Merge branch 'ui-179-filter-for-accessions-with-images' into 'master'

Ui 179 filter for accessions with images

See merge request genesys-pgr/genesys-server!329

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

@@ -239,6 +239,21 @@ public class AccessionController {
 		return accessionService.getAccessionDetails(accession);
 	}
 
+	@PreAuthorize("isAuthenticated()")
+	@RequestMapping(value = "/auditlog/10.{doi1:[0-9]+}/{doi2:.+}", method = RequestMethod.GET, produces = MediaType.APPLICATION_JSON_VALUE)
+	@JsonView(JsonViews.Root.class)
+	public AccessionService.AccessionAuditLog getAccessionAuditLogByDoi(@PathVariable("doi1") String doi1, @PathVariable("doi2") String doi2) {
+		Accession accession = accessionService.getByDoi("10." + doi1 + "/" + doi2);
+		return accessionService.getAuditLog(accession);
+	}
+
+	@PreAuthorize("isAuthenticated()")
+	@GetMapping(value = "/auditlog/{uuid:\\w{8}\\-\\w{4}.+}", produces = MediaType.APPLICATION_JSON_VALUE)
+	@JsonView(JsonViews.Root.class)
+	public AccessionService.AccessionAuditLog getAccessionAuditLogByUUID(@PathVariable("uuid") final UUID uuid) {
+		Accession accession = accessionService.getByUuid(uuid);
+		return accessionService.getAuditLog(accession);
+	}
 
 	@PostMapping(value = "/mapinfo", produces = MediaType.APPLICATION_JSON_VALUE)
 	@JsonView({ JsonViews.Public.class })

src/main/java/org/genesys2/server/model/genesys/AccessionId.java

@@ -27,6 +27,7 @@ import javax.persistence.Column;
 import javax.persistence.ElementCollection;
 import javax.persistence.Entity;
 import javax.persistence.FetchType;
+import javax.persistence.Index;
 import javax.persistence.Inheritance;
 import javax.persistence.InheritanceType;
 import javax.persistence.JoinColumn;
@@ -65,7 +66,8 @@ import com.fasterxml.jackson.annotation.ObjectIdGenerators;
  */
 @Entity
 @Inheritance(strategy = InheritanceType.JOINED)
-@Table(name = "acce")
+@Table(name = "acce", indexes = { 
+		@Index(name = "IX_imageCount", columnList = "imageCount") })
 @Audited
 public class AccessionId extends AuditedVersionedModel implements IdUUID {
 

src/main/java/org/genesys2/server/mvc/admin/AdminController.java

@@ -616,6 +616,13 @@ public class AdminController {
 							if (accession != null) {
 								LOG.warn("Folder for accession {}:{} is {}", instCode, accession.getAccessionNumber(), acceFolder.getPath());
 								accession.getAccessionId().setRepositoryFolder(acceFolder);
+								{
+									// Get number of images in the gallery
+									ImageGallery gallery = acceFolder.getGallery();
+									if (gallery != null) {
+										accession.getAccessionId().setImageCount(gallery.getImages().size());
+									}
+								}
 								accessionIdRepository.save(accession.getAccessionId());
 							} else {
 								LOG.warn("No accession {}:{} for folder {}", instCode, acceFolder.getName(), acceFolder.getPath());

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

@@ -30,6 +30,7 @@ import org.genesys2.server.model.impl.Subset;
 import org.genesys2.server.service.filter.AccessionFilter;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
+import org.genesys.blocks.auditlog.model.AuditLog;
 
 public interface AccessionService {
 
@@ -85,6 +86,14 @@ public interface AccessionService {
 	 */
 	AccessionDetails getAccessionDetails(Accession accession);
 
+	/**
+	 * Gets accession audit log, requires authentication
+	 *
+	 * @param accession the accession
+	 * @return the accession audit log
+	 */
+	AccessionAuditLog getAuditLog(Accession accession);
+
 	/**
 	 * Get only available for distribution  accessions id-s.
 	 *
@@ -150,4 +159,11 @@ public interface AccessionService {
 		public ImageGallery imageGallery;
 		public List<RepositoryFile> files;
 	}
+
+	class AccessionAuditLog {
+		public Map<String, List<AuditLog>> auditAccession;
+		public Map<String, List<AuditLog>> auditAccessionId;
+		public Map<String, List<AuditLog>> auditAccessionCollect;
+		public Map<String, List<AuditLog>> auditAccessionGeo;
+	}
 }

src/main/java/org/genesys2/server/service/filter/AccessionFilter.java

@@ -35,6 +35,8 @@ import com.querydsl.core.types.Predicate;
  */
 public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession> implements Serializable {
 
+	private static final long serialVersionUID = -1441103961567816877L;
+
 	/** The historic. */
 	public Boolean historic;
 
@@ -94,6 +96,9 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
 
 	/** accession aliases */
 	public StringFilter alias;
+	
+	/** accessions with images */
+	public Boolean images;
 
 
 	/* (non-Javadoc)
@@ -178,9 +183,19 @@ public class AccessionFilter extends UuidModelFilter<AccessionFilter, Accession>
 		}
 		// TODO Do we have to change this?
 		if (sgsv != null) {
-			and.and(accession.accessionId.duplSite.any().eq("NOR051"));
+			if (sgsv == Boolean.TRUE) {
+				and.and(accession.accessionId.duplSite.any().eq("NOR051"));
+			} else {
+				and.andNot(accession.accessionId.duplSite.any().eq("NOR051"));
+			}
+		}
+		if (images != null) {
+			if (images == Boolean.TRUE) {
+				and.and(accession.accessionId.imageCount.gt(0));
+			} else {
+				and.and(accession.accessionId.imageCount.eq(0));
+			}
 		}
-		
 		return and;
 	}
 

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

@@ -15,7 +15,6 @@
  */
 package org.genesys2.server.service.impl;
 
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
@@ -28,14 +27,13 @@ import java.util.UUID;
 import java.util.stream.Collectors;
 
 import org.apache.commons.collections.CollectionUtils;
-import org.apache.commons.lang3.StringUtils;
+import org.genesys.blocks.auditlog.service.AuditTrailService;
 import org.genesys.catalog.model.dataset.Dataset;
 import org.genesys.catalog.service.DatasetService;
 import org.genesys.filerepository.InvalidRepositoryPathException;
 import org.genesys.filerepository.model.ImageGallery;
 import org.genesys.filerepository.model.RepositoryFolder;
 import org.genesys.filerepository.service.ImageGalleryService;
-import org.genesys.filerepository.service.RepositoryService;
 import org.genesys2.server.exception.NotFoundElement;
 import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.model.genesys.AccessionData;
@@ -57,6 +55,7 @@ import org.springframework.context.annotation.Lazy;
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.PageImpl;
 import org.springframework.data.domain.Pageable;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
@@ -96,7 +95,7 @@ public class AccessionServiceImpl implements AccessionService {
 	private ImageGalleryService imageGalleryService;
 
 	@Autowired
-	private RepositoryService repositoryService;
+	private AuditTrailService auditService;
 
 	private <T extends AccessionData> T lazyLoad(T accession) {
 		if (accession != null) {
@@ -150,42 +149,47 @@ public class AccessionServiceImpl implements AccessionService {
 
 	@Override
 	public AccessionDetails getAccessionDetails(Accession accession) {
-			if (accession == null) {
-				throw new ResourceNotFoundException();
-			}
+		if (accession == null) {
+			throw new ResourceNotFoundException();
+		}
+		accession = accessionRepository.findOneByUuid(accession.getUuid());
 
-			List<Dataset> datasets = datasetService.listByAccession(accession);
-			List<Subset> subsets = subsetService.listByAccession(accession);
+		List<Dataset> datasets = datasetService.listByAccession(accession);
+		List<Subset> subsets = subsetService.listByAccession(accession);
 
-			AccessionDetails accessionDetails = new AccessionDetails();
-			accessionDetails.details = accession;
-			accessionDetails.pdci = accession.getAccessionId().getPdci();
-			accessionDetails.datasets = datasets;
-			accessionDetails.subsets = subsets;
+		AccessionDetails accessionDetails = new AccessionDetails();
+		accessionDetails.details = accession;
+		accessionDetails.pdci = accession.getAccessionId().getPdci();
+		accessionDetails.datasets = datasets;
+		accessionDetails.subsets = subsets;
 
-			try {
-				if (StringUtils.contains(accession.getAccessionNumber(), "/")) {
-					throw new InvalidRepositoryPathException("AccessionNumber contains /, cannot load folder for " + accession.getAccessionNumber());
+		RepositoryFolder folder = accession.getAccessionId().getRepositoryFolder();
+		if (folder != null) {
+			accessionDetails.files = folder.getFiles().stream().filter((file) -> !file.getContentType().contains("image/")).collect(Collectors.toList());
+
+			ImageGallery imageGallery = imageGalleryService.getImageGallery(folder);
+			if (imageGallery != null) {
+				if (imageGallery.getImages() != null) {
+					imageGallery.getImages().size();
 				}
+				accessionDetails.imageGallery = imageGallery;
+			}
+		}
 
-				RepositoryFolder folder = repositoryService.getFolder(Paths.get("/wiews", accession.getInstCode(), "acn", accession.getAccessionNumber()));
-				if (folder != null) {
-					accessionDetails.files = folder.getFiles().stream().filter((file) -> !file.getContentType().contains("image/")).collect(Collectors.toList());
+		return accessionDetails;
+	}
 
-					ImageGallery imageGallery = imageGalleryService.loadImageGallery(folder.getFolderPath());
-					if (imageGallery != null) {
-						if (imageGallery.getImages() != null) {
-							imageGallery.getImages().size();
-						}
-						accessionDetails.imageGallery = imageGallery;
-					}
+	@Override
+	@PreAuthorize("isAuthenticated()")
+	public AccessionAuditLog getAuditLog(Accession accession) {
+		AccessionAuditLog auditLog = new AccessionAuditLog();
 
-				}
-			} catch (InvalidRepositoryPathException e) {
-				LOG.warn("Error loading files folder for accession={}. {}", accession.getAccessionNumber(), e.getMessage());
-			}
+		auditLog.auditAccession = auditService.auditLogs(accession);
+		auditLog.auditAccessionId = auditService.auditLogs(accession.getAccessionId());
+		auditLog.auditAccessionCollect = auditService.auditLogs(accession.getAccessionId().getColl());
+		auditLog.auditAccessionGeo = auditService.auditLogs(accession.getAccessionId().getGeo());
 
-			return accessionDetails;
+		return auditLog;
 	}
 
 	@Override

src/main/resources/liquibase/liquibase-changeLog.yml

@@ -4761,3 +4761,15 @@ databaseChangeLog:
         columnNames:             folderId
         constraintName:          UK_3x3s9vul09xif4y29o2rwx939
         tableName:               acce
+
+- changeSet:
+    id:                          1547568102000-1
+    author:                      mobreza
+    comment:                     Add index on acce#imageCount
+    changes:
+    - createIndex:
+        columns:
+        - column:
+            name:              imageCount
+        indexName:             IX_imageCount
+        tableName:             acce