Merge pull request #72 from TheJacksonLaboratory/issue-71

Issue 71
TheJacksonLaboratory · Sep 9, 2024 · 099b63a · 099b63a
2 parents 14d0100 + 0591b41
commit 099b63a
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Showing 5 changed files with 9 additions and 5 deletions.
diff --git a/build.gradle b/build.gradle
@@ -7,7 +7,7 @@ plugins {
     id("com.dorongold.task-tree") version "3.0.0"
 }
 
-version = "0.5.16"
+version = "0.5.17"
 group = "org.jacksonlaboratory"
 
 repositories {

diff --git a/src/main/java/org/jacksonlaboratory/Application.java b/src/main/java/org/jacksonlaboratory/Application.java
@@ -8,7 +8,7 @@
     info = @Info(
             title = "ontology-service-${ontology}",
             description = "A restful service for the ${ontology} ontology.",
-            version = "0.5.16",
+            version = "0.5.17",
             contact = @Contact(name = "Michael Gargano", email = "[email protected]")
     )
 )

diff --git a/src/main/java/org/jacksonlaboratory/service/DataInitializer.java b/src/main/java/org/jacksonlaboratory/service/DataInitializer.java
@@ -57,7 +57,8 @@ public void init() {
 			log.info(String.format("Loading %s ontology terms..", graphService.ontologyName));
 			try {
 				this.termRepository.configure();
-				List<OntologyTerm> terms = graphService.getOntology().getTerms().stream().distinct().map(term ->
+				List<OntologyTerm> terms = graphService.getOntology().getTerms().stream().distinct()
+						.filter(Predicate.not(term -> !term.id().getPrefix().toLowerCase().contains(graphService.ontologyName))).map(term ->
 					 new OntologyTermBuilder(term.id(), term.getName())
 							.setDefinition(term.getDefinition()).setComment(term.getComment())
 							.setSynonyms( term.getSynonyms().stream()

diff --git a/src/main/java/org/jacksonlaboratory/service/GraphService.java b/src/main/java/org/jacksonlaboratory/service/GraphService.java
@@ -10,6 +10,9 @@
 import org.jacksonlaboratory.repository.TermRepository;
 import org.jacksonlaboratory.repository.TranslationRepository;
 import org.monarchinitiative.phenol.io.MinimalOntologyLoader;
+import org.monarchinitiative.phenol.io.OntologyLoader;
+import org.monarchinitiative.phenol.io.OntologyLoaderOptions;
+import org.monarchinitiative.phenol.io.utils.CurieUtilBuilder;
 import org.monarchinitiative.phenol.ontology.data.Identified;
 import org.monarchinitiative.phenol.ontology.data.MinimalOntology;
 import org.monarchinitiative.phenol.ontology.data.Term;
@@ -112,7 +115,7 @@ public void initialize() {
 		log.info(String.format("Loading %s ontology json..", ontologyName));
 		this.dataResolver = OntologyDataResolver.of(Path.of(directory), this.ontologyName);
 		File file = new File(dataResolver.ontologyJson().toUri());
-		this.ontology = MinimalOntologyLoader.loadOntology(file, ontologyName.toUpperCase());
+		this.ontology = OntologyLoader.loadOntology(file, ontologyName.toUpperCase());
 		log.info("Finished loading ontology json.");
 	}
 }
diff --git a/src/test/groovy/org/jacksonlaboratory/service/GraphServiceSpec.groovy b/src/test/groovy/org/jacksonlaboratory/service/GraphServiceSpec.groovy
@@ -30,7 +30,7 @@ class GraphServiceSpec extends Specification {
         when:
         def ontology = graphService.getOntology()
         then:
-        ontology.getTerms().size() == 5
+        ontology.getTerms().size() == 6
     }
 
     void 'test graph service get most recent termid'() {