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SCRUM-4442 (update) Handle whitespace and lower-case characters in ref/alt sequences for HGVSg identifier generation #1707

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merged 4 commits into from
Nov 6, 2024
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SCRUM-4442 (update) Handle whitespace and lower-case characters in ref/alt sequences for HGVSg identifier generation #1707

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836e111
Handle whitespace an lower case ref/alt sequences
markquintontulloch Nov 6, 2024
fc3ad79
Bump LinkML version
markquintontulloch Nov 6, 2024
b8b7595
Relax amino acid criteria
markquintontulloch Nov 6, 2024
6590a75
Update test file
markquintontulloch Nov 6, 2024
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2 changes: 1 addition & 1 deletion src/main/java/org/alliancegenome/curation_api/constants/LinkMLSchemaConstants.java
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ public class LinkMLSchemaConstants {
private LinkMLSchemaConstants() {
// Hidden from view, as it is a utility class
}
public static final String LATEST_RELEASE = "2.8.0";
public static final String LATEST_RELEASE = "2.8.1";
public static final String MIN_ONTOLOGY_RELEASE = "1.2.4";
public static final String MAX_ONTOLOGY_RELEASE = LATEST_RELEASE;

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4 changes: 2 additions & 2 deletions .../java/org/alliancegenome/curation_api/services/helpers/variants/HgvsIdentifierHelper.java
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Expand Up @@ -20,12 +20,12 @@ public static String getHgvsIdentifier(VariantFmsDTO dto) {

String refSeq = "";
if (StringUtils.isNotBlank(dto.getGenomicReferenceSequence()) && !Objects.equals(dto.getGenomicReferenceSequence(), "N/A")) {
refSeq = dto.getGenomicReferenceSequence();
refSeq = StringUtils.deleteWhitespace(dto.getGenomicReferenceSequence().toUpperCase());
}

String varSeq = "";
if (StringUtils.isNotBlank(dto.getGenomicVariantSequence()) && !Objects.equals(dto.getGenomicVariantSequence(), "N/A")) {
varSeq = dto.getGenomicVariantSequence();
varSeq = StringUtils.deleteWhitespace(dto.getGenomicVariantSequence().toUpperCase());
}

String chrAccession = "";
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4 changes: 2 additions & 2 deletions ...a/org/alliancegenome/curation_api/services/validation/dto/fms/VariantFmsDTOValidator.java
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Expand Up @@ -258,13 +258,13 @@ public void validateCuratedVariantGenomicLocationAssociation(VariantFmsDTO dto,
association.setRelation(vocabularyTermService.getTermInVocabulary(VocabularyConstants.LOCATION_ASSOCIATION_RELATION_VOCABULARY, "located_on").getEntity());

if (StringUtils.isNotBlank(dto.getGenomicReferenceSequence()) && !Objects.equals(dto.getGenomicReferenceSequence(), "N/A")) {
association.setReferenceSequence(dto.getGenomicReferenceSequence());
association.setReferenceSequence(StringUtils.deleteWhitespace(dto.getGenomicReferenceSequence()));
} else {
association.setReferenceSequence(null);
}

if (StringUtils.isNotBlank(dto.getGenomicVariantSequence()) && !Objects.equals(dto.getGenomicVariantSequence(), "N/A")) {
association.setVariantSequence(dto.getGenomicVariantSequence());
association.setVariantSequence(StringUtils.deleteWhitespace(dto.getGenomicVariantSequence()));
} else {
association.setVariantSequence(null);
}
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2 changes: 1 addition & 1 deletion ...alliancegenome/curation_api/services/validation/dto/fms/VepTranscriptFmsDTOValidator.java
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Expand Up @@ -168,7 +168,7 @@ public PredictedVariantConsequence validateTranscriptLevelConsequence(VepTxtDTO
String variantAminoAcids = null;
if (StringUtils.isNotBlank(dto.getAminoAcids())) {
String[] refVarAminoAcids = dto.getAminoAcids().split("/");
if (refVarAminoAcids.length == 1 && (Objects.equals(dto.getAminoAcids(), "X") || dto.getConsequence().contains("synonymous_variant"))) {
if (refVarAminoAcids.length == 1) {
referenceAminoAcids = refVarAminoAcids[0];
variantAminoAcids = refVarAminoAcids[0];
} else if (refVarAminoAcids.length == 2) {
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2 changes: 1 addition & 1 deletion src/test/resources/bulk/fms/11_vep/IV_07_invalid_amino_acids.json
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Expand Up @@ -8,7 +8,7 @@
"cdnaPosition": "3-800",
"cdsPosition": "1-600",
"proteinPosition": "246-?",
"aminoAcids": "TI",
"aminoAcids": "T/I/A",
"codons": "aCc/aTc",
"extra": [
"IMPACT=MODERATE",
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