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Initial code for mapped super class for associations #1674

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Initial code for mapped super class for associations #1674

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37 changes: 27 additions & 10 deletions src/main/java/org/alliancegenome/curation_api/model/entities/AGMDiseaseAnnotation.java
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Expand Up @@ -6,8 +6,8 @@
import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
import org.alliancegenome.curation_api.view.View;
import org.eclipse.microprofile.openapi.annotations.media.Schema;
import org.hibernate.annotations.Fetch;
import org.hibernate.annotations.FetchMode;
import org.hibernate.annotations.OnDelete;
import org.hibernate.annotations.OnDeleteAction;
import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.Indexed;
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
Expand All @@ -22,6 +22,7 @@
import jakarta.persistence.JoinTable;
import jakarta.persistence.ManyToMany;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.Table;
import jakarta.persistence.Transient;
import lombok.Data;
import lombok.EqualsAndHashCode;
Expand All @@ -33,13 +34,33 @@
@Schema(name = "AGM_Disease_Annotation", description = "Annotation class representing a agm disease annotation")
@JsonTypeName("AGMDiseaseAnnotation")
@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { DiseaseAnnotation.class })

@Table(indexes = {
@Index(name = "AGMDiseaseAnnotation_curie_index", columnList = "curie"),
@Index(name = "AGMDiseaseAnnotation_uniqueId_index", columnList = "uniqueId"),
@Index(name = "AGMDiseaseAnnotation_modEntityId_index", columnList = "modEntityId"),
@Index(name = "AGMDiseaseAnnotation_modInternalId_index", columnList = "modInternalId"),
@Index(name = "AGMDiseaseAnnotation_createdBy_index", columnList = "createdBy_id"),
@Index(name = "AGMDiseaseAnnotation_updatedBy_index", columnList = "updatedBy_id"),
@Index(name = "AGMDiseaseAnnotation_singleReference_index", columnList = "singleReference_id"),
@Index(name = "AGMDiseaseAnnotation_dataProvider_index", columnList = "dataProvider_id"),
@Index(name = "AGMDiseaseAnnotation_annotationType_index", columnList = "annotationType_id"),
@Index(name = "AGMDiseaseAnnotation_diseaseAnnotationObject_index", columnList = "diseaseAnnotationObject_id"),
@Index(name = "AGMDiseaseAnnotation_diseaseGeneticModifierRelation_index", columnList = "diseaseGeneticModifierRelation_id"),
@Index(name = "AGMDiseaseAnnotation_geneticSex_index", columnList = "geneticSex_id"),
@Index(name = "AGMDiseaseAnnotation_relation_index", columnList = "relation_id"),
@Index(name = "AGMDiseaseAnnotation_secondaryDataProvider_index", columnList = "secondaryDataProvider_id"),
@Index(name = "AGMDiseaseAnnotation_assertedAllele_index", columnList = "assertedAllele_id"),
@Index(name = "AGMDiseaseAnnotation_diseaseAnnotationSubject_index", columnList = "diseaseAnnotationSubject_id"),
@Index(name = "AGMDiseaseAnnotation_inferredAllele_index", columnList = "inferredAllele_id"),
@Index(name = "AGMDiseaseAnnotation_inferredGene_index", columnList = "inferredGene_id")
})
public class AGMDiseaseAnnotation extends DiseaseAnnotation {

@IndexedEmbedded(includePaths = {"name", "name_keyword", "curie", "curie_keyword", "modEntityId", "modEntityId_keyword", "modInternalId", "modInternalId_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@Fetch(FetchMode.SELECT)
@org.hibernate.annotations.OnDelete(action = org.hibernate.annotations.OnDeleteAction.CASCADE)
@OnDelete(action = OnDeleteAction.CASCADE)
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
private AffectedGenomicModel diseaseAnnotationSubject;

Expand All @@ -53,7 +74,6 @@ public class AGMDiseaseAnnotation extends DiseaseAnnotation {
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@Fetch(FetchMode.SELECT)
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
private Gene inferredGene;

Expand All @@ -66,7 +86,6 @@ public class AGMDiseaseAnnotation extends DiseaseAnnotation {
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@Fetch(FetchMode.SELECT)
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
private Allele inferredAllele;

Expand All @@ -80,10 +99,9 @@ public class AGMDiseaseAnnotation extends DiseaseAnnotation {
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@Fetch(FetchMode.SELECT)
@JoinTable(indexes = {
@Index(name = "association_agmdiseaseannotation_index", columnList = "agmdiseaseannotation_id"),
@Index(name = "association_assertedgenes_index", columnList = "assertedgenes_id")
@Index(columnList = "agmdiseaseannotation_id"),
@Index(columnList = "assertedgenes_id")
})
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
private List<Gene> assertedGenes;
Expand All @@ -97,7 +115,6 @@ public class AGMDiseaseAnnotation extends DiseaseAnnotation {
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@Fetch(FetchMode.SELECT)
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
private Allele assertedAllele;

Expand Down
17 changes: 2 additions & 15 deletions src/main/java/org/alliancegenome/curation_api/model/entities/Annotation.java
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Expand Up @@ -7,8 +7,6 @@
import org.alliancegenome.curation_api.model.entities.base.AuditedObject;
import org.alliancegenome.curation_api.view.View;
import org.eclipse.microprofile.openapi.annotations.media.Schema;
import org.hibernate.annotations.Fetch;
import org.hibernate.annotations.FetchMode;
import org.hibernate.search.engine.backend.types.Aggregable;
import org.hibernate.search.engine.backend.types.Searchable;
import org.hibernate.search.engine.backend.types.Sortable;
Expand All @@ -22,17 +20,15 @@

import jakarta.persistence.CascadeType;
import jakarta.persistence.Column;
import jakarta.persistence.Entity;
import jakarta.persistence.Index;
import jakarta.persistence.JoinTable;
import jakarta.persistence.ManyToMany;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.MappedSuperclass;
import jakarta.persistence.OneToMany;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.ToString;

@Entity
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@ToString(callSuper = true)
Expand Down Expand Up @@ -72,10 +68,6 @@ public class Annotation extends SingleReferenceAssociation {
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.PhenotypeAnnotationView.class, View.ForPublic.class })
@JoinTable(indexes = {
@Index(name = "association_annotation_conditionrelation_index", columnList = "annotation_id"),
@Index(name = "association_annotation_conditionrelations_index", columnList = "conditionrelations_id")
})
private List<ConditionRelation> conditionRelations;

@IndexedEmbedded(includePaths = {"freeText", "noteType.name", "references.curie",
Expand All @@ -85,17 +77,12 @@ public class Annotation extends SingleReferenceAssociation {
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@OneToMany(cascade = CascadeType.ALL, orphanRemoval = true)
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JoinTable(indexes = {
@Index(name = "association_annotation_annotation_index", columnList = "annotation_id"),
@Index(name = "association_relatednotes_index", columnList = "relatednotes_id")
})
private List<Note> relatedNotes;

@IndexedEmbedded(includePaths = {"sourceOrganization.abbreviation", "sourceOrganization.fullName", "sourceOrganization.shortName", "crossReference.displayName", "crossReference.referencedCurie",
"sourceOrganization.abbreviation_keyword", "sourceOrganization.fullName_keyword", "sourceOrganization.shortName_keyword", "crossReference.displayName_keyword", "crossReference.referencedCurie_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@Fetch(FetchMode.SELECT)
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
protected DataProvider dataProvider;

Expand Down
19 changes: 8 additions & 11 deletions src/main/java/org/alliancegenome/curation_api/model/entities/Association.java
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Expand Up @@ -5,24 +5,20 @@
import org.alliancegenome.curation_api.model.entities.base.AuditedObject;
import org.eclipse.microprofile.openapi.annotations.media.Schema;

import jakarta.persistence.DiscriminatorColumn;
import jakarta.persistence.Entity;
import jakarta.persistence.Index;
import jakarta.persistence.Inheritance;
import jakarta.persistence.InheritanceType;
import jakarta.persistence.Table;
import jakarta.persistence.MappedSuperclass;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.ToString;

@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@DiscriminatorColumn(name = "AssociationType", length = 96)
@Entity
//@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
//@DiscriminatorColumn(name = "AssociationType", length = 96)
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@ToString(callSuper = true)
@Schema(name = "association", description = "POJO that represents an association")
@Table(indexes = {
//@Table(indexes = {
/*
@Index(name = "association_curie_index", columnList = "curie"),
@Index(name = "association_modEntityId_index", columnList = "modEntityId"),
@Index(name = "association_modInternalId_index", columnList = "modInternalId"),
Expand Down Expand Up @@ -82,7 +78,8 @@

@Index(name = "association_createdby_index", columnList = "createdBy_id"),
@Index(name = "association_updatedby_index", columnList = "updatedBy_id")
})
*/
//})

@AGRCurationSchemaVersion(min = "1.9.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { AuditedObject.class })
public class Association extends AuditedObject {
Expand Down
28 changes: 2 additions & 26 deletions src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java
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Expand Up @@ -9,8 +9,6 @@
import org.alliancegenome.curation_api.model.entities.ontology.ECOTerm;
import org.alliancegenome.curation_api.view.View;
import org.eclipse.microprofile.openapi.annotations.media.Schema;
import org.hibernate.annotations.Fetch;
import org.hibernate.annotations.FetchMode;
import org.hibernate.search.engine.backend.types.Aggregable;
import org.hibernate.search.engine.backend.types.Searchable;
import org.hibernate.search.engine.backend.types.Sortable;
Expand All @@ -28,19 +26,17 @@
import com.fasterxml.jackson.annotation.JsonView;

import jakarta.persistence.Column;
import jakarta.persistence.Entity;
import jakarta.persistence.Index;
import jakarta.persistence.JoinTable;
import jakarta.persistence.ManyToMany;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.MappedSuperclass;
import jakarta.persistence.Transient;
import lombok.Data;
import lombok.EqualsAndHashCode;

@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
@JsonSubTypes({ @Type(value = AGMDiseaseAnnotation.class, name = "AGMDiseaseAnnotation"), @Type(value = AlleleDiseaseAnnotation.class, name = "AlleleDiseaseAnnotation"),
@Type(value = GeneDiseaseAnnotation.class, name = "GeneDiseaseAnnotation") })
@Entity
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { Annotation.class })
Expand All @@ -51,7 +47,6 @@ public abstract class DiseaseAnnotation extends Annotation {
"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "namespace_keyword" })
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@Fetch(FetchMode.SELECT)
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
private DOTerm diseaseAnnotationObject;

Expand All @@ -72,10 +67,6 @@ public abstract class DiseaseAnnotation extends Annotation {
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JoinTable(indexes = {
@Index(name = "association_diseaseannotation_diseaseannotation_index", columnList = "diseaseannotation_id"),
@Index(name = "association_diseaseannotation_evidencecodes_index", columnList = "evidencecodes_id")
})
private List<ECOTerm> evidenceCodes;

@IndexedEmbedded(includePaths = {
Expand All @@ -88,11 +79,6 @@ public abstract class DiseaseAnnotation extends Annotation {
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@Fetch(FetchMode.SELECT)
@JoinTable(indexes = {
@Index(name = "association_diseaseannotation_gene_index", columnList = "diseaseannotation_id"),
@Index(name = "association_diseaseannotation_with_index", columnList = "with_id")
})
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
private List<Gene> with;

Expand All @@ -106,10 +92,6 @@ public abstract class DiseaseAnnotation extends Annotation {
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JoinTable(indexes = {
@Index(name = "association_diseaseannotation_vt_diseaseannotation_index", columnList = "diseaseannotation_id"),
@Index(name = "association_diseaseannotation_diseasequalifiers_index", columnList = "diseasequalifiers_id")
})
private List<VocabularyTerm> diseaseQualifiers;

@IndexedEmbedded(includePaths = {"name", "name_keyword"})
Expand All @@ -122,19 +104,13 @@ public abstract class DiseaseAnnotation extends Annotation {
"sourceOrganization.abbreviation_keyword", "sourceOrganization.fullName_keyword", "sourceOrganization.shortName_keyword", "crossReference.displayName_keyword", "crossReference.referencedCurie_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@Fetch(FetchMode.SELECT)
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
private DataProvider secondaryDataProvider;

@IndexedEmbedded(includeDepth = 1)
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@Fetch(FetchMode.SELECT)
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JoinTable(indexes = {
@Index(name = "association_diseaseannotation_BiologicalEntity_index", columnList = "diseaseannotation_id"),
@Index(name = "association_diseaseannotation_dgms_index", columnList = "diseasegeneticmodifiers_id")
})
private List<BiologicalEntity> diseaseGeneticModifiers;

@IndexedEmbedded(includePaths = {"name", "name_keyword"})
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/alliancegenome/curation_api/model/entities/EvidenceAssociation.java
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Expand Up @@ -12,14 +12,14 @@

import com.fasterxml.jackson.annotation.JsonView;

import jakarta.persistence.Entity;
import jakarta.persistence.Index;
import jakarta.persistence.JoinTable;
import jakarta.persistence.ManyToMany;
import jakarta.persistence.MappedSuperclass;
import lombok.Data;
import lombok.EqualsAndHashCode;

@Entity
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@Schema(name = "evidenceAssociation", description = "POJO that represents an association supported by any number of information content entities")
Expand Down
8 changes: 2 additions & 6 deletions src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionAnnotation.java
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Expand Up @@ -14,24 +14,20 @@
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;

import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonSubTypes;
import com.fasterxml.jackson.annotation.JsonTypeInfo;
import com.fasterxml.jackson.annotation.JsonView;

import jakarta.persistence.CascadeType;
import jakarta.persistence.Column;
import jakarta.persistence.Entity;
import jakarta.persistence.JoinColumn;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.MappedSuperclass;
import jakarta.persistence.OneToOne;
import jakarta.persistence.Transient;
import lombok.Data;
import lombok.EqualsAndHashCode;


@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
@JsonSubTypes({ @JsonSubTypes.Type(value = GeneExpressionAnnotation.class, name = "GeneExpressionAnnotation") })
@Entity
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@AGRCurationSchemaVersion(min = "2.2.3", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { Annotation.class })
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/alliancegenome/curation_api/model/entities/PhenotypeAnnotation.java
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Expand Up @@ -23,11 +23,11 @@
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.MappedSuperclass;
import jakarta.persistence.OneToOne;
import jakarta.persistence.Transient;
import lombok.Data;
Expand All @@ -36,7 +36,7 @@
@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
@JsonSubTypes({ @Type(value = AGMPhenotypeAnnotation.class, name = "AGMPhenotypeAnnotation"), @Type(value = AllelePhenotypeAnnotation.class, name = "AllelePhenotypeAnnotation"),
@Type(value = GenePhenotypeAnnotation.class, name = "GenePhenotypeAnnotation") })
@Entity
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@AGRCurationSchemaVersion(min = "2.2.3", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { Annotation.class })
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/org/alliancegenome/curation_api/model/entities/SingleReferenceAssociation.java
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Expand Up @@ -10,12 +10,12 @@

import com.fasterxml.jackson.annotation.JsonView;

import jakarta.persistence.Entity;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.MappedSuperclass;
import lombok.Data;
import lombok.EqualsAndHashCode;

@Entity
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@Schema(name = "singleReferenceAssociation", description = "POJO that represents an association supported by a single reference")
Expand Down
4 changes: 2 additions & 2 deletions ...on_api/model/entities/associations/alleleAssociations/AlleleGenomicEntityAssociation.java
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Expand Up @@ -15,14 +15,14 @@
import com.fasterxml.jackson.annotation.JsonView;

import jakarta.persistence.CascadeType;
import jakarta.persistence.Entity;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.MappedSuperclass;
import jakarta.persistence.OneToOne;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.ToString;

@Entity
@MappedSuperclass
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@ToString(callSuper = true)
Expand Down
3 changes: 1 addition & 2 deletions .../model/entities/associations/constructAssociations/ConstructGenomicEntityAssociation.java
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Expand Up @@ -26,7 +26,6 @@
import jakarta.persistence.JoinTable;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.OneToMany;
import jakarta.persistence.OneToOne;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.ToString;
Expand Down Expand Up @@ -58,7 +57,7 @@ public class ConstructGenomicEntityAssociation extends EvidenceAssociation {

@IndexedEmbedded(includeDepth = 1)
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@OneToOne
@ManyToOne
@JsonView({ View.FieldsOnly.class })
@JsonIgnoreProperties({
"alleleGeneAssociations", "constructGenomicEntityAssociations", "sequenceTargetingReagentGeneAssociations",
Expand Down
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