-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
11 changed files
with
421 additions
and
66 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
164 changes: 164 additions & 0 deletions
164
oan-rest/src/test/java/org/jax/oan/controller/AnnotationControllerTest.java
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,164 @@ | ||
| package org.jax.oan.controller; | ||
|
|
||
| import io.micronaut.http.server.types.files.SystemFile; | ||
| import io.micronaut.runtime.EmbeddedApplication; | ||
| import io.micronaut.test.annotation.MockBean; | ||
| import io.micronaut.test.extensions.junit5.annotation.MicronautTest; | ||
| import io.restassured.specification.RequestSpecification; | ||
| import jakarta.inject.Inject; | ||
| import org.jax.oan.core.*; | ||
| import org.jax.oan.service.DiseaseService; | ||
| import org.jax.oan.service.DownloadService; | ||
| import org.jax.oan.service.GeneService; | ||
| import org.jax.oan.service.PhenotypeService; | ||
| import org.junit.jupiter.api.Test; | ||
| import org.monarchinitiative.phenol.ontology.data.TermId; | ||
|
|
||
| import static org.hamcrest.CoreMatchers.*; | ||
|
|
||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.io.PrintWriter; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
|
|
||
| import static org.mockito.Mockito.mock; | ||
| import static org.mockito.Mockito.when; | ||
|
|
||
| @MicronautTest | ||
| class AnnotationControllerTest { | ||
|
|
||
| @Inject | ||
| EmbeddedApplication<?> application; | ||
|
|
||
| @Inject | ||
| private PhenotypeService phenotypeService; | ||
| @Inject | ||
| private GeneService geneService; | ||
|
|
||
| @Inject | ||
| private DiseaseService diseaseService; | ||
|
|
||
| @Inject | ||
| private DownloadService downloadService; | ||
|
|
||
| @Test | ||
| void positive_by_disease(RequestSpecification spec) { | ||
| when(diseaseService.findAll(TermId.of("OMIM:039293"))) | ||
| .thenReturn(new DiseaseAnnotationDto(Map.of("limbs", phenotypes()), genes())); | ||
| spec.when().get("/api/annotation/OMIM:039293").then() | ||
| .statusCode(200).body("genes.id", | ||
| hasItems("NCBIGene:00093", "NCBIGene:02002")); | ||
| } | ||
|
|
||
| @Test | ||
| void positive_by_phenotype(RequestSpecification spec) { | ||
| when(phenotypeService.findAll(TermId.of("HP:0000001"))) | ||
| .thenReturn(new PhenotypeAnnotationDto(diseases(), genes(), assays())); | ||
| spec.when().get("/api/annotation/HP:0000001").then() | ||
| .statusCode(200) | ||
| .body("diseases.id", hasItems("MONDO:099233", "DECIPHER:434444")) | ||
| .body("genes.id", hasItems("NCBIGene:00093", "NCBIGene:02002")) | ||
| .body("assays.id", hasItem("LOINC:55555")); | ||
|
|
||
| } | ||
|
|
||
| @Test | ||
| void positive_by_gene(RequestSpecification spec) { | ||
| when(geneService.findAll(TermId.of("NCBIGene:093232"))) | ||
| .thenReturn(new GeneAnnotationDto(diseases(), phenotypes())); | ||
| spec.when().get("/api/annotation/NCBIGene:093232").then() | ||
| .statusCode(200) | ||
| .body("diseases.id", hasItems("MONDO:099233", "DECIPHER:434444")) | ||
| .body("phenotypes.id", hasItems("HP:099233", "HP:434444")); | ||
| } | ||
|
|
||
| @Test | ||
| void negative_by_no_prefix(RequestSpecification spec){ | ||
| spec.when().get("/api/annotation/FAKE:093232").then().statusCode(400); | ||
| } | ||
|
|
||
| @Test | ||
| void negative_by_incorrect_term(RequestSpecification spec){ | ||
| spec.when().get("/api/annotation/not-right").then().statusCode(400); | ||
| } | ||
|
|
||
| @Test | ||
| void positive_download_file(RequestSpecification spec) throws IOException { | ||
| when(downloadService.associations(TermId.of("OMIM:0392932"), SupportedEntity.DISEASE, SupportedEntity.GENE)) | ||
| .thenReturn(buildSimpleSpreadSheet()); | ||
| spec.when().get("/api/annotation/OMIM:0392932/download/gene").then() | ||
| .statusCode(200).contentType("text/tab-separated-values"); | ||
| } | ||
|
|
||
| @Test | ||
| void negative_download_file_no_prefix(RequestSpecification spec){ | ||
| spec.when().get("/api/annotation/FAKE:093232/download/gene").then().statusCode(400); | ||
| } | ||
|
|
||
| @Test | ||
| void negative_download_file_incorrect_term(RequestSpecification spec){ | ||
| spec.when().get("/api/annotation/not-right/download/disease").then().statusCode(400); | ||
| } | ||
|
|
||
| @Test | ||
| 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)) { | ||
| pw.println(String.format("%s \t %s", "id", "name")); | ||
| pw.println(String.format("%s \t %s", "NCBIGene:301", "TX2")); | ||
| } | ||
| return new SystemFile(file).attach(file.getName()); | ||
| } | ||
|
|
||
| @MockBean(DiseaseService.class) | ||
| DiseaseService diseaseService() { | ||
| return mock(DiseaseService.class); | ||
| } | ||
|
|
||
| @MockBean(GeneService.class) | ||
| GeneService geneService() { | ||
| return mock(GeneService.class); | ||
| } | ||
|
|
||
| @MockBean(PhenotypeService.class) | ||
| PhenotypeService phenotypeService() { | ||
| return mock(PhenotypeService.class); | ||
| } | ||
|
|
||
| @MockBean(DownloadService.class) | ||
| DownloadService downloadService() { | ||
| return mock(DownloadService.class); | ||
| } | ||
| } |
Oops, something went wrong.