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Refactored vocab server
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agr_indexer/src/main/java/org/alliancegenome/indexer/indexers/curation/service/GeneDiseaseAnnotationService.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -38,7 +38,7 @@ public class GeneDiseaseAnnotationService extends BaseDiseaseAnnotationService {
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private final GeneDiseaseAnnotationInterface geneApi = RestProxyFactory.createProxy(GeneDiseaseAnnotationInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config);
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private final GeneToGeneOrthologyGeneratedInterface orthologyApi = RestProxyFactory.createProxy(GeneToGeneOrthologyGeneratedInterface.class, ConfigHelper.getCurationApiUrl(), RestConfig.config);
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private VocabularyTermService vocabService = new VocabularyTermService();
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private VocabularyTermService vocabularyTermService = new VocabularyTermService();
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private EcoTermService ecoTermService = new EcoTermService();
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private OrganizationService orgService = new OrganizationService();
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private ReferenceService referenceService = new ReferenceService();
@@ -108,8 +108,8 @@ public Map<Gene, List<DiseaseAnnotation>> getOrthologousGeneDiseaseAnnotations(M
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params.put("obsolete", false);
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params.put("strictFilter", true);
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VocabularyTerm isMarkerViaOrthology = vocabService.getDiseaseRelationTerms().get("is_marker_via_orthology");
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VocabularyTerm isImplicatedViaOrthology = vocabService.getDiseaseRelationTerms().get("is_implicated_via_orthology");
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VocabularyTerm isMarkerViaOrthology = vocabularyTermService.getDiseaseRelationTerms().get("is_marker_via_orthology");
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VocabularyTerm isImplicatedViaOrthology = vocabularyTermService.getDiseaseRelationTerms().get("is_implicated_via_orthology");
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ECOTerm ecoTermIEA = ecoTermService.getEcoTerm("ECO:0000501");
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// hard code MGI:6194238 with corresponding AGRKB ID
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Reference allianceReference = referenceService.getReference("AGRKB:101000000828456");

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