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Merged
oblodgett merged 1 commit into from
Apr 1, 2026
Merged

Switch out download files for Species full name #1547

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2 changes: 1 addition & 1 deletion agr_api/src/main/java/org/alliancegenome/api/service/ExpressionRibbonESService.java
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Expand Up @@ -153,7 +153,7 @@ private RibbonEntity getExpressionRibbonSummary(String geneID) {
dataProvider = annotation.getDataProvider().getAbbreviation();
entity.setLabel(gene.getGeneSymbol().getDisplayText());
entity.setTaxonID(gene.getTaxon().getCurie());
entity.setTaxonName(gene.getTaxon().getName());
entity.setTaxonName(gene.getTaxon().getSpecies().getFullName());
} else {
Map<String, Object> geneDoc = getGene(geneID);
SpeciesType type = SpeciesType.getTypeByNameField(geneDoc.get("species").toString());
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6 changes: 3 additions & 3 deletions ...rc/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java
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Expand Up @@ -191,19 +191,19 @@ private static void extracted(DiseaseAnnotationDocument annotation, org.alliance
if (annotation instanceof GeneDiseaseAnnotationDocument document) {
org.alliancegenome.curation_api.model.entities.Gene subject = document.getSubject();
subjectTaxonCurie = subject.getTaxon().getCurie();
subjectTaxonName = subject.getTaxon().getName();
subjectTaxonName = subject.getTaxon().getSpecies().getFullName();
subjectID = subject.getIdentifier();
subjectSymbol = subject.getGeneSymbol().getDisplayText();
} else if (annotation instanceof AlleleDiseaseAnnotationDocument document) {
org.alliancegenome.curation_api.model.entities.Allele subject = document.getSubject();
subjectTaxonCurie = subject.getTaxon().getCurie();
subjectTaxonName = subject.getTaxon().getName();
subjectTaxonName = subject.getTaxon().getSpecies().getFullName();
subjectID = subject.getIdentifier();
subjectSymbol = subject.getAlleleSymbol().getDisplayText();
} else if (annotation instanceof AGMDiseaseAnnotationDocument document) {
org.alliancegenome.curation_api.model.entities.AffectedGenomicModel subject = document.getSubject();
subjectTaxonCurie = subject.getTaxon().getCurie();
subjectTaxonName = subject.getTaxon().getName();
subjectTaxonName = subject.getTaxon().getSpecies().getFullName();
subjectID = subject.getIdentifier();
subjectSymbol = subject.getAgmFullName().getDisplayText();
row.setEntityType(subject.getSubtype().getName());
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4 changes: 2 additions & 2 deletions agr_api/src/test/java/org/alliancegenome/api/tests/integration/GeneIT.java
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Expand Up @@ -176,7 +176,7 @@ public void checkExpressionAnnotation() {
String terms = String.join(",", termList);
// String stages = String.join(",", stageList);
String symbols = String.join(",", symbolList);
assertThat("first element species", response.getResults().get(0).getGeneExpressionAnnotation().getExpressionAnnotationSubject().getTaxon().getName(), equalTo("Danio rerio"));
assertThat("first element species", response.getResults().get(0).getGeneExpressionAnnotation().getExpressionAnnotationSubject().getTaxon().getSpecies().getFullName(), equalTo("Danio rerio"));
assertThat("first element symbol", response.getResults().get(0).getGeneExpressionAnnotation().getExpressionAnnotationSubject().getGeneSymbol().getDisplayText(), equalTo("abcb4"));
assertThat("list of terms", terms, equalTo("bile canaliculus,head,head,head,head,head,head,head,head,hepatocyte intracellular canaliculus,intestinal bulb,intestine,intestine,intestine,intestine"));
// assertThat("list of stages", stages, equalTo("ZFS:0000029,ZFS:0000030,ZFS:0000031,ZFS:0000032,ZFS:0000033,ZFS:0000034,ZFS:0000035,ZFS:0000036,ZFS:0000037,ZFS:0000029,ZFS:0000030,ZFS:0000031,ZFS:0000032,ZFS:0000033,ZFS:0000034"));
Expand Down Expand Up @@ -261,7 +261,7 @@ public void checkExpressionAnnotationFilter() {
String terms = String.join(",", termList);
// String stages = String.join(",", stageList);
String symbols = String.join(",", symbolList);
assertThat("first element species", response.getResults().get(0).getGeneExpressionAnnotation().getExpressionAnnotationSubject().getTaxon().getName(), equalTo("Danio rerio"));
assertThat("first element species", response.getResults().get(0).getGeneExpressionAnnotation().getExpressionAnnotationSubject().getTaxon().getSpecies().getFullName(), equalTo("Danio rerio"));
assertThat("first element symbol", response.getResults().get(0).getGeneExpressionAnnotation().getExpressionAnnotationSubject().getGeneSymbol().getDisplayText(), equalTo("shha"));
assertThat("list of terms", terms, equalTo("anal fin,anterior neural keel,anterior neural keel ventral region,anterior neural rod,axial chorda mesoderm,axial chorda mesoderm"));
// assertThat("list of stages", stages, equalTo("ZFS:0000029,ZFS:0000030,ZFS:0000031,ZFS:0000032,ZFS:0000033,ZFS:0000034,ZFS:0000035,ZFS:0000036,ZFS:0000044"));
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4 changes: 2 additions & 2 deletions ...ava_core/src/main/java/org/alliancegenome/core/translators/tdf/AlleleToTdfTranslator.java
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Expand Up @@ -16,10 +16,10 @@
import org.alliancegenome.curation_api.model.entities.Allele;
import org.alliancegenome.curation_api.model.entities.CrossReference;
import org.alliancegenome.curation_api.model.entities.Note;
import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
import org.alliancegenome.curation_api.model.entities.Reference;
import org.alliancegenome.curation_api.model.entities.TransgenicAlleleConstruct;
import org.alliancegenome.curation_api.model.entities.Variant;
import org.alliancegenome.curation_api.model.entities.PredictedVariantConsequence;
import org.alliancegenome.curation_api.model.entities.associations.CuratedVariantGenomicLocationAssociation;
import org.alliancegenome.curation_api.model.entities.associations.TranscriptGeneAssociation;
import org.alliancegenome.curation_api.model.entities.ontology.SOTerm;
Expand Down Expand Up @@ -163,7 +163,7 @@ private TransgenicAlleleDownloadRow getBaseDownloadAlleleTransgenicRow(Transgeni
TransgenicAlleleDownloadRow row = new TransgenicAlleleDownloadRow();
Allele allele = transgenicAlleleSummaryDocument.getAllele();

row.setSpecies(allele.getTaxon().getName());
row.setSpecies(allele.getTaxon().getSpecies().getFullName());
row.setAlleleID(allele.getPrimaryExternalId());
row.setAlleleSymbol(allele.getAlleleSymbol().getFormatText());
row.setTgConstructID(transgenicAlleleConstruct.getConstruct().getPrimaryExternalId());
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2 changes: 1 addition & 1 deletion ...core/src/main/java/org/alliancegenome/core/translators/tdf/ExpressionToTdfTranslator.java
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Expand Up @@ -59,7 +59,7 @@ private String buildRow(
StringJoiner joiner = new StringJoiner("\t");
if (isMultipleGenes) {
var subject = annotation.getExpressionAnnotationSubject();
joiner.add(subject.getTaxon().getName())
joiner.add(subject.getTaxon().getSpecies().getFullName())
.add(subject.getGeneSymbol().getDisplayText())
.add(subject.getPrimaryExternalId());
}
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2 changes: 1 addition & 1 deletion ...n/java/org/alliancegenome/core/translators/tdf/GeneGeneticInteractionToTdfTranslator.java
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Expand Up @@ -56,7 +56,7 @@ public String getAllRows(List<GeneGeneticInteractionDocument> interactions) {
joiner.add(interaction.getGeneGeneticInteraction().getGeneGeneAssociationObject().getIdentifier());
joiner.add(interaction.getGeneGeneticInteraction().getGeneGeneAssociationObject().getGeneSymbol().getDisplayText());
joiner.add(interaction.getGeneGeneticInteraction().getGeneGeneAssociationObject().getTaxon().getCurie());
joiner.add(interaction.getGeneGeneticInteraction().getGeneGeneAssociationObject().getTaxon().getName());
joiner.add(interaction.getGeneGeneticInteraction().getGeneGeneAssociationObject().getTaxon().getSpecies().getFullName());

joiner.add(interaction.getGeneGeneticInteraction().getInteractorBType().getCurie());
joiner.add(interaction.getGeneGeneticInteraction().getInteractorBType().getName());
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2 changes: 1 addition & 1 deletion ...java/org/alliancegenome/core/translators/tdf/GeneMolecularInteractionToTdfTranslator.java
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Expand Up @@ -56,7 +56,7 @@ public String getAllRows(List<GeneMolecularInteractionDocument> interactions) {
joiner.add(interaction.getGeneMolecularInteraction().getGeneGeneAssociationObject().getIdentifier());
joiner.add(interaction.getGeneMolecularInteraction().getGeneGeneAssociationObject().getGeneSymbol().getDisplayText());
joiner.add(interaction.getGeneMolecularInteraction().getGeneGeneAssociationObject().getTaxon().getCurie());
joiner.add(interaction.getGeneMolecularInteraction().getGeneGeneAssociationObject().getTaxon().getName());
joiner.add(interaction.getGeneMolecularInteraction().getGeneGeneAssociationObject().getTaxon().getSpecies().getFullName());

joiner.add(interaction.getGeneMolecularInteraction().getInteractorBType().getCurie());
joiner.add(interaction.getGeneMolecularInteraction().getInteractorBType().getName());
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2 changes: 1 addition & 1 deletion ...rc/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java
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Expand Up @@ -32,7 +32,7 @@ public List<VariantSearchResultDocument> convertToVariantSearchDocument(List<Var

if (variantLocation.getVariantAssociationSubject() != null) {
if (variantLocation.getVariantAssociationSubject().getTaxon() != null) {
vsd.setSpecies(variantLocation.getVariantAssociationSubject().getTaxon().getName());
vsd.setSpecies(variantLocation.getVariantAssociationSubject().getTaxon().getSpecies().getFullName());
}
if (variantLocation.getVariantAssociationSubject().getVariantType() != null && variantLocation.getVariantAssociationSubject().getVariantType().getName() != null) {
vsd.setVariantType(List.of(variantLocation.getVariantAssociationSubject().getVariantType().getName()));
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