DwCA download of selected accessions

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

@@ -143,10 +143,8 @@ public interface GenesysService {
 
 	long countDatasets(FaoInstitute faoInstitute);
 
-	void writeAccessions(FaoInstitute faoInstitute, OutputStream outputStream) throws IOException;
-
 	void writeAccessions(String jsonFilter, OutputStream outputStream) throws IOException;
-	
+
 	void saveAliases(List<AccessionAlias> aliases);
 
 	void removeAliases(List<AccessionAlias> aliases);
@@ -179,5 +177,4 @@ public interface GenesysService {
 	Set<Long> listAccessions(FaoInstitute holdingInstitute, Set<Long> accessionIds);
 
 	int countAccessions(String jsonFilter);
-
 }

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

@@ -94,6 +94,7 @@ public class DirectMysqlQuery {
 	}
 
 	protected DirectMysqlQuery filter(ObjectNode jsonTree, MethodResolver methodResolver) {
+		createQuery(whereBuffer, "a.id", jsonTree.get("id"), params);
 		createQuery(whereBuffer, "a.taxGenus", jsonTree.get("genusId"), params);
 		createQuery(whereBuffer, "a.taxSpecies", jsonTree.get("speciesId"), params);
 		createQuery(whereBuffer, "a.acceNumb", jsonTree.get("acceNumb"), params);

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

@@ -849,11 +849,6 @@ public class GenesysServiceImpl implements GenesysService, TraitService, Dataset
 		}
 	}
 
-	@Override
-	public void writeAccessions(final FaoInstitute faoInstitute, OutputStream outputStream) throws IOException {
-		writeAccessions("{\"instCode\":[\"" + faoInstitute.getCode() + "\"]}", outputStream);
-	}
-
 	@Override
 	// TODO FIXME Need proper term URLs
 	public void writeAccessions(String jsonFilter, OutputStream outputStream) throws IOException {

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

@@ -347,7 +347,7 @@ public class ExplorerController extends BaseController {
 		return "/accession/map";
 	}
 
-	@RequestMapping(value = "/explore/dwca", method = RequestMethod.GET)
+	@RequestMapping(value = "/explore/dwca", method = RequestMethod.POST)
 	public void dwca(ModelMap model, @RequestParam(value = "crop", required = false, defaultValue = "") String cropName,
 			@RequestParam(value = "filter", required = false, defaultValue = "{}") String jsonFilter, HttpServletResponse response) throws IOException {
 

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

@@ -16,10 +16,14 @@
 
 package org.genesys2.server.servlet.controller;
 
+import java.io.IOException;
+import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
+import javax.servlet.http.HttpServletResponse;
+
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionGeo;
 import org.genesys2.server.service.GenesysService;
@@ -37,11 +41,17 @@ 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;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
 @Controller
 @Scope("request")
 @RequestMapping("/sel")
 public class SelectionController extends BaseController {
 
+	private ObjectMapper mapper = new ObjectMapper();
+	
 	@Autowired
 	private SelectionBean selectionBean;
 
@@ -104,6 +114,40 @@ public class SelectionController extends BaseController {
 		return "redirect:/sel/";
 	}
 
+	/**
+	 * Download DwCA of selected accessions
+	 * 
+	 * @param model
+	 * @param cropName
+	 * @param jsonFilter
+	 * @param response
+	 * @throws IOException
+	 */
+	@RequestMapping(value = "/dwca", method = RequestMethod.POST)
+	public void dwca(ModelMap model, HttpServletResponse response) throws IOException {
+		// Create JSON filter
+		ObjectNode jsonTree = mapper.createObjectNode();
+		ArrayNode arr = jsonTree.putArray("id");
+		for (long id : selectionBean.copy()) {
+			arr.add(id);
+		}
+
+		int countFiltered = selectionBean.size();
+		_logger.info("Attempting to download DwCA for " + countFiltered + " accessions");
+		if (countFiltered > 100000) {
+			throw new RuntimeException("Refusing to export more than 100,000 entries");
+		}
+
+		response.setContentType("application/zip");
+		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-selected.zip\""));
+
+		// Write Darwin Core Archive to the stream.
+		OutputStream outputStream = response.getOutputStream();
+
+		genesysService.writeAccessions(jsonTree.toString(), outputStream);
+		response.flushBuffer();
+	}
+
 	// TODO REMOVE
 	@RequestMapping(value = "/json/count", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
 	@ResponseBody

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

@@ -43,11 +43,17 @@ import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
+
 @Controller
 @Scope("request")
 @RequestMapping("/wiews")
 public class WiewsController extends BaseController {
 
+	private ObjectMapper mapper = new ObjectMapper();
+
 	@Autowired
 	private InstituteService instituteService;
 
@@ -198,22 +204,25 @@ public class WiewsController extends BaseController {
 		return "/accession/data";
 	}
 
-	@RequestMapping(value="/{wiewsCode}/dwca", method=RequestMethod.POST)
+	@RequestMapping(value = "/{wiewsCode}/dwca", method = RequestMethod.POST)
 	public void viewData(ModelMap model, @PathVariable(value = "wiewsCode") String wiewsCode, HttpServletResponse response) throws IOException {
-		_logger.debug("Viewing country " + wiewsCode);
 		FaoInstitute faoInstitute = instituteService.getInstitute(wiewsCode);
 		if (faoInstitute == null) {
 			throw new ResourceNotFoundException();
 		}
-
 		_logger.warn("Searching accessions of: " + faoInstitute);
+
+		// Create JSON filter
+		ObjectNode jsonTree = mapper.createObjectNode();
+		ArrayNode arr = jsonTree.putArray("instCode");
+		arr.add(faoInstitute.getCode());
+
+		// Write Darwin Core Archive to the stream.
 		response.setContentType("application/zip");
 		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-accessions-%1$s.zip\"", faoInstitute.getCode()));
 
-		// Write Darwin Core Archive to the stream.
 		OutputStream outputStream = response.getOutputStream();
-
-		genesysService.writeAccessions(faoInstitute, outputStream);
+		genesysService.writeAccessions(jsonTree.toString(), outputStream);
 		response.flushBuffer();
 	}
 }

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

@@ -12,12 +12,22 @@
 	</h1>
 
 	<div class="main-col-header clearfix">
-	<div class="nav-header pull-left">
-		<div class="results"><spring:message code="accessions.number" arguments="${pagedData.totalElements}" />
-		<a href="<c:url value="/explore/map"><c:param name="crop" value="${crop.shortName}" /><c:param name="filter">${jsonFilter}</c:param></c:url>">Map</a>
+	<div class="nav-header">
 		<c:if test="${pagedData.totalElements le 100000}">
-		<a href="<c:url value="/explore/dwca"><c:param name="crop" value="${crop.shortName}" /><c:param name="filter">${jsonFilter}</c:param></c:url>"><spring:message code="filter.download-dwca" /></a>
+		<form class="pull-right form-horizontal" method="post" action="/explore/dwca">
+			<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
+			<input type="hidden" name="crop" value="${crop.shortName}" />
+			<input type="hidden" name="filter" value="<c:out value="${jsonFilter}" />" />
+			<div class="row" style="margin-top: 2em;">
+				<div class="col-sm-4">
+					<button class="btn btn-default" type="submit"><spring:message code="filter.download-dwca" /></button>
+				</div>
+			</div>
+		</form>
 		</c:if>
+
+		<div class="results"><spring:message code="accessions.number" arguments="${pagedData.totalElements}" />
+		<a href="<c:url value="/explore/map"><c:param name="crop" value="${crop.shortName}" /><c:param name="filter">${jsonFilter}</c:param></c:url>">Map</a>
 		</div> 
 		<div class="pagination">
 			<spring:message code="paged.pageOfPages" arguments="${pagedData.number+1},${pagedData.totalPages}" />

src/main/webapp/WEB-INF/jsp/selection/index.jsp

@@ -20,8 +20,18 @@
 	<c:if test="${pagedData != null}">
 		
 		<div class="main-col-header clearfix">
-		<div class="nav-header pull-left">
+		<div class="nav-header">
+			<form class="pull-right form-horizontal" method="post" action="/sel/dwca">
+				<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
+				<div class="row" style="margin-top: 2em;">
+					<div class="col-sm-4">
+						<button class="btn btn-default" type="submit"><spring:message code="filter.download-dwca" /></button>
+					</div>
+				</div>
+			</form>
+
 			<div class="results"><spring:message code="accessions.number" arguments="${pagedData.totalElements}" /></div>
+			
 			<div class="pagination">
 				<spring:message code="paged.pageOfPages" arguments="${pagedData.number+1},${pagedData.totalPages}" />
 				<a href="<spring:url value=""><spring:param name="page" value="${pagedData.number eq 0 ? 1 : pagedData.number}" /><spring:param name="filter" value="${jsonFilter}" /></spring:url>"><spring:message code="pagination.previous-page" /></a>