Download datasets as Darwin Core Archive

src/main/java/org/genesys2/server/model/genesys/ExperimentAccessionTrait.java

+/**
+ * Copyright 2013 Global Crop Diversity Trust
+ * 
+ * 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 org.genesys2.server.model.genesys;
+
+/*
+ * Looks like {@link AccessionTrait}
+ */
+public class ExperimentAccessionTrait {
+	private long experimentId;
+	private long accessionId;
+	private Object value;
+
+	public ExperimentAccessionTrait(final long experimentId, final long accessionId, final Object value) {
+		this.experimentId = experimentId;
+		this.accessionId=accessionId;
+		this.value = value;
+	}
+
+	public long getExperimentId() {
+		return experimentId;
+	}
+
+	public void setExperimentId(final long experimentId) {
+		this.experimentId = experimentId;
+	}
+	
+	public long getAccessionId() {
+		return accessionId;
+	}
+	
+	public void setAccessionId(long accessionId) {
+		this.accessionId = accessionId;
+	}
+
+	public Object getValue() {
+		return value;
+	}
+
+	public void setValue(final Object value) {
+		this.value = value;
+	}
+
+	@Override
+	public String toString() {
+		return "{" + value + ", " + experimentId + "}";
+	}
+}

src/main/java/org/genesys2/server/model/genesys/TraitCode.java

@@ -87,4 +87,12 @@ public class TraitCode {
 		}
 		return map;
 	}
+	
+	public static Map<String, String> parseCodeMap(final String options) {
+		final Map<String, String> map = new HashMap<String, String>();
+		for (final TraitCode code : parseOptions(options)) {
+			map.put(code.getCode(), code.getValue());
+		}
+		return map;
+	}
 }

src/main/java/org/genesys2/server/persistence/domain/TraitValueRepository.java

@@ -22,6 +22,7 @@ import java.util.Set;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionTrait;
+import org.genesys2.server.model.genesys.ExperimentAccessionTrait;
 import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.MetadataMethod;
@@ -33,6 +34,8 @@ public interface TraitValueRepository {
 	//
 	// List<ExperimentTrait> getValues(Accession accession, Method method);
 
+	List<ExperimentAccessionTrait> getValues(Metadata metadata, Method method);
+	
 	Map<Long, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits);
 
 	Map<Long, Map<Long, List<Object>>> getValues(Metadata metadata, List<Method> methods, List<Accession> accessions);
@@ -69,4 +72,5 @@ public interface TraitValueRepository {
 	 */
 	void updateMetadataMethods(Metadata metadata, Set<Long> methodIds);
 
+
 }
\ No newline at end of file

src/main/java/org/genesys2/server/persistence/domain/TraitValueRepositoryImpl.java

@@ -16,7 +16,9 @@
 
 package org.genesys2.server.persistence.domain;
 
+import java.sql.Connection;
 import java.sql.PreparedStatement;
+import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.HashMap;
@@ -31,6 +33,7 @@ import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionTrait;
+import org.genesys2.server.model.genesys.ExperimentAccessionTrait;
 import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.MetadataMethod;
@@ -38,7 +41,9 @@ import org.genesys2.server.model.genesys.Method;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.jdbc.core.BatchPreparedStatementSetter;
 import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.PreparedStatementCreator;
 import org.springframework.jdbc.core.PreparedStatementSetter;
+import org.springframework.jdbc.core.RowMapper;
 import org.springframework.stereotype.Repository;
 import org.springframework.transaction.annotation.Transactional;
 
@@ -90,6 +95,25 @@ public class TraitValueRepositoryImpl implements TraitValueRepository {
 	// return ret;
 	// }
 
+	@Override
+	public List<ExperimentAccessionTrait> getValues(final Metadata metadata, final Method method) {
+		final long metadataId = metadata.getId();
+		return this.jdbcTemplate.query(new PreparedStatementCreator() {
+			@Override
+			public PreparedStatement createPreparedStatement(Connection conn) throws SQLException {
+				PreparedStatement pst = conn.prepareStatement("select `ALIS_Id` as accessionId, `" + method.getFieldName() + "` as traitvalue from `"
+						+ method.getId() + "` where `Meta_Id`=?");
+				pst.setLong(1, metadataId);
+				return pst;
+			}
+		}, new RowMapper<ExperimentAccessionTrait>() {
+			@Override
+			public ExperimentAccessionTrait mapRow(ResultSet rs, int pos) throws SQLException {
+				return new ExperimentAccessionTrait(metadataId, rs.getLong(1), rs.getObject(2));
+			}
+		});
+	}
+
 	@Override
 	public Map<Long, List<ExperimentTrait>> getValues(List<AccessionTrait> accessionTraits) {
 		if (accessionTraits == null) {

src/main/java/org/genesys2/server/service/DatasetService.java

@@ -16,6 +16,8 @@
 
 package org.genesys2.server.service;
 
+import java.io.IOException;
+import java.io.OutputStream;
 import java.util.List;
 import java.util.Map;
 
@@ -38,4 +40,13 @@ public interface DatasetService {
 	void touch(@Param("metadata") Metadata metadata);
 
 	void upsertAccessionData(Metadata metadata, Accession accession, Map<Long, List<Object>> methodValues);
+
+	/**
+	 * Writes a Darwin Core Archive to the specified output stream
+	 * 
+	 * @param metadata
+	 * @param outputStream
+	 * @throws IOException 
+	 */
+	void writeDataset(Metadata metadata, OutputStream outputStream) throws IOException;
 }

src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java

@@ -16,12 +16,18 @@
 
 package org.genesys2.server.service.impl;
 
+import java.io.BufferedWriter;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipOutputStream;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.logging.Log;
@@ -33,12 +39,14 @@ import org.genesys2.server.model.genesys.AllAcqBreeding;
 import org.genesys2.server.model.genesys.AllAcqCollect;
 import org.genesys2.server.model.genesys.AllAcqExchange;
 import org.genesys2.server.model.genesys.AllEnvironment;
+import org.genesys2.server.model.genesys.ExperimentAccessionTrait;
 import org.genesys2.server.model.genesys.ExperimentTrait;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.genesys.SvalbardData;
 import org.genesys2.server.model.genesys.Taxonomy;
+import org.genesys2.server.model.genesys.TraitCode;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.Crop;
@@ -70,6 +78,7 @@ import org.genesys2.server.service.TraitService;
 import org.genesys2.spring.SecurityContextUtil;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.repository.query.Param;
 import org.springframework.security.access.prepost.PreAuthorize;
@@ -77,6 +86,8 @@ import org.springframework.security.acls.domain.BasePermission;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 
+import au.com.bytecode.opencsv.CSVWriter;
+
 @Service
 @Transactional(readOnly = true)
 public class GenesysServiceImpl implements GenesysService, TraitService, DatasetService {
@@ -554,4 +565,101 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		// traitValueRepository.updateMetadataMethods(metadata,
 		// methodValues.keySet());
 	}
+
+	@Override
+	public void writeDataset(Metadata metadata, OutputStream outputStream) throws IOException {
+		// Methods: A CSV is generated for each method
+		List<Method> metadataMethods = listMethods(metadata);
+
+		CSVWriter csv = null;
+
+		// UTF8 is used for encoding entry names
+		ZipOutputStream zos = new ZipOutputStream(outputStream);
+		zos.setComment("Genesys Dataset " + metadata.getUuid());
+
+		ZipEntry coreEntry = new ZipEntry("core.csv");
+		coreEntry.setComment("Accession information");
+		coreEntry.setTime(System.currentTimeMillis());
+		zos.putNextEntry(coreEntry);
+
+		// Accessions
+		csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
+		csv.writeNext(new String[] { "coreId", "instCode", "acceNumb", "genus" });
+
+		// Write accession information
+		Page<Accession> datasetAccessions = null;
+		int page = 0;
+		do {
+			datasetAccessions = listMetadataAccessions(metadata.getId(), new PageRequest(page++, 50));
+			for (Accession accn : datasetAccessions.getContent()) {
+				csv.writeNext(new String[] { String.valueOf(accn.getId()), accn.getInstituteCode(), accn.getAccessionName(), accn.getGenus() });
+			}
+		} while (datasetAccessions.hasNextPage());
+
+		csv.flush();
+		zos.closeEntry();
+
+		for (Method method : metadataMethods) {
+			ZipEntry methodEntry = new ZipEntry(String.format("%1$s.csv", method.getFieldName().toLowerCase()));
+			methodEntry.setComment(method.getMethod());
+			methodEntry.setTime(System.currentTimeMillis());
+			zos.putNextEntry(methodEntry);
+
+			List<ExperimentAccessionTrait> vals = traitValueRepository.getValues(metadata, method);
+			csv = new CSVWriter(new BufferedWriter(new OutputStreamWriter(zos)), ',', '"', '\\', "\n");
+			csv.writeNext(new String[] { "coreId", "datasetId", "value" });
+
+			Map<String, String> codeMap = null;
+			if (method.isCoded()) {
+				codeMap = TraitCode.parseCodeMap(method.getOptions());
+			}
+			for (ExperimentAccessionTrait et : vals) {
+				if (et.getValue() == null)
+					continue;
+				if (codeMap == null) {
+					csv.writeNext(new String[] { String.valueOf(et.getAccessionId()), String.valueOf(et.getExperimentId()), et.getValue().toString() });
+				} else {
+					csv.writeNext(new String[] { String.valueOf(et.getAccessionId()), String.valueOf(et.getExperimentId()), codeMap.get(et.getValue()) });
+				}
+			}
+
+			csv.flush();
+			zos.closeEntry();
+		}
+
+		ZipEntry metaEntry = new ZipEntry("meta.xml");
+		metaEntry.setComment("Darwin Core Archive metadata");
+		metaEntry.setTime(System.currentTimeMillis());
+		zos.putNextEntry(metaEntry);
+		BufferedWriter osw = new BufferedWriter(new OutputStreamWriter(zos));
+		osw.write("<?xml version='1.0' encoding='utf-8'?>\n");
+		osw.write("<archive xmlns=\"http://rs.tdwg.org/dwc/text/\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:schemaLocation=\"http://rs.tdwg.org/dwc/text/ http://rs.tdwg.org/dwc/text/tdwg_dwc_text.xsd\">\n");
+		osw.write("<core encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
+		osw.write("\t<files><location>core.csv</location></files>\n");
+		osw.write("\t<id index=\"0\" />\n");
+		osw.write("\t<field index=\"1\" term=\"http://purl.org/germplasm/germplasmType#wiewsInstituteID\"/>\n");
+		osw.write("\t<field index=\"2\" term=\"http://purl.org/germplasm/germplasmTerm#germplasmIdentifier\"/>\n");
+		osw.write("\t<field index=\"3\" term=\"http://rs.tdwg.org/dwc/terms/genus\"/>\n");
+		osw.write("</core>\n");
+
+		for (int i = 0; i < metadataMethods.size(); i++) {
+			Method method = metadataMethods.get(i);
+
+			osw.write("<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
+			osw.write("\t<files><location>");
+			osw.write(method.getFieldName().toLowerCase());
+			osw.write(".csv</location></files>\n");
+			osw.write("\t<coreid index=\"0\" />\n");
+			osw.write("\t<field index=\"1\" term=\"http://rs.tdwg.org/dwc/terms/datasetID\"/>\n");
+			osw.write("\t<field index=\"2\" term=\"http://www.genesys-pgr.org/descriptors//");
+			osw.write(String.valueOf(method.getId()));
+			osw.write("\"/>\n");
+			osw.write("</extension>\n");
+		}
+		osw.write("</archive>\n");
+		osw.flush();
+		zos.closeEntry();
+
+		zos.finish();
+	}
 }

src/main/java/org/genesys2/server/servlet/controller/DatasetController.java

@@ -16,8 +16,14 @@
 
 package org.genesys2.server.servlet.controller;
 
+import java.io.IOException;
+import java.io.OutputStream;
+
+import javax.servlet.http.HttpServletResponse;
+
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.Metadata;
+import org.genesys2.server.service.DatasetService;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -29,6 +35,7 @@ import org.springframework.ui.ModelMap;
 import org.springframework.validation.Validator;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
 /**
@@ -41,10 +48,13 @@ public class DatasetController extends BaseController {
 
 	@Autowired
 	private SelectionBean selectionBean;
-	
+
 	@Autowired
 	private GenesysService genesysService;
 
+	@Autowired
+	private DatasetService datasetService;
+
 	@Autowired
 	private Validator validator;
 
@@ -72,8 +82,25 @@ public class DatasetController extends BaseController {
 		model.addAttribute("accessionMethods", genesysService.getMetadataTraitValues(metadata, accessions.getContent()));
 
 		model.addAttribute("selection", selectionBean);
-		
+
 		return "/metadata/view";
 	}
 
+	@RequestMapping(value = "/view/{id}/dwca", method = RequestMethod.GET, produces = "application/zip")
+	public void downloadDwca(@PathVariable(value = "id") long metadataId, HttpServletResponse response) throws IOException {
+		_logger.debug("Downloading data for " + metadataId);
+
+		Metadata metadata = genesysService.getMetadata(metadataId);
+		if (metadata == null) {
+			throw new ResourceNotFoundException();
+		}
+		response.setContentType("application/zip");
+		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-dataset-%1$s.zip\"", metadata.getUuid()));
+
+		// Write Darwin Core Archive to the stream.
+		OutputStream outputStream = response.getOutputStream();
+
+		datasetService.writeDataset(metadata, outputStream);
+		response.flushBuffer();
+	}
 }

src/main/resources/content/language.properties

@@ -250,6 +250,7 @@ search.button.label=Search
 admin.page.title=Genesys 2 Administration
 metadata.page.title=Datasets
 metadata.page.view.title=Dataset details
+metadata.download-dwca=Download dataset (Darwin Core Archive)
 page.login=Login
 
 traits.page.title=Descriptors

src/main/resources/spring/spring.properties

@@ -24,7 +24,7 @@ db.url=jdbc:mysql://127.0.0.1/genesys2?useUnicode=true&characterEncoding=UTF-8&u
 db.driverClassName = com.mysql.jdbc.Driver
 db.username = root
 db.password = 
-db.showSql=true
+db.showSql=false
 db.hbm2ddl=do-nothing
 
 c3p0.acquireIncrement=1

src/main/webapp/WEB-INF/jsp/metadata/view.jsp

@@ -49,6 +49,7 @@
 		</div>
 
 
+		<div><a href="<c:url value="/data/view/${metadata.id}/dwca" />"><spring:message code="metadata.download-dwca" /></a></div>
 		<h3>Observations</h3>
 	</c:if>