JSP: Accession details page

src/main/java/org/genesys/catalog/model/dataset/AccessionIdentifier.java

@@ -17,12 +17,8 @@ package org.genesys.catalog.model.dataset;
 
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
-import javax.persistence.FetchType;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
 import java.io.Serializable;
 
-import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.server.model.impl.AccessionIdentifier3;
 
 /**
@@ -58,11 +54,6 @@ public class AccessionIdentifier implements AccessionIdentifier3, Serializable {
 	@Column(nullable = true, length = 100)
 	private String species;
 
-	/** The accession. */
-	@ManyToOne(optional = true, fetch = FetchType.LAZY, cascade = {})
-	@JoinColumn(name = "accessionId", nullable = true)
-	private AccessionId accession;
-
 	/**
 	 * Gets the doi.
 	 *
@@ -153,24 +144,6 @@ public class AccessionIdentifier implements AccessionIdentifier3, Serializable {
 		this.species = species;
 	}
 
-	/**
-	 * Gets the accession.
-	 *
-	 * @return the accession
-	 */
-	public AccessionId getAccession() {
-		return accession;
-	}
-
-	/**
-	 * Sets the accession.
-	 *
-	 * @param accession the new accession
-	 */
-	public void setAccession(final AccessionId accession) {
-		this.accession = accession;
-	}
-
 	/**
 	 * Gets holding institute code.
 	 *
@@ -250,19 +223,6 @@ public class AccessionIdentifier implements AccessionIdentifier3, Serializable {
 		} else if (!species.equals(other.species)) {
 			return false;
 		}
-		if (accession == null) {
-			if (other.accession != null) {
-				return false;
-			}
-		} else {
-			if (other.accession != null) {
-				if (!accession.getUuid().equals(other.accession.getUuid())) {
-					return false;
-				}
-			} else {
-				return false;
-			}
-		}
 		return true;
 	}
 }

src/main/java/org/genesys/catalog/model/dataset/Dataset.java

@@ -15,6 +15,7 @@
  */
 package org.genesys.catalog.model.dataset;
 
+import com.fasterxml.jackson.annotation.JsonIdentityReference;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import com.fasterxml.jackson.annotation.JsonView;
 import org.genesys.blocks.auditlog.annotations.Audited;
@@ -29,6 +30,7 @@ import org.genesys.catalog.model.traits.Descriptor;
 import org.genesys.catalog.service.PublishValidationInterface;
 import org.genesys.filerepository.model.RepositoryFile;
 import org.genesys2.server.model.PublishState;
+import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.util.MCPDUtil;
 import org.springframework.data.elasticsearch.annotations.Document;
 import org.springframework.data.elasticsearch.annotations.Field;
@@ -79,6 +81,12 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 	@JsonView({ JsonViews.Public.class })
 	private Set<AccessionIdentifier> accessionIdentifiers;
 
+	/** The accessions. */
+	@ManyToMany(cascade = {}, fetch = FetchType.LAZY)
+	@JoinTable(name = "dataset_acce", joinColumns = @JoinColumn(name = "datasetId"), inverseJoinColumns = @JoinColumn(name = "acce_id"))
+	@JsonIdentityReference(alwaysAsId = true)
+	private List<AccessionId> accessions;
+
 	/** The descriptors. */
 	@ManyToMany(fetch = FetchType.LAZY, cascade = {})
 	@JoinTable(name = "dataset_descriptor", joinColumns = @JoinColumn(name = "datasetId", referencedColumnName = "id"), inverseJoinColumns = @JoinColumn(name = "descriptorId", referencedColumnName = "id"))
@@ -529,6 +537,24 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 		this.accessionIdentifiers = accessionIdentifiers;
 	}
 
+	/**
+	 * Gets the accessions.
+	 *
+	 * @return the accessions
+	 */
+	public List<AccessionId> getAccessions() {
+		return accessions;
+	}
+
+	/**
+	 * Sets the accessions.
+	 *
+	 * @param accessions the new accessions
+	 */
+	public void setAccessions(final List<AccessionId> accessions) {
+		this.accessions = accessions;
+	}
+
 	/**
 	 * Gets the descriptors.
 	 *

src/main/java/org/genesys/catalog/service/DatasetService.java

@@ -24,6 +24,7 @@ import org.genesys.filerepository.InvalidRepositoryFileDataException;
 import org.genesys.filerepository.InvalidRepositoryPathException;
 import org.genesys.filerepository.NoSuchRepositoryFileException;
 import org.genesys.filerepository.model.RepositoryFile;
+import org.genesys2.server.model.genesys.AccessionId;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.data.domain.Page;
@@ -112,6 +113,14 @@ public interface DatasetService {
 	 */
 	Dataset loadDataset(UUID uuid, int version);
 
+	/**
+	 * List published datasets by accession.
+	 *
+	 * @param accessionId the accessionId
+	 * @return list of Dataset
+	 */
+	List<Dataset> listByAccession(AccessionId accessionId);
+
 	/**
 	 * List published datasets matching the filter.
 	 *

src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java

@@ -27,6 +27,7 @@ import java.util.Set;
 import java.util.UUID;
 import java.util.stream.Collectors;
 
+import com.google.common.collect.Lists;
 import org.apache.commons.lang.StringUtils;
 import org.genesys.blocks.security.service.CustomAclService;
 import org.genesys.catalog.exceptions.InvalidApiUsageException;
@@ -49,6 +50,7 @@ import org.genesys.filerepository.service.RepositoryService;
 import org.genesys2.server.model.PublishState;
 import org.genesys2.server.model.UserRole;
 import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionId;
 import org.genesys2.server.security.SecurityUtils;
 import org.genesys2.server.service.GenesysService;
 import org.genesys2.server.service.impl.NonUniqueAccessionException;
@@ -126,7 +128,8 @@ public class DatasetServiceImpl implements DatasetService {
 		dataset.setCrops(source.getCrops());
 
 		if (source.getAccessionIdentifiers() != null && !source.getAccessionIdentifiers().isEmpty()) {
-			dataset.setAccessionIdentifiers(lookupMatchingAccessions(new HashSet<>(source.getAccessionIdentifiers())));
+			dataset.setAccessionIdentifiers(new HashSet<>(source.getAccessionIdentifiers()));
+			dataset.setAccessions(lookupMatchingAccessions(dataset.getAccessionIdentifiers()));
 		}
 
 		copyDescriptors(dataset, source.getDescriptors());
@@ -174,7 +177,8 @@ public class DatasetServiceImpl implements DatasetService {
 		LOG.info("Update AccessionIdentifiers. Input dataset: {}, input accessionIdentifiers {}", dataset, accessionIdentifiers);
 		dataset = loadDataset(dataset);
 		dataset.getAccessionIdentifiers().clear();
-		dataset.setAccessionIdentifiers(lookupMatchingAccessions(new HashSet<>(accessionIdentifiers)));
+		dataset.setAccessionIdentifiers(new HashSet<>(accessionIdentifiers));
+		dataset.setAccessions(lookupMatchingAccessions(dataset.getAccessionIdentifiers()));
 		return lazyLoad(datasetRepository.save(dataset));
 	}
 
@@ -315,6 +319,15 @@ public class DatasetServiceImpl implements DatasetService {
 		return lazyLoad(dataset);
 	}
 
+	/**
+	 * {@inheritDoc}
+	 */
+	@Override
+	public List<Dataset> listByAccession(final AccessionId accessionId) {
+		final Iterable<Dataset> datasets = datasetRepository.findAll(dataset.accessions.contains(accessionId).and(dataset.state.in(PublishState.PUBLISHED)));
+		return Lists.newArrayList(datasets);
+	}
+
 	/**
 	 * {@inheritDoc}
 	 */
@@ -430,7 +443,8 @@ public class DatasetServiceImpl implements DatasetService {
 			throw new NotFoundElement("Dataset doesn't exist");
 		}
 		loadedDataset.setState(PublishState.DRAFT);
-		loadedDataset.setAccessionIdentifiers(lookupMatchingAccessions(new HashSet<>(accessionIdentifiers)));
+		loadedDataset.setAccessionIdentifiers(new HashSet<>(accessionIdentifiers));
+		loadedDataset.setAccessions(lookupMatchingAccessions(loadedDataset.getAccessionIdentifiers()));
 		return lazyLoad(datasetRepository.save(loadedDataset));
 	}
 
@@ -594,27 +608,31 @@ public class DatasetServiceImpl implements DatasetService {
 	}
 
 	/**
-	 * Looking for matching Accession and then sets that to AccessionIdentifier
+	 * Looking for matching Accession
 	 *
-	 * @param accessionIdentifiers the accessionIdentifiers
-	 * @return accessionIdentifiers with matching accessions from Genesys
+	 * @param identifiers the accessionIdentifiers
+	 * @return list of matching accessions from Genesys
 	 */
-	private Set<AccessionIdentifier> lookupMatchingAccessions(final Set<AccessionIdentifier> accessionIdentifiers) {
-		accessionIdentifiers.forEach(accei -> {
-			Accession foundAccession = null;
-			if (!StringUtils.isBlank(accei.getDoi())) {
-				foundAccession = genesysService.getAccessionByDOI(accei.getDoi());
-			} else {
-				try {
-					foundAccession = genesysService.getAccession(accei.getInstCode(), accei.getDoi(), accei.getAcceNumb(), accei.getGenus());
-				} catch (final NonUniqueAccessionException e) {
-					LOG.warn(e.getMessage());
+	private List<AccessionId> lookupMatchingAccessions(final Set<AccessionIdentifier> identifiers) {
+		final List<AccessionId> accessions = new ArrayList<>();
+		if (!identifiers.isEmpty()) {
+			identifiers.forEach(accei -> {
+				Accession foundAccession = null;
+				if (!StringUtils.isBlank(accei.getDoi())) {
+					foundAccession = genesysService.getAccessionByDOI(accei.getDoi());
+				} else {
+					try {
+						foundAccession = genesysService.getAccession(accei.getInstCode(), accei.getDoi(), accei.getAcceNumb(), accei.getGenus());
+					} catch (final NonUniqueAccessionException e) {
+						LOG.warn(e.getMessage());
+					}
 				}
-			}
-			accei.setAccession(foundAccession != null ? foundAccession.getAccessionId() : null);
-		});
-
-		return accessionIdentifiers;
+				if (foundAccession != null) {
+					accessions.add(foundAccession.getAccessionId());
+				}
+			});
+		}
+		return accessions.stream().distinct().collect(Collectors.toList());
 	}
 
 }

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

@@ -26,6 +26,7 @@ import java.util.UUID;
 import javax.servlet.http.HttpServletResponse;
 
 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.genesys.filerepository.service.ImageGalleryService;
@@ -99,6 +100,9 @@ public class AccessionController extends BaseController {
 	
 	@Autowired
 	private AuditTrailService auditService;
+
+	@Autowired
+	private DatasetService datasetService;
 	
 	@Value("${base.url}")
 	private String baseUrl;
@@ -145,7 +149,8 @@ public class AccessionController extends BaseController {
 
 		model.addAttribute("accessionNames", genesysService.listAccessionNames(accessionId));
 		model.addAttribute("accessionAliases", accessionId.getAliases());
-		
+		model.addAttribute("accessionDatasets", datasetService.listByAccession(accessionId));
+
 		model.addAttribute("accessionExchange", accession);
 		
 		AccessionCollect accessionCollect = accessionId.getColl();

src/main/resources/content/language.properties

@@ -306,6 +306,7 @@ accession.breeding=Breeder information
 accession.breederCode=Breeder Code
 accession.pedigree=Pedigree
 accession.collecting=Collecting information
+accession.datasets=List of Datasets
 accession.collecting.site=Location of collecting site
 accession.collecting.institute=Collecting institute
 accession.collecting.number=Collecting number

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

@@ -3739,3 +3739,64 @@ databaseChangeLog:
     - sql:
         sql: >-
           update accession_historic ah right join acce ac on ac.id = ah.id right join accession_geo geo on geo.id = ac.geoId set ah.tileIndex = geo.tileIndex;
+
+- changeSet:
+    id:                        1534922647579-1
+    author:                    mborodenko
+    changes:
+    - dropForeignKeyConstraint:
+        baseTableName:         dataset_accessions
+        constraintName:        FK_ekss0g19xg9h2tsp1zl8g9h2t
+    - dropColumn:
+        tableName:             dataset_accessions
+        columnName:            accessionId
+
+- changeSet:
+    id:                        1534922647579-2
+    author:                    mborodenko
+    changes:
+    - createTable:
+        columns:
+        - column:
+            constraints:
+              nullable:        false
+            name:              datasetId
+            type:              BIGINT
+        - column:
+            constraints:
+              nullable:        false
+            name:              acce_id
+            type:              BIGINT
+        tableName:             dataset_acce
+    - createIndex:
+        columns:
+        - column:
+            name:              datasetId
+        indexName:             FK_17w5b5xt9tbw0l6eefqayh33q
+        tableName:             dataset_acce
+    - createIndex:
+        columns:
+        - column:
+            name:              acce_id
+        indexName:             FK_7jyg2if8kyxyw8toq5qyy5vj2
+        tableName:             dataset_acce
+    - addForeignKeyConstraint:
+        baseColumnNames:       acce_id
+        baseTableName:         dataset_acce
+        constraintName:        FK_7jyg2if8kyxyw8toq5qyy5vj2
+        deferrable:            false
+        initiallyDeferred:     false
+        onDelete:              NO ACTION
+        onUpdate:              NO ACTION
+        referencedColumnNames: id
+        referencedTableName:   acce
+    - addForeignKeyConstraint:
+        baseColumnNames:       datasetId
+        baseTableName:         dataset_acce
+        constraintName:        FK_17w5b5xt9tbw0l6eefqayh33q
+        deferrable:            false
+        initiallyDeferred:     false
+        onDelete:              NO ACTION
+        onUpdate:              NO ACTION
+        referencedColumnNames: id
+        referencedTableName:   dataset

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

@@ -1072,6 +1072,30 @@
           </div>
         </c:if>
 
+        <c:if test="${accessionDatasets ne null and accessionDatasets.size() gt 0}">
+          <div class="collect-info">
+            <h4 class="row section-heading"><spring:message code="accession.datasets"/></h4>
+            <div class="section-inner-content clearfix">
+              <div class="terms-table">
+                <c:forEach items="${accessionDatasets}" var="dataset" varStatus="status">
+                  <div class="row">
+                    <div class="col-lg-6 col-md-6 col-sm-6 col-xs-8">
+                      <p>
+                        <a class="" title="Dataset" href="<c:url value='${genesysCatalogUrl}/datasets/${dataset.uuid}' />">
+                          <c:out value="${dataset.title}" />
+                        </a>
+                      </p>
+                    </div>
+                    <div class="col-lg-6 col-md-6 col-sm-6 col-xs-4 text-left">
+                      <p><fmt:formatNumber value="${dataset.descriptorCount}" /></p>
+                    </div>
+                  </div>
+                </c:forEach>
+              </div>
+            </div>
+          </div>
+        </c:if>
+
         <div class="collect-info">
           <div class="section-inner-content clearfix">
             <p>

src/test/java/org/genesys/test/catalog/services/AbstractDatasetServiceTest.java

@@ -46,6 +46,14 @@ import org.springframework.beans.factory.annotation.Autowired;
 public abstract class AbstractDatasetServiceTest extends CatalogServiceTest {
 
 	protected static final String TEST_INSTCODE = "XYZ001";
+	protected static final String TEST_INSTCODE2 = "XYZ002";
+	protected static final String TEST_INSTCODE3 = "XYZ003";
+	protected static final String TEST_ACCNUM = "TestAccNum1";
+	protected static final String TEST_ACCNUM2 = "TestAccNum2";
+	protected static final String TEST_ACCNUM3 = "TestAccNum3";
+	protected static final String TEST_GEN = "TestGen1";
+	protected static final String TEST_GEN2 = "TestGen2";
+	protected static final String TEST_GEN3= "TestGen3";
 	protected static final String DATASET_TITLE_1 = "Dataset title 1";
 	protected static final String DATASET_TITLE_2 = "Dataset title 2";
 	protected static final String DATASET_DESCRIPTION_1 = "Test description 1";

src/test/java/org/genesys/test/catalog/services/DatasetServiceTest.java

@@ -17,6 +17,7 @@ package org.genesys.test.catalog.services;
 
 import static org.hamcrest.Matchers.*;
 import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertThat;
 
 import java.io.File;
@@ -154,11 +155,6 @@ public class DatasetServiceTest extends AbstractDatasetServiceTest {
 		assertThat(input, not(nullValue()));
 		assertThat(input.getAccessionIdentifiers().size(), is(1));
 		assertThat(input.getAccessionIdentifiers().iterator().next(), is(accessionIdentifiers.iterator().next()));
-
-		AccessionIdentifier accessionIdentifier = input.getAccessionIdentifiers().stream().findFirst().orElse(null);
-		assertThat(accessionIdentifier, notNullValue());
-		AccessionId accessionId = accessionIdentifier.getAccession();
-		assertThat(accessionId, nullValue());
 	}
 
 	@Test
@@ -184,12 +180,76 @@ public class DatasetServiceTest extends AbstractDatasetServiceTest {
 		assertThat(input.getAccessionIdentifiers().size(), is(1));
 		assertThat(input.getAccessionIdentifiers().iterator().next(), is(accessionIdentifiers.iterator().next()));
 
-		final AccessionIdentifier accessionIdentifier = input.getAccessionIdentifiers().stream().findFirst().orElse(null);
-		assertThat(accessionIdentifier, notNullValue());
-		final AccessionId accessionId = accessionIdentifier.getAccession();
+		final AccessionId accessionId = input.getAccessions().stream().findFirst().orElse(null);
+		assertThat(accessionId, notNullValue());
 		assertThat(accessionId.getUuid(), is(accession.getAccessionId().getUuid()));
 	}
 
+	@Test
+	public void testCreateAndUpdateAccessionsInDataset() {
+		final Accession accession1 = buildAndSaveAccession(TEST_ACCNUM, TEST_INSTCODE, TEST_GEN);
+		final Accession accession2 = buildAndSaveAccession(TEST_ACCNUM2, TEST_INSTCODE2, TEST_GEN2);
+		final Accession accession3 = buildAndSaveAccession(TEST_ACCNUM3, TEST_INSTCODE3, TEST_GEN3);
+
+		Dataset input = buildDataset(DATASET_TITLE_1, DATASET_DESCRIPTION_1, partner, null, PublishState.DRAFT);
+		input = datasetService.createDataset(input);
+
+		final Set<AccessionIdentifier> accessionIdentifiers = new HashSet<AccessionIdentifier>() {
+			/**
+			 *
+			 */
+			private static final long serialVersionUID = 8866546652858324614L;
+
+			{
+				add(makeAccessionIdentifier(TEST_INSTCODE, TEST_ACCNUM, TEST_GEN, null));
+				add(makeAccessionIdentifier(TEST_INSTCODE2, TEST_ACCNUM2, TEST_GEN2, null));
+				add(makeAccessionIdentifier(TEST_INSTCODE3, TEST_ACCNUM3, TEST_GEN3, null));
+			}
+		};
+
+		input = datasetService.updateAccessionIdentifiers(input, accessionIdentifiers);
+		assertThat(input, not(nullValue()));
+		assertThat(input.getAccessionIdentifiers().size(), is(3));
+		assertThat(input.getAccessions().size(), is(3));
+		assertThat(input.getAccessionIdentifiers().size(), is(accessionIdentifiers.size()));
+
+		// remove one accession
+		final Set<AccessionIdentifier> accessionIdentifiers2 = accessionIdentifiers.stream().filter(accessionIdentifier -> !accessionIdentifier.getInstCode().equals(TEST_INSTCODE)).collect(Collectors.toSet());
+		assertThat(accessionIdentifiers2.size(), is(2));
+
+		// update dataset with a new list of accessions
+		input = datasetService.updateAccessionIdentifiers(input, accessionIdentifiers2);
+		assertThat(input, not(nullValue()));
+
+		// test if dataset has a new set of accessions
+		assertThat(input.getAccessionIdentifiers().size(), is(2));
+		assertThat(input.getAccessions().size(), is(2));
+
+		assertFalse(input.getAccessions().stream().anyMatch(accessionId -> accessionId.getUuid() == accession2.getAccessionId().getUuid()));
+	}
+
+	@Test
+	public void testListDatasetsByAccession() {
+		final Accession accession = buildAndSaveAccession(TEST_ACCNUM, TEST_INSTCODE, TEST_GEN);
+
+		Dataset input = buildDataset(DATASET_TITLE_1, DATASET_DESCRIPTION_1, partner, null, PublishState.PUBLISHED);
+		input = datasetService.createDataset(input);
+
+		// add accessionIdentifier to dataset
+		final Set<AccessionIdentifier> accessionIdentifiers = new HashSet<>();
+		accessionIdentifiers.add(makeAccessionIdentifier(TEST_INSTCODE, TEST_ACCNUM, TEST_GEN, null));
+		input = datasetService.updateAccessionIdentifiers(input, accessionIdentifiers);
+		assertThat(input.getAccessionIdentifiers().size(), is(1));
+
+		// make sure that accession from Genesys also be added
+		assertThat(input.getAccessions().size(), is(1));
+
+		List<Dataset> datasets = datasetService.listByAccession(accession.getAccessionId());
+		assertThat(datasets.size(), is(1));
+
+		assertEquals(input.getUuid(), datasets.get(0).getUuid());
+	}
+
 	/**
 	 * Fail to update Dataset when isPublished() = true
 	 */