Merge pull request #51 from TheJacksonLaboratory/hotfix/tests

property collision with environment variables, renaming to be more sp…
TheJacksonLaboratory · Apr 2, 2024 · bff325e · bff325e
2 parents 15eedc2 + 3da3152
commit bff325e
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Showing 8 changed files with 18 additions and 17 deletions.
diff --git a/.github/workflows/ontology-build-deploy.yml b/.github/workflows/ontology-build-deploy.yml
@@ -41,7 +41,7 @@ env:
     GCLOUD_REGISTRY_PROJECT_ID: ${{ secrets.GCLOUD_REGISTRY_PROJECT_ID }}
     GCLOUD_REGISTRY_IMAGE_ENV: docker
     GCLOUD_REGISTRY_IMAGE_PROJECT: ontology
-    ONTOLOGY: ${{ inputs.ontology }}
+    ONTOLOGY_SERVICE_ONTOLOGY: ${{ inputs.ontology }}
     ONTOLOGY_SERVICE_LOAD: ${{ inputs.load }}
     ONTOLOGY_SERVICE_INTERNATIONAL: ${{ inputs.international }}
     SERVICE_NAME: ontology-service-${{ inputs.ontology }}
@@ -79,7 +79,7 @@ jobs:
           echo "PROJECT_VERSION=$(./gradlew properties -q | awk '/^version:/ {print $2}')" >> $GITHUB_ENV
       - name: Get ontology data
         run: |
-          bash ontology.sh ${ONTOLOGY}
+          bash ontology.sh ${ONTOLOGY_SERVICE_ONTOLOGY}
       - name: Docker Login
         run: |
           gcloud auth configure-docker "${GCLOUD_GCR}"

diff --git a/.github/workflows/ontology-sanity.yml b/.github/workflows/ontology-sanity.yml
@@ -1,7 +1,7 @@
 name: Sanity Check Application
 on: pull_request
 env:
-  ONTOLOGY: hp
+  ONTOLOGY_SERVICE_ONTOLOGY: hp
   ONTOLOGY_SERVICE_LOAD: true
 jobs:
   build:

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 = "0.5.9",
+            version = "0.5.10",
             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
@@ -54,7 +54,7 @@ public DataInitializer(TermRepository termRepository,
 	@Transactional
 	public void init() {
 		if(shouldLoad){
-			log.info("Loading ontology terms..");
+			log.info(String.format("Loading %s ontology terms..", graphService.ontologyName));
 			try {
 				this.termRepository.configure();
 				List<OntologyTerm> terms = graphService.getOntology().getTerms().stream().distinct().map(term ->

diff --git a/src/main/java/org/jacksonlaboratory/service/GraphService.java b/src/main/java/org/jacksonlaboratory/service/GraphService.java
@@ -30,7 +30,6 @@
  * Stores a {@link MinimalOntology} and provides associated methods for traversal
  */
 @Singleton
-@Requires(property = "ontology")
 @Transactional
 public class GraphService {
 
@@ -41,8 +40,8 @@ public class GraphService {
 
 	private OntologyDataResolver dataResolver;
 
-	@Property(name = "ontology") String ontologyName;
-	@Property(name = "workingdir") String directory;
+	@Value("${ontology}") String ontologyName;
+	@Value("${workingdir}") String directory;
 
 	@Value("${international}")
 	boolean international;
@@ -101,7 +100,7 @@ public OntologyDataResolver getDataResolver() {
 
 	@PostConstruct
 	public void initialize() {
-		log.info("Loading ontology json..");
+		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());

diff --git a/src/main/resources/application-test.yml b/src/main/resources/application-test.yml
@@ -2,7 +2,7 @@ micronaut:
   server:
     port: 8086
   application:
-    name: ontology-service-${ONTOLOGY:hp}
+    name: ontology-service-hp
   router:
     static-resources:
       swagger:

diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
@@ -3,7 +3,7 @@ micronaut:
     cors:
       enabled: true
   application:
-    name: ontology-service-${ONTOLOGY:unknown}
+    name: ontology-service-${ONTOLOGY_SERVICE_ONTOLOGY:unknown}
   router:
     static-resources:
       swagger:
@@ -47,7 +47,7 @@ jackson:
 
 api-url:
   prefix: /api
-ontology: ${ONTOLOGY:unknown}
+ontology: ${ONTOLOGY_SERVICE_ONTOLOGY:unknown}
 load: ${ONTOLOGY_SERVICE_LOAD:true}
 international: ${ONTOLOGY_SERVICE_INTERNATIONAL:false}
 workingdir: "data"
diff --git a/src/test/groovy/org/jacksonlaboratory/ingest/OntologyDataResolverSpec.groovy b/src/test/groovy/org/jacksonlaboratory/ingest/OntologyDataResolverSpec.groovy
@@ -6,10 +6,12 @@ import java.nio.file.Path
 
 class OntologyDataResolverSpec extends Specification {
 
-    void 'test of'(){
-        Path dataDirectory = Path.of("src/test/resources");
-        OntologyDataResolver dataResolver = HpoDataResolver.of(dataDirectory, "hp");
-        assertEquals(dataResolver.ontologyJson(), dataDirectory.resolve("hp-base.json"));
-        assertEquals(dataDirectory, dataResolver.dataDirectory());
+    void 'test of ontology data resolver'(){
+        given:
+            Path dataDirectory = Path.of("src/test/resources");
+            OntologyDataResolver dataResolver = OntologyDataResolver.of(dataDirectory, "hp");
+        expect:
+            dataResolver.ontologyJson() == dataDirectory.resolve("hp-base.json")
+            dataDirectory == dataResolver.dataDirectory()
     }
 }