MCPD XLSX

pom.xml

@@ -522,7 +522,12 @@
             <artifactId>transifex-client</artifactId>
             <version>0.2-SNAPSHOT</version>
         </dependency>
-    </dependencies>
+		 <dependency>
+		 	<groupId>org.apache.poi</groupId>
+		 	<artifactId>poi-ooxml</artifactId>
+		 	<version>3.10.1</version>
+		 </dependency>
+	</dependencies>
 
 	<build>
 		<plugins>

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

@@ -20,6 +20,7 @@ import org.genesys2.server.model.genesys.Method;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
+import org.springframework.data.domain.Sort;
 import org.springframework.jdbc.core.RowCallbackHandler;
 
 public interface GenesysLowlevelRepository {
@@ -53,4 +54,6 @@ public interface GenesysLowlevelRepository {
 
 	int countAccessions(AppliedFilters filter);
 
+	void listAccessionIds(AppliedFilters filter, Sort sort, RowCallbackHandler rowCallbackHandler);
+
 }

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

@@ -32,6 +32,7 @@ import org.genesys2.server.service.impl.DirectMysqlQuery;
 import org.genesys2.server.service.impl.DirectMysqlQuery.MethodResolver;
 import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Sort;
 import org.springframework.jdbc.BadSqlGrammarException;
 import org.springframework.jdbc.core.ArgumentPreparedStatementSetter;
 import org.springframework.jdbc.core.JdbcTemplate;
@@ -255,6 +256,34 @@ public class GenesysLowlevelRepositoryImpl implements GenesysLowlevelRepository
 			}
 		}, rowCallbackHandler);
 	}
+	
+
+	@Override
+	public void listAccessionIds(final AppliedFilters filter, final Sort sort, final RowCallbackHandler rowCallbackHandler) {
+		final DirectMysqlQuery directQuery = new DirectMysqlQuery("accession", "a");
+		directQuery.jsonFilter(filter, new MethodResolver() {
+			@Override
+			public Method getMethod(final long methodId) {
+				return GenesysLowlevelRepositoryImpl.this.methodRepository.findOne(methodId);
+			}
+		});
+		directQuery.sort(sort);
+
+		this.jdbcTemplate.query(new PreparedStatementCreator() {
+			@Override
+			public PreparedStatement createPreparedStatement(final Connection con) throws SQLException {
+				final PreparedStatement stmt = con.prepareStatement(directQuery
+						.getQuery("a.id"));
+
+				final ArgumentPreparedStatementSetter apss = new ArgumentPreparedStatementSetter(directQuery.getParameters());
+				apss.setValues(stmt);
+
+				// Set mysql JConnector to stream results
+//				stmt.setFetchSize(Integer.MIN_VALUE);
+				return stmt;
+			}
+		}, rowCallbackHandler);
+	}
 
 	@Override
 	public void listAccessionsGeo(final AppliedFilters filter, final RowCallbackHandler rowCallbackHandler) {

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

+/**
+ * Copyright 2014 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.service;
+
+import java.io.IOException;
+import java.io.OutputStream;
+
+import org.genesys2.server.service.impl.FilterHandler.AppliedFilters;
+
+/**
+ * Defines available downloads
+ * 
+ * @author matijaobreza
+ * 
+ */
+public interface DownloadService {
+
+	void writeXlsxMCPD(AppliedFilters filters, OutputStream outputStream) throws IOException;
+
+}

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

@@ -37,6 +37,7 @@ import org.genesys2.server.service.impl.FilterHandler.MinValueFilter;
 import org.genesys2.server.service.impl.FilterHandler.StartsWithFilter;
 import org.genesys2.server.service.impl.FilterHandler.ValueRangeFilter;
 import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Sort;
 import org.springframework.data.domain.Sort.Order;
 
 public class DirectMysqlQuery {
@@ -85,7 +86,9 @@ public class DirectMysqlQuery {
 		if (StringUtils.isNotBlank(alias)) {
 			sb.append(alias).append(StringUtils.SPACE);
 		}
-		sb.append("on ").append(onExpr).append(StringUtils.SPACE);
+		if (StringUtils.isNotBlank(onExpr)) {
+			sb.append("on ").append(onExpr).append(StringUtils.SPACE);
+		}
 		return this;
 	}
 
@@ -397,6 +400,30 @@ public class DirectMysqlQuery {
 		return params.toArray();
 	}
 
+	public DirectMysqlQuery sort(Sort sort) {
+		if (sortBuffer.length() != 0) {
+			throw new RuntimeException("sortBuffer is not blank, invalid use of #pageable(Pageable)");
+		}
+
+		sortBuffer.append("\n order by ");
+		for (final Order o : sort) {
+			if (LOG.isDebugEnabled()) {
+				LOG.debug("Order: " + o);
+			}
+			// ClassMetadata md =
+			// sessionFactory.getClassMetadata(Accession.class);
+			// md.
+			// EntityType<Accession> x =
+			// entityManager.getMetamodel().entity(Accession.class);
+			// System.err.println(x.getAttribute(o.getProperty()).getName());
+			// sb.append(x.getAttribute(o.getProperty()).getName());
+			sortBuffer.append("a.").append(o.getProperty());
+			sortBuffer.append(" ").append(o.getDirection());
+		}
+
+		return this;
+	}
+
 	public DirectMysqlQuery pageable(Pageable pageable) {
 		if (sortBuffer.length() != 0) {
 			throw new RuntimeException("sortBuffer is not blank, invalid use of #pageable(Pageable)");
@@ -407,21 +434,7 @@ public class DirectMysqlQuery {
 		}
 
 		if (pageable.getSort() != null) {
-			sortBuffer.append("\n order by ");
-			for (final Order o : pageable.getSort()) {
-				if (LOG.isDebugEnabled()) {
-					LOG.debug("Order: " + o);
-				}
-				// ClassMetadata md =
-				// sessionFactory.getClassMetadata(Accession.class);
-				// md.
-				// EntityType<Accession> x =
-				// entityManager.getMetamodel().entity(Accession.class);
-				// System.err.println(x.getAttribute(o.getProperty()).getName());
-				// sb.append(x.getAttribute(o.getProperty()).getName());
-				sortBuffer.append("a.").append(o.getProperty());
-				sortBuffer.append(" ").append(o.getDirection());
-			}
+			sort(pageable.getSort());
 		}
 		sortBuffer.append(" limit ");
 		if (LOG.isDebugEnabled()) {

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

@@ -38,6 +38,7 @@ import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.genesys.ParameterCategory;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.service.CropService;
+import org.genesys2.server.service.DownloadService;
 import org.genesys2.server.service.ElasticService;
 import org.genesys2.server.service.FilterConstants;
 import org.genesys2.server.service.GenesysFilterService;
@@ -57,6 +58,7 @@ import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Sort;
 import org.springframework.http.MediaType;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.ModelMap;
 import org.springframework.web.bind.annotation.PathVariable;
@@ -71,9 +73,11 @@ import com.jhlabs.image.MapColorsFilter;
 @Controller
 public class ExplorerController extends BaseController {
 
+	private static final int DOWNLOAD_LIMIT = 100000;
+
 	@Autowired
 	private GenesysFilterService filterService;
-	
+
 	@Autowired
 	private ElasticService elasticService;
 
@@ -98,6 +102,9 @@ public class ExplorerController extends BaseController {
 	@Autowired
 	private FilterHandler filterHandler;
 
+	@Autowired
+	private DownloadService downloadService;
+
 	private final ObjectMapper mapper = new ObjectMapper();
 
 	/**
@@ -161,11 +168,9 @@ public class ExplorerController extends BaseController {
 		}
 		model.addAttribute("crop", crop);
 
-		
 		// JSP works with JsonObject
 		final Map<?, ?> filters = mapper.readValue(appliedFilters.toString(), Map.class);
 		model.addAttribute("filters", filters);
-		
 
 		selectedFilters = appliedFilters.getFilterNames();
 		final List<GenesysFilter> currentFilters = filterHandler.selectFilters(selectedFilters);
@@ -187,7 +192,6 @@ public class ExplorerController extends BaseController {
 		return "/accession/explore";
 	}
 
-
 	/**
 	 * Browse all using Elasticsearch
 	 * 
@@ -195,7 +199,7 @@ public class ExplorerController extends BaseController {
 	 * @param page
 	 * @return
 	 * @throws IOException
-	 * @throws SearchException 
+	 * @throws SearchException
 	 */
 	@RequestMapping("/explore-es")
 	public String viewElasticFiltered(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page,
@@ -221,11 +225,9 @@ public class ExplorerController extends BaseController {
 		}
 		model.addAttribute("crop", crop);
 
-		
-		// JSP works with JsonObject  // TODO Handle -filter.key!!
+		// JSP works with JsonObject // TODO Handle -filter.key!!
 		final Map<?, ?> filters = mapper.readValue(appliedFilters.toString(), Map.class);
 		model.addAttribute("filters", filters);
-		
 
 		selectedFilters = appliedFilters.getFilterNames();
 		final List<GenesysFilter> currentFilters = filterHandler.selectFilters(selectedFilters);
@@ -247,7 +249,6 @@ public class ExplorerController extends BaseController {
 		return "/accession/explore-es";
 	}
 
-	
 	@RequestMapping(value = "/additional-filter", method = RequestMethod.GET)
 	public String getAdditionalFilters(ModelMap model, @RequestParam(value = "filter", required = true, defaultValue = "") String[] selectedFilters)
 			throws IOException {
@@ -332,6 +333,29 @@ public class ExplorerController extends BaseController {
 		response.flushBuffer();
 	}
 
+	@PreAuthorize("isAuthenticated()")
+	@RequestMapping(value = "/explore/download/mcpd", method = RequestMethod.POST)
+	public void downloadXlsxMCPD(ModelMap model, @RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter,
+			HttpServletResponse response) throws IOException {
+
+		final AppliedFilters appliedFilters = updateFilterWithCrop(null, jsonFilter);
+
+		final int countFiltered = genesysService.countAccessions(appliedFilters);
+		_logger.info("Attempting to download XLSX MCPD for " + countFiltered + " accessions");
+		if (countFiltered > DOWNLOAD_LIMIT) {
+			throw new RuntimeException("Refusing to export more than " + DOWNLOAD_LIMIT + " entries");
+		}
+
+		response.setContentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
+		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-filtered.xlsx\""));
+
+		// Write Darwin Core Archive to the stream.
+		final OutputStream outputStream = response.getOutputStream();
+
+		downloadService.writeXlsxMCPD(appliedFilters, outputStream);
+		response.flushBuffer();
+	}
+
 	private AppliedFilters updateFilterWithCrop(String cropName, String jsonFilter) throws IOException {
 		AppliedFilters appliedFilters = mapper.readValue(jsonFilter, AppliedFilters.class);
 
@@ -385,11 +409,10 @@ public class ExplorerController extends BaseController {
 	public void tile(@PathVariable("zoom") int zoom, @PathVariable("x") int x, @PathVariable("y") int y,
 			@RequestParam(value = "filter", required = true) String jsonFilter, @RequestParam(value = "color", required = false) String color,
 			HttpServletResponse response) {
-		
-		
+
 		try {
 			AppliedFilters appliedFilters = mapper.readValue(jsonFilter, AppliedFilters.class);
-			
+
 			byte[] image = mappingService.getTile(appliedFilters, zoom, x, y);
 			image = changeColor(color, image);
 			response.getOutputStream().write(image, 0, image.length);
@@ -444,7 +467,8 @@ public class ExplorerController extends BaseController {
 	}
 
 	@RequestMapping(value = "/explore/overview")
-	public String overview(ModelMap model, @RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter) throws IOException, SearchException {
+	public String overview(ModelMap model, @RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter) throws IOException,
+			SearchException {
 
 		AppliedFilters appliedFilters = mapper.readValue(jsonFilter, AppliedFilters.class);
 		String[] selectedFilters = appliedFilters.getFilterNames();

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

@@ -26,6 +26,7 @@ import javax.servlet.http.HttpServletResponse;
 
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.service.DownloadService;
 import org.genesys2.server.service.FilterConstants;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.impl.FilterHandler;
@@ -45,21 +46,20 @@ import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.ResponseBody;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-
 @Controller
 @Scope("request")
 @RequestMapping("/sel")
 public class SelectionController extends BaseController {
 
-	private final ObjectMapper mapper = new ObjectMapper();
-
 	@Autowired
 	private SelectionBean selectionBean;
 
 	@Autowired
 	private GenesysService genesysService;
 
+	@Autowired
+	private DownloadService downloadService;
+
 	@RequestMapping("/")
 	public String view(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page) {
 
@@ -151,6 +151,29 @@ public class SelectionController extends BaseController {
 		response.flushBuffer();
 	}
 
+	@RequestMapping(value = "/download/mcpd", method = RequestMethod.POST)
+	public void downloadXlsxMCPD(ModelMap model, HttpServletResponse response) throws IOException {
+		// Create JSON filter
+		final AppliedFilters appliedFilters = new AppliedFilters();
+		AppliedFilter arr = new FilterHandler.AppliedFilter().setFilterName(FilterConstants.ID);
+		for (final long id : selectionBean.copy()) {
+			arr.addFilterValue(new FilterHandler.LiteralValueFilter(id));
+		}
+		appliedFilters.add(arr);
+
+		final int countFiltered = genesysService.countAccessions(appliedFilters);
+		_logger.info("Attempting to download XLSX MCPD for " + countFiltered + " accessions");
+
+		response.setContentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
+		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-selected.xlsx\""));
+
+		// Write Darwin Core Archive to the stream.
+		final OutputStream outputStream = response.getOutputStream();
+
+		downloadService.writeXlsxMCPD(appliedFilters, outputStream);
+		response.flushBuffer();
+	}
+
 	// TODO REMOVE
 	@RequestMapping(value = "/json/count", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
 	@ResponseBody

src/main/resources/content/language.properties

@@ -358,6 +358,7 @@ filter.available=Available for distribution
 filter.donorCode=Donor institute
 filter.duplSite=Site of safety duplication
 filter.download-dwca=Download ZIP
+filter.download-mcpd=Download MCPD
 filter.add=Add filter
 filter.additional=Additional filters
 filter.apply=Apply

src/main/resources/template/download/.gitignore

+/~$*

src/main/webapp/WEB-INF/jsp/accession/explore.jsp

@@ -37,6 +37,13 @@
 					<button class="btn btn-default" type="submit"><spring:message code="filter.download-dwca" /></button>
 				</form>
 				</c:if>
+                <security:authorize access="isAuthenticated()">
+				<form style="display: inline-block" method="post" action="<c:url value="/explore/download/mcpd" />">
+					<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
+					<input type="hidden" name="filter" value="<c:out value="${jsonFilter}" />" />
+					<button class="btn btn-default" type="submit"><spring:message code="filter.download-mcpd" /></button>
+				</form>
+				</security:authorize>
 				<a class="btn btn-default" href="<c:url value="/explore/overview"><c:param name="filter">${jsonFilter}</c:param></c:url>"><span class="glyphicon glyphicon-eye-open"></span><span style="margin-left: 0.5em;"><spring:message code="data-overview.short" /></span></a>
 				<a class="btn btn-default" href="<c:url value="/explore/map"><c:param name="filter">${jsonFilter}</c:param></c:url>"><span class="glyphicon glyphicon-globe"></span><span style="margin-left: 0.5em;"><spring:message code="maps.view-map" /></span></a>
 			</div>