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Merge pull request #1665 from alliance-genome/fix_missing_indexs
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@oblodgett
oblodgett authored Sep 11, 2024
2 parents 353e4b5 + 202be7f commit 8ceabe9
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Showing 31 changed files with 776 additions and 251 deletions.
15 changes: 4 additions & 11 deletions src/main/java/org/alliancegenome/curation_api/model/entities/AGMDiseaseAnnotation.java
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Expand Up @@ -8,8 +8,6 @@
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 @@ -24,7 +22,6 @@
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 @@ -35,14 +32,7 @@
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@Schema(name = "AGM_Disease_Annotation", description = "Annotation class representing a agm disease annotation")
@JsonTypeName("AGMDiseaseAnnotation")
@OnDelete(action = OnDeleteAction.CASCADE)
@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { DiseaseAnnotation.class })
@Table(indexes = {
@Index(name = "AGMDiseaseAnnotation_inferredGene_index", columnList = "inferredGene_id"),
@Index(name = "AGMDiseaseAnnotation_inferredAllele_index", columnList = "inferredAllele_id"),
@Index(name = "AGMDiseaseAnnotation_assertedAllele_index", columnList = "assertedAllele_id"),
@Index(name = "AGMDiseaseAnnotation_DiseaseAnnotationSubject_index", columnList = "diseaseAnnotationSubject_id")
})
public class AGMDiseaseAnnotation extends DiseaseAnnotation {

@IndexedEmbedded(includePaths = {"name", "name_keyword", "curie", "curie_keyword", "modEntityId", "modEntityId_keyword", "modInternalId", "modInternalId_keyword"})
Expand Down Expand Up @@ -91,7 +81,10 @@ public class AGMDiseaseAnnotation extends DiseaseAnnotation {
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@Fetch(FetchMode.SELECT)
@JoinTable(indexes = @Index(name = "agmdiseaseannotation_gene_agmdiseaseannotation_index", columnList = "agmdiseaseannotation_id"))
@JoinTable(indexes = {
@Index(name = "association_agmdiseaseannotation_index", columnList = "agmdiseaseannotation_id"),
@Index(name = "association_assertedgenes_index", columnList = "assertedgenes_id")
})
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
private List<Gene> assertedGenes;

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11 changes: 2 additions & 9 deletions src/main/java/org/alliancegenome/curation_api/model/entities/AGMPhenotypeAnnotation.java
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Expand Up @@ -21,7 +21,6 @@
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 @@ -33,12 +32,6 @@
@Schema(name = "AGM_Phenotype_Annotation", description = "Annotation class representing a agm phenotype annotation")
@JsonTypeName("AGMPhenotypeAnnotation")
@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { PhenotypeAnnotation.class })
@Table(indexes = {
@Index(name = "AGMPhenotypeAnnotation_inferredGene_index", columnList = "inferredGene_id"),
@Index(name = "AGMPhenotypeAnnotation_inferredAllele_index", columnList = "inferredAllele_id"),
@Index(name = "AGMPhenotypeAnnotation_assertedAllele_index", columnList = "assertedAllele_id"),
@Index(name = "AGMPhenotypeAnnotation_PhenotypeAnnotationSubject_index", columnList = "phenotypeAnnotationSubject_id")
})
public class AGMPhenotypeAnnotation extends PhenotypeAnnotation {

@IndexedEmbedded(includePaths = {"name", "name_keyword", "curie", "curie_keyword", "modEntityId", "modEntityId_keyword", "modInternalId", "modInternalId_keyword"})
Expand Down Expand Up @@ -88,8 +81,8 @@ public class AGMPhenotypeAnnotation extends PhenotypeAnnotation {
@ManyToMany
@Fetch(FetchMode.SELECT)
@JoinTable(indexes = {
@Index(name = "agmphenotypeannotation_gene_agmphenotypeannotation_index", columnList = "agmphenotypeannotation_id"),
@Index(name = "agmphenotypeannotation_gene_assertedgenes_index", columnList = "assertedgenes_id")
@Index(name = "association_agmphenotypeannotation_index", columnList = "agmphenotypeannotation_id"),
@Index(name = "association_assertedgenes_index", columnList = "assertedgenes_id")
})
@JsonView({ View.FieldsAndLists.class, View.PhenotypeAnnotationView.class, View.ForPublic.class })
private List<Gene> assertedGenes;
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12 changes: 2 additions & 10 deletions src/main/java/org/alliancegenome/curation_api/model/entities/AlleleDiseaseAnnotation.java
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Expand Up @@ -8,8 +8,6 @@
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 @@ -24,7 +22,6 @@
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 @@ -35,12 +32,7 @@
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@Schema(name = "Allele_Disease_Annotation", description = "Annotation class representing a allele disease annotation")
@JsonTypeName("AlleleDiseaseAnnotation")
@OnDelete(action = OnDeleteAction.CASCADE)
@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { DiseaseAnnotation.class })
@Table(indexes = {
@Index(name = "AlleleDiseaseAnnotation_inferredGene_index", columnList = "inferredGene_id"),
@Index(name = "AlleleDiseaseAnnotation_DiseaseAnnotationSubject_index", columnList = "diseaseAnnotationSubject_id")
})
public class AlleleDiseaseAnnotation extends DiseaseAnnotation {

@IndexedEmbedded(includePaths = {
Expand Down Expand Up @@ -83,8 +75,8 @@ public class AlleleDiseaseAnnotation extends DiseaseAnnotation {
@ManyToMany
@Fetch(FetchMode.SELECT)
@JoinTable(indexes = {
@Index(name = "allelediseaseannotationgene_diseaseannotation_index", columnList = "allelediseaseannotation_id"),
@Index(name = "allelediseaseannotationgene_assertedgenes_index", columnList = "assertedgenes_id")
@Index(name = "association_allelediseaseannotation_index", columnList = "allelediseaseannotation_id"),
@Index(name = "association_assertedgenes_index", columnList = "assertedgenes_id")
})
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
private List<Gene> assertedGenes;
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9 changes: 2 additions & 7 deletions src/main/java/org/alliancegenome/curation_api/model/entities/AllelePhenotypeAnnotation.java
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Expand Up @@ -21,7 +21,6 @@
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 @@ -33,10 +32,6 @@
@Schema(name = "Allele_Phenotype_Annotation", description = "Annotation class representing a allele phenotype annotation")
@JsonTypeName("AllelePhenotypeAnnotation")
@AGRCurationSchemaVersion(min = "2.2.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { PhenotypeAnnotation.class })
@Table(indexes = {
@Index(name = "AllelePhenotypeAnnotation_inferredGene_index", columnList = "inferredGene_id"),
@Index(name = "AllelePhenotypeAnnotation_PhenotypeAnnotationSubject_index", columnList = "phenotypeAnnotationSubject_id")
})
public class AllelePhenotypeAnnotation extends PhenotypeAnnotation {

@IndexedEmbedded(includePaths = {
Expand Down Expand Up @@ -79,8 +74,8 @@ public class AllelePhenotypeAnnotation extends PhenotypeAnnotation {
@ManyToMany
@Fetch(FetchMode.SELECT)
@JoinTable(indexes = {
@Index(name = "allelephenotypeannotationgene_phenotypeannotation_index", columnList = "allelephenotypeannotation_id"),
@Index(name = "allelephenotypeannotationgene_assertedgenes_index", columnList = "assertedgenes_id")
@Index(name = "association_allelephenotypeannotation_index", columnList = "allelephenotypeannotation_id"),
@Index(name = "association_assertedgenes_index", columnList = "assertedgenes_id")
})
@JsonView({ View.FieldsAndLists.class, View.PhenotypeAnnotationView.class, View.ForPublic.class })
private List<Gene> assertedGenes;
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24 changes: 8 additions & 16 deletions src/main/java/org/alliancegenome/curation_api/model/entities/Annotation.java
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Expand Up @@ -28,8 +28,6 @@
import jakarta.persistence.ManyToMany;
import jakarta.persistence.ManyToOne;
import jakarta.persistence.OneToMany;
import jakarta.persistence.Table;
import jakarta.persistence.UniqueConstraint;
import lombok.Data;
import lombok.EqualsAndHashCode;
import lombok.ToString;
Expand All @@ -40,18 +38,6 @@
@ToString(callSuper = true)
@Schema(name = "annotation", description = "POJO that represents an annotation")
@AGRCurationSchemaVersion(min = "1.9.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { AuditedObject.class })
@Table(
indexes = {
@Index(name = "annotation_curie_index", columnList = "curie"),
@Index(name = "annotation_uniqueId_index", columnList = "uniqueId"),
@Index(name = "annotation_modEntityId_index", columnList = "modEntityId"),
@Index(name = "annotation_modInternalId_index", columnList = "modInternalId"),
@Index(name = "annotation_dataprovider_index", columnList = "dataProvider_id")
}, uniqueConstraints = {
@UniqueConstraint(name = "annotation_modentityid_uk", columnNames = "modEntityId"),
@UniqueConstraint(name = "annotation_modinternalid_uk", columnNames = "modInternalId")
}
)
public class Annotation extends SingleReferenceAssociation {

@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
Expand Down Expand Up @@ -86,7 +72,10 @@ 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 = "annotation_conditionrelation_annotation_index", columnList = "annotation_id"), @Index(name = "annotation_conditionrelation_conditionrelations_index", columnList = "conditionrelations_id")})
@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 @@ -96,7 +85,10 @@ 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 = "annotation_note_annotation_index", columnList = "annotation_id"), @Index(name = "annotation_note_relatednotes_index", columnList = "relatednotes_id")})
@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",
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66 changes: 63 additions & 3 deletions src/main/java/org/alliancegenome/curation_api/model/entities/Association.java
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Expand Up @@ -5,6 +5,7 @@
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;
Expand All @@ -14,16 +15,75 @@
import lombok.EqualsAndHashCode;
import lombok.ToString;

@Inheritance(strategy = InheritanceType.JOINED)
@Inheritance(strategy = InheritanceType.SINGLE_TABLE)
@DiscriminatorColumn(name = "AssociationType", length = 96)
@Entity
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@ToString(callSuper = true)
@Schema(name = "association", description = "POJO that represents an association")
@Table(indexes = {
@Index(name = "association_createdby_index", columnList = "createdBy_id"),
@Index(name = "association_updatedby_index", columnList = "updatedBy_id")
@Index(name = "association_curie_index", columnList = "curie"),
@Index(name = "association_modEntityId_index", columnList = "modEntityId"),
@Index(name = "association_modInternalId_index", columnList = "modInternalId"),
@Index(name = "association_uniqueId_index", columnList = "uniqueid"),
@Index(name = "association_whenexpressedstagename_index ", columnList = "whenexpressedstagename"),
@Index(name = "association_whereexpressedstatement_index", columnList = "whereexpressedstatement"),
@Index(name = "association_interactionId_index", columnList = "interactionid"),
@Index(name = "association_construct_subject_index", columnList = "constructassociationsubject_id"),
@Index(name = "association_construct_object_index", columnList = "constructgenomicentityassociationobject_id"),
@Index(name = "association_relation_index", columnList = "relation_id"),
@Index(name = "association_singlereference_index", columnList = "singleReference_id"),
@Index(name = "association_dataProvider_index", columnList = "dataProvider_id"),
@Index(name = "association_crossreference_index", columnList = "crossreference_id"),
@Index(name = "association_assertedAllele_index", columnList = "assertedAllele_id"),
@Index(name = "association_inferredAllele_index", columnList = "inferredAllele_id"),
@Index(name = "association_inferredGene_index", columnList = "inferredGene_id"),
@Index(name = "association_PhenotypeAnnotationSubject_index", columnList = "phenotypeAnnotationSubject_id"),
@Index(name = "association_sgdstrainbackground_index", columnList = "sgdstrainbackground_id"),
@Index(name = "association_expressionpattern_index", columnList = "expressionpattern_id"),
@Index(name = "association_expression_annotation_subject_index", columnList = "expressionannotationsubject_id"),
@Index(name = "association_expression_assay_used_index", columnList = "expressionassayused_id"),
@Index(name = "association_sqtr_subject_index", columnList = "sequencetargetingreagentassociationsubject_id"),
@Index(name = "association_sqtr_object_index", columnList = "sequencetargetingreagentgeneassociationobject_id"),
@Index(name = "association_evidencecode_index", columnList = "evidencecode_id"),
@Index(name = "association_relatednote_index", columnList = "relatednote_id"),
@Index(name = "association_geneassociationsubject_index", columnList = "geneassociationsubject_id"),
@Index(name = "association_genegeneassociationobject_index", columnList = "genegeneassociationobject_id"),
@Index(name = "association_transcript_subject_index", columnList = "transcriptassociationsubject_id"),
@Index(name = "association_transcript_gene_object_index", columnList = "transcriptgeneassociationobject_id"),
@Index(name = "association_exon_subject_index", columnList = "exonassociationsubject_id"),
@Index(name = "association_exon_object_index", columnList = "exongenomiclocationassociationobject_id"),
@Index(name = "association_annotationType_index", columnList = "annotationType_id"),
@Index(name = "association_DiseaseAnnotationObject_index", columnList = "diseaseAnnotationObject_id"),
@Index(name = "association_diseaseGeneticModifierRelation_index", columnList = "diseaseGeneticModifierRelation_id"),
@Index(name = "association_geneticSex_index", columnList = "geneticSex_id"),
@Index(name = "association_secondaryDataProvider_index", columnList = "secondaryDataProvider_id"),
@Index(name = "association_DiseaseAnnotationSubject_index", columnList = "diseaseAnnotationSubject_id"),
@Index(name = "association_interactionsource_index", columnList = "interactionsource_id"),
@Index(name = "association_interactiontype_index", columnList = "interactiontype_id"),
@Index(name = "association_interactorarole_index", columnList = "interactorarole_id"),
@Index(name = "association_interactorbrole_index", columnList = "interactorbrole_id"),
@Index(name = "association_interactoratype_index", columnList = "interactoratype_id"),
@Index(name = "association_interactorbtype_index", columnList = "interactorbtype_id"),
@Index(name = "association_interactorageneticperturbarion_index", columnList = "interactorageneticperturbation_id"),
@Index(name = "association_interactorbgeneticperturbarion_index", columnList = "interactorbgeneticperturbation_id"),
@Index(name = "association_alleleassociationsubject_index", columnList = "alleleassociationsubject_id"),
@Index(name = "association_allelegeneassociationobject_index", columnList = "allelegeneassociationobject_id"),
@Index(name = "association_transcript_exon_object_index", columnList = "transcriptexonassociationobject_id"),
@Index(name = "association_transcript_object_index", columnList = "transcriptgenomiclocationassociationobject_id"),
@Index(name = "association_cds_subject_index", columnList = "codingsequenceassociationsubject_id"),
@Index(name = "association_cds_object_index", columnList = "codingsequencegenomiclocationassociationobject_id"),
@Index(name = "association_aggregationdatabase_index", columnList = "aggregationdatabase_id"),
@Index(name = "association_detectionmethod_index", columnList = "detectionmethod_id"),
@Index(name = "association_transcript_cds_object_index", columnList = "transcriptcodingsequenceassociationobject_id"),

@Index(name = "association_associationtype_index", columnList = "associationtype"),

@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 {

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