package org.dnaerys.client;
import com.github.tomakehurst.wiremock.WireMockServer;
import io.quarkus.test.common.QuarkusTestResource;
import io.quarkus.test.junit.QuarkusTest;
import jakarta.inject.Inject;
import org.dnaerys.cluster.grpc.*;
import org.dnaerys.test.WireMockGrpcResource;
import org.dnaerys.test.WireMockGrpcResource.InjectWireMockGrpc;
import org.dnaerys.test.WireMockGrpcResource.InjectWireMockServer;
import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.DisplayName;
import org.junit.jupiter.api.Nested;
import org.junit.jupiter.api.Test;
import org.junit.jupiter.params.ParameterizedTest;
import org.junit.jupiter.params.provider.ValueSource;
import org.wiremock.grpc.dsl.WireMockGrpcService;
import java.util.Iterator;
import static org.assertj.core.api.Assertions.assertThat;
import static org.mockito.ArgumentMatchers.any;
import static org.mockito.ArgumentMatchers.argThat;
import static org.mockito.Mockito.*;
import static org.wiremock.grpc.dsl.WireMockGrpc.*;
/**
* Unit tests for DnaerysClient.
* Tests pagination logic, annotation building, input validation, and error handling.
*
* Test Case IDs: CLI-PAG-001 through CLI-ERR-004
*
* Uses WireMock gRPC for mocking non-streaming gRPC responses.
* Streaming tests (PaginationLogicTests) remain disabled due to WireMock gRPC 0.11.0 limitations.
*
* @see org.dnaerys.client.DnaerysClient
*/
@DisplayName("DnaerysClient Unit Tests")
@QuarkusTest
@QuarkusTestResource(WireMockGrpcResource.class)
class DnaerysClientTest {
@Inject
DnaerysClient client;
@InjectWireMockGrpc
WireMockGrpcService dnaerysService;
@InjectWireMockServer
WireMockServer wireMockServer;
// Mock stub used only by disabled PaginationLogicTests (streaming RPC tests)
// Kept for compilation only - not used by enabled tests
@SuppressWarnings("unused")
private DnaerysServiceGrpc.DnaerysServiceBlockingStub mockBlockingStub;
@BeforeEach
void setUp() {
// Reset all stubs between tests for isolation
if (wireMockServer != null) {
wireMockServer.resetAll();
}
// Initialize mock stub for disabled PaginationLogicTests (compilation only)
mockBlockingStub = mock(DnaerysServiceGrpc.DnaerysServiceBlockingStub.class);
}
// ========================================
// ANNOTATION BUILDING TESTS (CLI-ANN-*)
// ========================================
@Nested
@DisplayName("Annotation Building Tests")
class AnnotationBuildingTests {
@Test
@DisplayName("CLI-ANN-001: AF less than filter is set correctly")
void testAfLessThan() {
Annotations annotations = client.composeAnnotations(
0.01f, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getAfLt()).isEqualTo(0.01f);
assertThat(annotations.getAfGt()).isZero();
}
@Test
@DisplayName("CLI-ANN-002: AF greater than filter is set correctly")
void testAfGreaterThan() {
Annotations annotations = client.composeAnnotations(
null, 0.05f, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getAfGt()).isEqualTo(0.05f);
assertThat(annotations.getAfLt()).isZero();
}
@Test
@DisplayName("CLI-ANN-003: Impact filter parses CSV correctly")
void testImpactFilter() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
"HIGH,MODERATE", null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getImpactList())
.hasSize(2)
.containsExactlyInAnyOrder(Impact.HIGH, Impact.MODERATE);
}
@Test
@DisplayName("CLI-ANN-004: Combined filters are all set correctly")
void testCombinedFilters() {
Annotations annotations = client.composeAnnotations(
0.01f, 0.0001f, // AF lt, gt
0.05f, 0.001f, // gnomAD genome AF
0.02f, 0.0005f, // gnomAD exome AF
"HIGH", "PROTEIN_CODING", "TRANSCRIPT", "SNV",
"MISSENSE_VARIANT", "PATHOGENIC",
"LIKELY_PATHOGENIC", 0.9f, 0.5f,
true, false, true, false
);
assertThat(annotations.getAfLt()).isEqualTo(0.01f);
assertThat(annotations.getAfGt()).isEqualTo(0.0001f);
assertThat(annotations.getGnomadGenomesAfLt()).isEqualTo(0.05f);
assertThat(annotations.getGnomadGenomesAfGt()).isEqualTo(0.001f);
assertThat(annotations.getGnomadExomesAfLt()).isEqualTo(0.02f);
assertThat(annotations.getGnomadExomesAfGt()).isEqualTo(0.0005f);
assertThat(annotations.getImpactList()).contains(Impact.HIGH);
assertThat(annotations.getBioTypeList()).contains(BioType.PROTEIN_CODING);
assertThat(annotations.getFeatureTypeList()).contains(FeatureType.TRANSCRIPT);
assertThat(annotations.getVariantTypeList()).contains(VariantType.SNV);
assertThat(annotations.getConsequenceList()).contains(Consequence.MISSENSE_VARIANT);
assertThat(annotations.getClinsgnList()).contains(ClinSignificance.PATHOGENIC);
assertThat(annotations.getAmClassList()).contains(AlphaMissense.AM_LIKELY_PATHOGENIC);
assertThat(annotations.getAmScoreLt()).isEqualTo(0.9f);
assertThat(annotations.getAmScoreGt()).isEqualTo(0.5f);
assertThat(annotations.getBiallelicOnly()).isTrue();
assertThat(annotations.getMultiallelicOnly()).isFalse();
assertThat(annotations.getExcludeMales()).isTrue();
assertThat(annotations.getExcludeFemales()).isFalse();
}
@Test
@DisplayName("CLI-ANN-005: Empty/null filters produce empty annotations object")
void testEmptyFilters() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getAfLt()).isZero();
assertThat(annotations.getAfGt()).isZero();
assertThat(annotations.getImpactList()).isEmpty();
assertThat(annotations.getBioTypeList()).isEmpty();
assertThat(annotations.getConsequenceList()).isEmpty();
}
@Test
@DisplayName("CLI-ANN-006: Invalid values are filtered out from CSV")
void testInvalidValuesFiltered() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
"HIGH,INVALID,MODERATE", null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getImpactList())
.hasSize(2)
.containsExactlyInAnyOrder(Impact.HIGH, Impact.MODERATE)
.doesNotContain(Impact.UNRECOGNIZED);
}
@Test
@DisplayName("Negative AF values are not set")
void testNegativeAfNotSet() {
Annotations annotations = client.composeAnnotations(
-0.01f, -0.05f, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getAfLt()).isZero();
assertThat(annotations.getAfGt()).isZero();
}
@Test
@DisplayName("Zero AF values are not set")
void testZeroAfNotSet() {
Annotations annotations = client.composeAnnotations(
0.0f, 0.0f, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getAfLt()).isZero();
assertThat(annotations.getAfGt()).isZero();
}
@Test
@DisplayName("gnomAD genome AF filters are set correctly")
void testGnomadGenomeAf() {
Annotations annotations = client.composeAnnotations(
null, null, 0.05f, 0.001f, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getGnomadGenomesAfLt()).isEqualTo(0.05f);
assertThat(annotations.getGnomadGenomesAfGt()).isEqualTo(0.001f);
}
@Test
@DisplayName("gnomAD exome AF filters are set correctly")
void testGnomadExomeAf() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, 0.02f, 0.0005f,
null, null, null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getGnomadExomesAfLt()).isEqualTo(0.02f);
assertThat(annotations.getGnomadExomesAfGt()).isEqualTo(0.0005f);
}
@Test
@DisplayName("BioType filter parses CSV correctly")
void testBioTypeFilter() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, "PROTEIN_CODING,LNCRNA", null, null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getBioTypeList())
.hasSize(2)
.containsExactlyInAnyOrder(BioType.PROTEIN_CODING, BioType.LNCRNA);
}
@Test
@DisplayName("FeatureType filter parses CSV correctly")
void testFeatureTypeFilter() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, "TRANSCRIPT,REGULATORYFEATURE", null, null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getFeatureTypeList())
.hasSize(2)
.containsExactlyInAnyOrder(FeatureType.TRANSCRIPT, FeatureType.REGULATORYFEATURE);
}
@Test
@DisplayName("VariantType filter parses CSV correctly")
void testVariantTypeFilter() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, "SNV,INSERTION,DELETION", null, null,
null, null, null, null, null, null, null
);
assertThat(annotations.getVariantTypeList())
.hasSize(3)
.containsExactlyInAnyOrder(VariantType.SNV, VariantType.INSERTION, VariantType.DELETION);
}
@Test
@DisplayName("Consequences filter parses CSV correctly")
void testConsequencesFilter() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, null, "STOP_GAINED,FRAMESHIFT_VARIANT,MISSENSE_VARIANT", null,
null, null, null, null, null, null, null
);
assertThat(annotations.getConsequenceList())
.hasSize(3)
.containsExactlyInAnyOrder(
Consequence.STOP_GAINED,
Consequence.FRAMESHIFT_VARIANT,
Consequence.MISSENSE_VARIANT
);
}
@Test
@DisplayName("ClinSignificance filter parses CSV correctly")
void testClinSignificanceFilter() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, null, null, "PATHOGENIC,LIKELY_PATHOGENIC",
null, null, null, null, null, null, null
);
assertThat(annotations.getClinsgnList())
.hasSize(2)
.containsExactlyInAnyOrder(ClinSignificance.PATHOGENIC, ClinSignificance.LIKELY_PATHOGENIC);
}
@Test
@DisplayName("AlphaMissense filter parses CSV correctly")
void testAlphaMissenseFilter() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, null, null, null,
"LIKELY_PATHOGENIC,AMBIGUOUS", null, null, null, null, null, null
);
assertThat(annotations.getAmClassList())
.hasSize(2)
.containsExactlyInAnyOrder(AlphaMissense.AM_LIKELY_PATHOGENIC, AlphaMissense.AM_AMBIGUOUS);
}
@Test
@DisplayName("AlphaMissense score filters are set correctly")
void testAlphaMissenseScoreFilters() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, null, null, null,
null, 0.9f, 0.5f, null, null, null, null
);
assertThat(annotations.getAmScoreLt()).isEqualTo(0.9f);
assertThat(annotations.getAmScoreGt()).isEqualTo(0.5f);
}
@Test
@DisplayName("Boolean filters (biallelic, multiallelic) are set when true")
void testBooleanFiltersTrue() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, true, true, true, true
);
assertThat(annotations.getBiallelicOnly()).isTrue();
assertThat(annotations.getMultiallelicOnly()).isTrue();
assertThat(annotations.getExcludeMales()).isTrue();
assertThat(annotations.getExcludeFemales()).isTrue();
}
@Test
@DisplayName("Boolean filters are not set when false")
void testBooleanFiltersFalse() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, false, false, false, false
);
// When false, the flags should not be set (default is false)
assertThat(annotations.getBiallelicOnly()).isFalse();
assertThat(annotations.getMultiallelicOnly()).isFalse();
assertThat(annotations.getExcludeMales()).isFalse();
assertThat(annotations.getExcludeFemales()).isFalse();
}
@Test
@DisplayName("Empty string filters are treated as null")
void testEmptyStringFilters() {
Annotations annotations = client.composeAnnotations(
null, null, null, null, null, null,
"", "", "", "", "", "",
"", null, null, null, null, null, null
);
assertThat(annotations.getImpactList()).isEmpty();
assertThat(annotations.getBioTypeList()).isEmpty();
assertThat(annotations.getFeatureTypeList()).isEmpty();
assertThat(annotations.getVariantTypeList()).isEmpty();
assertThat(annotations.getConsequenceList()).isEmpty();
assertThat(annotations.getClinsgnList()).isEmpty();
assertThat(annotations.getAmClassList()).isEmpty();
}
}
// ========================================
// INPUT VALIDATION TESTS
// ========================================
@Nested
@DisplayName("Input Validation Tests")
class InputValidationTests {
@Test
@DisplayName("Invalid chromosome throws RuntimeException for count")
void testInvalidChromosomeCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInRegion(
"99", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null
)
);
assertThat(thrown.getMessage()).contains("Invalid Chromosome");
}
@Test
@DisplayName("Invalid chromosome throws RuntimeException for select")
void testInvalidChromosomeSelect() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.selectVariantsInRegion(
"99", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
null, null
)
);
assertThat(thrown.getMessage()).contains("Invalid Chromosome");
}
@Test
@DisplayName("Negative start position throws RuntimeException for count")
void testNegativeStartCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInRegion(
"1", -100, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null
)
);
assertThat(thrown.getMessage()).contains("Invalid 'start' or 'end'");
}
@Test
@DisplayName("Start > End throws RuntimeException for count")
void testInvertedCoordinatesCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInRegion(
"1", 2000, 1000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null
)
);
assertThat(thrown.getMessage()).contains("Invalid 'start' or 'end'");
}
@Test
@DisplayName("Start > End throws RuntimeException for select")
void testInvertedCoordinatesSelect() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.selectVariantsInRegion(
"1", 2000, 1000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
null, null
)
);
assertThat(thrown.getMessage()).contains("Invalid 'start' or 'end'");
}
@Test
@DisplayName("Null sample ID throws RuntimeException for count in sample")
void testNullSampleIdCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInRegionInSample(
"1", 1000, 2000, null, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null
)
);
assertThat(thrown.getMessage()).contains("Sample ID must not be empty");
}
@Test
@DisplayName("Empty sample ID throws RuntimeException for count in sample")
void testEmptySampleIdCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInRegionInSample(
"1", 1000, 2000, "", true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null
)
);
assertThat(thrown.getMessage()).contains("Sample ID must not be empty");
}
@ParameterizedTest(name = "Chromosome ''{0}'' is invalid")
@ValueSource(strings = {"0", "23", "99", "chrM", "invalid", ""}) // Note: "MT" is valid (maps to CHR_MT)
@DisplayName("Invalid chromosome values throw RuntimeException")
void testVariousInvalidChromosomes(String chromosome) {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInRegion(
chromosome, 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null
)
);
assertThat(thrown.getMessage()).contains("Invalid Chromosome");
}
@Test
@DisplayName("Variant min/max length normalization with valid coordinates")
void testVariantLengthNormalization() {
// Stub CountVariantsInRegion to return a count
CountAllelesResponse response = CountAllelesResponse.newBuilder()
.setCount(100L)
.build();
dnaerysService.stubFor(
method("CountVariantsInRegion")
.willReturn(message(response))
);
// Test that negative variant lengths are normalized (not rejected)
long count = client.countVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, -5, -10, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null
);
// Should succeed with normalized values
assertThat(count).isEqualTo(100L);
}
}
// ========================================
// HOMOZYGOUS REFERENCE INPUT VALIDATION TESTS
// ========================================
@Nested
@DisplayName("Homozygous Reference Input Validation Tests")
class HomozygousReferenceInputValidationTests {
@Test
@DisplayName("countSamplesHomozygousReference with invalid chromosome throws RuntimeException")
void testCountHomRefInvalidChromosome() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countSamplesHomozygousReference("99", 1000)
);
assertThat(thrown.getMessage()).contains("Invalid Chromosome");
}
@Test
@DisplayName("countSamplesHomozygousReference with invalid position throws RuntimeException")
void testCountHomRefInvalidPosition() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countSamplesHomozygousReference("1", 0)
);
assertThat(thrown.getMessage()).contains("Invalid position");
}
@Test
@DisplayName("countSamplesHomozygousReference with negative position throws RuntimeException")
void testCountHomRefNegativePosition() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countSamplesHomozygousReference("1", -100)
);
assertThat(thrown.getMessage()).contains("Invalid position");
}
@Test
@DisplayName("selectSamplesHomozygousReference with invalid chromosome throws RuntimeException")
void testSelectHomRefInvalidChromosome() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.selectSamplesHomozygousReference("99", 1000)
);
assertThat(thrown.getMessage()).contains("Invalid Chromosome");
}
@Test
@DisplayName("selectSamplesHomozygousReference with invalid position throws RuntimeException")
void testSelectHomRefInvalidPosition() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.selectSamplesHomozygousReference("1", 0)
);
assertThat(thrown.getMessage()).contains("Invalid position");
}
}
// ========================================
// KINSHIP INPUT VALIDATION TESTS
// Uses WireMock gRPC for mocking non-streaming DatasetInfo and KinshipDuo RPCs.
// ========================================
@Nested
@DisplayName("Kinship Input Validation Tests")
class KinshipInputValidationTests {
@Test
@DisplayName("Kinship with non-existent sample1 throws RuntimeException")
void testKinshipNonExistentSample1() {
// Stub datasetInfo to return empty cohorts (sample won't be found)
DatasetInfoResponse datasetResponse = DatasetInfoResponse.newBuilder().build();
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(message(datasetResponse))
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.kinship("NONEXISTENT", "HG00405")
);
assertThat(thrown.getMessage()).contains("does not exist");
}
@Test
@DisplayName("Kinship with non-existent sample2 throws RuntimeException")
void testKinshipNonExistentSample2() {
// Stub datasetInfo to return sample1 but not sample2
Cohort cohort = Cohort.newBuilder()
.addMaleSamplesNames("HG00403")
.build();
DatasetInfoResponse datasetResponse = DatasetInfoResponse.newBuilder()
.addCohorts(cohort)
.build();
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(message(datasetResponse))
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.kinship("HG00403", "NONEXISTENT")
);
assertThat(thrown.getMessage()).contains("does not exist");
}
@Test
@DisplayName("Kinship with null sample1 throws RuntimeException")
void testKinshipNullSample1() {
DatasetInfoResponse datasetResponse = DatasetInfoResponse.newBuilder().build();
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(message(datasetResponse))
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.kinship(null, "HG00405")
);
assertThat(thrown.getMessage()).contains("does not exist");
}
@Test
@DisplayName("Kinship with null sample2 throws RuntimeException")
void testKinshipNullSample2() {
Cohort cohort = Cohort.newBuilder()
.addMaleSamplesNames("HG00403")
.build();
DatasetInfoResponse datasetResponse = DatasetInfoResponse.newBuilder()
.addCohorts(cohort)
.build();
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(message(datasetResponse))
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.kinship("HG00403", null)
);
assertThat(thrown.getMessage()).contains("does not exist");
}
@Test
@DisplayName("Kinship with valid samples succeeds")
void testKinshipValidSamples() {
// Stub datasetInfo to return both samples
Cohort cohort = Cohort.newBuilder()
.addMaleSamplesNames("HG00403")
.addFemaleSamplesNames("HG00405")
.build();
DatasetInfoResponse datasetResponse = DatasetInfoResponse.newBuilder()
.addCohorts(cohort)
.build();
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(message(datasetResponse))
);
// Stub kinship response
Relatedness relatedness = Relatedness.newBuilder()
.setDegree(KinshipDegree.FIRST_DEGREE)
.build();
KinshipResponse kinshipResponse = KinshipResponse.newBuilder()
.addRel(relatedness)
.build();
dnaerysService.stubFor(
method("KinshipDuo")
.willReturn(message(kinshipResponse))
);
String result = client.kinship("HG00403", "HG00405");
assertThat(result).isEqualTo("FIRST_DEGREE");
}
}
// ========================================
// GRPC ERROR HANDLING TESTS
// Uses WireMock gRPC for mocking error responses.
// ========================================
@Nested
@DisplayName("gRPC Error Handling Tests")
class GrpcErrorHandlingTests {
@Test
@DisplayName("CLI-ERR-001: gRPC UNAVAILABLE error throws RuntimeException for getDatasetInfo")
void testGetDatasetInfoGrpcFailure() {
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(Status.UNAVAILABLE, "Connection failed")
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.getDatasetInfo()
);
assertThat(thrown.getMessage()).contains("UNAVAILABLE");
}
@Test
@DisplayName("CLI-ERR-002: gRPC UNAVAILABLE error throws RuntimeException for countSamplesHomozygousReference")
void testCountSamplesHomRefGrpcFailure() {
dnaerysService.stubFor(
method("CountSamplesHomReference")
.willReturn(Status.UNAVAILABLE, "Connection failed")
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countSamplesHomozygousReference("1", 1000)
);
assertThat(thrown.getMessage()).contains("UNAVAILABLE");
}
@Test
@DisplayName("CLI-ERR-003: gRPC UNAVAILABLE error throws RuntimeException for getSampleIds")
void testGetSampleIdsGrpcFailure() {
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(Status.UNAVAILABLE, "Connection failed")
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.getSampleIds(DnaerysClient.Gender.BOTH)
);
assertThat(thrown.getMessage()).contains("UNAVAILABLE");
}
@Test
@DisplayName("CLI-ERR-004: gRPC UNAVAILABLE error throws RuntimeException for kinship")
void testKinshipGrpcFailure() {
dnaerysService.stubFor(
method("DatasetInfo")
.willReturn(Status.UNAVAILABLE, "Connection failed")
);
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.kinship("HG00403", "HG00405")
);
assertThat(thrown.getMessage()).contains("UNAVAILABLE");
}
}
// ========================================
// PAGINATION LOGIC TESTS (Server Streaming RPC)
// These tests use SelectVariantsInRegion which is a server streaming RPC.
// WireMock gRPC 0.11.0 has limited streaming support (returns single message only).
// These tests remain disabled until WireMock gRPC adds full streaming support.
// ========================================
@Nested
@DisplayName("Pagination Logic Tests")
@org.junit.jupiter.api.Disabled("WireMock gRPC 0.11.0 has limited streaming RPC support")
class PaginationLogicTests {
@Test
@DisplayName("CLI-PAG-001: Null limit is normalized to MAX_RETURNED_ITEMS")
void testNullLimitNormalization() {
// Return empty iterator
@SuppressWarnings("unchecked")
Iterator<AllelesResponse> emptyIterator = mock(Iterator.class);
when(emptyIterator.hasNext()).thenReturn(false);
when(mockBlockingStub.selectVariantsInRegion(any(AllelesInRegionRequest.class)))
.thenReturn(emptyIterator);
// Call with null limit
client.selectVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
null, null // skip=null, limit=null
);
// Verify the request was made with limit=50 (MAX_RETURNED_ITEMS)
verify(mockBlockingStub).selectVariantsInRegion(argThat(request ->
request.getLimit() == 50 && request.getSkip() == 0
));
}
@Test
@DisplayName("CLI-PAG-002: Negative limit is normalized to MAX_RETURNED_ITEMS")
void testNegativeLimitNormalization() {
@SuppressWarnings("unchecked")
Iterator<AllelesResponse> emptyIterator = mock(Iterator.class);
when(emptyIterator.hasNext()).thenReturn(false);
when(mockBlockingStub.selectVariantsInRegion(any(AllelesInRegionRequest.class)))
.thenReturn(emptyIterator);
// Call with negative limit
client.selectVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
null, -1 // limit=-1
);
verify(mockBlockingStub).selectVariantsInRegion(argThat(request ->
request.getLimit() == 50
));
}
@Test
@DisplayName("CLI-PAG-003: Over-limit is normalized to MAX_RETURNED_ITEMS")
void testOverLimitNormalization() {
@SuppressWarnings("unchecked")
Iterator<AllelesResponse> emptyIterator = mock(Iterator.class);
when(emptyIterator.hasNext()).thenReturn(false);
when(mockBlockingStub.selectVariantsInRegion(any(AllelesInRegionRequest.class)))
.thenReturn(emptyIterator);
// Call with over limit
client.selectVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
null, 500 // limit=500 (over max)
);
verify(mockBlockingStub).selectVariantsInRegion(argThat(request ->
request.getLimit() == 50
));
}
@Test
@DisplayName("CLI-PAG-004: Valid limit is passed through")
void testValidLimitPassthrough() {
@SuppressWarnings("unchecked")
Iterator<AllelesResponse> emptyIterator = mock(Iterator.class);
when(emptyIterator.hasNext()).thenReturn(false);
when(mockBlockingStub.selectVariantsInRegion(any(AllelesInRegionRequest.class)))
.thenReturn(emptyIterator);
// Call with valid limit
client.selectVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
null, 25 // limit=25 (valid)
);
verify(mockBlockingStub).selectVariantsInRegion(argThat(request ->
request.getLimit() == 25
));
}
@Test
@DisplayName("CLI-PAG-005: Null skip is normalized to 0")
void testNullSkipNormalization() {
@SuppressWarnings("unchecked")
Iterator<AllelesResponse> emptyIterator = mock(Iterator.class);
when(emptyIterator.hasNext()).thenReturn(false);
when(mockBlockingStub.selectVariantsInRegion(any(AllelesInRegionRequest.class)))
.thenReturn(emptyIterator);
client.selectVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
null, 50 // skip=null
);
verify(mockBlockingStub).selectVariantsInRegion(argThat(request ->
request.getSkip() == 0
));
}
@Test
@DisplayName("CLI-PAG-006: Negative skip is normalized to 0")
void testNegativeSkipNormalization() {
@SuppressWarnings("unchecked")
Iterator<AllelesResponse> emptyIterator = mock(Iterator.class);
when(emptyIterator.hasNext()).thenReturn(false);
when(mockBlockingStub.selectVariantsInRegion(any(AllelesInRegionRequest.class)))
.thenReturn(emptyIterator);
client.selectVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
-10, 50 // skip=-10
);
verify(mockBlockingStub).selectVariantsInRegion(argThat(request ->
request.getSkip() == 0
));
}
@Test
@DisplayName("CLI-PAG-007: Valid skip is passed through")
void testValidSkipPassthrough() {
@SuppressWarnings("unchecked")
Iterator<AllelesResponse> emptyIterator = mock(Iterator.class);
when(emptyIterator.hasNext()).thenReturn(false);
when(mockBlockingStub.selectVariantsInRegion(any(AllelesInRegionRequest.class)))
.thenReturn(emptyIterator);
client.selectVariantsInRegion(
"1", 1000, 2000, true, true,
null, null, null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null,
200, 50 // skip=200 (valid)
);
verify(mockBlockingStub).selectVariantsInRegion(argThat(request ->
request.getSkip() == 200
));
}
}
// ========================================
// DATASET INFO RECORD TESTS
// ========================================
@Nested
@DisplayName("DatasetInfo Record Tests")
class DatasetInfoRecordTests {
@Test
@DisplayName("DatasetInfo record holds correct values")
void testDatasetInfoRecord() {
DnaerysClient.DatasetInfo info = new DnaerysClient.DatasetInfo(138044723, 3202, 1598, 1604);
assertThat(info.variantsTotal()).isEqualTo(138044723);
assertThat(info.samplesTotal()).isEqualTo(3202);
assertThat(info.samplesMaleCount()).isEqualTo(1598);
assertThat(info.samplesFemaleCount()).isEqualTo(1604);
}
@Test
@DisplayName("DatasetInfo record equality")
void testDatasetInfoEquality() {
DnaerysClient.DatasetInfo info1 = new DnaerysClient.DatasetInfo(1000, 100, 50, 50);
DnaerysClient.DatasetInfo info2 = new DnaerysClient.DatasetInfo(1000, 100, 50, 50);
assertThat(info1).isEqualTo(info2);
}
}
// ========================================
// GENDER ENUM TESTS
// ========================================
@Nested
@DisplayName("Gender Enum Tests")
class GenderEnumTests {
@Test
@DisplayName("Gender enum has all expected values")
void testGenderEnumValues() {
assertThat(DnaerysClient.Gender.values())
.containsExactly(
DnaerysClient.Gender.MALE,
DnaerysClient.Gender.FEMALE,
DnaerysClient.Gender.BOTH
);
}
}
}
