#284 Dataset AccessionIdentifier

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

@@ -17,8 +17,14 @@ 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;
+
 /**
  * Identifies an accession by it's INSTCODE, ACCENUMB and GENUS. Use of DOI
  * remains optional.
@@ -27,30 +33,35 @@ import java.io.Serializable;
  * @author Matija Obreza
  */
 @Embeddable
-public class AccessionIdentifier implements Serializable {
+public class AccessionIdentifier implements AccessionIdentifier3, Serializable {
 
 	/** The Constant serialVersionUID. */
 	private static final long serialVersionUID = 1L;
 
 	/** The DOI. */
 	@Column(length = 100)
-	public String doi;
+	private String doi;
 
 	/** The inst code. */
 	@Column(length = 10, nullable = false)
-	public String instCode;
+	private String instCode;
 
 	/** The acce numb. */
 	@Column(nullable = false, length = 50)
-	public String acceNumb;
+	private String acceNumb;
 
 	/** The genus. */
 	@Column(nullable = false, length = 100)
-	public String genus;
+	private String genus;
 
 	/** The species. */
 	@Column(nullable = true, length = 100)
-	public String species;
+	private String species;
+
+	/** The accession. */
+	@ManyToOne(optional = true, fetch = FetchType.LAZY, cascade = {})
+	@JoinColumn(name = "accessionId", nullable = true)
+	private AccessionId accession;
 
 	/**
 	 * Gets the doi.
@@ -142,6 +153,44 @@ public class AccessionIdentifier implements 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.
+	 *
+	 * @return the instCode
+	 */
+	@Override
+	public String getHoldingInstitute() {
+		return instCode;
+	}
+
+	/**
+	 * Gets accession number.
+	 *
+	 * @return the acceNumb
+	 */
+	@Override
+	public String getAccessionNumber() {
+		return acceNumb;
+	}
+
 	@Override
 	public int hashCode() {
 		final int prime = 31;
@@ -201,6 +250,19 @@ public class AccessionIdentifier implements 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/service/impl/DatasetServiceImpl.java

@@ -27,6 +27,7 @@ import java.util.Set;
 import java.util.UUID;
 import java.util.stream.Collectors;
 
+import org.apache.commons.lang.StringUtils;
 import org.genesys.blocks.security.service.CustomAclService;
 import org.genesys.catalog.exceptions.InvalidApiUsageException;
 import org.genesys.catalog.exceptions.NotFoundElement;
@@ -46,7 +47,10 @@ import org.genesys.filerepository.NoSuchRepositoryFileException;
 import org.genesys.filerepository.model.RepositoryFile;
 import org.genesys.filerepository.service.RepositoryService;
 import org.genesys2.server.model.UserRole;
+import org.genesys2.server.model.genesys.Accession;
 import org.genesys2.server.security.SecurityUtils;
+import org.genesys2.server.service.GenesysService;
+import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.dao.ConcurrencyFailureException;
@@ -88,6 +92,9 @@ public class DatasetServiceImpl implements DatasetService {
 	@Autowired
 	private SecurityUtils securityUtils;
 
+	@Autowired
+	private GenesysService genesysService;
+
 	/** The file repository path. */
 	@Value("${file.repository.datasets.folder}")
 	public String datasetRepositoryPath;
@@ -115,7 +122,7 @@ public class DatasetServiceImpl implements DatasetService {
 		dataset.setCrops(source.getCrops());
 
 		if (source.getAccessionIdentifiers() != null && !source.getAccessionIdentifiers().isEmpty()) {
-			dataset.setAccessionIdentifiers(new HashSet<>(source.getAccessionIdentifiers()));
+			dataset.setAccessionIdentifiers(lookupMatchingAccessions(new HashSet<>(source.getAccessionIdentifiers())));
 		}
 
 		copyDescriptors(dataset, source.getDescriptors());
@@ -162,7 +169,7 @@ public class DatasetServiceImpl implements DatasetService {
 		LOG.info("Update AccessionIdentifiers. Input dataset: {}, input accessionIdentifiers {}", dataset, accessionIdentifiers);
 		dataset = loadDataset(dataset);
 		dataset.getAccessionIdentifiers().clear();
-		dataset.setAccessionIdentifiers(new HashSet<>(accessionIdentifiers));
+		dataset.setAccessionIdentifiers(lookupMatchingAccessions(new HashSet<>(accessionIdentifiers)));
 		return lazyLoad(datasetRepository.save(dataset));
 	}
 
@@ -408,7 +415,7 @@ public class DatasetServiceImpl implements DatasetService {
 		if (loadedDataset == null) {
 			throw new NotFoundElement("Dataset doesn't exist");
 		}
-		loadedDataset.setAccessionIdentifiers(new HashSet<>(accessionIdentifiers));
+		loadedDataset.setAccessionIdentifiers(lookupMatchingAccessions(new HashSet<>(accessionIdentifiers)));
 		return lazyLoad(datasetRepository.save(loadedDataset));
 	}
 
@@ -536,4 +543,28 @@ public class DatasetServiceImpl implements DatasetService {
 		target.getDescriptors().addAll(descriptors.stream().distinct().collect(Collectors.toList()));
 	}
 
+	/**
+	 * Looking for matching Accession and then sets that to AccessionIdentifier
+	 *
+	 * @param accessionIdentifiers the accessionIdentifiers
+	 * @return accessionIdentifiers with 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());
+				}
+			}
+			accei.setAccession(foundAccession != null ? foundAccession.getAccessionId() : null);
+		});
+
+		return accessionIdentifiers;
+	}
+
 }

src/main/java/org/genesys2/server/persistence/AccessionRepositoryCustomImpl.java

@@ -45,6 +45,7 @@ import org.genesys2.server.service.impl.NonUniqueAccessionException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.InitializingBean;
+import org.springframework.dao.IncorrectResultSizeDataAccessException;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.support.Querydsl;
 import org.springframework.stereotype.Repository;
@@ -217,7 +218,7 @@ public class AccessionRepositoryCustomImpl implements AccessionRepositoryCustom,
 
 		if (doi != null) {
 			restrictions.add(criteriaBuilder.equal(root.get("doi"), doi));
-		} else if (institute.hasUniqueAcceNumbs()) {
+		} else if (institute != null && institute.hasUniqueAcceNumbs()) {
 			restrictions.add(criteriaBuilder.equal(root.get("accessionNumber"), acceNumb));
 		} else {
 			restrictions.add(criteriaBuilder.and(criteriaBuilder.equal(root.get("accessionNumber"), acceNumb), criteriaBuilder.equal(tax.get("genus"), genus)));
@@ -225,7 +226,17 @@ public class AccessionRepositoryCustomImpl implements AccessionRepositoryCustom,
 
 		cq.where(criteriaBuilder.and(criteriaBuilder.equal(root.get("institute"), institute), criteriaBuilder.or(restrictions.toArray(new Predicate[] {}))));
 
-		return em.createQuery(cq).getSingleResult();
+		List<Accession> result = em.createQuery(cq).getResultList();
+
+		if (result.isEmpty()) {
+			return null;
+		}
+
+		if (result.size() > 1) {
+			throw new IncorrectResultSizeDataAccessException(1, result.size());
+		}
+
+		return result.get(0);
 	}
 
 	@Override

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

@@ -319,8 +319,8 @@ public class GenesysServiceImpl implements GenesysService, DatasetService {
 			Accession accession = accessionRepository.findOne(instituteRepository.findByCode(instCode), doi, acceNumb, genus);
 			return lazyLoadAccession(accession);
 		} catch (IncorrectResultSizeDataAccessException e) {
-			LOG.error("Duplicate accession name instCode={} acceNumb={}", instCode, acceNumb);
-			throw new NonUniqueAccessionException(instCode, acceNumb);
+			LOG.error("Duplicate accession name instCode={} acceNumb={} genus={}", instCode, acceNumb, genus);
+			throw new NonUniqueAccessionException(instCode, acceNumb, genus);
 		}
 	}
 

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

@@ -3565,3 +3565,39 @@ databaseChangeLog:
     - sql:
         sql: >-
            CREATE INDEX UK_1my8xep8hi5fv42o3ivu0t41o ON short_filter(json(250))
+
+- changeSet:
+    id: 1533138107794-1
+    author: mborodenko
+    comment: Add column `accessionId` to dataset_accessions table
+    changes:
+    - addColumn:
+        columns:
+        - column:
+            constraints:
+              nullable: true
+            name: accessionId
+            type: BIGINT(20)
+        tableName: dataset_accessions
+
+- changeSet:
+    id: 1533138107794-2
+    author: mborodenko
+    comment: Add constraints
+    changes:
+    - addForeignKeyConstraint:
+        baseColumnNames: accessionId
+        baseTableName: dataset_accessions
+        constraintName: FK_ekss0g19xg9h2tsp1zl8g9h2t
+        deferrable: false
+        initiallyDeferred: false
+        onDelete: NO ACTION
+        onUpdate: NO ACTION
+        referencedColumnNames: id
+        referencedTableName: acce
+    - createIndex:
+        columns:
+        - column:
+            name: accessionId
+        indexName: FK_ekss0g19xg9h2tsp1zl8g9h2t
+        tableName: dataset_accessions

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

@@ -18,6 +18,7 @@ package org.genesys.test.catalog.services;
 import java.util.HashSet;
 import java.util.Set;
 
+import com.google.common.collect.Lists;
 import org.genesys.catalog.model.Partner;
 import org.genesys.catalog.model.dataset.AccessionIdentifier;
 import org.genesys.catalog.model.dataset.Dataset;
@@ -28,6 +29,14 @@ import org.genesys.catalog.persistence.dataset.DatasetVersionsRepository;
 import org.genesys.catalog.service.DatasetCreatorService;
 import org.genesys.catalog.service.DatasetService;
 import org.genesys.filerepository.persistence.RepositoryFilePersistence;
+import org.genesys2.server.model.genesys.Accession;
+import org.genesys2.server.model.genesys.AccessionId;
+import org.genesys2.server.model.genesys.Taxonomy2;
+import org.genesys2.server.model.impl.FaoInstitute;
+import org.genesys2.server.persistence.AccessionRepository;
+import org.genesys2.server.persistence.FaoInstituteRepository;
+import org.genesys2.server.service.InstituteService;
+import org.genesys2.server.service.TaxonomyService;
 import org.junit.After;
 import org.junit.Before;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -50,6 +59,14 @@ public abstract class AbstractDatasetServiceTest extends CatalogServiceTest {
 	protected RepositoryFilePersistence repositoryFilePersistence;
 	@Autowired
 	protected DatasetCreatorService datasetCreatorService;
+	@Autowired
+	protected AccessionRepository accessionRepository;
+	@Autowired
+	protected FaoInstituteRepository instituteRepository;
+	@Autowired
+	private InstituteService instituteService;
+	@Autowired
+	private TaxonomyService taxonomyService;
 
 	public AbstractDatasetServiceTest() {
 		super();
@@ -68,6 +85,8 @@ public abstract class AbstractDatasetServiceTest extends CatalogServiceTest {
 		datasetVersionsRepository.deleteAll();
 		descriptorRepository.deleteAll();
 		repositoryFilePersistence.deleteAll();
+		accessionRepository.deleteAll();
+		instituteRepository.deleteAll();
 		super.cleanup();
 	}
 
@@ -130,4 +149,21 @@ public abstract class AbstractDatasetServiceTest extends CatalogServiceTest {
 		return accessionIdentifier;
 	}
 
+	protected Accession buildAndSaveAccession(final String acceNumb, final String instCode, final String genus) {
+		FaoInstitute institute = new FaoInstitute();
+		institute.setCode(instCode);
+		institute.setFullName("Test institute " + instCode);
+		instituteService.update(Lists.newArrayList(institute));
+		institute = instituteService.getInstitute(instCode);
+
+		Accession a = new Accession();
+		a.setAccessionId(new AccessionId());
+		a.setInstitute(institute);
+		a.setAccessionNumber(acceNumb);
+		Taxonomy2 taxon = new Taxonomy2();
+		taxon.setGenus(genus);
+		a.setTaxonomy(taxonomyService.ensureTaxonomy(taxon));
+		return accessionRepository.save(a);
+	}
+
 }
\ No newline at end of file

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

@@ -42,6 +42,8 @@ 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.Accession;
+import org.genesys2.server.model.genesys.AccessionId;
 import org.junit.Test;
 import org.springframework.dao.ConcurrencyFailureException;
 import org.springframework.dao.DataIntegrityViolationException;
@@ -149,6 +151,40 @@ 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
+	public void testLookupAccessionsForAccessionIdentifiersInDataset() {
+		final Accession accession = buildAndSaveAccession("TestAccNum", TEST_INSTCODE, "TestGen");
+
+		Dataset input = buildDataset(DATASET_TITLE_1, DATASET_DESCRIPTION_1, partner, null, false);
+		input = datasetService.createDataset(input);
+
+		final Set<AccessionIdentifier> accessionIdentifiers = new HashSet<AccessionIdentifier>() {
+			/**
+			 *
+			 */
+			private static final long serialVersionUID = 8866546652858324612L;
+
+			{
+				add(makeAccessionIdentifier(TEST_INSTCODE, "TestAccNum", "TestGen", null));
+			}
+		};
+
+		input = datasetService.updateAccessionIdentifiers(input, accessionIdentifiers);
+		assertThat(input, not(nullValue()));
+		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();
+		assertThat(accessionId.getUuid(), is(accession.getAccessionId().getUuid()));
 	}
 
 	/**