Merge branch '393-download-genesys1-descriptor-lists-by-crop' into 'master'

Resolve "Download Genesys1 descriptor lists by crop"

Closes #393

See merge request genesys-pgr/genesys-server!313

src/main/java/org/genesys2/server/api/v0/CropsController.java

@@ -16,8 +16,12 @@
 
 package org.genesys2.server.api.v0;
 
+import java.io.EOFException;
+import java.io.IOException;
+import java.io.OutputStream;
 import java.util.List;
 
+import javax.servlet.http.HttpServletResponse;
 import javax.xml.bind.ValidationException;
 
 import org.genesys2.server.api.ApiBaseController;
@@ -38,6 +42,7 @@ import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.ui.ModelMap;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestBody;
 import org.springframework.web.bind.annotation.RequestMapping;
@@ -224,5 +229,27 @@ public class CropsController extends ApiBaseController {
 
 		cropService.rebuildTaxonomies(crop);
 	}
+	
+
+	@RequestMapping(value = "/{shortName}/descriptors/xlsx", method = RequestMethod.POST)
+	public void downloadExcel(ModelMap model, @PathVariable(value = "shortName") String shortName, HttpServletResponse response) throws IOException {
+		final Crop crop = cropService.getCrop(shortName);
+		if (crop == null) {
+			throw new ResourceNotFoundException();
+		}
+		LOG.debug("Downloading descriptors for crop {}", shortName);
+
+		// Write descriptors to the stream.
+		response.setContentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
+		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-descriptors-%1$s.xlsx\"", crop.getShortName()));
+
+		final OutputStream outputStream = response.getOutputStream();
+		try {
+			traitService.writeDescriptorsXlsx(crop, outputStream);
+			response.flushBuffer();
+		} catch (EOFException e) {
+			LOG.warn("Download was aborted: {}", e.getMessage());
+		}
+	}
 
 }

src/main/java/org/genesys2/server/mvc/CropController.java

@@ -16,15 +16,17 @@
 
 package org.genesys2.server.mvc;
 
+import java.io.EOFException;
 import java.io.IOException;
+import java.io.OutputStream;
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 import java.util.stream.Collectors;
 
-import com.fasterxml.jackson.databind.node.ArrayNode;
-import com.fasterxml.jackson.databind.node.ObjectNode;
+import javax.servlet.http.HttpServletResponse;
+
 import org.apache.commons.lang3.StringUtils;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.CropRule;
@@ -53,13 +55,15 @@ 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;
+import org.springframework.web.bind.annotation.ResponseBody;
 
 import com.fasterxml.jackson.core.JsonParseException;
 import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.core.type.TypeReference;
 import com.fasterxml.jackson.databind.JsonMappingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
-import org.springframework.web.bind.annotation.ResponseBody;
+import com.fasterxml.jackson.databind.node.ArrayNode;
+import com.fasterxml.jackson.databind.node.ObjectNode;
 
 @Controller
 @RequestMapping("/c")
@@ -298,4 +302,25 @@ public class CropController extends BaseController {
 		return "/descr/index";
 	}
 
+	@RequestMapping(value = "/{shortName}/descriptors/xlsx", method = RequestMethod.POST)
+	public void downloadExcel(ModelMap model, @PathVariable(value = "shortName") String shortName, HttpServletResponse response) throws IOException {
+		final Crop crop = cropService.getCrop(shortName);
+		if (crop == null) {
+			throw new ResourceNotFoundException();
+		}
+		LOG.debug("Downloading descriptors for crop {}", shortName);
+
+		// Write descriptors to the stream.
+		response.setContentType("application/vnd.openxmlformats-officedocument.spreadsheetml.sheet");
+		response.addHeader("Content-Disposition", String.format("attachment; filename=\"genesys-descriptors-%1$s.xlsx\"", crop.getShortName()));
+
+		final OutputStream outputStream = response.getOutputStream();
+		try {
+			traitService.writeDescriptorsXlsx(crop, outputStream);
+			response.flushBuffer();
+		} catch (EOFException e) {
+			LOG.warn("Download was aborted: {}", e.getMessage());
+		}
+	}
+
 }

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

@@ -24,6 +24,7 @@ import java.util.List;
 import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys.catalog.model.traits.Descriptor;
 import org.genesys2.server.model.genesys.Metadata;
+import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.service.filter.AccessionFilter;
 
 /**
@@ -46,4 +47,6 @@ public interface DownloadService {
 
 	void writeXlsxMetadata(Metadata metadata, OutputStream outputStream) throws IOException;
 
+	void writeXlsxGenesys1Descriptors(Crop crop, OutputStream outputStream) throws IOException;
+
 }

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

-/**
- * Copyright 2014 Global Crop Diversity Trust
+/*
+ * Copyright 2018 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.
@@ -12,10 +12,12 @@
  * 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 java.util.List;
 import java.util.Map;
 
@@ -144,4 +146,13 @@ public interface TraitService {
 
 	Page<Method> listMethods(Pageable pageable);
 
+	/**
+	 * Write descriptors as Excel to output stream.
+	 *
+	 * @param crop the crop
+	 * @param outputStream the output stream
+	 * @throws IOException 
+	 */
+	void writeDescriptorsXlsx(Crop crop, OutputStream outputStream) throws IOException;
+
 }

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

@@ -24,6 +24,7 @@ import java.lang.reflect.Method;
 import java.net.URLEncoder;
 import java.sql.ResultSet;
 import java.sql.SQLException;
+import java.text.MessageFormat;
 import java.util.Collection;
 import java.util.Date;
 import java.util.HashMap;
@@ -66,15 +67,18 @@ import org.genesys2.server.model.genesys.AccessionRemark;
 import org.genesys2.server.model.genesys.ExperimentAccessionTrait;
 import org.genesys2.server.model.genesys.Metadata;
 import org.genesys2.server.model.genesys.PDCI;
+import org.genesys2.server.model.genesys.Parameter;
 import org.genesys2.server.model.genesys.Taxonomy2;
 import org.genesys2.server.model.genesys.TraitCode;
 import org.genesys2.server.model.impl.Country;
+import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.mvc.JspHelper;
 import org.genesys2.server.persistence.GenesysLowlevelRepository;
 import org.genesys2.server.persistence.TraitValueRepository;
 import org.genesys2.server.service.DownloadService;
 import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.TraitService;
 import org.genesys2.server.service.filter.AccessionFilter;
 import org.genesys2.server.service.worker.AccessionProcessor;
 import org.genesys2.util.MCPDUtil;
@@ -84,6 +88,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Qualifier;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.i18n.LocaleContextHolder;
+import org.springframework.data.domain.PageRequest;
 import org.springframework.jdbc.core.RowCallbackHandler;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
@@ -148,6 +153,9 @@ public class DownloadServiceImpl implements DownloadService {
 	@Autowired
 	private GenesysService genesysService;
 
+	@Autowired
+	private TraitService traitService;
+
 	@Value("${base.url}")
 	private String baseUrl;
 
@@ -832,41 +840,8 @@ public class DownloadServiceImpl implements DownloadService {
 
 			for (final org.genesys2.server.model.genesys.Method method : metadataMethods) {
 				item++;
-
 				final Row nextRow = sheet.createRow(item);
-
-				updateCell(nextRow, 1, ""); // method.getUuid().toString());
-				updateCell(nextRow, 2, ""); // method.getVersion());
-				updateCell(nextRow, 3, method.getParameter().getCrop() == null ? "" : method.getParameter().getCrop().getShortName());
-				updateCell(nextRow, 4, "");
-				updateCell(nextRow, 5, method.getParameter().getTitle());
-				updateCell(nextRow, 6, catalogDescriptorCategory(method.getParameter().getCategory().getName()));
-				updateCell(nextRow, 7, method.getMethod());
-				updateCell(nextRow, 8, catalogDataType(method.getFieldType()));
-				updateCell(nextRow, 9, 2 == method.getFieldType() ? "TRUE" : 1 == method.getFieldType() ? "FALSE" : "");
-				// updateCell(nextRow, 10, method.getMinValue());
-				// updateCell(nextRow, 11, method.getMaxValue());
-
-				// if (method.getVocabulary() != null) {
-				// updateCell(nextRow, 12, method.getVocabulary().getUuid().toString());
-				// }
-
-				final StringBuilder codes = new StringBuilder();
-				final StringBuilder codeTitles = new StringBuilder();
-				final StringBuilder codeDescriptions = new StringBuilder();
-				
-				for (final TraitCode traitCode : TraitCode.parseOptions(method.getOptions())) {
-					codes.append(NEW_LINE).append(traitCode.getCode());
-					codeTitles.append(NEW_LINE).append(traitCode.getValue());
-					String description = ""; // traitCode.getDescription();
-					codeDescriptions.append(NEW_LINE).append(description != null ? description.replace(NEW_LINE, "; ") : "");
-				}
-				updateCell(nextRow, 13, codes.toString().replaceFirst(NEW_LINE, ""));
-				updateCell(nextRow, 14, codeTitles.toString().replaceFirst(NEW_LINE, ""));
-				updateCell(nextRow, 15, codeDescriptions.toString().replaceFirst(NEW_LINE, ""));
-
-				updateCell(nextRow, 16, method.getFieldName());
-				updateCell(nextRow, 17, method.getUnit());
+				writeGenesys1Method(method, nextRow);
 			}
 		});
 
@@ -961,6 +936,120 @@ public class DownloadServiceImpl implements DownloadService {
 		workbook.dispose();
 		outputStream.flush();
 	}
+	
+
+	@Override
+	public void writeXlsxGenesys1Descriptors(Crop crop, OutputStream outputStream) throws IOException {
+		final XSSFWorkbook template = new XSSFWorkbook(getClass().getResourceAsStream("/template/download/CATALOG-DESCRIPTORS.xlsx"));
+
+		final SuperSXSSFWorkbook workbook = new SuperSXSSFWorkbook(template, 50);
+		WorkbookStyles wbStyles = WorkbookStyles.create(workbook);
+
+		final Sheet datasetSheet = workbook.getXSSFSheet("metadata");
+
+		List<Parameter> parameters = traitService.listTraits(crop, new PageRequest(0, 1000)).getContent();
+		
+		String crops = parameters.stream().map(parameter -> parameter.getCrop().getShortName()).distinct().collect(Collectors.joining(";"));
+		descriptors1WriteMetadata(crop, crops, datasetSheet, wbStyles);
+
+		final SuperSXSSFSheet descriptorsSheet = workbook.getStreamingSheet("descriptors");
+		descriptorsSheet.setRowGenerator((sheet) -> {
+			int item = 5;
+
+			for (Parameter p: parameters) {
+				for (final org.genesys2.server.model.genesys.Method method : traitService.getTraitMethods(p)) {
+					item++;
+					final Row nextRow = sheet.createRow(item);
+					writeGenesys1Method(method, nextRow);
+				}
+			}
+		});
+
+		workbook.write(outputStream);
+		workbook.close();
+		workbook.dispose();
+		outputStream.flush();
+	}
+
+	private void writeGenesys1Method(final org.genesys2.server.model.genesys.Method method, final Row nextRow) {
+		updateCell(nextRow, 1, ""); // method.getUuid().toString());
+		updateCell(nextRow, 2, ""); // method.getVersion());
+		updateCell(nextRow, 3, method.getParameter().getCrop() == null ? "" : method.getParameter().getCrop().getShortName());
+		updateCell(nextRow, 4, "genesys1");
+		updateCell(nextRow, 5, StringUtils.trimToNull(method.getParameter().getTitle()));
+		updateCell(nextRow, 6, catalogDescriptorCategory(method.getParameter().getCategory().getName()));
+		updateCell(nextRow, 7, StringUtils.trimToNull(method.getMethod()));
+		updateCell(nextRow, 8, catalogDataType(method.getFieldType()));
+		updateCell(nextRow, 9, 2 == method.getFieldType() ? "TRUE" : 1 == method.getFieldType() ? "FALSE" : "");
+		// updateCell(nextRow, 10, method.getMinValue());
+		// updateCell(nextRow, 11, method.getMaxValue());
+
+		// if (method.getVocabulary() != null) {
+		// updateCell(nextRow, 12, method.getVocabulary().getUuid().toString());
+		// }
+
+		final StringBuilder codes = new StringBuilder();
+		final StringBuilder codeTitles = new StringBuilder();
+		final StringBuilder codeDescriptions = new StringBuilder();
+		
+		for (final TraitCode traitCode : TraitCode.parseOptions(method.getOptions())) {
+			codes.append(NEW_LINE).append(traitCode.getCode());
+			codeTitles.append(NEW_LINE).append(traitCode.getValue());
+			String description = ""; // traitCode.getDescription();
+			codeDescriptions.append(NEW_LINE).append(description != null ? description.replace(NEW_LINE, "; ") : "");
+		}
+		updateCell(nextRow, 13, codes.toString().replaceFirst(NEW_LINE, ""));
+		updateCell(nextRow, 14, codeTitles.toString().replaceFirst(NEW_LINE, ""));
+		updateCell(nextRow, 15, codeDescriptions.toString().replaceFirst(NEW_LINE, ""));
+
+		updateCell(nextRow, 16, StringUtils.trimToNull(method.getFieldName()));
+		updateCell(nextRow, 17, StringUtils.trimToNull(method.getUnit()));
+	}
+
+	private void descriptors1WriteMetadata(Crop crop, String crops, Sheet sheet, WorkbookStyles wbStyles) {
+		int row = 1, col = 5;
+		// 1 uuid
+		// updateCell(sheet.getRow(row++), col, metadata.getUuid().toString());
+		row++;
+		// 2 version
+		// updateCell(sheet.getRow(row++), col, metadata.getVersion());
+		row++;
+
+		// 3 Dataset provider
+		updateCell(sheet.getRow(row++), col, "Genesys");
+		// 4 Title
+		updateCell(sheet.getRow(row++), col, MessageFormat.format("Genesys 1 descriptors for {0}", crop.getName()));
+		// 5 Version
+		updateCell(sheet.getRow(row++), col, "genesys1");
+		// 6 Dataset description
+		updateCell(sheet.getRow(row++), col, MessageFormat.format("Descriptors for {0} as used by Genesys 1 trait database.", crop.getName()));
+		// 7 Dataset URL
+		updateCellUrl(sheet.getRow(row++), col, MessageFormat.format("https://www.genesys-pgr.org/c/{0}/descriptors", crop.getShortName()));
+		// 8 Date of registration of the dataset
+		updateCell(sheet.getRow(row++), col, new Date(), wbStyles.dateStyle);
+		// 9 License
+		updateCell(sheet.getRow(row++), col, "CC-BY");
+		// 10 Language of the dataset
+		updateCell(sheet.getRow(row++), col, "en");
+		// 11 Related resources
+		updateCell(sheet.getRow(row++), col, "");
+
+		// 12 Crops
+		if (crops != null) {
+			updateCell(sheet.getRow(row++), col, crops);
+		}
+
+		// 13 Dataset provider email
+		updateCellEmail(sheet.getRow(row++), col, "helpdesk@genesys-pgr.org");
+		// 14 Dataset provider addresss
+		updateCell(sheet.getRow(row++), col, "");
+
+		// 15 Recommended citation
+		{
+			// updateCell(sheet.getRow(row++), col, metadata.getCitation());
+			row++;
+		}
+	}
 
 	private String catalogDescriptorCategory(String name) {
 		switch (name) {
@@ -1157,4 +1246,5 @@ public class DownloadServiceImpl implements DownloadService {
 			return name;
 		return otherNames + ";" + name;
 	}
+
 }

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

@@ -16,6 +16,8 @@
 
 package org.genesys2.server.service.impl;
 
+import java.io.IOException;
+import java.io.OutputStream;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
@@ -38,6 +40,7 @@ import org.genesys2.server.persistence.MethodRepository;
 import org.genesys2.server.persistence.ParameterCategoryRepository;
 import org.genesys2.server.persistence.ParameterRepository;
 import org.genesys2.server.persistence.TraitValueRepository;
+import org.genesys2.server.service.DownloadService;
 import org.genesys2.server.service.HtmlSanitizer;
 import org.genesys2.server.service.TraitService;
 import org.slf4j.Logger;
@@ -64,6 +67,10 @@ public class TraitServiceImpl implements TraitService {
 	private GenesysLowlevelRepository genesysLowlevelRepository;
 	@Autowired
 	private CustomAclService aclService;
+
+	@Autowired
+	private DownloadService downloadService;
+
 	@Autowired
 	private HtmlSanitizer htmlSanitizer;
 
@@ -323,4 +330,9 @@ public class TraitServiceImpl implements TraitService {
 
 		return paramMethods;
 	}
+	
+	@Override
+	public void writeDescriptorsXlsx(Crop crop, OutputStream outputStream) throws IOException {
+		downloadService.writeXlsxGenesys1Descriptors(crop, outputStream);
+	}
 }

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

@@ -20,6 +20,16 @@
 	<div class="nav-header pull-left">
 		<local:paginate2 page="${pagedData}" />
 	</div>
+	<div class="pull-right list-view-controls">
+		<security:authorize access="isAuthenticated()">
+		<form class="form-horizontal" method="post" action="<c:url value="/c/${crop.shortName}/descriptors/xlsx" />">
+			<input type="hidden" name="${_csrf.parameterName}" value="${_csrf.token}"/>
+			<div class="col-sm-4">
+				<button class="btn btn-primary" type="submit"><spring:message code="metadata.download-xlsx" /></button>
+			</div>
+		</form>
+		</security:authorize>
+	</div>
 	</div>
 	
 	<c:if test="${crop ne null}">