unit test for oan-etl load

README.md

@@ -14,7 +14,7 @@ Micronaut 4.1.2
 ### Modules
 
 #### OAN-ETL
-    A module to load our graph data which includes phenotypes, diseases, genes, assays. There
+    A ontologyModule to load our graph data which includes phenotypes, diseases, genes, assays. There
     are multiple loaders for the different ontologies that are supported
 
 Running
@@ -30,7 +30,7 @@ Testing
 ```
 
 #### OAN-REST
-    A module that exposes our graph via a REST-API. This will be used for the hpo web application
+    A ontologyModule that exposes our graph via a REST-API. This will be used for the hpo web application
     and deployed to google cloud.
 
 Running

oan-etl/build.gradle

@@ -1,6 +1,7 @@
 plugins {
     id("com.github.johnrengelman.shadow") version "8.1.1"
     id("io.micronaut.application") version "4.0.3"
+    id('jacoco')
 }
 
 group = 'org.jacksonlaboratory'
@@ -52,3 +53,15 @@ micronaut {
         annotations("org.jacksonlaboratory.*")
     }
 }
+
+test {
+    finalizedBy jacocoTestReport // report is always generated after tests run
+}
+jacocoTestReport {
+    dependsOn test // tests are required to run before generating the report
+    reports {
+        xml.required = false
+        csv.required = false
+        html.outputLocation = layout.buildDirectory.dir('jacocoHtml')
+    }
+}

oan-etl/src/main/java/org/jacksonlaboratory/GraphCommand.java

@@ -3,7 +3,6 @@
 import io.micronaut.configuration.picocli.PicocliRunner;
 import jakarta.inject.Inject;
 import org.jacksonlaboratory.graph.Operations;
-import org.jacksonlaboratory.model.Module;
 import org.jacksonlaboratory.ontology.HpoGraphLoader;
 import picocli.CommandLine.Command;
 import picocli.CommandLine.Option;

oan-etl/src/main/java/org/jacksonlaboratory/graph/Operations.java

@@ -1,14 +1,12 @@
 package org.jacksonlaboratory.graph;
 
 import jakarta.inject.Singleton;
-import org.jacksonlaboratory.model.Module;
+import org.jacksonlaboratory.model.OntologyModule;
 import org.neo4j.driver.Driver;
 import org.neo4j.driver.Transaction;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.util.List;
-
 @Singleton
 public class Operations {
 	private static final Logger logger = LoggerFactory.getLogger(Operations.class);
@@ -27,9 +25,9 @@ public void truncate(){
 		}
 	}
 
-	public void createIndexes(Module module){
+	public void createIndexes(OntologyModule ontologyModule){
 		Transaction tx = driver.session().beginTransaction();
-		if (module.equals(Module.HPO)){
+		if (ontologyModule.equals(OntologyModule.HPO)){
 			logger.info("Creating Indexes...");
 			tx.run("CREATE INDEX phenotype_id FOR (n:Phenotype) ON (n.id)");
 			tx.run("CREATE INDEX disease_id FOR (n:Disease) ON (n.id)");
@@ -41,9 +39,9 @@ public void createIndexes(Module module){
 		tx.close();
 	}
 
-	public void dropIndexes(Module module){
+	public void dropIndexes(OntologyModule ontologyModule){
 		Transaction tx = driver.session().beginTransaction();
-		if(module.equals(Module.HPO)){
+		if(ontologyModule.equals(OntologyModule.HPO)){
 			logger.info("Dropping Indexes...");
 			tx.run("DROP INDEX phenotype_id IF EXISTS");
 			tx.run("DROP INDEX disease_id IF EXISTS");

oan-etl/src/main/java/org/jacksonlaboratory/model/Module.java → oan-etl/src/main/java/org/jacksonlaboratory/model/OntologyModule.java

@@ -1,5 +1,7 @@
 package org.jacksonlaboratory.model;
 
-public enum Module {
+public enum OntologyModule {
 	HPO, MAXO
+
 }
+

oan-etl/src/main/java/org/jacksonlaboratory/ontology/HpoGraphLoader.java

@@ -2,7 +2,7 @@
 
 import io.micronaut.context.annotation.Context;
 import org.jacksonlaboratory.graph.Operations;
-import org.jacksonlaboratory.model.Module;
+import org.jacksonlaboratory.model.OntologyModule;
 import org.monarchinitiative.phenol.annotations.assoc.MissingPhenolResourceException;
 import org.monarchinitiative.phenol.annotations.formats.AnnotationReference;
 import org.monarchinitiative.phenol.annotations.formats.hpo.HpoAssociationData;
@@ -56,12 +56,12 @@ public void load(String folder) throws IOException, MissingPhenolResourceExcepti
 		final HpoAssociationData associations = HpoAssociationData.builder(hpoOntology).orphaToGenePath(orphaToGenePath).mim2GeneMedgen(omimToGenePath)
 				.hpoDiseases(diseases).hgncCompleteSetArchive(hgncPath).build();
 		List<TermId> phenotypes = diseases.stream().flatMap(d -> d.annotationLines().stream().map(HpoAnnotationLine::phenotypeTermId)).distinct().toList();
-		operations.dropIndexes(Module.HPO);
+		operations.dropIndexes(OntologyModule.HPO);
 		try (Session session = driver.session()) {
 			phenotypes(session, phenotypes, hpoOntology);
 			diseases(session, diseases);
 			genes(session, associations);
-			operations.createIndexes(Module.HPO);
+			operations.createIndexes(OntologyModule.HPO);
 			diseaseToPhenotype(session, diseases, hpoOntology);
 			diseaseToGene(session, associations);
 			assayToPhenotype(session, loincPath);

oan-etl/src/test/java/org/jacksonlaboratory/graph/OperationsTest.java

@@ -0,0 +1,49 @@
+package org.jacksonlaboratory.graph;
+
+import io.micronaut.test.extensions.junit5.annotation.MicronautTest;
+import org.jacksonlaboratory.model.OntologyModule;
+import org.junit.jupiter.api.Test;
+import org.neo4j.driver.Driver;
+import org.neo4j.driver.Record;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@MicronautTest
+class OperationsTest {
+
+	Driver driver;
+	Operations operations;
+	public OperationsTest(Driver driver, Operations operations) {
+		this.driver = driver;
+		this.operations = operations;
+	}
+
+	@Test
+	void truncate() {
+		// Create fake nodes
+		// expect nodes to be 0.
+		driver.session().executeWriteWithoutResult(tx -> tx.run("CREATE (sample1),(sample2),(sample3),(sample4),(sample5)"));
+		int current = driver.session().executeWrite(tx -> tx.run("MATCH (x) RETURN COUNT(x)").single().values().get(0).asInt());
+		assertEquals(5, current);
+		operations.truncate();
+		current = driver.session().executeWrite(tx -> tx.run("MATCH (x) RETURN COUNT(x)").single().values().get(0).asInt());
+		assertEquals(0, current);
+	}
+
+	@Test
+	void createAndDropIndexes() {
+		driver.session().executeWriteWithoutResult(tx ->
+				tx.run("CREATE (p: Phenotype {id: 'HP:000001'}),(d: Disease {id: 'OMIM:1000'}),(g: Gene {id: 'NCBIGene:30'}),(a: Assay {id: 'LOINC:09103-3'})"));
+
+		operations.createIndexes(OntologyModule.HPO);
+		List<Record> indexes = driver.session().executeWrite(tx -> tx.run("SHOW INDEXES YIELD name, labelsOrTypes, properties, type").list()).stream().filter(r -> r.get("type").asString().equals("RANGE")).collect(Collectors.toList());
+		assertEquals(4, indexes.size());
+		operations.dropIndexes(OntologyModule.HPO);
+		indexes = driver.session().executeWrite(tx -> tx.run("SHOW INDEXES YIELD name, labelsOrTypes, properties, type").list()).stream().filter(r -> r.get("type").asString().equals("RANGE")).collect(Collectors.toList());;
+		assertEquals(0, indexes.size());
+		operations.truncate();
+	}
+}

oan-etl/src/test/java/org/jacksonlaboratory/model/OntologyModuleTest.java

@@ -0,0 +1,21 @@
+package org.jacksonlaboratory.model;
+
+import org.junit.jupiter.api.Test;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+class OntologyModuleTest {
+
+	@Test
+	void values() {
+		assertEquals(OntologyModule.HPO, OntologyModule.HPO);
+		assertNotEquals(OntologyModule.HPO, OntologyModule.MAXO);
+		assertEquals(OntologyModule.values().length, 2);
+	}
+
+	@Test
+	void valueOf() {
+		assertEquals(OntologyModule.valueOf("HPO"), OntologyModule.HPO);
+		assertEquals(OntologyModule.valueOf("MAXO"), OntologyModule.MAXO);
+	}
+}