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SCRUM-3952: change vocabularyterm to ontologyterm after LinkML change #1667

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Sep 20, 2024
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SCRUM-3952: change vocabularyterm to ontologyterm after LinkML change #1667

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023f56d
SCRUM-3952: change vocabularyterm to ontologyterm after LinkML change
abecerra Sep 12, 2024
4efba46
SCRUM-3952: fix integration tests
abecerra Sep 19, 2024
d28cc2e
SCRUM-3952: fix indentation and remove commented code
abecerra Sep 19, 2024
6a499ad
SCRUM-3952: use vocabulary term sets in test
abecerra Sep 20, 2024
16c7616
SCRUM-3952: increase LinkML version
abecerra Sep 20, 2024
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4 changes: 2 additions & 2 deletions src/main/java/org/alliancegenome/curation_api/constants/LinkMLSchemaConstants.java
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Expand Up @@ -5,8 +5,8 @@ public class LinkMLSchemaConstants {
private LinkMLSchemaConstants() {
// Hidden from view, as it is a utility class
}
public static final String LATEST_RELEASE = "2.6.1";
public static final String LATEST_RELEASE = "2.7.0";
public static final String MIN_ONTOLOGY_RELEASE = "1.2.4";
public static final String MAX_ONTOLOGY_RELEASE = LATEST_RELEASE;

}
}
7 changes: 5 additions & 2 deletions src/main/java/org/alliancegenome/curation_api/constants/VocabularyConstants.java
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Expand Up @@ -69,14 +69,17 @@ 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 TRANSCRIPT_RELATION_VOCABULARY = "transcript_relation";
public static final String TRANSCRIPT_CHILD_TERM = "is_child_of";
public static final String TRANSCRIPT_PARENT_TERM = "is_parent_of";

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";
public static final String SPATIAL_EXPRESSION_QUALIFIERS = "spatial_expression_qualifiers";
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public static final String ANATOMICAL_STRUCTURE_QUALIFIER = "anatomical_structure_qualifier";
public static final String ANATOMICAL_SUBSTRUCTURE_QUALIFIER = "anatomical_subtructure_qualifier";
public static final String CELLULAR_COMPONENT_QUALIFIER = "cellular_component_qualifier";

public static final String HTP_DATASET_CATEGORY_TAGS = "data_set_category_tags";
public static final String HTP_DATASET_NOTE_TYPE_VOCABULARY_TERM_SET = "htp_expression_dataset_note_type";
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11 changes: 6 additions & 5 deletions src/main/java/org/alliancegenome/curation_api/model/entities/AnatomicalSite.java
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Expand Up @@ -11,6 +11,7 @@
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.OntologyTerm;
import org.alliancegenome.curation_api.model.entities.ontology.UBERONTerm;
import org.alliancegenome.curation_api.view.View;
import org.eclipse.microprofile.openapi.annotations.media.Schema;
Expand All @@ -30,7 +31,7 @@
@Entity
@Data
@EqualsAndHashCode(onlyExplicitlyIncluded = true, callSuper = true)
@AGRCurationSchemaVersion(min = "2.6.1", max = LinkMLSchemaConstants.LATEST_RELEASE)
@AGRCurationSchemaVersion(min = "2.7.0", 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"),
Expand All @@ -55,7 +56,7 @@ public class AnatomicalSite extends AuditedObject {
@ManyToOne
@JsonView({View.FieldsOnly.class})
private GOTerm cellularComponentTerm;

//celullar compoent ribbon -- slim
@IndexedEmbedded(includePaths = {"name", "name_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
Expand All @@ -79,7 +80,7 @@ public class AnatomicalSite extends AuditedObject {
@Index(name = "anatomicalstructurequalifiers_anatomicalsite_index", columnList = "anatomicalsite_id"),
@Index(name = "anatomicalstructurequalifiers_structurequalifiers_index", columnList = "anatomicalstructurequalifiers_id")}
)
private List<VocabularyTerm> anatomicalStructureQualifiers;
private List<OntologyTerm> anatomicalStructureQualifiers;

@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
@KeywordField(name = "anatomicalsubstructurequalifiers_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
Expand All @@ -91,7 +92,7 @@ public class AnatomicalSite extends AuditedObject {
@Index(name = "anatomicalsubstructurequalifiers_anatomicalsite_index", columnList = "anatomicalsite_id"),
@Index(name = "anatomicalsubstructurequalifiers_qualifiers_index", columnList = "anatomicalsubstructurequalifiers_id")}
)
private List<VocabularyTerm> anatomicalSubstructureQualifiers;
private List<OntologyTerm> anatomicalSubstructureQualifiers;

@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
@KeywordField(name = "cellularcomponentqualifiers_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
Expand All @@ -103,7 +104,7 @@ public class AnatomicalSite extends AuditedObject {
@Index(name = "cellularcomponentqualifiers_anatomicalsite_index", columnList = "anatomicalsite_id"),
@Index(name = "cellularcomponentqualifiers_cellularcomponentqualifiers_index", columnList = "cellularcomponentqualifiers_id")}
)
private List<VocabularyTerm> cellularComponentQualifiers;
private List<OntologyTerm> cellularComponentQualifiers;

@FullTextField(analyzer = "autocompleteAnalyzer", searchAnalyzer = "autocompleteSearchAnalyzer")
@KeywordField(name = "anatomicalstructureuberonterms_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES, normalizer = "sortNormalizer")
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74 changes: 33 additions & 41 deletions ...ome/curation_api/services/validation/dto/fms/GeneExpressionAnnotationFmsDTOValidator.java
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@@ -1,28 +1,15 @@
package org.alliancegenome.curation_api.services.validation.dto.fms;

import java.time.OffsetDateTime;
import java.time.format.DateTimeParseException;
import java.util.ArrayList;
import java.util.List;

import jakarta.enterprise.context.RequestScoped;
import jakarta.inject.Inject;
import org.alliancegenome.curation_api.constants.ValidationConstants;
import org.alliancegenome.curation_api.constants.VocabularyConstants;
import org.alliancegenome.curation_api.dao.GeneExpressionAnnotationDAO;
import org.alliancegenome.curation_api.enums.BackendBulkDataProvider;
import org.alliancegenome.curation_api.exceptions.ValidationException;
import org.alliancegenome.curation_api.exceptions.ObjectValidationException;
import org.alliancegenome.curation_api.model.entities.AnatomicalSite;
import org.alliancegenome.curation_api.model.entities.ExpressionPattern;
import org.alliancegenome.curation_api.model.entities.Gene;
import org.alliancegenome.curation_api.model.entities.GeneExpressionAnnotation;
import org.alliancegenome.curation_api.model.entities.Reference;
import org.alliancegenome.curation_api.model.entities.TemporalContext;
import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
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.MMOTerm;
import org.alliancegenome.curation_api.model.entities.ontology.StageTerm;
import org.alliancegenome.curation_api.model.entities.ontology.UBERONTerm;
import org.alliancegenome.curation_api.model.entities.*;
import org.alliancegenome.curation_api.model.entities.ontology.*;
import org.alliancegenome.curation_api.model.ingest.dto.fms.GeneExpressionFmsDTO;
import org.alliancegenome.curation_api.model.ingest.dto.fms.UberonSlimTermDTO;
import org.alliancegenome.curation_api.response.ObjectResponse;
Expand All @@ -32,16 +19,14 @@
import org.alliancegenome.curation_api.services.ReferenceService;
import org.alliancegenome.curation_api.services.VocabularyTermService;
import org.alliancegenome.curation_api.services.helpers.annotations.GeneExpressionAnnotationUniqueIdHelper;
import org.alliancegenome.curation_api.services.ontology.AnatomicalTermService;
import org.alliancegenome.curation_api.services.ontology.GoTermService;
import org.alliancegenome.curation_api.services.ontology.MmoTermService;
import org.alliancegenome.curation_api.services.ontology.StageTermService;
import org.alliancegenome.curation_api.services.ontology.UberonTermService;
import org.alliancegenome.curation_api.services.ontology.*;
import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang3.ObjectUtils;

import jakarta.enterprise.context.RequestScoped;
import jakarta.inject.Inject;
import java.time.OffsetDateTime;
import java.time.format.DateTimeParseException;
import java.util.ArrayList;
import java.util.List;

@RequestScoped
public class GeneExpressionAnnotationFmsDTOValidator {
Expand All @@ -57,6 +42,7 @@ public class GeneExpressionAnnotationFmsDTOValidator {
@Inject GoTermService goTermService;
@Inject UberonTermService uberonTermService;
@Inject StageTermService stageTermService;
@Inject OntologyTermService ontologyTermService;

public GeneExpressionAnnotation validateAnnotation(GeneExpressionFmsDTO geneExpressionFmsDTO, BackendBulkDataProvider dataProvider) throws ValidationException {
ObjectResponse<GeneExpressionAnnotation> response = new ObjectResponse<>();
Expand Down Expand Up @@ -118,7 +104,7 @@ public GeneExpressionAnnotation validateAnnotation(GeneExpressionFmsDTO geneExpr

ObjectResponse<AnatomicalSite> anatomicalSiteObjectResponse = validateAnatomicalSite(geneExpressionFmsDTO);
if (anatomicalSiteObjectResponse.hasErrors()) {
response.addErrorMessage("whereExpressed", anatomicalSiteObjectResponse.errorMessagesString());
response.addErrorMessage("expressionPattern", anatomicalSiteObjectResponse.errorMessagesString());
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} else {
geneExpressionAnnotation.setWhereExpressedStatement(geneExpressionFmsDTO.getWhereExpressed().getWhereExpressedStatement());
AnatomicalSite anatomicalSite = updateAnatomicalSite(anatomicalSiteObjectResponse, geneExpressionAnnotation);
Expand All @@ -127,7 +113,7 @@ public GeneExpressionAnnotation validateAnnotation(GeneExpressionFmsDTO geneExpr

ObjectResponse<TemporalContext> temporalContextObjectResponse = validateTemporalContext(geneExpressionFmsDTO);
if (temporalContextObjectResponse.hasErrors()) {
response.addErrorMessage("whenExpressed", temporalContextObjectResponse.errorMessagesString());
response.addErrorMessage("expressionPattern", temporalContextObjectResponse.errorMessagesString());
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} else {
geneExpressionAnnotation.setWhenExpressedStageName(geneExpressionFmsDTO.getWhenExpressed().getStageName());
TemporalContext temporalContext = updateTemporalContext(temporalContextObjectResponse, geneExpressionAnnotation);
Expand Down Expand Up @@ -238,31 +224,37 @@ private ObjectResponse<AnatomicalSite> validateAnatomicalSite(GeneExpressionFmsD

if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureQualifierTermId())) {
String anatomicalstructurequalifiertermId = geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureQualifierTermId();
VocabularyTerm anatomicalStructureQualifierTerm = vocabularyTermService.getTermInVocabulary(VocabularyConstants.ANATOMICAL_STRUCTURE_UBERON_SLIM_TERMS, anatomicalstructurequalifiertermId).getEntity();
if (anatomicalStructureQualifierTerm == null) {
response.addErrorMessage("whereExpressed - anatomicalStructureQualifierTermId", ValidationConstants.INVALID_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed().getAnatomicalStructureTermId() + ")");
} else {
anatomicalSite.setAnatomicalStructureQualifiers(List.of(anatomicalStructureQualifierTerm));
if (vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.ANATOMICAL_STRUCTURE_QUALIFIER, anatomicalstructurequalifiertermId) != null) {
OntologyTerm anatomicalStructureQualifierTerm = ontologyTermService.findByCurieOrSecondaryId(anatomicalstructurequalifiertermId);
if (anatomicalStructureQualifierTerm == null) {
response.addErrorMessage("whereExpressed - anatomicalStructureQualifierTermId", ValidationConstants.INVALID_MESSAGE + " (" + anatomicalstructurequalifiertermId + ")");
} else {
anatomicalSite.setAnatomicalStructureQualifiers(List.of(anatomicalStructureQualifierTerm));
}
}
}

if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureQualifierTermId())) {
String anatomicalsubstructurequalifierId = geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureQualifierTermId();
VocabularyTerm anatomicalSubStructureQualifierTerm = vocabularyTermService.getTermInVocabulary(VocabularyConstants.ANATOMICAL_STRUCTURE_UBERON_SLIM_TERMS, anatomicalsubstructurequalifierId).getEntity();
if (anatomicalSubStructureQualifierTerm == null) {
response.addErrorMessage("whereExpressed - anatomicalSubStructureQualifierTermId", ValidationConstants.INVALID_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed().getAnatomicalSubStructureTermId() + ")");
} else {
anatomicalSite.setAnatomicalSubstructureQualifiers(List.of(anatomicalSubStructureQualifierTerm));
if (vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.ANATOMICAL_SUBSTRUCTURE_QUALIFIER, anatomicalsubstructurequalifierId) != null) {
OntologyTerm anatomicalSubStructureQualifierTerm = ontologyTermService.findByCurieOrSecondaryId(anatomicalsubstructurequalifierId);
if (anatomicalSubStructureQualifierTerm == null) {
response.addErrorMessage("whereExpressed - anatomicalSubStructureQualifierTermId", ValidationConstants.INVALID_MESSAGE + " (" + anatomicalsubstructurequalifierId + ")");
} else {
anatomicalSite.setAnatomicalSubstructureQualifiers(List.of(anatomicalSubStructureQualifierTerm));
}
}
}

if (!ObjectUtils.isEmpty(geneExpressionFmsDTO.getWhereExpressed().getCellularComponentQualifierTermId())) {
String cellularComponentQualifierTermId = geneExpressionFmsDTO.getWhereExpressed().getCellularComponentQualifierTermId();
VocabularyTerm cellularComponentQualifierTerm = vocabularyTermService.getTermInVocabulary(VocabularyConstants.CELLULAR_COMPONENT_QUALIFIERS, cellularComponentQualifierTermId).getEntity();
if (cellularComponentQualifierTerm == null) {
response.addErrorMessage("whereExpressed - cellularComponentQualifierTermId", ValidationConstants.INVALID_MESSAGE + " (" + geneExpressionFmsDTO.getWhereExpressed().getCellularComponentQualifierTermId() + ")");
} else {
anatomicalSite.setCellularComponentQualifiers(List.of(cellularComponentQualifierTerm));
if (vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.CELLULAR_COMPONENT_QUALIFIER, cellularComponentQualifierTermId) != null) {
OntologyTerm cellularComponentQualifierTerm = ontologyTermService.findByCurieOrSecondaryId(cellularComponentQualifierTermId);
if (cellularComponentQualifierTerm == null) {
response.addErrorMessage("whereExpressed - cellularComponentQualifierTermId", ValidationConstants.INVALID_MESSAGE + " (" + cellularComponentQualifierTermId + ")");
} else {
anatomicalSite.setCellularComponentQualifiers(List.of(cellularComponentQualifierTerm));
}
}
}

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