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RGD load and category tag validation change #1685

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Oct 9, 2024
Merged

RGD load and category tag validation change #1685

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3 changes: 3 additions & 0 deletions ...n/java/org/alliancegenome/curation_api/model/entities/HTPExpressionDatasetAnnotation.java
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Expand Up @@ -9,6 +9,8 @@
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.engine.backend.types.Aggregable;
import org.hibernate.search.engine.backend.types.Projectable;
import org.hibernate.search.engine.backend.types.Searchable;
Expand Down Expand Up @@ -87,6 +89,7 @@ public class HTPExpressionDatasetAnnotation extends AuditedObject {
@IndexedEmbedded(includePaths = {"name", "name_keyword"})
@IndexingDependency(reindexOnUpdate = ReindexOnUpdate.SHALLOW)
@ManyToMany
@OnDelete(action = OnDeleteAction.CASCADE)
@JsonView({ View.FieldsAndLists.class })
@JoinTable(name = "htpexpressiondatasetannotation_categorytags", indexes = { @Index(name = "htpdatasetannotation_htpdatasetid_index", columnList = "htpexpressiondatasetannotation_id"), @Index(name = "htpdatasetannotation_categorytags_index", columnList = "categorytags_id")})
List<VocabularyTerm> categoryTags;
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3 changes: 3 additions & 0 deletions src/main/java/org/alliancegenome/curation_api/model/entities/ResourceDescriptor.java
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Expand Up @@ -7,6 +7,8 @@
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 Down Expand Up @@ -61,6 +63,7 @@ public class ResourceDescriptor extends AuditedObject {
@KeywordField(name = "synoynyms_keyword", aggregable = Aggregable.YES, sortable = Sortable.YES, searchable = Searchable.YES)
@ElementCollection
@JoinTable(indexes = @Index(columnList = "resourcedescriptor_id"))
@Fetch(FetchMode.JOIN)
@JsonView({ View.ResourceDescriptorView.class, View.FieldsAndLists.class })
private List<String> synonyms;

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28 changes: 22 additions & 6 deletions ...ration_api/services/validation/dto/fms/HTPExpressionDatasetAnnotationFmsDTOValidator.java
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Expand Up @@ -15,6 +15,7 @@
import org.alliancegenome.curation_api.model.entities.HTPExpressionDatasetAnnotation;
import org.alliancegenome.curation_api.model.entities.Note;
import org.alliancegenome.curation_api.model.entities.Reference;
import org.alliancegenome.curation_api.model.input.Pagination;
import org.alliancegenome.curation_api.model.entities.VocabularyTerm;
import org.alliancegenome.curation_api.model.ingest.dto.fms.HTPExpressionDatasetAnnotationFmsDTO;
import org.alliancegenome.curation_api.model.ingest.dto.fms.PublicationFmsDTO;
Expand Down Expand Up @@ -117,18 +118,33 @@ public HTPExpressionDatasetAnnotation validateHTPExpressionDatasetAnnotationFmsD
}

if (CollectionUtils.isNotEmpty(dto.getCategoryTags())) {
List<VocabularyTerm> categoryTags = new ArrayList<>();
Map<String, VocabularyTerm> categoryTags = new HashMap<>();
for (String categoryTag : dto.getCategoryTags()) {
if (StringUtils.isNotEmpty(categoryTag)) {
VocabularyTerm tag = vocabularyTermService.getTermInVocabulary(VocabularyConstants.HTP_DATASET_CATEGORY_TAGS, categoryTag).getEntity();
if (tag == null) {
Map<String, Object> params = new HashMap<>();
params.put("name", categoryTag);
params.put("query_operator", "or");
params.put("synonyms", categoryTag);
SearchResponse<VocabularyTerm> searchResponse = vocabularyTermService.findByParams(new Pagination(), params);
boolean added = false;
if (searchResponse.getTotalResults() > 0) {
for (VocabularyTerm tag : searchResponse.getResults()) {
if (tag.getVocabulary().getName().equals("Data Set Category Tags") && (tag.getName().equals(categoryTag) || tag.getSynonyms().contains(categoryTag))) {
if (categoryTags.containsKey(categoryTag)) {
htpAnnotationResponse.addErrorMessage("categoryTags", ValidationConstants.INVALID_MESSAGE + " Multiple Tags found in the Vocabulary " + " (" + categoryTag + ")");
} else {
categoryTags.put(categoryTag, tag);
added = true;
}
}
}
}
if (!added) {
htpAnnotationResponse.addErrorMessage("categoryTags", ValidationConstants.INVALID_MESSAGE + " (" + categoryTag + ")");
} else {
categoryTags.add(tag);
}
}
}
htpannotation.setCategoryTags(categoryTags);
htpannotation.setCategoryTags(new ArrayList<>(categoryTags.values()));
} else {
htpAnnotationResponse.addErrorMessage("categoryTags", ValidationConstants.REQUIRED_MESSAGE);
}
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13 changes: 13 additions & 0 deletions src/main/resources/db/migration/v0.37.0.58__htp_tags_fix.sql
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@@ -0,0 +1,13 @@
DELETE FROM htpexpressiondatasetannotation_categorytags WHERE categorytags_id IN (SELECT id FROM vocabularyterm WHERE name = 'strain study');
DELETE FROM vocabularyterm_synonyms WHERE vocabularyterm_id IN (SELECT id FROM vocabularyterm WHERE name = 'strain study');

DELETE FROM vocabularyterm WHERE name = 'strain study';

DELETE FROM vocabularyterm_synonyms WHERE vocabularyterm_id IN (SELECT id FROM vocabularyterm WHERE name = 'anatomical structure');
DELETE FROM vocabularyterm_synonyms WHERE vocabularyterm_id IN (SELECT id FROM vocabularyterm WHERE name = 'chemical stimulus');

INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'tissue type study' FROM vocabularyterm WHERE name = 'anatomical structure';
INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'tissue specific' FROM vocabularyterm WHERE name = 'anatomical structure';

INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'chemical stimulus study' FROM vocabularyterm WHERE name = 'chemical stimulus';
INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'response to chemical' FROM vocabularyterm WHERE name = 'chemical stimulus';
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