diff --git a/agr_api/src/main/java/org/alliancegenome/api/service/ExpressionRibbonESService.java b/agr_api/src/main/java/org/alliancegenome/api/service/ExpressionRibbonESService.java index 07cf21089..72afc62cc 100644 --- a/agr_api/src/main/java/org/alliancegenome/api/service/ExpressionRibbonESService.java +++ b/agr_api/src/main/java/org/alliancegenome/api/service/ExpressionRibbonESService.java @@ -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 geneDoc = getGene(geneID); SpeciesType type = SpeciesType.getTypeByNameField(geneDoc.get("species").toString()); diff --git a/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java b/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java index 71bcf419b..8fc181b3d 100644 --- a/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java +++ b/agr_api/src/main/java/org/alliancegenome/api/translators/tdf/DiseaseAnnotationToTdfTranslator.java @@ -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()); diff --git a/agr_api/src/test/java/org/alliancegenome/api/tests/integration/GeneIT.java b/agr_api/src/test/java/org/alliancegenome/api/tests/integration/GeneIT.java index 44ca52cc2..1b3d9c6cc 100644 --- a/agr_api/src/test/java/org/alliancegenome/api/tests/integration/GeneIT.java +++ b/agr_api/src/test/java/org/alliancegenome/api/tests/integration/GeneIT.java @@ -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")); @@ -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")); diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/AlleleToTdfTranslator.java b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/AlleleToTdfTranslator.java index b86536cb4..013997130 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/AlleleToTdfTranslator.java +++ b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/AlleleToTdfTranslator.java @@ -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; @@ -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()); diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/ExpressionToTdfTranslator.java b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/ExpressionToTdfTranslator.java index b203b0efc..a7fab1e2e 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/ExpressionToTdfTranslator.java +++ b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/ExpressionToTdfTranslator.java @@ -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()); } diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneGeneticInteractionToTdfTranslator.java b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneGeneticInteractionToTdfTranslator.java index e2dca441c..9562ec9a0 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneGeneticInteractionToTdfTranslator.java +++ b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneGeneticInteractionToTdfTranslator.java @@ -56,7 +56,7 @@ public String getAllRows(List 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()); diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneMolecularInteractionToTdfTranslator.java b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneMolecularInteractionToTdfTranslator.java index 10557a9e9..c6f6ca192 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneMolecularInteractionToTdfTranslator.java +++ b/agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneMolecularInteractionToTdfTranslator.java @@ -56,7 +56,7 @@ public String getAllRows(List 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()); diff --git a/agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java b/agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java index 2cc2e92fa..ce48ec79a 100644 --- a/agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java +++ b/agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java @@ -32,7 +32,7 @@ public List convertToVariantSearchDocument(List