Merge pull request #1627 from alliance-genome/SCRUM-3952

SCRUM-3952: add ExpressionPattern, TemporalContext and AnatomicalSite
alliance-genome · Jul 31, 2024 · cdf2c3b · cdf2c3b
2 parents 60bc6f4 + 326bf0f
commit cdf2c3b
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Showing 21 changed files with 1,233 additions and 94 deletions.
diff --git a/src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java b/src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java
@@ -69,5 +69,8 @@ private VocabularyConstants() {
 
 	public static final String GENE_EXPRESSION_VOCABULARY = "gene_expression";
 	public static final String GENE_EXPRESSION_RELATION_TERM = "is_expressed_in";
+	public static final String STAGE_UBERON_SLIM_TERMS = "stage_uberon_slim_terms";
+	public static final String ANATOMICAL_STRUCTURE_UBERON_SLIM_TERMS = "anatomical_structure_uberon_slim_terms";
+	public static final String CELLULAR_COMPONENT_QUALIFIERS = "cellular_component_qualifiers";
 
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/AnatomicalSite.java b/src/main/java/org/alliancegenome/curation_api/model/entities/AnatomicalSite.java
@@ -0,0 +1,116 @@
+package org.alliancegenome.curation_api.model.entities;
+
+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.entities.base.AuditedObject;
+import org.alliancegenome.curation_api.model.entities.ontology.AnatomicalTerm;
+import org.alliancegenome.curation_api.model.entities.ontology.GOTerm;
+import org.alliancegenome.curation_api.model.entities.ontology.UBERONTerm;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.search.engine.backend.types.Aggregable;
+import org.hibernate.search.engine.backend.types.Searchable;
+import org.hibernate.search.engine.backend.types.Sortable;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
+
+import java.util.List;
+
+@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
+@Entity
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
+@AGRCurationSchemaVersion(min = "2.2.3", max = LinkMLSchemaConstants.LATEST_RELEASE)
+@Schema(name = "Anatomical_Site", description = "Anatomical part of an expression pattern")
+@Table(indexes = {
+	@Index(name = "anatomicalsite_anatomicalstructure_index ", columnList = "anatomicalstructure_id"),
+	@Index(name = "anatomicalsite_anatomicalsubstructure_index", columnList = "anatomicalsubstructure_id"),
+	@Index(name = "anatomicalsite_cellularcomponentterm_index", columnList = "cellularcomponentterm_id")}
+)
+public class AnatomicalSite extends AuditedObject {
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({View.FieldsOnly.class})
+	private AnatomicalTerm anatomicalStructure;
+
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({View.FieldsOnly.class})
+	private AnatomicalTerm anatomicalSubstructure;
+
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({View.FieldsOnly.class})
+	private GOTerm cellularComponentTerm;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "anatomicalstructurequalifiers_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ManyToMany
+	@JsonView({View.FieldsOnly.class})
+	@JoinTable(
+		name = "anatomicalsite_anatomicalstructurequalifiers",
+		indexes = {
+			@Index(name = "anatomicalstructurequalifiers_anatomicalsite_index", columnList = "anatomicalsite_id"),
+			@Index(name = "anatomicalstructurequalifiers_structurequalifiers_index", columnList = "anatomicalstructurequalifiers_id")}
+	)
+	private List<VocabularyTerm> anatomicalStructureQualifiers;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "anatomicalsubstructurequalifiers_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ManyToMany
+	@JsonView({View.FieldsOnly.class})
+	@JoinTable(
+		name = "anatomicalsite_anatomicalsubstructurequalifiers",
+		indexes = {
+			@Index(name = "anatomicalsubstructurequalifiers_anatomicalsite_index", columnList = "anatomicalsite_id"),
+			@Index(name = "anatomicalsubstructurequalifiers_qualifiers_index", columnList = "anatomicalsubstructurequalifiers_id")}
+	)
+	private List<VocabularyTerm> anatomicalSubstructureQualifiers;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "cellularcomponentqualifiers_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ManyToMany
+	@JsonView({View.FieldsOnly.class})
+	@JoinTable(
+		name = "anatomicalsite_cellularcomponentqualifiers",
+		indexes = {
+			@Index(name = "cellularcomponentqualifiers_anatomicalsite_index", columnList = "anatomicalsite_id"),
+			@Index(name = "cellularcomponentqualifiers_cellularcomponentqualifiers_index", columnList = "cellularcomponentqualifiers_id")}
+	)
+	private List<VocabularyTerm> cellularComponentQualifiers;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "anatomicalstructureuberonterms_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ManyToMany
+	@JsonView({View.FieldsOnly.class})
+	@JoinTable(
+		name = "anatomicalsite_anatomicalstructureuberonterms",
+		indexes = {
+			@Index(name = "anatomicalstructureuberonterms_anatomicalsite_index", columnList = "anatomicalsite_id"),
+			@Index(name = "anatomicalstructureuberonterms_uberonterms_index", columnList = "anatomicalstructureuberonterms_id")}
+	)
+	private List<UBERONTerm> anatomicalStructureUberonTerms;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "anatomicalsubstructureuberonterms_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ManyToMany
+	@JsonView({View.FieldsOnly.class})
+	@JoinTable(
+		name = "anatomicalsite_anatomicalsubstructureuberonterms",
+		indexes = {
+			@Index(name = "anatomicalsubstructureuberonterms_anatomicalsite_index", columnList = "anatomicalsite_id"),
+			@Index(name = "anatomicalsubstructureuberonterms_uberonterms_index", columnList = "anatomicalsubstructureuberonterms_id")}
+	)
+	private List<UBERONTerm> anatomicalSubstructureUberonTerms;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionAnnotation.java
@@ -30,26 +30,32 @@
 @Schema(name = "Expression_Annotation", description = "Annotation class representing an expression annotation")
 @Table(indexes = {
 	@Index(name = "expressionannotation_whenexpressedstagename_index ", columnList = "whenexpressedstagename"),
-	@Index(name = "expressionannotation_whereexpressedstatement_index", columnList = "whereexpressedstatement")
+	@Index(name = "expressionannotation_whereexpressedstatement_index", columnList = "whereexpressedstatement"),
+	@Index(name = "expressionannotation_expressionpattern_index", columnList = "expressionpattern_id")
 })
 public abstract class ExpressionAnnotation extends Annotation {
 
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class})
 	private VocabularyTerm relation;
 
 	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
 	@KeywordField(name = "whenExpressedStageName_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class})
 	private String whenExpressedStageName;
 
 	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
 	@KeywordField(name = "whereExpressedStatement_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({ View.FieldsOnly.class})
 	private String whereExpressedStatement;
 
+	@OneToOne(cascade = CascadeType.ALL, orphanRemoval = true)
+	@JoinColumn(name = "expressionpattern_id", referencedColumnName = "id")
+	@JsonView({ View.FieldsOnly.class})
+	private ExpressionPattern expressionPattern;
+
 	@Transient
 	@JsonIgnore
 	public String getDataProviderString() {

diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionPattern.java b/src/main/java/org/alliancegenome/curation_api/model/entities/ExpressionPattern.java
@@ -0,0 +1,38 @@
+package org.alliancegenome.curation_api.model.entities;
+
+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.entities.base.AuditedObject;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+
+@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, include = JsonTypeInfo.As.PROPERTY, property = "type")
+@Entity
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
+@AGRCurationSchemaVersion(min = "2.2.3", max = LinkMLSchemaConstants.LATEST_RELEASE)
+@Schema(name = "Expression_Pattern", description = "Annotation class representing an expression pattern")
+
+@Table(indexes = {
+	@Index(name = "expressionpattern_whenexpressed_index", columnList = "whenexpressed_id"),
+	@Index(name = "expressionpattern_whereexpressed_index", columnList = "whereexpressed_id")
+})
+public class ExpressionPattern extends AuditedObject {
+
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@OneToOne(cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsOnly.class})
+	private TemporalContext whenExpressed;
+
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@OneToOne(cascade = CascadeType.ALL, orphanRemoval = true)
+	@JsonView({ View.FieldsOnly.class})
+	private AnatomicalSite whereExpressed;
+}
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/GeneExpressionAnnotation.java b/src/main/java/org/alliancegenome/curation_api/model/entities/GeneExpressionAnnotation.java
@@ -34,13 +34,13 @@ public class GeneExpressionAnnotation extends ExpressionAnnotation {
 	@IndexedEmbedded(includePaths = {"geneSymbol.displayText", "geneSymbol.formatText", "geneSymbol.displayText_keyword", "geneSymbol.formatText_keyword", "curie", "curie_keyword", "taxon.curie", "taxon.name", "taxon.curie_keyword", "taxon.name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class })
 	private Gene expressionAnnotationSubject;
 
 	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
 	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
 	@ManyToOne
-	@JsonView({ View.FieldsOnly.class, View.ForPublic.class })
+	@JsonView({View.FieldsOnly.class})
 	private MMOTerm expressionAssayUsed;
 
 }
diff --git a/src/main/java/org/alliancegenome/curation_api/model/entities/TemporalContext.java b/src/main/java/org/alliancegenome/curation_api/model/entities/TemporalContext.java
@@ -0,0 +1,78 @@
+package org.alliancegenome.curation_api.model.entities;
+
+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.entities.base.AuditedObject;
+import org.alliancegenome.curation_api.model.entities.ontology.StageTerm;
+import org.alliancegenome.curation_api.view.View;
+import org.eclipse.microprofile.openapi.annotations.media.Schema;
+import org.hibernate.search.engine.backend.types.Aggregable;
+import org.hibernate.search.engine.backend.types.Searchable;
+import org.hibernate.search.engine.backend.types.Sortable;
+import org.hibernate.search.mapper.pojo.automaticindexing.ReindexOnUpdate;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.FullTextField;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexedEmbedded;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.IndexingDependency;
+import org.hibernate.search.mapper.pojo.mapping.definition.annotation.KeywordField;
+
+import java.util.List;
+
+@JsonTypeInfo(use = JsonTypeInfo.Id.NAME, property = "type")
+@Entity
+@Data
+@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
+@AGRCurationSchemaVersion(min = "2.2.3", max = LinkMLSchemaConstants.LATEST_RELEASE)
+@Schema(name = "Temporal_Context", description = "Temporal expression pattern")
+@Table(indexes = {
+	@Index(name = "temporalcontext_developmentalstagestart_index ", columnList = "developmentalstagestart_id"),
+	@Index(name = "temporalcontext_developmentalstagestop_index ", columnList = "developmentalstagestop_id"),
+	@Index(name = "temporalcontext_age_index ", columnList = "age")
+})
+public class TemporalContext extends AuditedObject {
+
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({View.FieldsOnly.class})
+	private StageTerm developmentalStageStart;
+
+	@IndexedEmbedded(includePaths = {"name", "name_keyword"})
+	@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
+	@ManyToOne
+	@JsonView({View.FieldsOnly.class})
+	private StageTerm developmentalStageStop;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "age_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@JsonView({View.FieldsOnly.class})
+	private String age;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "temporalqualifiers_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ManyToMany
+	@JsonView({View.FieldsOnly.class})
+	@JoinTable(
+		name = "temporalcontext_temporalqualifiers",
+		indexes = {
+			@Index(name = "temporalqualifiers_temporalcontext_index", columnList = "temporalcontext_id"),
+			@Index(name = "temporalqualifiers_temporalqualifiers_index", columnList = "temporalqualifiers_id")}
+	)
+	private List<VocabularyTerm> temporalQualifiers;
+
+	@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
+	@KeywordField(name = "stageuberonslimterms_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
+	@ManyToMany
+	@JsonView({View.FieldsOnly.class})
+	@JoinTable(
+		name = "temporalcontext_stageuberonslimterms",
+		indexes = {
+			@Index(name = "stageuberonslimterms_temporalcontext_index", columnList = "temporalcontext_id"),
+			@Index(name = "stageuberonslimterms_uberonterms_index", columnList = "stageuberonslimterms_id")}
+	)
+	private List<VocabularyTerm> stageUberonSlimTerms;
+}