test coverage for oan-rest, updating models to have equals and hashco…

…de, adding neo4j harness for tests

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

@@ -28,7 +28,7 @@ public class GraphCommand implements Runnable {
 	@Option(names = {"-m", "--modules"}, description = "The list of modules to load into the graph.")
 	List<String> modules;
 
-	public static void main(String[] args) throws Exception {
+	public static void main(String[] args) {
 		PicocliRunner.run(GraphCommand.class, args);
 	}
 

oan-model/src/main/java/org/jax/oan/core/Assay.java

@@ -7,4 +7,14 @@ public class Assay extends OntologyClass {
 	public Assay(TermId id, String name) {
 		super(id, name);
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		return super.equals(o);
+	}
+
+	@Override
+	public int hashCode() {
+		return super.hashCode();
+	}
 }

oan-model/src/main/java/org/jax/oan/core/Disease.java

@@ -7,4 +7,14 @@ public class Disease extends OntologyClass {
 	public Disease(TermId id, String name) {
 		super(id, name);
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		return super.equals(o);
+	}
+
+	@Override
+	public int hashCode() {
+		return super.hashCode();
+	}
 }

oan-model/src/main/java/org/jax/oan/core/Gene.java

@@ -6,4 +6,14 @@ public class Gene extends OntologyClass {
 	public Gene(TermId id, String name) {
 		super(id, name);
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		return super.equals(o);
+	}
+
+	@Override
+	public int hashCode() {
+		return super.hashCode();
+	}
 }

oan-model/src/main/java/org/jax/oan/core/MedicalAction.java

@@ -6,4 +6,14 @@ public class MedicalAction extends OntologyClass {
 	public MedicalAction(TermId id, String name) {
 		super(id, name);
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		return super.equals(o);
+	}
+
+	@Override
+	public int hashCode() {
+		return super.hashCode();
+	}
 }

oan-model/src/main/java/org/jax/oan/core/OntologyClass.java

@@ -2,6 +2,8 @@
 
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
+import java.util.Objects;
+
 public abstract class OntologyClass {
 
 	TermId id;
@@ -20,4 +22,17 @@ public String getId() {
 	public String getName() {
 		return name;
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		OntologyClass that = (OntologyClass) o;
+		return Objects.equals(id, that.id) && Objects.equals(name, that.name);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(id, name);
+	}
 }

oan-model/src/main/java/org/jax/oan/core/Phenotype.java

@@ -2,6 +2,7 @@
 
 import org.monarchinitiative.phenol.ontology.data.TermId;
 
+import java.util.Objects;
 import java.util.Optional;
 
 public class Phenotype extends OntologyClass {
@@ -33,4 +34,19 @@ public Optional<PhenotypeMetadata> getMetadata() {
 	public String getCategory() {
 		return category;
 	}
+
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		if (!super.equals(o)) return false;
+		Phenotype phenotype = (Phenotype) o;
+		return Objects.equals(metadata, phenotype.metadata) && Objects.equals(category, phenotype.category);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(super.hashCode(), metadata, category);
+	}
 }

oan-model/src/main/java/org/jax/oan/core/PhenotypeMetadata.java

@@ -1,6 +1,7 @@
 package org.jax.oan.core;
 
 import java.util.List;
+import java.util.Objects;
 
 public class PhenotypeMetadata {
 
@@ -31,4 +32,17 @@ public String getFrequency() {
 	public List<String> getSources() {
 		return sources;
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) return true;
+		if (o == null || getClass() != o.getClass()) return false;
+		PhenotypeMetadata that = (PhenotypeMetadata) o;
+		return Objects.equals(sex, that.sex) && Objects.equals(onset, that.onset) && Objects.equals(frequency, that.frequency) && Objects.equals(sources, that.sources);
+	}
+
+	@Override
+	public int hashCode() {
+		return Objects.hash(sex, onset, frequency, sources);
+	}
 }

oan-rest/build.gradle

@@ -33,6 +33,11 @@ dependencies {
     testImplementation('org.junit.jupiter:junit-jupiter')
     testImplementation("io.micronaut.test:micronaut-test-junit5")
     testImplementation("org.mockito:mockito-junit-jupiter")
+    testRuntimeOnly('javax.ws.rs:javax.ws.rs-api:2.1.1')
+    testRuntimeOnly("javax.validation:validation-api:2.0.1.Final")
+    testRuntimeOnly("javax.annotation:javax.annotation-api:1.3.2")
+    testRuntimeOnly("org.neo4j.test:neo4j-harness")
+
 }
 
 

oan-rest/src/main/java/org/jax/oan/repository/DiseaseRepository.java

@@ -12,7 +12,10 @@
 import org.neo4j.driver.Value;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
+import java.util.function.Predicate;
+import java.util.stream.Collectors;
 
 import static org.neo4j.driver.Values.parameters;
 
@@ -56,7 +59,7 @@ public List<Phenotype> findPhenotypesByDisease(TermId termId){
 				Record r = result.next();
 				Value p = r.get("p");
 				Value pm = r.get("pm");
-				PhenotypeMetadata phenotypeMetadata = new PhenotypeMetadata(pm.get("sex").asString(), pm.get("onset").asString(), pm.get("frequency").asString(), List.of(pm.get("sources").asString().split(";")));
+				PhenotypeMetadata phenotypeMetadata = new PhenotypeMetadata(pm.get("sex").asString(), pm.get("onset").asString(), pm.get("frequency").asString(), Arrays.stream(pm.get("sources").asString().split(";")).filter(Predicate.not(String::isBlank)).collect(Collectors.toList()));
 				Phenotype phenotype = new Phenotype(TermId.of(p.get("id").asString()), p.get("name").asString(), p.get("category").asString(), phenotypeMetadata);
 				phenotypes.add(phenotype);
 			}

oan-rest/src/main/java/org/jax/oan/repository/PhenotypeRepository.java

@@ -72,8 +72,8 @@ public List<Assay> findAssaysByTerm(TermId termId){
 			Result result = tx.run("MATCH (a: Assay)-[:MEASURES]-(p: Phenotype {id: $id}) RETURN a", parameters("id", termId.getValue()));
 
 			while (result.hasNext()) {
-				Record record = result.next();
-				Assay assay = new Assay(TermId.of(record.get("id").asString()), record.get("name").asString());
+				Value value = result.next().get("a");
+				Assay assay = new Assay(TermId.of(value.get("id").asString()), value.get("name").asString());
 				assays.add(assay);
 			}
 		}

oan-rest/src/main/java/org/jax/oan/service/DownloadService.java

@@ -52,10 +52,13 @@ public SystemFile associations(TermId termId, SupportedEntity source, SupportedE
 			case PHENOTYPE -> {
 				if(target.equals(SupportedEntity.DISEASE)){
 					List<Disease> diseases = this.phenotypeRepository.findDiseasesByTerm(termId);
-					return buildFile(String.format("dieases_for_%s", termId.getValue()), diseases);
-				} else {
+					return buildFile(String.format("diseases_for_%s", termId.getValue()), diseases);
+				} else if(target.equals(SupportedEntity.GENE)) {
 					List<Gene> genes = this.phenotypeRepository.findGenesByTerm(termId);
 					return buildFile(String.format("genes_for_%s", termId.getValue()), genes);
+				} else {
+					List<Assay> assays = this.phenotypeRepository.findAssaysByTerm(termId);
+					return buildFile(String.format("assays_for_%s", termId.getValue()), assays);
 				}
 			}
 			default -> throw new OntologyAnnotationNetworkRuntimeException(String.format("Downloading %s association for %s failed because source type is not supported.", target.toString().toLowerCase(), termId.getValue()));

oan-rest/src/main/resources/application-test.properties

@@ -0,0 +1 @@
+neo4j.embedded.ephemeral=true

oan-rest/src/test/java/org/jax/oan/TestData.java

@@ -0,0 +1,38 @@
+package org.jax.oan;
+
+import org.jax.oan.core.Assay;
+import org.jax.oan.core.Disease;
+import org.jax.oan.core.Gene;
+import org.jax.oan.core.Phenotype;
+import org.monarchinitiative.phenol.ontology.data.TermId;
+
+import java.util.List;
+
+public class TestData {
+	public static List<Disease> diseases(){
+		return List.of(
+				new Disease(TermId.of("MONDO:099233"),"Really bad one"),
+				new Disease(TermId.of("DECIPHER:434444"),"Kinda bad one")
+		);
+	}
+
+	public static List<Phenotype> phenotypes(){
+		return List.of(
+				new Phenotype(TermId.of("HP:099233"),"Long legs"),
+				new Phenotype(TermId.of("HP:434444"),"Big bicep small arm")
+		);
+	}
+
+	public static List<Assay> assays(){
+		return List.of(
+				new Assay(TermId.of("LOINC:55555"),"Special bicep test")
+		);
+	}
+
+	public static List<Gene> genes(){
+		return List.of(
+				new Gene(TermId.of("NCBIGene:00093"),"TP4"),
+				new Gene(TermId.of("NCBIGene:02002"),"YZ")
+		);
+	}
+}

oan-rest/src/test/java/org/jax/oan/controller/AnnotationControllerTest.java

@@ -19,9 +19,11 @@
 import java.io.File;
 import java.io.IOException;
 import java.io.PrintWriter;
+import java.nio.file.Files;
 import java.util.List;
 import java.util.Map;
 
+import static org.jax.oan.TestData.*;
 import static org.mockito.Mockito.mock;
 import static org.mockito.Mockito.when;
 
@@ -85,10 +87,12 @@ void negative_by_incorrect_term(RequestSpecification spec){
 
 	@Test
 	void positive_download_file(RequestSpecification spec) throws IOException {
+		SystemFile file = buildSimpleSpreadSheet();
 		when(downloadService.associations(TermId.of("OMIM:0392932"), SupportedEntity.DISEASE, SupportedEntity.GENE))
-				.thenReturn(buildSimpleSpreadSheet());
+				.thenReturn(file);
 		spec.when().get("/api/annotation/OMIM:0392932/download/gene").then()
 				.statusCode(200).contentType("text/tab-separated-values");
+		Files.deleteIfExists(file.getFile().toPath());
 	}
 
 	@Test
@@ -106,33 +110,6 @@ void negative_download_file_bad_type(RequestSpecification spec){
 		spec.when().get("/api/annotation/OMIM:0392932/download/disease").then().statusCode(400);
 	}
 
-	private static List<Gene> genes(){
-		return List.of(
-				new Gene(TermId.of("NCBIGene:00093"),"TP4"),
-				new Gene(TermId.of("NCBIGene:02002"),"YZ")
-		);
-	}
-
-	private static List<Disease> diseases(){
-		return List.of(
-				new Disease(TermId.of("MONDO:099233"),"Really bad one"),
-				new Disease(TermId.of("DECIPHER:434444"),"Kinda bad one")
-		);
-	}
-
-	private static List<Phenotype> phenotypes(){
-		return List.of(
-				new Phenotype(TermId.of("HP:099233"),"Long legs"),
-				new Phenotype(TermId.of("HP:434444"),"Big bicep small arm")
-		);
-	}
-
-	private static List<Assay> assays(){
-		return List.of(
-				new Assay(TermId.of("LOINC:55555"),"Special bicep test")
-		);
-	}
-
 	private static SystemFile buildSimpleSpreadSheet() throws IOException {
 		File file = File.createTempFile("test", ".tsv");
 		try (PrintWriter pw = new PrintWriter(file)) {

oan-rest/src/test/java/org/jax/oan/repository/DiseaseRepositoryTest.java

@@ -0,0 +1,70 @@
+package org.jax.oan.repository;
+
+import io.micronaut.test.extensions.junit5.annotation.MicronautTest;
+import jakarta.inject.Inject;
+import org.jax.oan.core.Gene;
+import org.jax.oan.core.Phenotype;
+import org.jax.oan.core.PhenotypeMetadata;
+import org.junit.jupiter.api.AfterAll;
+import org.junit.jupiter.api.BeforeAll;
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.TestInstance;
+import org.monarchinitiative.phenol.ontology.data.TermId;
+import org.neo4j.driver.Driver;
+import org.neo4j.driver.Session;
+import org.neo4j.driver.Transaction;
+
+import java.util.List;
+
+import static org.junit.jupiter.api.Assertions.*;
+
+@TestInstance(TestInstance.Lifecycle.PER_CLASS)
+@MicronautTest
+class DiseaseRepositoryTest {
+
+	@Inject
+	Driver driver;
+
+	@Inject
+	DiseaseRepository diseaseRepository;
+
+	@BeforeAll
+	void initialize() {
+		try(Transaction tx = driver.session().beginTransaction()){
+			tx.run("CREATE (d:Disease {id: 'OMIM:092320', name: 'Some bad disease'})");
+			tx.run("CREATE (p: Phenotype {id: 'HP:000001', name: 'short stature', category: ''})");
+			tx.run("CREATE (g:Gene {id: 'NCBIGene:9999', name: 'TX2'})");
+			tx.run("CREATE (g:Gene {id: 'NCBIGene:7777', name: 'MNN'})");
+			tx.run("MATCH (d:Disease {id: 'OMIM:092320'}), (p:Phenotype {id: 'HP:000001'})" +
+					"MERGE (d)-[:MANIFESTS]->(p)<-[:WITH_METADATA {context: 'OMIM:092320'}]-(pm: PhenotypeMetadata {onset: '', frequency: '1/1', sex: 'female'," +
+					"sources: '' })");
+			tx.run("MATCH (d:Disease {id: 'OMIM:092320'}), (g:Gene {id: 'NCBIGene:7777'}) " +
+					"MERGE (d)-[:EXPRESSES]->(g)");
+			tx.run("MATCH (d:Disease {id: 'OMIM:092320'}), (g:Gene {id: 'NCBIGene:9999'}) " +
+					"MERGE (d)-[:EXPRESSES]->(g)");
+			tx.commit();
+		}
+	}
+
+	@Test
+	void findGenesByDisease() {
+		List<Gene> genes = diseaseRepository.findGenesByDisease(TermId.of("OMIM:092320"));
+		List<Gene> expected = List.of(
+				new Gene(TermId.of("NCBIGene:9999"),"TX2"),
+				new Gene(TermId.of("NCBIGene:7777"),"MNN")
+				);
+		assertTrue(
+				expected.containsAll(genes)
+		);
+	}
+
+	@Test
+	void findPhenotypesByDisease() {
+		List<Phenotype> phenotypes = diseaseRepository.findPhenotypesByDisease(TermId.of("OMIM:092320"));
+		List<Phenotype> expected = List.of(
+				new Phenotype(TermId.of("HP:000001"), "short stature", "", new PhenotypeMetadata("female", "", "1/1", List.of()))
+		);
+
+		assertTrue(phenotypes.containsAll(expected));
+	}
+}