Feature #26151 Specifying columns to include in accession list /explore

src/main/java/org/genesys2/server/model/json/Api1Constants.java

@@ -21,6 +21,8 @@ package org.genesys2.server.model.json;
  */
 public interface Api1Constants {
 	public static interface Accession {
+
+		public static final String CROPE_NAME = "cropName";
 		/**
 		 * WIEWS code of accession holding institute.
 		 */
@@ -183,10 +185,12 @@ public interface Api1Constants {
 		 */
 		public static final String ACCEURL = "acceUrl";
 
+		public static final String SCIENTIFIC_NAME = "scientificName";
 	}
 
 	public static interface Collecting {
 
+		public static final String MISSION_ID = "collectingMissionID";
 		/**
 		 * Corresponds to COLLDATE
 		 */
@@ -230,6 +234,7 @@ public interface Api1Constants {
 
 	public static interface Geo {
 
+		public static final String LATITUDE_LONGITUDE = "latitudeAndLongitude";
 		/**
 		 * Latitude
 		 */

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

@@ -57,17 +57,20 @@ import org.springframework.data.domain.Pageable;
 public interface GenesysService {
 
 	/**
-	 * Return the number of active ({@link Accession#historic} == false) accession records
+	 * Return the number of active ({@link Accession#historic} == false)
+	 * accession records
 	 */
 	long countByInstitute(FaoInstitute institute);
 
 	/**
-	 * Return the number of active ({@link Accession#historic} == false) accession records
+	 * Return the number of active ({@link Accession#historic} == false)
+	 * accession records
 	 */
 	long countByOrigin(Country country);
 
 	/**
-	 * Return the number of active ({@link Accession#historic} == false) accession records
+	 * Return the number of active ({@link Accession#historic} == false)
+	 * accession records
 	 */
 	long countByLocation(Country country);
 
@@ -131,7 +134,7 @@ public interface GenesysService {
 	void updateAccessionInstitueRefs();
 
 	List<Accession> saveAccessions(FaoInstitute institute, List<Accession> matching);
-	
+
 	List<SvalbardData> saveSvalbards(List<SvalbardData> svalbards);
 
 	long countAvailableForDistribution(Set<Long> accessionIds);
@@ -139,7 +142,7 @@ public interface GenesysService {
 	Set<Long> filterAvailableForDistribution(Set<Long> accessionIds);
 
 	AccessionData saveAccession(AccessionData accession);
-	
+
 	List<Accession> saveAccessions(Iterable<Accession> accession);
 
 	void updateAccessionCount(FaoInstitute institute);
@@ -171,7 +174,7 @@ public interface GenesysService {
 	List<AccessionGeo> listAccessionsGeo(Set<Long> copy);
 
 	List<AccessionHistoric> removeAccessions(FaoInstitute institute, List<Accession> toDelete);
-	
+
 	void setInSvalbard(List<Accession> matching);
 
 	void addAccessions(List<Accession> accessions);
@@ -210,6 +213,10 @@ public interface GenesysService {
 
 	List<Long> listAccessionsIds(Taxonomy2 taxonomy);
 
+	List<String> columnsForDisplay();
+
+	List<String> defaultViewColumns();
+
 	public static class AllStuff {
 		public AllStuff(long id) {
 			this.id = id;

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

@@ -72,6 +72,7 @@ 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.model.impl.Organization;
+import org.genesys2.server.model.json.Api1Constants;
 import org.genesys2.server.persistence.domain.AccessionAliasRepository;
 import org.genesys2.server.persistence.domain.AccessionBreedingRepository;
 import org.genesys2.server.persistence.domain.AccessionCollectRepository;
@@ -1068,8 +1069,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		zos.putNextEntry(metaEntry);
 		final 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("<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");
@@ -1336,8 +1336,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		zos.putNextEntry(metaEntry);
 		final 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("<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");
@@ -1349,8 +1348,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		for (int i = 0; i < metadataMethods.size(); i++) {
 			final Method method = metadataMethods.get(i);
 
-			osw.write(
-					"<extension encoding=\"UTF-8\" fieldsTerminatedBy=\",\" linesTerminatedBy=\"\\n\" fieldsEnclosedBy=\"&quot;\" ignoreHeaderLines=\"0\">\n");
+			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");
@@ -1531,6 +1529,29 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		return toRemove;
 	}
 
+	@Override
+	public List<String> columnsForDisplay() {
+		List<String> columnList = new ArrayList<>();
+		columnList.add(Api1Constants.Accession.GENUS);
+		columnList.add(Api1Constants.Accession.SPECIES);
+		columnList.add(Api1Constants.Accession.SUBTAXA);
+		columnList.add(Api1Constants.Accession.CROPE_NAME);
+		columnList.add(Api1Constants.Geo.LATITUDE_LONGITUDE);
+		columnList.add(Api1Constants.Collecting.MISSION_ID);
+		return columnList;
+	}
+
+	@Override
+	public List<String> defaultViewColumns() {
+		List<String> columnList = new ArrayList<>();
+		columnList.add(Api1Constants.Accession.ACCENUMB);
+		columnList.add(Api1Constants.Accession.SCIENTIFIC_NAME);
+		columnList.add(Api1Constants.Accession.ORIGCTY);
+		columnList.add(Api1Constants.Accession.SAMPSTAT);
+		columnList.add(Api1Constants.Accession.INSTCODE);
+		return columnList;
+	}
+
 	@Override
 	public List<Long> listAccessionsIds(Taxonomy2 taxonomy) {
 		return accessionRepository.listAccessionsIds(taxonomy);

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

 /**
  * Copyright 2015 Global Crop Diversity Trust
- *
+ * <p/>
  * 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
- *
+ * <p/>
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * <p/>
  * 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.
@@ -25,10 +25,13 @@ import java.io.IOException;
 import java.io.OutputStream;
 import java.net.URI;
 import java.net.URISyntaxException;
+import java.util.Arrays;
+import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
 import javax.imageio.ImageIO;
+import javax.servlet.http.Cookie;
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang.ArrayUtils;
@@ -65,6 +68,7 @@ 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.CookieValue;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
@@ -142,15 +146,31 @@ public class ExplorerController extends BaseController {
 
 	/**
 	 * Browse all
-	 * 
+	 *
 	 * @param model
 	 * @param page
 	 * @return
 	 * @throws IOException
 	 */
 	@RequestMapping("/explore")
-	public String viewFiltered(ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page,
-			@RequestParam(value = "filter", required = true, defaultValue = "{}") String jsonFilter) throws IOException {
+	public String viewFiltered(HttpServletResponse response, ModelMap model, @RequestParam(value = "page", required = false, defaultValue = "1") int page,
+			@RequestParam(value = "filter", required = true, defaultValue = "{}") String jsonFilter,
+			@RequestParam(value = "columns", required = true, defaultValue = "") String columns,
+			@CookieValue(value = "columns", defaultValue = "") String cookieColumns) throws IOException {
+
+		if (columns != null && !columns.isEmpty()) {
+			String columnsForCookie = "";
+			for (String clmn : Arrays.asList(columns.split(","))) {
+				columnsForCookie += clmn + ",";
+			}
+			columnsForCookie = !columnsForCookie.isEmpty() && columnsForCookie.substring(columnsForCookie.length() - 1).equals(",") ? columnsForCookie
+					.substring(0, columnsForCookie.length() - 1) : columnsForCookie;
+			Cookie cookie = new Cookie("columns", columnsForCookie);
+			response.addCookie(cookie);
+			model.addAttribute("selectedColumns", columnsForCookie.isEmpty() ? Collections.emptyList() : Arrays.asList(columnsForCookie.split(",")));
+		} else if (!cookieColumns.isEmpty()) {
+			model.addAttribute("selectedColumns", Arrays.asList(cookieColumns.split(",")));
+		}
 
 		String[] selectedFilters = null;
 
@@ -187,6 +207,8 @@ public class ExplorerController extends BaseController {
 
 		_logger.info("Got: " + accessions);
 
+		model.addAttribute("defaultColumns", genesysService.defaultViewColumns());
+		model.addAttribute("availableColumns", genesysService.columnsForDisplay());
 		model.addAttribute("crops", cropService.list(getLocale()));
 		model.addAttribute("pagedData", accessions);
 		model.addAttribute("appliedFilters", appliedFilters);
@@ -198,7 +220,7 @@ public class ExplorerController extends BaseController {
 
 	/**
 	 * Browse all using Elasticsearch
-	 * 
+	 *
 	 * @param model
 	 * @param page
 	 * @return
@@ -401,7 +423,7 @@ public class ExplorerController extends BaseController {
 
 	/**
 	 * Change color of the tile
-	 * 
+	 *
 	 * @param color
 	 * @param imageBytes
 	 * @return
@@ -477,8 +499,8 @@ 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();
@@ -538,12 +560,13 @@ public class ExplorerController extends BaseController {
 	@RequestMapping(value = "/explore/shorten-url", method = RequestMethod.POST, produces = MediaType.APPLICATION_JSON_VALUE)
 	@ResponseBody
 	public Object getBriefURL(@RequestParam(value = "filter", required = false, defaultValue = "") String jsonFilter,
-			@RequestParam(value = "page", required = false, defaultValue = "1") int page) throws IOException, URISyntaxException {
+			@RequestParam(value = "page", required = false, defaultValue = "1") int page, @CookieValue(value = "columns") String columns) throws IOException,
+			URISyntaxException {
 
 		AppliedFilters appliedFilters = mapper.readValue(jsonFilter, AppliedFilters.class);
 
-		URI longUrl = new URIBuilder(baseUrl).setPath("/explore").addParameter("filter", appliedFilters.toString()).addParameter("page", Integer.toString(page))
-				.build();
+		URI longUrl = new URIBuilder(baseUrl).setPath("/explore").addParameter("filter", appliedFilters.toString())
+				.addParameter("page", Integer.toString(page)).addParameter("columns", columns).build();
 
 		final String shortenedUrl = urlShortenerService.shortenUrl(longUrl.toURL());
 

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

@@ -17,11 +17,13 @@
 package org.genesys2.server.servlet.controller;
 
 import java.text.DateFormatSymbols;
+import java.util.List;
 import java.util.Locale;
 
 import org.apache.commons.lang.StringUtils;
 import org.apache.commons.lang.math.RandomUtils;
 import org.genesys2.server.exception.UserException;
+import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.impl.Country;
 import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.User;
@@ -38,23 +40,23 @@ import com.fasterxml.jackson.databind.ObjectMapper;
 @Component
 public class JspHelper {
 
-    private static final String regExpr="[^\\w]+";
+	private static final String regExpr = "[^\\w]+";
 
-    private static final String delimiter="-";
-    
-    @Autowired
+	private static final String delimiter = "-";
+
+	@Autowired
 	private UserService userService;
-	
-    @Autowired
+
+	@Autowired
 	private GeoService geoService;
-	
-    @Autowired
+
+	@Autowired
 	private CropService cropService;
-	
-    @Autowired
+
+	@Autowired
 	private ObjectMapper objectMapper;
-	
-    @Autowired
+
+	@Autowired
 	private HtmlConverter htmlConverter;
 
 	public String userFullName(Long userId) {
@@ -84,6 +86,10 @@ public class JspHelper {
 		return cropService.getCrop(shortName);
 	}
 
+	public List<Crop> getCropsByAccession(Accession accession) {
+		return cropService.getCrops(accession.getTaxonomy());
+	}
+
 	public String toJson(Object object) throws JsonProcessingException {
 		return objectMapper.writer().writeValueAsString(object);
 	}

src/main/resources/content/language.properties

@@ -332,6 +332,7 @@ accession.availability.false=Not available
 accession.historic.true=Historic
 accession.historic.false=Active
 accession.acceUrl=Additional accession URL
+accession.scientificName=Scientific name
 
 accession.page.profile.title=Accession profile: {0}
 accession.page.resolve.title=Multiple accessions found
@@ -369,6 +370,7 @@ selection.add-many.button=Add to selection list
 savedmaps=Remember current map
 savedmaps.list=Map list
 savedmaps.save=Remember map
+taxonomy.subtaxa=Subtaxa
 
 filter.enter.title=Enter filter title
 filters.page.title=Data filters
@@ -423,6 +425,20 @@ filter.internal.message.more=More than {0}
 filter.internal.message.less=Less than {0}
 filter.lists=Listed on accession list
 
+columns.add=View
+columns.applay=Applay
+columns.genus=Genus
+columns.species=Species
+columns.subtaxa=Subtaxa
+columns.cropName=Crop name
+columns.latitudeAndLongitude=Latitude & Longitude
+columns.collectingMissionID=Collecting mission ID
+
+columns.acceNumb=Accession number
+columns.scientificName=Scientific name
+columns.orgCty=Country of origin
+columns.sampStat=Biological status of accession
+columns.instCode=Holding institute
 
 search.page.title=Full-text Search
 search.no-results=No matches found for your query.