Merge branch '436-accession-page-url' into 'master'

Resolve "Accession page URL"

Closes #436

See merge request genesys-pgr/genesys-server!389

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

@@ -19,41 +19,28 @@ package org.genesys2.server.mvc;
 import java.io.EOFException;
 import java.io.IOException;
 import java.io.OutputStreamWriter;
-import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
 
 import javax.servlet.http.HttpServletResponse;
 
 import org.apache.commons.lang.StringUtils;
-import org.genesys.blocks.auditlog.service.AuditTrailService;
-import org.genesys.catalog.service.DatasetService;
-import org.genesys.filerepository.InvalidRepositoryPathException;
-import org.genesys.filerepository.model.ImageGallery;
 import org.genesys2.server.exception.NotFoundElement;
 import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.genesys.Accession;
-import org.genesys2.server.model.genesys.AccessionCollect;
-import org.genesys2.server.model.genesys.AccessionGeo;
-import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.server.model.genesys.Taxonomy2;
-import org.genesys2.server.model.impl.Crop;
 import org.genesys2.server.model.impl.FaoInstitute;
 import org.genesys2.server.service.AccessionService;
-import org.genesys2.server.service.ClimateDataService;
 import org.genesys2.server.service.DownloadService;
 import org.genesys2.server.service.FilterConstants;
 import org.genesys2.server.service.GenesysService;
-import org.genesys2.server.service.InstituteFilesService;
 import org.genesys2.server.service.InstituteService;
 import org.genesys2.server.service.TaxonomyService;
-import org.genesys2.server.service.TraitService;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
-import org.springframework.security.core.context.SecurityContextHolder;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.ModelMap;
 import org.springframework.web.bind.annotation.GetMapping;
@@ -77,26 +64,13 @@ public class AccessionController extends BaseController {
 	@Autowired
 	private GenesysService genesysService;
 
-	@Autowired
-	private TraitService traitService;
 
 	@Autowired
 	private TaxonomyService taxonomyService;
 
-	@Autowired
-	private InstituteFilesService instituteFilesService;
-
-	@Autowired
-	private ClimateDataService climateDataService;
 
 	@Autowired
 	private DownloadService downloadService;
-	
-	@Autowired
-	private AuditTrailService auditService;
-
-	@Autowired
-	private DatasetService datasetService;
 
 	@Autowired
 	private AccessionService accessionService;
@@ -104,8 +78,9 @@ public class AccessionController extends BaseController {
 	@Value("${base.url}")
 	private String baseUrl;
 
-	@RequestMapping(value = "/id/{accessionId}", produces = { MediaType.APPLICATION_JSON_VALUE })
-	public @ResponseBody AccessionDetails viewJson(ModelMap model, @PathVariable(value = "accessionId") long accessionId) {
+	@RequestMapping(value = "/id/{accessionId}", produces = {MediaType.APPLICATION_JSON_VALUE})
+	public @ResponseBody
+	AccessionDetails viewJson(ModelMap model, @PathVariable(value = "accessionId") long accessionId) {
 		AccessionDetails ad = genesysService.getAccessionDetails(accessionId);
 		if (ad == null) {
 			throw new NotFoundElement();
@@ -116,94 +91,24 @@ public class AccessionController extends BaseController {
 	@RequestMapping(value = "/id/{accessionId}")
 	public ModelAndView view(ModelMap model, @PathVariable(value = "accessionId") long accessionId) {
 		LOG.debug("Viewing ACN {}", accessionId);
+
 		final Accession accession = genesysService.getAccession(accessionId);
-		
+
 		if (accession == null) {
 			throw new NotFoundElement();
 		}
 
-		if (accession.getDoi() != null) {
-			// Permanent HTTP redirect to the DOI URL
-			RedirectView rv = new RedirectView();
-		    rv.setStatusCode(HttpStatus.MOVED_PERMANENTLY);
-		    rv.setUrl(baseUrl + "/" + accession.getDoi());
-		    return new ModelAndView(rv);
-		}
-		
-		return displayAccession(model, accession);
-	}
-
-	/**
-	 * Load the details to display full accession details page
-	 * 
-	 * @param accession
-	 * @return
-	 */
-	public ModelAndView displayAccession(ModelMap model, Accession accession) {
-		AccessionId accessionId = accession.getAccessionId();
-
-		model.addAttribute("accession", accession);
-
-		model.addAttribute("accessionNames", genesysService.listAccessionNames(accessionId));
-		model.addAttribute("accessionAliases", accessionId.getAliases());
-		model.addAttribute("accessionDatasets", datasetService.listByAccession(accession));
-
-		model.addAttribute("accessionExchange", accession);
-		
-		AccessionCollect accessionCollect = accessionId.getColl();
-		model.addAttribute("accessionCollect", accessionCollect);
-
-		model.addAttribute("accessionBreeding", accession);
-		
-		AccessionGeo accessionGeo = accessionId.getGeo();
-		model.addAttribute("accessionGeo", accessionGeo);
-
-		if (SecurityContextHolder.getContext().getAuthentication().isAuthenticated()) {
-			// only for authenticated users
-			model.addAttribute("auditAccession", auditService.auditLogs(accession));
-			model.addAttribute("auditAccessionId", auditService.auditLogs(accessionId));
-			model.addAttribute("auditAccessionCollect", auditService.auditLogs(accessionCollect));
-			model.addAttribute("auditAccessionGeo", auditService.auditLogs(accessionGeo));
-		}
-
-		model.addAttribute("svalbardDeposits", genesysService.getSvalbardData(accessionId));
-		model.addAttribute("accessionRemarks", accessionId.getRemarks());
-
-		model.addAttribute("metadatas", genesysService.listMetadata(accessionId));
-		model.addAttribute("methods", traitService.listMethods(accessionId));
-		model.addAttribute("methodValues", genesysService.getAccessionTraitValues(accessionId));
-
-		if (accession.getCrop() != null) {
-			List<Crop> crops = new ArrayList<Crop>();
-			crops.add(accession.getCrop());
-			model.addAttribute("crops", crops);
+		RedirectView rv = new RedirectView();
+		rv.setStatusCode(HttpStatus.MOVED_PERMANENTLY);
+		if (StringUtils.isNotEmpty(accession.getDoi())) {
+			rv.setUrl("/" + accession.getDoi());
 		} else {
-			// TODO Remove
-			// model.addAttribute("crops", cropService.getCrops(accession.getTaxonomy()));
-		}
-
-		// Worldclim data
-		if (accessionGeo != null && accessionGeo.getTileIndex() != null) {
-			model.addAttribute("worldclimJson", climateDataService.jsonForTile(accessionGeo.getTileIndex()));
+			rv.setUrl("/a/" + accession.getUuid().toString());
 		}
-
-		model.addAttribute("pdci", accessionId.getPdci());
-		model.addAttribute("institutePDCI", accession.getInstitute().getStatisticsPDCI());
-
-		ImageGallery imageGallery = null;
-		try {
-			imageGallery = this.instituteFilesService.loadImageGallery(accession.getInstitute(), accession);
-		} catch (InvalidRepositoryPathException e) {
-			LOG.warn("Error loading image gallery for accession={}. {}", accession.getAccessionNumber(), e.getMessage());
-		}
-		if (imageGallery != null) {
-			model.addAttribute("thumbnailFormat", "200x200");
-			model.addAttribute("imageGallery", imageGallery);
-		}
-
-		return new ModelAndView("/accession/details", model);
+		return new ModelAndView(rv);
 	}
 
+
 	@RequestMapping("/{holdingInstitute}/{genus}/{accessionName:.+}")
 	public String viewInstituteAccession(ModelMap model, @PathVariable(value = "holdingInstitute") String holdingInstitute,
 			@PathVariable(value = "genus") String genus, @PathVariable(value = "accessionName") String accessionName) {
@@ -218,7 +123,7 @@ public class AccessionController extends BaseController {
 			if (accession == null) {
 				throw new NotFoundElement();
 			} else {
-				return "redirect:/acn/id/" + accession.getId();
+				return "redirect:/a/" + accession.getUuid();
 			}
 		} catch (NonUniqueAccessionException e) {
 			return "redirect:/acn/" + holdingInstitute + "/" + accessionName;
@@ -238,7 +143,7 @@ public class AccessionController extends BaseController {
 			throw new NotFoundElement();
 		}
 		if (accessions.size() == 1) {
-			return "redirect:/acn/id/" + accessions.get(0).getId();
+			return "redirect:/a/" + accessions.get(0).getUuid();
 		}
 
 		model.addAttribute("faoInstitute", faoInstitute);
@@ -249,17 +154,21 @@ public class AccessionController extends BaseController {
 	}
 
 	@GetMapping(value = "/{uuid:\\w{8}\\-\\w{4}.+}")
-	public String viewAccessionByUUID(final ModelMap model, @PathVariable("uuid") final UUID uuid) {
+	public ModelAndView viewAccessionByUUID(final ModelMap model, @PathVariable("uuid") final UUID uuid) {
 		final Accession accession = accessionService.getByUuid(uuid);
 
 		if (accession == null) {
 			throw new NotFoundElement();
 		}
+
+		RedirectView rv = new RedirectView();
+		rv.setStatusCode(HttpStatus.MOVED_PERMANENTLY);
 		if (StringUtils.isNotEmpty(accession.getDoi())) {
-			return "redirect:/" + accession.getDoi();
+			rv.setUrl("/" + accession.getDoi());
 		} else {
-			return "redirect:/acn/id/" + accession.getId();
+			rv.setUrl("/a/" + accession.getUuid().toString());
 		}
+		return new ModelAndView(rv);
 	}
 
 	/**

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

+/*
+ * Copyright 2019 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.mvc;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+
+import org.genesys.blocks.auditlog.service.AuditTrailService;
+import org.genesys.catalog.service.DatasetService;
+import org.genesys.filerepository.InvalidRepositoryPathException;
+import org.genesys.filerepository.model.ImageGallery;
+import org.genesys2.server.exception.NotFoundElement;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionCollect;
+import org.genesys2.server.model.genesys.AccessionGeo;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.impl.Crop;
+import org.genesys2.server.service.AccessionService;
+import org.genesys2.server.service.ClimateDataService;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.InstituteFilesService;
+import org.genesys2.server.service.TraitService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import org.springframework.security.core.context.SecurityContextHolder;
+import org.springframework.stereotype.Controller;
+import org.springframework.ui.ModelMap;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.view.RedirectView;
+
+/**
+ * Handles accession display on `/a/...` URL prefix using UUID
+ */
+@Controller
+@RequestMapping("/a")
+public class AcnController extends BaseController {
+
+	@Autowired
+	private GenesysService genesysService;
+
+	@Autowired
+	private TraitService traitService;
+
+	@Autowired
+	private AuditTrailService auditService;
+
+	@Autowired
+	private DatasetService datasetService;
+
+	@Autowired
+	private InstituteFilesService instituteFilesService;
+
+	@Autowired
+	private ClimateDataService climateDataService;
+
+	@Autowired
+	private AccessionService accessionService;
+
+	@RequestMapping(value = "/{uuid:\\w{8}\\-\\w{4}.+}")
+	public ModelAndView view(ModelMap model, @PathVariable(value = "uuid") UUID uuid) {
+		final Accession accession = accessionService.getByUuid(uuid);
+
+		if (accession == null) {
+			throw new NotFoundElement();
+		}
+
+		if (accession.getDoi() != null) {
+			// Permanent HTTP redirect to the DOI URL
+			RedirectView rv = new RedirectView();
+			rv.setStatusCode(HttpStatus.MOVED_PERMANENTLY);
+			rv.setUrl("/" + accession.getDoi());
+			return new ModelAndView(rv);
+		}
+
+		return displayAccession(model, accession);
+	}
+
+
+	/**
+	 * Load the details to display full accession details page
+	 *
+	 * @param accession
+	 * @return
+	 */
+	public ModelAndView displayAccession(ModelMap model, Accession accession) {
+		AccessionId accessionId = accession.getAccessionId();
+
+		model.addAttribute("accession", accession);
+
+		model.addAttribute("accessionNames", genesysService.listAccessionNames(accessionId));
+		model.addAttribute("accessionAliases", accessionId.getAliases());
+		model.addAttribute("accessionDatasets", datasetService.listByAccession(accession));
+
+		model.addAttribute("accessionExchange", accession);
+
+		AccessionCollect accessionCollect = accessionId.getColl();
+		model.addAttribute("accessionCollect", accessionCollect);
+
+		model.addAttribute("accessionBreeding", accession);
+
+		AccessionGeo accessionGeo = accessionId.getGeo();
+		model.addAttribute("accessionGeo", accessionGeo);
+
+		if (SecurityContextHolder.getContext().getAuthentication().isAuthenticated()) {
+			// only for authenticated users
+			model.addAttribute("auditAccession", auditService.auditLogs(accession));
+			model.addAttribute("auditAccessionId", auditService.auditLogs(accessionId));
+			model.addAttribute("auditAccessionCollect", auditService.auditLogs(accessionCollect));
+			model.addAttribute("auditAccessionGeo", auditService.auditLogs(accessionGeo));
+		}
+
+		model.addAttribute("svalbardDeposits", genesysService.getSvalbardData(accessionId));
+		model.addAttribute("accessionRemarks", accessionId.getRemarks());
+
+		model.addAttribute("metadatas", genesysService.listMetadata(accessionId));
+		model.addAttribute("methods", traitService.listMethods(accessionId));
+		model.addAttribute("methodValues", genesysService.getAccessionTraitValues(accessionId));
+
+		if (accession.getCrop() != null) {
+			List<Crop> crops = new ArrayList<Crop>();
+			crops.add(accession.getCrop());
+			model.addAttribute("crops", crops);
+		}
+
+		// Worldclim data
+		if (accessionGeo != null && accessionGeo.getTileIndex() != null) {
+			model.addAttribute("worldclimJson", climateDataService.jsonForTile(accessionGeo.getTileIndex()));
+		}
+
+		model.addAttribute("pdci", accessionId.getPdci());
+		model.addAttribute("institutePDCI", accession.getInstitute().getStatisticsPDCI());
+
+		ImageGallery imageGallery = null;
+		try {
+			imageGallery = this.instituteFilesService.loadImageGallery(accession.getInstitute(), accession);
+		} catch (InvalidRepositoryPathException e) {
+			LOG.warn("Error loading image gallery for accession={}. {}", accession.getAccessionNumber(), e.getMessage());
+		}
+		if (imageGallery != null) {
+			model.addAttribute("thumbnailFormat", "200x200");
+			model.addAttribute("imageGallery", imageGallery);
+		}
+
+		return new ModelAndView("/accession/details", model);
+	}
+
+}
\ No newline at end of file

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

@@ -44,7 +44,7 @@ public class DoiController extends BaseController {
 	private GenesysService genesysService;
 
 	@Autowired
-	private AccessionController accessionController;
+	private AcnController accessionController;
 
 	@RequestMapping(value = "/10.{dummy:[0-9]+}/**")
 	public ModelAndView view(HttpServletRequest request, ModelMap model) {

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

@@ -75,7 +75,7 @@ public class ResolverController {
 		}
 
 		if (resolved instanceof Accession) {
-			return "redirect:/acn/id/" + ((Accession) resolved).getId();
+			return "redirect:/a/" + uuid;
 		}
 
 		if (resolved instanceof AccessionHistoric) {

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

@@ -259,6 +259,7 @@ public class SelectionController extends BaseController {
 				g.lat = acnGeo.getLatitude();
 				g.lng = acnGeo.getLongitude();
 				AccessionData a = genesysService.getAccession(g.id);
+				g.uuid = a.getUuid().toString();
 				g.accessionName = a.getAccessionNumber();
 				g.instCode = a.getInstituteCode();
 				geo.add(g);
@@ -294,6 +295,7 @@ public class SelectionController extends BaseController {
 	}
 
 	public static class AccessionGeoJson {
+		public String uuid;
 		public long id;
 		public Double lat;
 		public Double lng;

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

@@ -434,7 +434,7 @@ public class GenesysFilterServiceImpl implements GenesysFilterService {
 			@Override
 			public PreparedStatement createPreparedStatement(Connection con) throws SQLException {
 				final PreparedStatement stmt = con.prepareStatement(directQuery.getQuery(distinct ? "distinct geo.longitude, geo.latitude"
-						: "a.id, a.acceNumb, a.instCode, geo.longitude, geo.latitude, geo.datum, geo.uncertainty "));
+						: "a.id, acce.uuid, a.acceNumb, a.instCode, geo.longitude, geo.latitude, geo.datum, geo.uncertainty "));
 				// Set mysql JConnector to stream results
 				stmt.setFetchSize(Integer.MIN_VALUE);
 				new ArgumentPreparedStatementSetter(directQuery.getParameters()).setValues(stmt);

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

@@ -22,10 +22,12 @@ import java.io.ByteArrayOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.OutputStreamWriter;
+import java.nio.ByteBuffer;
 import java.sql.ResultSet;
 import java.sql.SQLException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.UUID;
 import java.util.concurrent.atomic.AtomicInteger;
 
 import javax.imageio.ImageIO;
@@ -143,6 +145,8 @@ public class MappingServiceImpl implements MappingService, InitializingBean {
 
 					ObjectNode properties;
 					feature.set("properties", properties = feature.objectNode());
+					ByteBuffer bb = ByteBuffer.wrap(rs.getBytes("uuid"));
+					properties.put("uuid", new UUID(bb.getLong(), bb.getLong()).toString());
 					properties.put("acceNumb", rs.getString("acceNumb"));
 					properties.put("instCode", rs.getString("instCode"));
 					properties.put("datum", rs.getString("datum"));

src/main/webapp/WEB-INF/jsp/accession/details-turtle.jsp

@@ -22,7 +22,7 @@
         <c:set var = "accessionDetailUrl" value = "/${accession.doi}"/>
     </c:when>
     <c:otherwise>
-        <c:set var = "accessionDetailUrl" value = "/acn/id/${accession.id}"/>
+        <c:set var = "accessionDetailUrl" value = "/a/${accession.uuid}"/>
     </c:otherwise>
 </c:choose>
   <${baseUrl}<c:out value="${fn:trim(accessionDetailUrl)}" />>

src/main/webapp/WEB-INF/jsp/accession/explore2.jsp

@@ -1038,7 +1038,7 @@
                     text: pagedData.content[i].acceNumb
                 }).appendTo(