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SCRUM-4603 add convenience method for relation plus negation #1738

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merged 3 commits into from
Nov 22, 2024
Merged

SCRUM-4603 add convenience method for relation plus negation #1738

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8c31fe1
SCRUM-4603 add convenience method for relation plus negation
cmpich Nov 22, 2024
3ba1aa4
add braces
cmpich Nov 22, 2024
5d4252a
handle null relation
cmpich Nov 22, 2024
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117 changes: 61 additions & 56 deletions src/main/java/org/alliancegenome/curation_api/model/entities/DiseaseAnnotation.java
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Original file line number Diff line number Diff line change
@@ -1,7 +1,13 @@
package org.alliancegenome.curation_api.model.entities;

import java.util.List;

import com.fasterxml.jackson.annotation.JsonIgnore;
import com.fasterxml.jackson.annotation.JsonSubTypes;
import com.fasterxml.jackson.annotation.JsonSubTypes.Type;
import com.fasterxml.jackson.annotation.JsonTypeInfo;
import com.fasterxml.jackson.annotation.JsonView;
import jakarta.persistence.*;
import lombok.Data;
import lombok.EqualsAndHashCode;
import org.alliancegenome.curation_api.constants.LinkMLSchemaConstants;
import org.alliancegenome.curation_api.interfaces.AGRCurationSchemaVersion;
import org.alliancegenome.curation_api.model.bridges.BooleanValueBridge;
Expand All @@ -19,25 +25,7 @@
import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
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.JsonSubTypes.Type;
import com.fasterxml.jackson.annotation.JsonTypeInfo;
import com.fasterxml.jackson.annotation.JsonView;

import jakarta.persistence.Column;
import jakarta.persistence.Entity;
import jakarta.persistence.Index;
import jakarta.persistence.Inheritance;
import jakarta.persistence.InheritanceType;
import jakarta.persistence.JoinColumn;
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;
import java.util.List;

@Inheritance(strategy = InheritanceType.JOINED)
@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
Expand All @@ -49,7 +37,7 @@
@Entity
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = { Annotation.class })
@AGRCurationSchemaVersion(min = "2.8.0", max = LinkMLSchemaConstants.LATEST_RELEASE, dependencies = {Annotation.class})
@Schema(name = "Disease_Annotation", description = "Annotation class representing a disease annotation")
@Table(indexes = {
@Index(name = "DiseaseAnnotation_internal_index", columnList = "internal"),
Expand All @@ -73,29 +61,29 @@
public abstract class DiseaseAnnotation extends Annotation {

@IndexedEmbedded(includePaths = {"curie", "name", "secondaryIdentifiers", "synonyms.name", "namespace",
"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "namespace_keyword" })
"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "namespace_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
@JsonView({View.FieldsOnly.class, View.ForPublic.class})
private DOTerm diseaseAnnotationObject;

@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer", valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
@KeywordField(name = "negated_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, valueBridge = @ValueBridgeRef(type = BooleanValueBridge.class))
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
@JsonView({View.FieldsOnly.class, View.ForPublic.class})
@Column(columnDefinition = "boolean default false", nullable = false)
private Boolean negated = false;

@IndexedEmbedded(includePaths = {"name", "name_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
@JsonView({View.FieldsOnly.class, View.ForPublic.class})
private VocabularyTerm relation;

@IndexedEmbedded(includePaths = {"curie", "name", "secondaryIdentifiers", "synonyms.name", "abbreviation",
"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "abbreviation_keyword" })
"curie_keyword", "name_keyword", "secondaryIdentifiers_keyword", "synonyms.name_keyword", "abbreviation_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
@JoinTable(
joinColumns = @JoinColumn(name = "diseaseannotation_id"),
inverseJoinColumns = @JoinColumn(name = "evidencecodes_id"),
Expand All @@ -107,16 +95,16 @@ public abstract class DiseaseAnnotation extends Annotation {
private List<ECOTerm> evidenceCodes;

@IndexedEmbedded(includePaths = {
"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
@JoinTable(
joinColumns = @JoinColumn(name = "diseaseannotation_id"),
inverseJoinColumns = @JoinColumn(name = "with_id"),
Expand All @@ -130,13 +118,13 @@ public abstract class DiseaseAnnotation extends Annotation {
@IndexedEmbedded(includePaths = {"name", "name_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
@JsonView({View.FieldsOnly.class, View.ForPublic.class})
private VocabularyTerm annotationType;

@IndexedEmbedded(includePaths = {"name", "name_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
@JoinTable(
joinColumns = @JoinColumn(name = "diseaseannotation_id"),
inverseJoinColumns = @JoinColumn(name = "diseasequalifiers_id"),
Expand All @@ -150,27 +138,27 @@ public abstract class DiseaseAnnotation extends Annotation {
@IndexedEmbedded(includePaths = {"name", "name_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
@JsonView({View.FieldsOnly.class, View.ForPublic.class})
private VocabularyTerm geneticSex;

@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"})
"sourceOrganization.abbreviation_keyword", "sourceOrganization.fullName_keyword", "sourceOrganization.shortName_keyword", "crossReference.displayName_keyword", "crossReference.referencedCurie_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
@JsonView({View.FieldsOnly.class, View.ForPublic.class})
private DataProvider secondaryDataProvider;

@IndexedEmbedded(includePaths = {
"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
"geneSymbol.formatText", "geneSymbol.displayText", "geneSymbol.formatText_keyword", "geneSymbol.displayText_keyword",
"geneFullName.formatText", "geneFullName.displayText", "geneFullName.formatText_keyword", "geneFullName.displayText_keyword",
"geneSystematicName.formatText", "geneSystematicName.displayText", "geneSystematicName.formatText_keyword", "geneSystematicName.displayText_keyword",
"geneSynonyms.formatText", "geneSynonyms.displayText", "geneSynonyms.formatText_keyword", "geneSynonyms.displayText_keyword",
"geneSecondaryIds.secondaryId", "geneSecondaryIds.secondaryId_keyword", "name", "name_keyword", "symbol", "symbol_keyword"
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
@JoinTable(
name = "diseaseannotation_modifiergene",
joinColumns = @JoinColumn(name = "diseaseannotation_id"),
Expand All @@ -183,15 +171,15 @@ public abstract class DiseaseAnnotation extends Annotation {
private List<Gene> diseaseGeneticModifierGenes;

@IndexedEmbedded(includePaths = {
"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
"alleleSymbol.formatText", "alleleSymbol.displayText", "alleleSymbol.formatText_keyword", "alleleSymbol.displayText_keyword",
"alleleFullName.formatText", "alleleFullName.displayText", "alleleFullName.formatText_keyword", "alleleFullName.displayText_keyword",
"alleleSynonyms.formatText", "alleleSynonyms.displayText", "alleleSynonyms.formatText_keyword", "alleleSynonyms.displayText_keyword",
"alleleSecondaryIds.secondaryId", "alleleSecondaryIds.secondaryId_keyword"
"curie", "modEntityId", "modInternalId", "curie_keyword", "modEntityId_keyword", "modInternalId_keyword",
"alleleSymbol.formatText", "alleleSymbol.displayText", "alleleSymbol.formatText_keyword", "alleleSymbol.displayText_keyword",
"alleleFullName.formatText", "alleleFullName.displayText", "alleleFullName.formatText_keyword", "alleleFullName.displayText_keyword",
"alleleSynonyms.formatText", "alleleSynonyms.displayText", "alleleSynonyms.formatText_keyword", "alleleSynonyms.displayText_keyword",
"alleleSecondaryIds.secondaryId", "alleleSecondaryIds.secondaryId_keyword"
})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
@JoinTable(
name = "diseaseannotation_modifierallele",
joinColumns = @JoinColumn(name = "diseaseannotation_id"),
Expand All @@ -206,7 +194,7 @@ public abstract class DiseaseAnnotation extends Annotation {
@IndexedEmbedded(includePaths = {"name", "name_keyword", "curie", "curie_keyword", "modEntityId", "modEntityId_keyword", "modInternalId", "modInternalId_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@JsonView({ View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class })
@JsonView({View.FieldsAndLists.class, View.DiseaseAnnotation.class, View.ForPublic.class})
@JoinTable(
name = "diseaseannotation_modifieragm",
joinColumns = @JoinColumn(name = "diseaseannotation_id"),
Expand All @@ -221,7 +209,7 @@ public abstract class DiseaseAnnotation extends Annotation {
@IndexedEmbedded(includePaths = {"name", "name_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToOne
@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
@JsonView({View.FieldsOnly.class, View.ForPublic.class})
private VocabularyTerm diseaseGeneticModifierRelation;

@Transient
Expand All @@ -232,7 +220,7 @@ public abstract class DiseaseAnnotation extends Annotation {

@Transient
public abstract String getSubjectSpeciesName();

@Transient
public abstract String getSubjectIdentifier();

Expand All @@ -246,4 +234,21 @@ public String getDataProviderString() {
}
return builder.toString();
}

@Transient
public String getFullRelationString() {
if (relation == null) {
return null;
}
if (!negated) {
return relation.getName();
}

if (relation.getName().equals("is_model_of")) {
return "does_not_model";
}
return relation.getName().replaceFirst("_", "_not_");
}


}
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