DOI resolver for accessions

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

@@ -285,9 +285,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public Accession getAccession(AccessionIdentifier3 aid3) throws NonUniqueAccessionException {
 		try {
 			Accession accession = accessionRepository.findOne(aid3.getHoldingInstitute(), aid3.getAccessionName(), aid3.getGenus());
-			if (accession != null)
-				accession.getStoRage().size();
-			return accession;
+			return lazyLoadAccession(accession);
 		} catch (IncorrectResultSizeDataAccessException e) {
 			LOG.error("Duplicate accession name instCode=" + aid3.getHoldingInstitute() + " acceNumb=" + aid3.getAccessionName() + " genus=" + aid3.getGenus());
 			throw new NonUniqueAccessionException(aid3.getHoldingInstitute(), aid3.getAccessionName(), aid3.getGenus());
@@ -298,9 +296,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 	public Accession getAccession(String instCode, String acceNumb) throws NonUniqueAccessionException {
 		try {
 			Accession accession = accessionRepository.findByInstituteCodeAndAccessionName(instCode, acceNumb);
-			if (accession != null)
-				accession.getStoRage().size();
-			return accession;
+			return lazyLoadAccession(accession);
 		} catch (IncorrectResultSizeDataAccessException e) {
 			LOG.error("Duplicate accession name instCode=" + instCode + " acceNumb=" + acceNumb);
 			throw new NonUniqueAccessionException(instCode, acceNumb);
@@ -314,9 +310,7 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 		}
 		try {
 			Accession accession = accessionRepository.findOne(instCode, acceNumb, genus);
-			if (accession != null)
-				accession.getStoRage().size();
-			return accession;
+			return lazyLoadAccession(accession);
 		} catch (IncorrectResultSizeDataAccessException e) {
 			LOG.error("Duplicate accession name instCode=" + instCode + " acceNumb=" + acceNumb);
 			throw new NonUniqueAccessionException(instCode, acceNumb);
@@ -338,7 +332,14 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 
 	@Override
 	public Accession getAccessionByDOI(final String doi) {
-		return accessionRepository.findByDoi(doi);
+		Accession accession = accessionRepository.findByDoi(doi);
+		return lazyLoadAccession(accession);
+	}
+
+	private Accession lazyLoadAccession(Accession accession) {
+		if (accession != null)
+			accession.getStoRage().size();
+		return accession;
 	}
 
 	@Override

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

@@ -23,6 +23,8 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
 
+import javax.servlet.http.HttpServletResponse;
+
 import org.genesys2.server.filerepository.model.ImageGallery;
 import org.genesys2.server.filerepository.service.ImageGalleryService;
 import org.genesys2.server.model.dataset.DS;
@@ -46,6 +48,8 @@ import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.genesys2.server.service.impl.PDCICalculator;
 import org.genesys2.spring.ResourceNotFoundException;
 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.stereotype.Controller;
 import org.springframework.ui.ModelMap;
@@ -54,8 +58,8 @@ 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 javax.servlet.http.HttpServletResponse;
+import org.springframework.web.servlet.ModelAndView;
+import org.springframework.web.servlet.view.RedirectView;
 
 @Controller
 @RequestMapping("/acn")
@@ -92,6 +96,9 @@ public class AccessionController extends BaseController {
 
 	@Autowired
 	private DownloadService downloadService;
+	
+	@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) {
@@ -103,12 +110,32 @@ public class AccessionController extends BaseController {
 	}
 
 	@RequestMapping(value = "/id/{accessionId}")
-	public String view(ModelMap model, @PathVariable(value = "accessionId") long accessionId) {
+	public ModelAndView view(ModelMap model, @PathVariable(value = "accessionId") long accessionId) {
 		_logger.debug("Viewing ACN " + accessionId);
 		final Accession accession = genesysService.getAccession(accessionId);
+		
 		if (accession == null) {
 			throw new ResourceNotFoundException();
 		}
+
+		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) {
 		model.addAttribute("accession", accession);
 		model.addAttribute("accessionNames", genesysService.listAccessionNames(accession.getAccessionId()));
 		model.addAttribute("accessionAliases", genesysService.listAccessionAliases(accession.getAccessionId()));
@@ -173,7 +200,7 @@ public class AccessionController extends BaseController {
 			model.addAttribute("imageGallery", imageGallery);
 		}
 
-		return "/accession/details";
+		return new ModelAndView("/accession/details", model);
 	}
 
 	@RequestMapping("/{holdingInstitute}/{genus}/{accessionName:.+}")

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

+/*
+ * Copyright 2017 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.servlet.controller;
 
+import javax.servlet.http.HttpServletRequest;
+
+import org.genesys2.server.model.elastic.AccessionDetails;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.MediaType;
 import org.springframework.stereotype.Controller;
-import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.ui.ModelMap;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.servlet.HandlerMapping;
+import org.springframework.web.servlet.ModelAndView;
 
 /**
+ * View resolver for DOIs handles: Accessions
+ * 
  * @author Maxym Borodenko
+ * @author Matija Obreza
  */
 @Controller
 public class DoiController extends BaseController {
 
-    @Autowired
-    private GenesysService genesysService;
-
-    @RequestMapping("/{firstPartDOI:10\\.[0-9]+}/{secondPartDOI:.+}")
-    public String view(@PathVariable String firstPartDOI, @PathVariable String secondPartDOI) {
-        final String doi = firstPartDOI + "/" + secondPartDOI;
-
-        _logger.info("Lookup accession by DOI");
-        Accession accession = genesysService.getAccessionByDOI(doi);
-        if (accession == null) {
-            throw new ResourceNotFoundException();
-        } else {
-            return "forward:/acn/id/" + accession.getId().toString();
-        }
-    }
+	@Autowired
+	private GenesysService genesysService;
+
+	@Autowired
+	private AccessionController accessionController;
+
+	@RequestMapping(value = "/10.{dummy:[0-9]+}/**")
+	public ModelAndView view(HttpServletRequest request, ModelMap model) {
+		final String fullpath = (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
+		final String doi = fullpath.substring(1);
+
+		_logger.debug("Lookup accession by DOI=" + doi);
+
+		Accession accession = genesysService.getAccessionByDOI(doi);
+		if (accession == null) {
+			throw new ResourceNotFoundException();
+		} else {
+			return accessionController.displayAccession(model, accession);
+		}
+	}
+
+	@RequestMapping(value = "/10.{dummy:[0-9]+}/**}", headers = { "Accept: application/json" }, produces = { MediaType.APPLICATION_JSON_VALUE })
+	public @ResponseBody AccessionDetails viewJson(HttpServletRequest request, ModelMap model) {
+		final String fullpath = (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
+		final String doi = fullpath.substring(1);
+
+		_logger.debug("Lookup accession by DOI=" + doi);
+
+		Accession accession = genesysService.getAccessionByDOI(doi);
+		if (accession == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		AccessionDetails ad = genesysService.getAccessionDetails(accession.getId());
+		if (ad == null) {
+			throw new ResourceNotFoundException();
+		}
+		return ad;
+	}
 }

src/main/java/org/genesys2/server/servlet/filter/EnvVariablesFilter.java

@@ -37,6 +37,9 @@ public class EnvVariablesFilter extends OncePerRequestFilter {
 	@Value("${cdn.flags.url}")
 	private String cdnFlagsUrl;
 
+	@Value("${base.url}")
+	private String baseUrl;
+
 	@Override
 	public void afterPropertiesSet() throws ServletException {
 		super.afterPropertiesSet();
@@ -54,7 +57,11 @@ public class EnvVariablesFilter extends OncePerRequestFilter {
 		if (cdnFlagsUrl != null) {
 			request.setAttribute("cdnFlagsUrl", cdnFlagsUrl);
 		}
-
+		
+		if (baseUrl != null) {
+			request.setAttribute("baseUrl", baseUrl);
+		}
+		
 		filterChain.doFilter(request, response);
 	}