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cbioportal import user
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Dec 27, 2024
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4 changes: 2 additions & 2 deletions
4
src/main/resources/fed-sources.properties → src/main/resources/federator.properties
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| fed.sources[0].name=Test cBioPortal 1 | ||
| fed.sources[0].base-url=https://test.cbioportal.dev.aws.mskcc.org/api-fed | ||
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| fed.sources[0].name=Test cBioPortal 2 | ||
| fed.sources[0].base-url=https://test2.cbioportal.dev.aws.mskcc.org/api-fed | ||
| fed.sources[1].name=Test cBioPortal 2 | ||
| fed.sources[1].base-url=https://test2.cbioportal.dev.aws.mskcc.org/api-fed |
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182 changes: 182 additions & 0 deletions
182
src/test/java/org/cbioportal/service/impl/FederatedViewServiceImplTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,182 @@ | ||
| package org.cbioportal.service.impl; | ||
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| import org.cbioportal.model.ClinicalAttribute; | ||
| import org.cbioportal.model.Sample; | ||
| import org.cbioportal.persistence.ClinicalAttributeRepository; | ||
| import org.cbioportal.persistence.ClinicalDataRepository; | ||
| import org.cbioportal.persistence.SampleRepository; | ||
| import org.cbioportal.service.ClinicalAttributeService; | ||
| import org.cbioportal.service.ClinicalDataService; | ||
| import org.cbioportal.service.exception.FederationException; | ||
| import org.junit.Assert; | ||
| import org.junit.Before; | ||
| import org.junit.Test; | ||
| import org.junit.runner.RunWith; | ||
| import org.mockito.InjectMocks; | ||
| import org.mockito.Mock; | ||
| import org.mockito.Mockito; | ||
| import org.mockito.Spy; | ||
| import org.mockito.junit.MockitoJUnitRunner; | ||
| import org.springframework.test.util.ReflectionTestUtils; | ||
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| import java.util.List; | ||
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| @RunWith(MockitoJUnitRunner.class) | ||
| public class FederatedViewServiceImplTest extends BaseServiceImplTest { | ||
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| @InjectMocks | ||
| private FederatedViewServiceImpl federatedViewService; | ||
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| @Mock | ||
| private List<String> dataSourceStudies = List.of( | ||
| STUDY_ID, | ||
| STUDY_ID_2 | ||
| ); | ||
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| @Mock | ||
| private ClinicalAttributeService clinicalAttributeService; | ||
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| @Mock | ||
| private ClinicalDataService clinicalDataService; | ||
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| private List<ClinicalAttribute> mockClinicalAttributes() { | ||
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| var attrib11 = new ClinicalAttribute(); | ||
| attrib11.setDisplayName("Sex"); | ||
| attrib11.setDescription("Sex"); | ||
| attrib11.setDatatype("STRING"); | ||
| attrib11.setPatientAttribute(false); | ||
| attrib11.setPriority("1"); | ||
| attrib11.setAttrId("SEX"); | ||
| attrib11.setCancerStudyIdentifier(STUDY_ID); | ||
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| var attrib21 = new ClinicalAttribute(); | ||
| attrib21.setDisplayName("Age"); | ||
| attrib21.setDescription("Age"); | ||
| attrib21.setDatatype("NUMBER"); | ||
| attrib21.setPatientAttribute(false); | ||
| attrib21.setPriority("1"); | ||
| attrib21.setAttrId("AGE"); | ||
| attrib21.setCancerStudyIdentifier(STUDY_ID); | ||
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| var attrib12 = new ClinicalAttribute(); | ||
| attrib12.setDisplayName("Sex"); | ||
| attrib12.setDescription("Sex"); | ||
| attrib12.setDatatype("STRING"); | ||
| attrib12.setPatientAttribute(false); | ||
| attrib12.setPriority("1"); | ||
| attrib12.setAttrId("SEX"); | ||
| attrib12.setCancerStudyIdentifier(STUDY_ID_2); | ||
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| var attrib22 = new ClinicalAttribute(); | ||
| attrib22.setDisplayName("Age"); | ||
| attrib22.setDescription("Age"); | ||
| attrib22.setDatatype("NUMBER"); | ||
| attrib22.setPatientAttribute(false); | ||
| attrib22.setPriority("1"); | ||
| attrib22.setAttrId("AGE"); | ||
| attrib22.setCancerStudyIdentifier(STUDY_ID_2); | ||
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| return List.of(attrib11, attrib21, attrib12, attrib22); | ||
| } | ||
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| private List<Sample> mockSamples() { | ||
| var sample1 = new Sample(); | ||
| sample1.setStableId(SAMPLE_ID1); | ||
| sample1.setPatientStableId(PATIENT_ID_1); | ||
| sample1.setCancerStudyIdentifier(STUDY_ID); | ||
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| var sample2 = new Sample(); | ||
| sample2.setStableId(SAMPLE_ID2); | ||
| sample2.setPatientStableId(PATIENT_ID_2); | ||
| sample2.setCancerStudyIdentifier(STUDY_ID); | ||
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| var sample3 = new Sample(); | ||
| sample3.setStableId(SAMPLE_ID3); | ||
| sample3.setPatientStableId(PATIENT_ID_3); | ||
| sample3.setCancerStudyIdentifier(STUDY_ID_2); | ||
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| return List.of(sample1, sample2, sample3); | ||
| } | ||
|
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| @Before | ||
| public void setup() { | ||
| ReflectionTestUtils.setField(federatedViewService, "federationMode", FederationMode.DATASOURCE); | ||
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| List<ClinicalAttribute> attribs = mockClinicalAttributes(); | ||
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| // Methods used by fetchClinicalAttributes | ||
| } | ||
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| @Test | ||
| public void fetchClinicalAttributes() throws FederationException { | ||
| // Arrange | ||
| var expected = mockClinicalAttributes(); | ||
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| // Act | ||
| var result = federatedViewService.fetchClinicalAttributes(); | ||
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| // Assert | ||
| Assert.assertEquals(expected, result); | ||
| } | ||
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| // @Test | ||
| // public void fetchClinicalDataCountsNoFilter() throws FederationException { | ||
| // // Arrange | ||
| // // Mock out: the cohort, ie. | ||
| // // - 1 person is this race & this age & this study | ||
| // // - .. 2 other people .. | ||
| // var filter = new ClinicalDataCountFilter(); | ||
| // // First we get the cohort | ||
| //// Mockito.when( | ||
| //// studyViewFilterApplier.apply() | ||
| //// ).thenReturn( | ||
| //// | ||
| //// ); | ||
| // // Then we extract the study and sample IDs from this cohort | ||
| // Mockito.when().thenReturn(); | ||
| // // Then we call clinicalDataService | ||
| // Mockito.when( | ||
| // clinicalDataService.fetchClinicalDataCounts( | ||
| // studyIds, | ||
| // sampleIds, | ||
| // attributeIds | ||
| // ) | ||
| // ).thenReturn( | ||
| // /* ... */ | ||
| // ); | ||
| // | ||
| // // Act | ||
| // var result = federatedViewService.fetchClinicalDataCounts(filter); | ||
| // | ||
| // // Assert | ||
| // // - Returns some list of SampleIdentifiers | ||
| // // - Extracts them into study ID + sample ID list | ||
| // // - Calls fetchClinicalDataCounts() | ||
| // } | ||
| // | ||
| // // TODO test with filter | ||
| // | ||
| // @Test | ||
| // public void fetchClinicalDataBinCountsNoFilter() throws FederationException { | ||
| // // Arrange | ||
| // var filter = new ClinicalDataBinCountFilter(); | ||
| // Mockito.when( | ||
| // clinicalDataBinUtil.fetchClinicalDataBinCounts( | ||
| // DataBinMethod.STATIC, | ||
| // filter, | ||
| // false | ||
| // ) | ||
| // ).thenReturn( | ||
| // /* ... */ | ||
| // ); | ||
| // | ||
| // // Act | ||
| // var result = federatedViewService.fetchClinicalDataBinCounts(); | ||
| // | ||
| // // Assert ... | ||
| // } | ||
| // | ||
| // // TODO test with filter | ||
| } |
46 changes: 46 additions & 0 deletions
46
src/test/java/org/cbioportal/test/integration/FederatedApiIntegrationTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,46 @@ | ||
| package org.cbioportal.test.integration; | ||
|
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| import org.cbioportal.model.ClinicalAttribute; | ||
| import org.cbioportal.model.Sample; | ||
| import org.cbioportal.persistence.ClinicalAttributeRepository; | ||
| import org.cbioportal.persistence.ClinicalDataRepository; | ||
| import org.cbioportal.persistence.SampleRepository; | ||
| import org.cbioportal.service.ClinicalDataService; | ||
| import org.cbioportal.service.FederatedViewService; | ||
| import org.cbioportal.web.FederatedViewController; | ||
| import org.cbioportal.web.config.TestConfig; | ||
| import org.junit.Before; | ||
| import org.junit.Test; | ||
| import org.junit.runner.RunWith; | ||
| import org.springframework.beans.factory.annotation.Autowired; | ||
| import org.springframework.boot.test.autoconfigure.web.servlet.AutoConfigureMockMvc; | ||
| import org.springframework.boot.test.autoconfigure.web.servlet.WebMvcTest; | ||
| import org.springframework.boot.test.context.SpringBootTest; | ||
| import org.springframework.boot.test.mock.mockito.MockBean; | ||
| import org.springframework.context.annotation.ComponentScan; | ||
| import org.springframework.http.MediaType; | ||
| import org.springframework.security.test.context.support.WithMockUser; | ||
| import org.springframework.test.context.ContextConfiguration; | ||
| import org.springframework.test.context.junit4.SpringJUnit4ClassRunner; | ||
| import org.springframework.test.web.servlet.MockMvc; | ||
| import org.springframework.test.web.servlet.request.MockMvcRequestBuilders; | ||
|
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| import java.util.List; | ||
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| import static org.mockito.ArgumentMatchers.any; | ||
| import static org.mockito.Mockito.when; | ||
| import static org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.csrf; | ||
| import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*; | ||
| import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.jsonPath; | ||
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| @RunWith(SpringJUnit4ClassRunner.class) | ||
| //@WebMvcTest | ||
| //@AutoConfigureMockMvc // load the whole Spring Boot application context | ||
| @ContextConfiguration(classes = { | ||
| FederatedViewController.class, | ||
| FederatedViewService.class, | ||
| ClinicalDataService.class, | ||
| TestConfig.class | ||
| }) | ||
| public class FederatedApiIntegrationTest { | ||
| } |
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