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Adding vocabulary terms to genetic sex vocabulary #1708

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merged 4 commits into from
Nov 8, 2024
Merged

Adding vocabulary terms to genetic sex vocabulary #1708

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42a29ce
Adding vocabulary terms to genetic sex vocabulary
VarunReddy1111 Nov 7, 2024
531d8b6
changing migration version
VarunReddy1111 Nov 8, 2024
f8d6832
Merge branch 'alpha' into SCRUM-4509
VarunReddy1111 Nov 8, 2024
0a3db5a
Merge branch 'alpha' into SCRUM-4509
VarunReddy1111 Nov 8, 2024
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28 changes: 22 additions & 6 deletions ..._api/services/validation/dto/fms/HTPExpressionDatasetSampleAnnotationFmsDTOValidator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
import org.alliancegenome.curation_api.model.ingest.dto.fms.BioSampleGenomicInformationFmsDTO;
import org.alliancegenome.curation_api.model.ingest.dto.fms.HTPExpressionDatasetSampleAnnotationFmsDTO;
import org.alliancegenome.curation_api.model.ingest.dto.fms.WhereExpressedFmsDTO;
import org.alliancegenome.curation_api.model.input.Pagination;
import org.alliancegenome.curation_api.response.ObjectResponse;
import org.alliancegenome.curation_api.response.SearchResponse;
import org.alliancegenome.curation_api.services.AffectedGenomicModelService;
Expand Down Expand Up @@ -167,7 +168,7 @@ public HTPExpressionDatasetSampleAnnotation validateHTPExpressionDatasetSampleAn
} else if (htpSampleAnnotation.getGenomicInformation().getBioSampleAllele() != null) {
identifierString = htpSampleAnnotation.getGenomicInformation().getBioSampleAllele().getIdentifier();
}
if (!identifierString.equals(dto.getGenomicInformation().getBiosampleId())) {
if (!identifierString.equals(dto.getGenomicInformation().getBiosampleId()) || htpSampleAnnotation.getGenomicInformation().getBioSampleAgmType() == null && StringUtils.isNotEmpty(dto.getGenomicInformation().getIdType())) {
validateGenomicInformation(dto.getGenomicInformation(), htpSampleAnnotation, htpSampleAnnotationResponse);
}
if (StringUtils.isNotEmpty(dto.getGenomicInformation().getBioSampleText())) {
Expand All @@ -181,9 +182,22 @@ public HTPExpressionDatasetSampleAnnotation validateHTPExpressionDatasetSampleAn
}

if (StringUtils.isNotEmpty(dto.getSex())) {
VocabularyTerm geneticSex = vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.GENETIC_SEX_VOCABULARY, dto.getSex()).getEntity();
if (geneticSex != null) {
htpSampleAnnotation.setGeneticSex(geneticSex);
Map<String, Object> params = new HashMap<>();
params.put("name", dto.getSex());
params.put("query_operator", "or");
params.put("synonyms", dto.getSex());
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("Genetic Sex") && (tag.getName().equals(dto.getSex()) || tag.getSynonyms().contains(dto.getSex()))) {
htpSampleAnnotation.setGeneticSex(tag);
added = true;
}
}
}
if (!added) {
htpSampleAnnotationResponse.addErrorMessage("Sex", ValidationConstants.INVALID_MESSAGE + " (" + dto.getSex() + ")");
}
}

Expand Down Expand Up @@ -221,7 +235,7 @@ public HTPExpressionDatasetSampleAnnotation validateHTPExpressionDatasetSampleAn
}

if (StringUtils.isNotEmpty(dto.getSequencingFormat())) {
VocabularyTerm sequencingFormat = vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.HTP_DATASET_SAMPLE_SEQUENCE_FORMAT_VOCABULARY, dto.getSequencingFormat()).getEntity();
VocabularyTerm sequencingFormat = vocabularyTermService.getTermInVocabulary(VocabularyConstants.HTP_DATASET_SAMPLE_SEQUENCE_FORMAT_VOCABULARY, dto.getSequencingFormat()).getEntity();
if (sequencingFormat != null) {
htpSampleAnnotation.setSequencingFormat(sequencingFormat);
}
Expand Down Expand Up @@ -281,9 +295,11 @@ protected void validateGenomicInformation(BioSampleGenomicInformationFmsDTO dto,
htpSampleAnnotationResponse.addErrorMessage("GenomicInformation - BioSampleId", ValidationConstants.INVALID_MESSAGE + " (" + identifierString + ")");
} else {
htpSampleAnnotation.getGenomicInformation().setBioSampleAgm(agm);
VocabularyTerm agmType = vocabularyTermService.getTermInVocabularyTermSet(VocabularyConstants.AGM_SUBTYPE_VOCABULARY, dto.getIdType()).getEntity();
VocabularyTerm agmType = vocabularyTermService.getTermInVocabulary(VocabularyConstants.AGM_SUBTYPE_VOCABULARY, dto.getIdType()).getEntity();
if (agmType != null) {
htpSampleAnnotation.getGenomicInformation().setBioSampleAgmType(agmType);
} else {
htpSampleAnnotationResponse.addErrorMessage("GenomicInformation - IdType", ValidationConstants.INVALID_MESSAGE + " (" + dto.getIdType() + ")");
}
}
}
Expand Down
2 changes: 2 additions & 0 deletions src/main/resources/db/migration/v0.38.0.4__adding_synonyms_htpsample_genetic_sex.sql
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@@ -0,0 +1,2 @@
INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'unknown' FROM vocabularyterm WHERE name = 'unknown sex';
INSERT INTO vocabularyterm_synonyms (vocabularyterm_id, synonyms) SELECT id, 'pooled' FROM vocabularyterm WHERE name = 'pooled sexes';
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