Merge pull request #1547 from alliance-genome/SCRUM-5953

Switch out download files for Species full name

Author: oblodgett

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<String, Object> geneDoc = getGene(geneID);
 			SpeciesType type = SpeciesType.getTypeByNameField(geneDoc.get("species").toString());

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());

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"));

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());

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());
 		}

agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneGeneticInteractionToTdfTranslator.java

@@ -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());

agr_java_core/src/main/java/org/alliancegenome/core/translators/tdf/GeneMolecularInteractionToTdfTranslator.java

@@ -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());

agr_java_core/src/main/java/org/alliancegenome/core/variant/converters/VariantSearchResultConverter.java

@@ -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()));