Scrum 4436

src/main/java/org/alliancegenome/curation_api/dao/ReferenceDAO.java

@@ -1,11 +1,13 @@
 package org.alliancegenome.curation_api.dao;
 
-import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
-import org.alliancegenome.curation_api.model.entities.Reference;
-
 import jakarta.enterprise.context.ApplicationScoped;
 import jakarta.persistence.Query;
 import jakarta.transaction.Transactional;
+import org.alliancegenome.curation_api.dao.base.BaseSQLDAO;
+import org.alliancegenome.curation_api.model.entities.Reference;
+
+import java.util.*;
+import java.util.stream.Collectors;
 
 @ApplicationScoped
 public class ReferenceDAO extends BaseSQLDAO<Reference> {
@@ -35,4 +37,53 @@ protected void deleteReferenceForeignKey(String table, String column, String ori
 		jpqlQuery.executeUpdate();
 	}
 
+	public HashMap<String, Reference> getReferenceMap() {
+		HashMap<String, Reference> referenceIdMap = new HashMap<>();
+		Query q = entityManager.createNativeQuery("""
+					SELECT ref.id, cr.referencedcurie
+					FROM Reference as ref, reference_crossreference as assoc, Crossreference as cr
+					where assoc.reference_id = ref.id
+					and assoc.crossreferences_id = cr.id
+			""");
+		List<Object[]> ids = q.getResultList();
+		Set<Long> refIDs = ids.stream().map(object -> (Long) object[0]).collect(Collectors.toSet());
+		Map<Long, List<Object[]>> idMap = ids.stream().collect(Collectors.groupingBy(o -> (Long) o[0]));
+		List<Reference> refs = new ArrayList<>();
+		refIDs.forEach(id -> {
+			Reference reference = entityManager.getReference(Reference.class, id);
+			refs.add(reference);
+			referenceIdMap.put(String.valueOf(id), reference);
+			if (idMap.get(id) != null) {
+				idMap.get(id).forEach(objects -> {
+					referenceIdMap.put((String) objects[1], reference);
+				});
+			}
+		});
+		return referenceIdMap;
+	}
+
+	public HashMap<String, Reference> getShallowReferenceMap() {
+		HashMap<String, Reference> referenceIdMap = new HashMap<>();
+		Query q = entityManager.createNativeQuery("""
+					SELECT ref.id, cr.referencedcurie
+					FROM Reference as ref, reference_crossreference as assoc, Crossreference as cr
+					where assoc.reference_id = ref.id
+					and assoc.crossreferences_id = cr.id
+			""");
+		List<Object[]> ids = q.getResultList();
+		Set<Long> refIDs = ids.stream().map(object -> (Long) object[0]).collect(Collectors.toSet());
+		Map<Long, List<Object[]>> idMap = ids.stream().collect(Collectors.groupingBy(o -> (Long) o[0]));
+		List<Reference> refs = new ArrayList<>();
+		refIDs.forEach(id -> {
+			Reference reference = getShallowEntity(Reference.class, id);
+			refs.add(reference);
+			referenceIdMap.put(String.valueOf(id), reference);
+			if (idMap.get(id) != null) {
+				idMap.get(id).forEach(objects -> {
+					referenceIdMap.put((String) objects[1], reference);
+				});
+			}
+		});
+		return referenceIdMap;
+	}
 }

src/main/java/org/alliancegenome/curation_api/model/entities/AffectedGenomicModel.java

@@ -4,6 +4,7 @@
 
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
+import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.view.View;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
@@ -26,7 +27,7 @@
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@ToString(exclude = { "agmDiseaseAnnotations" }, callSuper = true)
+@ToString(exclude = { "agmDiseaseAnnotations", "constructGenomicEntityAssociations" }, callSuper = true)
 @Schema(name = "AffectedGenomicModel", description = "POJO that represents the AGM")
 @AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class }, partial = true)
 public class AffectedGenomicModel extends GenomicEntity {
@@ -43,4 +44,15 @@ public class AffectedGenomicModel extends GenomicEntity {
 	@ManyToOne
 	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
 	private VocabularyTerm subtype;
+
+	@IndexedEmbedded(includePaths = {
+		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
+		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
+		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
+		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
+	})
+	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
+	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
+
 }

src/main/java/org/alliancegenome/curation_api/model/entities/Allele.java

@@ -2,11 +2,13 @@
 
 import java.util.List;
 
+import jakarta.persistence.*;
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
 import org.alliancegenome.curation_api.model.bridges.BooleanAndNullValueBridge;
 import org.alliancegenome.curation_api.model.entities.associations.alleleAssociations.AlleleGeneAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.alleleAssociations.AlleleVariantAssociation;
+import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.model.entities.slotAnnotations.alleleSlotAnnotations.AlleleDatabaseStatusSlotAnnotation;
 import org.alliancegenome.curation_api.model.entities.slotAnnotations.alleleSlotAnnotations.AlleleFullNameSlotAnnotation;
 import org.alliancegenome.curation_api.model.entities.slotAnnotations.alleleSlotAnnotations.AlleleFunctionalImpactSlotAnnotation;
@@ -34,15 +36,6 @@
 import com.fasterxml.jackson.annotation.JsonManagedReference;
 import com.fasterxml.jackson.annotation.JsonView;
 
-import jakarta.persistence.CascadeType;
-import jakarta.persistence.Entity;
-import jakarta.persistence.Index;
-import jakarta.persistence.JoinTable;
-import jakarta.persistence.ManyToMany;
-import jakarta.persistence.ManyToOne;
-import jakarta.persistence.OneToMany;
-import jakarta.persistence.OneToOne;
-import jakarta.persistence.Table;
 import lombok.Data;
 import lombok.EqualsAndHashCode;
 import lombok.ToString;
@@ -55,7 +48,7 @@
 	exclude = {
 		"alleleGeneAssociations", "alleleVariantAssociations", "alleleDiseaseAnnotations", "alleleMutationTypes", "alleleSymbol", "alleleFullName", "alleleSynonyms",
 		"alleleSecondaryIds", "alleleInheritanceModes", "alleleFunctionalImpacts", "alleleGermlineTransmissionStatus", "alleleDatabaseStatus",
-		"alleleNomenclatureEvents"
+		"alleleNomenclatureEvents", "constructGenomicEntityAssociations"
 	},
 	callSuper = true
 )
@@ -212,4 +205,15 @@ public class Allele extends GenomicEntity {
 		@Index(name = "allele_note_relatednotes_index", columnList = "relatedNotes_id")})
 	private List<Note> relatedNotes;
 
+
+	@IndexedEmbedded(includePaths = {
+		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
+		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
+		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
+		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
+	})
+	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
+	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
+
 }

src/main/java/org/alliancegenome/curation_api/model/entities/Gene.java

@@ -5,6 +5,7 @@
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
 import org.alliancegenome.curation_api.model.entities.associations.alleleAssociations.AlleleGeneAssociation;
+import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.geneAssociations.GeneGenomicLocationAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.sequenceTargetingReagentAssociations.SequenceTargetingReagentGeneAssociation;
 import org.alliancegenome.curation_api.model.entities.associations.transcriptAssociations.TranscriptGeneAssociation;
@@ -40,7 +41,7 @@
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
 @ToString(exclude = { "geneDiseaseAnnotations", "geneGeneAssociations", "geneSymbol", "geneFullName", "geneSystematicName", "geneSynonyms", "geneSecondaryIds",
-		"geneGenomicLocationAssociations", "alleleGeneAssociations", "sequenceTargetingReagentGeneAssociations", "transcriptGeneAssociations" }, callSuper = true)
+		"geneGenomicLocationAssociations", "alleleGeneAssociations", "sequenceTargetingReagentGeneAssociations", "transcriptGeneAssociations", "constructGenomicEntityAssociations" }, callSuper = true)
 @Schema(name = "Gene", description = "POJO that represents the Gene")
 @AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { GenomicEntity.class }, partial = true)
 @Table(indexes = { @Index(name = "gene_genetype_index", columnList = "geneType_id") })
@@ -119,4 +120,16 @@ public class Gene extends GenomicEntity {
 	@OneToMany(mappedBy = "geneAssociationSubject", cascade = CascadeType.ALL, orphanRemoval = true)
 	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
 	private List<GeneGenomicLocationAssociation> geneGenomicLocationAssociations;
+
+
+	@IndexedEmbedded(includePaths = {
+		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
+		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
+		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
+		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
+	})
+	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
+	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
+
 }

src/main/java/org/alliancegenome/curation_api/model/entities/GenomicEntity.java

@@ -1,31 +1,24 @@
 package org.alliancegenome.curation_api.model.entities;
 
-import java.util.List;
-
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.persistence.*;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
-import org.alliancegenome.curation_api.model.entities.associations.constructAssociations.ConstructGenomicEntityAssociation;
 import org.alliancegenome.curation_api.view.View;
 import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
 
-import com.fasterxml.jackson.annotation.JsonView;
-
-import jakarta.persistence.CascadeType;
-import jakarta.persistence.Entity;
-import jakarta.persistence.Index;
-import jakarta.persistence.JoinTable;
-import jakarta.persistence.OneToMany;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
-import lombok.ToString;
+import java.util.List;
 
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
-@ToString(exclude = { "constructGenomicEntityAssociations" }, callSuper = true)
-@AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { BiologicalEntity.class })
+@ToString(callSuper = true)
+@AGRCurationSchemaVersion(min = "1.5.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {BiologicalEntity.class})
 public class GenomicEntity extends BiologicalEntity {
 
 	@IndexedEmbedded(includePaths = {"referencedCurie", "displayName", "resourceDescriptorPage.name", "referencedCurie_keyword", "displayName_keyword", "resourceDescriptorPage.name_keyword"})
@@ -37,18 +30,8 @@ public class GenomicEntity extends BiologicalEntity {
 		@Index(columnList = "crossreferences_id", name = "genomicentity_crossreference_crossreferences_index")
 	})
 	@EqualsAndHashCode.Include
-	@JsonView({ View.FieldsAndLists.class, View.AlleleView.class, View.GeneView.class, View.AffectedGenomicModelView.class, View.VariantView.class })
+	@JsonView({View.FieldsAndLists.class, View.AlleleView.class, View.GeneView.class, View.AffectedGenomicModelView.class, View.VariantView.class})
 	private List<CrossReference> crossReferences;
-
 
-	@IndexedEmbedded(includePaths = {
-		"constructAssociationSubject.curie", "constructAssociationSubject.constructSymbol.displayText", "constructAssociationSubject.constructSymbol.formatText",
-		"constructAssociationSubject.constructFullName.displayText", "constructAssociationSubject.constructFullName.formatText", "constructAssociationSubject.modEntityId",
-		"constructAssociationSubject.curie_keyword", "constructAssociationSubject.constructSymbol.displayText_keyword", "constructAssociationSubject.constructSymbol.formatText_keyword",
-		"constructAssociationSubject.constructFullName.displayText_keyword", "constructAssociationSubject.constructFullName.formatText_keyword", "constructAssociationSubject.modEntityId_keyword"
-	})
-	@OneToMany(mappedBy = "constructGenomicEntityAssociationObject", cascade = CascadeType.ALL, orphanRemoval = true)
-	@JsonView({ View.FieldsAndLists.class, View.GeneDetailView.class })
-	private List<ConstructGenomicEntityAssociation> constructGenomicEntityAssociations;
 
 }

src/main/java/org/alliancegenome/curation_api/model/entities/associations/constructAssociations/ConstructGenomicEntityAssociation.java

@@ -1,14 +1,14 @@
 package org.alliancegenome.curation_api.model.entities.associations.constructAssociations;
 
-import java.util.List;
-
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+import com.fasterxml.jackson.annotation.JsonView;
+import jakarta.persistence.*;
+import lombok.Data;
+import lombok.EqualsAndHashCode;
+import lombok.ToString;
 import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
 import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
-import org.alliancegenome.curation_api.model.entities.Construct;
-import org.alliancegenome.curation_api.model.entities.EvidenceAssociation;
-import org.alliancegenome.curation_api.model.entities.GenomicEntity;
-import org.alliancegenome.curation_api.model.entities.Note;
-import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
+import org.alliancegenome.curation_api.model.entities.*;
 import org.alliancegenome.curation_api.view.View;
 import org.eclipse.microprofile.openapi.annotations.media.Schema;
 import org.hibernate.annotations.Fetch;
@@ -17,26 +17,13 @@
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
 import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
 
-import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
-import com.fasterxml.jackson.annotation.JsonView;
-
-import jakarta.persistence.CascadeType;
-import jakarta.persistence.Entity;
-import jakarta.persistence.Index;
-import jakarta.persistence.JoinColumn;
-import jakarta.persistence.JoinTable;
-import jakarta.persistence.ManyToOne;
-import jakarta.persistence.OneToMany;
-import jakarta.persistence.Table;
-import lombok.Data;
-import lombok.EqualsAndHashCode;
-import lombok.ToString;
+import java.util.List;
 
 @Entity
 @Data
 @EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
 @ToString(callSuper = true)
-@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { EvidenceAssociation.class })
+@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {EvidenceAssociation.class})
 @Schema(name = "ConstructGenomicEntityAssociation", description = "POJO representing an association between a construct and a genomic entity")
 
 @Table(indexes = {
@@ -57,21 +44,21 @@ public class ConstructGenomicEntityAssociation extends EvidenceAssociation {
 		"curie_keyword", "constructSymbol.displayText_keyword", "constructSymbol.formatText_keyword",
 		"constructFullName.displayText_keyword", "constructFullName.formatText_keyword", "modEntityId_keyword", "modInternalId_keyword"})
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class })
+	@JsonView({View.FieldsOnly.class})
 	@JsonIgnoreProperties("constructGenomicEntityAssociations")
 	@Fetch(FetchMode.JOIN)
 	private Construct constructAssociationSubject;
-	
+
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class })
+	@JsonView({View.FieldsOnly.class})
 	private VocabularyTerm relation;
-	
+
 	@IndexedEmbedded(includeDepth = 1)
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class })
+	@JsonView({View.FieldsOnly.class})
 	@JsonIgnoreProperties({
 		"alleleGeneAssociations", "constructGenomicEntityAssociations", "sequenceTargetingReagentGeneAssociations",
 		"transcriptGenomicLocationAssociations", "exonGenomicLocationAssociations", "codingSequenceGenomicLocationAssociations",
@@ -85,7 +72,7 @@ public class ConstructGenomicEntityAssociation extends EvidenceAssociation {
 	})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
-	@JsonView({ View.FieldsAndLists.class, View.ConstructView.class })
+	@JsonView({View.FieldsAndLists.class, View.ConstructView.class})
 	@JoinTable(
 		joinColumns = @JoinColumn(name = "constructgenomicentityassociation_id"),
 		inverseJoinColumns = @JoinColumn(name = "relatedNotes_id"),

src/main/java/org/alliancegenome/curation_api/services/InformationContentEntityService.java

@@ -28,4 +28,5 @@ public InformationContentEntity retrieveFromDbOrLiteratureService(String curieOr
 
 		return ice;
 	}
+
 }