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Commit bf425918 authored by Matija Obreza's avatar Matija Obreza
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DOI resolver for accessions

parent 02eb36bf
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src/main/java/org/genesys2/server/service/impl/GenesysServiceImpl.java
View file @ bf425918
......@@ -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
View file @ bf425918
......@@ -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
View file @ bf425918
/*
* 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
View file @ bf425918
......@@ -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);
}
......
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