Merge branch '314-accesssion-api-v1-details' into 'master'

Resolve "Accesssion API v1: details"

Closes #314

See merge request genesys-pgr/genesys-server!214

src/main/java/org/genesys2/server/api/v1/AccessionController.java

@@ -26,29 +26,28 @@ import javax.servlet.http.HttpServletRequest;
 
 import org.genesys.blocks.model.JsonViews;
 import org.genesys.catalog.api.FilteredPage;
+import org.genesys.catalog.model.dataset.Dataset;
+import org.genesys.catalog.service.DatasetService;
 import org.genesys.catalog.service.ShortFilterService;
 import org.genesys2.server.api.ApiBaseController;
 import org.genesys2.server.api.model.AccessionHeaderJson;
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.PDCI;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
+import org.genesys2.server.model.impl.Subset;
 import org.genesys2.server.service.AccessionService;
 import org.genesys2.server.service.ElasticsearchService;
 import org.genesys2.server.service.ElasticsearchService.TermResult;
+import org.genesys2.server.service.SubsetService;
 import org.genesys2.server.service.filter.AccessionFilter;
 import org.genesys2.server.service.impl.SearchException;
+import org.genesys2.spring.ResourceNotFoundException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.data.domain.Sort;
 import org.springframework.http.MediaType;
 import org.springframework.security.access.prepost.PreAuthorize;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestBody;
-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.RestController;
+import org.springframework.web.bind.annotation.*;
 import org.springframework.web.servlet.HandlerMapping;
 
 import com.fasterxml.jackson.annotation.JsonView;
@@ -83,6 +82,12 @@ public class AccessionController {
 	@Autowired
 	private ElasticsearchService elasticsearchService;
 
+	@Autowired
+	private DatasetService datasetService;
+
+	@Autowired
+	private SubsetService subsetService;
+
 	private final Set<String> terms = Sets.newHashSet("institute.code", "institute.country.code3", "cropName", "crop.shortName", "taxonomy.genus", "taxonomy.species",
 		"taxonomy.genusSpecies", "countryOfOrigin.code3", "sampStat", "available", "mlsStatus", "donorCode", "sgsv", "storage", "duplSite", "breederCode");
 
@@ -175,6 +180,40 @@ public class AccessionController {
 		return accessionService.toUUID(identifiers);
 	}
 
+	@RequestMapping(value = "/details/10.{dummy:[0-9]+}/**}", method = RequestMethod.GET, produces = { MediaType.APPLICATION_JSON_VALUE })
+	@JsonView(JsonViews.Minimal.class)
+	public AccessionDetailsJson getAccessionDetailsByDoi(HttpServletRequest request) {
+		final String fullPath = (String) request.getAttribute(HandlerMapping.PATH_WITHIN_HANDLER_MAPPING_ATTRIBUTE);
+		final String doi = fullPath.substring(API_BASE.length() + 1);
+
+		Accession accession = accessionService.getByDoi(doi);
+
+		return  getAccessionDetails(accession);
+	}
+
+	@GetMapping(value="/details/{UUID}", consumes = MediaType.APPLICATION_JSON_VALUE)
+	@JsonView(JsonViews.Minimal.class)
+	public AccessionDetailsJson getAccessionDetailsByUUID(@PathVariable("UUID") final UUID uuid) {
+		Accession accession = accessionService.getByUuid(uuid);
+		return getAccessionDetails(accession);
+	}
+
+	private AccessionDetailsJson getAccessionDetails(Accession accession) {
+		if (accession == null) {
+			throw new ResourceNotFoundException();
+		}
+
+		List<Dataset> datasets = datasetService.listByAccession(accession.getAccessionId());
+		List<Subset> subsets = subsetService.listByAccession(accession.getAccessionId());
+
+		AccessionDetailsJson accessionDetails = new AccessionDetailsJson();
+		accessionDetails.details = accession;
+		accessionDetails.pdci = accession.getAccessionId().getPdci();
+		accessionDetails.datasets = datasets;
+		accessionDetails.subsets = subsets;
+
+		return accessionDetails;
+	}
 
 	/**
 	 * Get term overview for filters
@@ -238,4 +277,11 @@ public class AccessionController {
 		return objectMapper.readValue(objectMapper.writeValueAsString(filter), AccessionFilter.class);
 	}
 
+	public static class AccessionDetailsJson {
+		public Accession details;
+		public PDCI pdci;
+		public List<Dataset> datasets;
+		public List<Subset> subsets;
+	}
+
 }

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

@@ -16,9 +16,11 @@
 
 package org.genesys2.server.service;
 
+import java.util.List;
 import java.util.Set;
 import java.util.UUID;
 
+import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.server.model.impl.Subset;
 import org.genesys2.server.service.filter.SubsetFilter;
 import org.springframework.data.domain.Page;
@@ -131,4 +133,6 @@ public interface SubsetService {
      */
     Subset approveSubset(Subset subset);
 
+    List<Subset> listByAccession(AccessionId accessionId);
+
 }

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

@@ -333,4 +333,9 @@ public class SubsetServiceImpl implements SubsetService {
 
 		return deepLoad(subsetRepository.save(loaded));
 	}
+
+	@Override
+	public List<Subset> listByAccession(AccessionId accessionId) {
+		return (List<Subset>) subsetRepository.findAll(QSubset.subset.accessions.contains(accessionId));
+	}
 }