325 @@
+/*
+ * 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.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Properties;
+
+import javax.activation.DataHandler;
+import javax.activation.DataSource;
+import javax.mail.util.ByteArrayDataSource;
+
+import org.apache.commons.io.FileUtils;
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.common.exceptions.Status;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.mail.EMailAddress;
+import ch.systemsx.cisd.common.utilities.MD5ChecksumCalculator;
+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.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+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.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
+
+/**
+ * Processing plugin for exporting meta data of a flow lane as a SOFT file.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataSetToSOFT implements IProcessingPluginTask
+{
+ 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(
+ "${flow-lane}_${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 class SOFTBuilder
+ {
+ private final StringBuilder builder = new StringBuilder();
+
+ void addSample(Sample sample, String propertyTypeCode)
+ {
+ addLine('^', "SAMPLE", getProperty(sample, propertyTypeCode));
+ }
+
+ void addSampleProperty(String key, Sample sample, String propertyTypeCode, Map<String, String> translation)
+ {
+ String property = getProperty(sample, propertyTypeCode);
+ String translatedProperty = translation.get(property);
+ addProperty(key, translatedProperty == null ? property : translatedProperty);
+ }
+
+ void addSampleProperty(String key, Sample sample, String propertyTypeCode)
+ {
+ addProperty(key, getProperty(sample, propertyTypeCode));
+ }
+
+ void addProperty(String key, String property)
+ {
+ addLine('!', "Sample_" + key, property);
+ }
+
+ private void addLine(char prefix, String key, String value)
+ {
+ builder.append(prefix).append(key).append(" = ").append(value).append('\n');
+ }
+
+ private String getProperty(Sample sample, String propertyTypeCode)
+ {
+ String property = tryToGetProperty(sample, propertyTypeCode);
+ return property == null ? EMPTY : property;
+ }
+
+ @Override
+ public String toString()
+ {
+ return builder.toString();
+ }
+ }
+
+ private static final String tryToGetProperty(Sample sample, String propertyTypeCode)
+ {
+ List<IEntityProperty> properties = sample.getProperties();
+ for (IEntityProperty property : properties)
+ {
+ if (property.getPropertyType().getCode().equals(propertyTypeCode))
+ {
+ return property.tryGetAsString();
+ }
+ }
+ 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;
+
+ public DataSetToSOFT(Properties properties, File storeRoot)
+ {
+ this.storeRoot = storeRoot;
+ translation = new HashMap<String, String>();
+ translation.put("GENOMIC_DNA", "genomic");
+ translation.put("FRAGMENTED_GENOMIC_DNA", "genomic");
+ translation.put("CHIP", "genomic");
+ translation.put("BISULFITE", "genomic");
+ translation.put("NON_GENOMIC", "non-genomic");
+ translation.put("SYNTHETIC", "synthetic");
+ translation.put("VIRAL_RNA", "viral RNA");
+ translation.put("SMALL_RNA", "other");
+ translation.put("TOTAL_RNA", "other");
+ translation.put("MRNA", "other");
+ translation.put("PROCESSED_DNA_LIBRARY", "<<<NEED_TO_BE_FILLED>>>");
+ }
+
+ public ProcessingStatus process(List<DatasetDescription> datasets,
+ DataSetProcessingContext context)
+ {
+ EMailAddress address = new EMailAddress(context.getUserEmailOrNull());
+ IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
+ ProcessingStatus status = new ProcessingStatus();
+ for (DatasetDescription datasetDescription : datasets)
+ {
+ try
+ {
+ String dataSetCode = datasetDescription.getDatasetCode();
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("Create SOFT file for data set " + dataSetCode);
+ }
+ ExternalData srfDataSet = service.tryGetDataSet(dataSetCode);
+ Sample flowLaneSample = getFlowLaneSample(srfDataSet);
+ Sample flowCellSample = getFlowCellSample(flowLaneSample);
+ Sample sequencingSample = getSequencingSample(flowLaneSample);
+ File srfFile = tryToFindSrfFile(datasetDescription);
+ if (srfFile == null)
+ {
+ status.addDatasetStatus(datasetDescription,
+ Status.createError("Data set " + dataSetCode + " has no srf file."));
+ continue;
+ }
+ String checkSum = calculateCheckSum(srfFile);
+
+ SOFTBuilder softBuilder = new SOFTBuilder();
+ softBuilder.addSample(sequencingSample, EXTERNAL_SAMPLE_NAME_PROPERTY);
+ softBuilder.addProperty("type", "SRA");
+ softBuilder.addSampleProperty("title", sequencingSample, EXTERNAL_SAMPLE_NAME_PROPERTY);
+ softBuilder.addSampleProperty("source_name", sequencingSample, "SAMPLE_SOURCE_NAME");
+ softBuilder.addSampleProperty("organism", sequencingSample, "NCBI_ORGANISM_TAXONOMY");
+ softBuilder.addSampleProperty("characteristics", sequencingSample, "SAMPLE_CHARACTERISTICS");
+ 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("library_strategy", sequencingSample, "SEQUENCING_APPLICATION");
+ softBuilder.addSampleProperty("library_source", sequencingSample, "SAMPLE_KIND", translation);
+ softBuilder.addSampleProperty("library_selection", sequencingSample, "SAMPLE_KIND");
+ softBuilder.addSampleProperty("instrument_model", flowCellSample, "GENOME_ANALYZER");
+ softBuilder.addProperty("raw_file_1", srfFile.getName());
+ softBuilder.addProperty("raw_file_type_1", "srf");
+ softBuilder.addProperty("file_checksum_1", checkSum);
+
+ String subject = createSubject(sequencingSample);
+ String content = createContent(sequencingSample, flowLaneSample, srfDataSet);
+ String fileName = createSoftFileName(sequencingSample, flowLaneSample);
+ DataSource dataSource = createDataSource(softBuilder.toString());
+ context.getMailClient().sendEmailMessageWithAttachment(subject, content, fileName,
+ new DataHandler(dataSource), null, null, address);
+ status.addDatasetStatus(datasetDescription, Status.OK);
+ } catch (Exception ex)
+ {
+ status.addDatasetStatus(datasetDescription, Status.createError("Exception occured: " + ex));
+ operationLog.error("Exception occured while processing " + datasetDescription, ex);
+ }
+ }
+ return status;
+ }
+
+ private String createSubject(Sample sequencingSample)
+ {
+ Template template = E_MAIL_SUBJECT_TEMPLATE.createFreshCopy();
+ bindExternalSampleName(template, sequencingSample);
+ return template.createText();
+ }
+
+ private String createContent(Sample sequencingSample, Sample flowLaneSample, ExternalData dataSet)
+ {
+ Template template = E_MAIL_CONTENT_TEMPLATE.createFreshCopy();
+ bindExternalSampleName(template, sequencingSample);
+ template.bind("flow-lane", flowLaneSample.getIdentifier());
+ template.bind("data-set", dataSet.getCode());
+ return template.createText();
+ }
+
+ private String createSoftFileName(Sample sequencingSample, Sample flowLaneSample)
+ {
+ Template template = SOFT_FILE_NAME_TEMPLATE.createFreshCopy();
+ bindExternalSampleName(template, sequencingSample);
+ template.bind("flow-lane", flowLaneSample.getCode().replace(':', '-'));
+ return template.createText();
+ }
+
+ private void bindExternalSampleName(Template template, Sample sequencingSample)
+ {
+ String externalSampleName = tryToGetProperty(sequencingSample, EXTERNAL_SAMPLE_NAME_PROPERTY);
+ template.bind("external-sample-name", externalSampleName);
+ }
+
+ private String calculateCheckSum(File srfFile)
+ {
+ String checkSum;
+ try
+ {
+ checkSum = MD5ChecksumCalculator.calculate(FileUtils.readFileToByteArray(srfFile));
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ return checkSum;
+ }
+
+ private File tryToFindSrfFile(DatasetDescription datasetDescription)
+ {
+ File root = new File(storeRoot, datasetDescription.getDataSetLocation());
+ return tryToFindSrfFile(root);
+ }
+
+ private File tryToFindSrfFile(File file)
+ {
+ if (file.isFile() && file.getName().endsWith(".srf"))
+ {
+ return file;
+ }
+ if (file.isDirectory())
+ {
+ File[] files = file.listFiles();
+ for (File child : files)
+ {
+ File srfFile = tryToFindSrfFile(child);
+ if (srfFile != null)
+ {
+ return srfFile;
+ }
+ }
+ }
+ return null;
+ }
+
+ private Sample getFlowLaneSample(ExternalData dataSet)
+ {
+ IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
+ SampleIdentifier identifier = SampleIdentifierFactory.parse(dataSet.getSampleIdentifier());
+ return service.tryGetSampleWithExperiment(identifier);
+ }
+
+ private Sample getFlowCellSample(Sample flowLaneSample)
+ {
+ IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
+ SampleIdentifier identifier = SampleIdentifierFactory.parse(flowLaneSample.getContainer().getIdentifier());
+ return service.tryGetSampleWithExperiment(identifier);
+ }
+
+ private Sample getSequencingSample(Sample flowLaneSample)
+ {
+ IEncapsulatedOpenBISService service = ServiceProvider.getOpenBISService();
+ List<Sample> parents = service.listSamples(ListSampleCriteria.createForChild(new TechId(flowLaneSample.getId())));
+ return parents.get(0);
+ }
+
+ private DataSource createDataSource(final String softData)
+ {
+ try
+ {
+ return new ByteArrayDataSource(softData, "text/plain");
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+
+
+}
--
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