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 org.dnaerys.mcp.OneKGPdMCPServer.GenomicRegion;
import org.dnaerys.mcp.OneKGPdMCPServer.SelectByAnnotations;
import java.util.Iterator;
import java.util.List;
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;
private static final SelectByAnnotations NO_ANNOTATIONS = new SelectByAnnotations(
null, null, null, null, null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null, null, null);
@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(
new SelectByAnnotations(0.01f, null, null, 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(
new SelectByAnnotations(null, 0.05f, null, null, 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(
new SelectByAnnotations(null, null, null, null, null, null,
null, "HIGH,MODERATE", null, 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(
new SelectByAnnotations(
0.01f, 0.0001f, // AF lt, gt
0.02f, 0.0005f, // gnomAD exome AF
0.05f, 0.001f, // gnomAD genome AF
"PATHOGENIC", // clinSignificance
"HIGH", // vepImpact
"TRANSCRIPT", // vepFeature
"PROTEIN_CODING", // vepBiotype
"SNV", // vepVariantType
"MISSENSE_VARIANT", // vepConsequences
"LIKELY_PATHOGENIC", // alphaMissenseClass
0.9f, 0.5f, // AM score lt, gt
true, false, // biallelic, multiallelic
true, false, // excludeMales, excludeFemales
null, null) // minLen, maxLen
);
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(
new SelectByAnnotations(null, null, 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 throw RuntimeException")
void testInvalidValuesThrow() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.composeAnnotations(
new SelectByAnnotations(null, null, null, null, null, null,
null, "HIGH,INVALID,MODERATE", null, null, null, null,
null, null, null, null, null, null, null, null, null)
)
);
assertThat(thrown.getMessage()).contains("Invalid parameter");
}
@Test
@DisplayName("Negative AF values throw RuntimeException")
void testNegativeAfThrows() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.composeAnnotations(
new SelectByAnnotations(-0.01f, -0.05f, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, null)
)
);
assertThat(thrown.getMessage()).contains("Invalid parameter");
}
@Test
@DisplayName("Zero AF values are not set")
void testZeroAfNotSet() {
Annotations annotations = client.composeAnnotations(
new SelectByAnnotations(0.0f, 0.0f, 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();
}
@Test
@DisplayName("gnomAD genome AF filters are set correctly")
void testGnomadGenomeAf() {
Annotations annotations = client.composeAnnotations(
new SelectByAnnotations(null, null, 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(
new SelectByAnnotations(null, null, 0.02f, 0.0005f, null, null,
null, null, 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(
new SelectByAnnotations(null, null, 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(
new SelectByAnnotations(null, null, null, null, null, null,
null, null, "TRANSCRIPT,REGULATORYFEATURE", null, null, 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(
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, "SNV,INSERTION,DELETION", null,
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(
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, "STOP_GAINED,FRAMESHIFT_VARIANT,MISSENSE_VARIANT",
null, 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(
new SelectByAnnotations(null, null, null, null, null, null,
"PATHOGENIC,LIKELY_PATHOGENIC", null, null, null, null, null,
null, null, 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(
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, null,
"LIKELY_PATHOGENIC,AMBIGUOUS", null, null, 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(
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, null,
null, 0.9f, 0.5f, null, null, 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(
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, true, true, true, true, null, null)
);
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(
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, false, false, false, false, null, null)
);
// 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(
new SelectByAnnotations(null, null, 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.countVariants(
List.of(new GenomicRegion("99", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS
)
);
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.selectVariants(
List.of(new GenomicRegion("99", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, 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.countVariants(
List.of(new GenomicRegion("1", -100, 2000, null, null)), true, true,
NO_ANNOTATIONS
)
);
assertThat(thrown.getMessage()).contains("Invalid genomic region");
}
@Test
@DisplayName("Start > End throws RuntimeException for count")
void testInvertedCoordinatesCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariants(
List.of(new GenomicRegion("1", 2000, 1000, null, null)), true, true,
NO_ANNOTATIONS
)
);
assertThat(thrown.getMessage()).contains("Invalid genomic region");
}
@Test
@DisplayName("Start > End throws RuntimeException for select")
void testInvertedCoordinatesSelect() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.selectVariants(
List.of(new GenomicRegion("1", 2000, 1000, null, null)), true, true,
NO_ANNOTATIONS, null, null
)
);
assertThat(thrown.getMessage()).contains("Invalid genomic region");
}
@Test
@DisplayName("Null samples list throws RuntimeException for count in samples")
void testNullSamplesCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInSamples(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), null, true, true,
NO_ANNOTATIONS
)
);
assertThat(thrown.getMessage()).contains("Samples ID must not be empty");
}
@Test
@DisplayName("Empty samples list throws RuntimeException for count in samples")
void testEmptySamplesCount() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariantsInSamples(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), List.of(), true, true,
NO_ANNOTATIONS
)
);
assertThat(thrown.getMessage()).contains("Samples 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.countVariants(
List.of(new GenomicRegion(chromosome, 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS
)
);
assertThat(thrown.getMessage()).contains("Invalid Chromosome");
}
@Test
@DisplayName("Negative minVariantLengthBp throws RuntimeException")
void testNegativeMinVariantLengthThrows() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, -5, null)
)
);
assertThat(thrown.getMessage()).contains("'minVariantLengthBp' must be >= 0");
}
@Test
@DisplayName("Empty regions list throws RuntimeException")
void testEmptyRegionsList() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariants(
List.of(), true, true, NO_ANNOTATIONS
)
);
assertThat(thrown.getMessage()).contains("'regions' list cannot be empty");
}
@Test
@DisplayName("Null regions list throws RuntimeException")
void testNullRegionsList() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariants(
null, true, true, NO_ANNOTATIONS
)
);
assertThat(thrown.getMessage()).contains("'regions' list cannot be empty");
}
@Test
@DisplayName("Negative maxVariantLengthBp throws RuntimeException")
void testNegativeMaxVariantLengthThrows() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, null, -10)
)
);
assertThat(thrown.getMessage()).contains("'maxVariantLengthBp' must be >= 0");
}
@Test
@DisplayName("minVariantLengthBp > maxVariantLengthBp throws RuntimeException")
void testMinGreaterThanMaxVariantLengthThrows() {
RuntimeException thrown = org.junit.jupiter.api.Assertions.assertThrows(
RuntimeException.class,
() -> client.countVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
new SelectByAnnotations(null, null, null, null, null, null,
null, null, null, null, null, null,
null, null, null, null, null, null, null, 50, 10)
)
);
assertThat(thrown.getMessage()).contains("'minVariantLengthBp' must be <= 'maxVariantLengthBp'");
}
}
// ========================================
// 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("'position' must be >= 0");
}
@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("'position' must be >= 0");
}
@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("'position' must be >= 0");
}
}
// ========================================
// 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.selectVariantsInMultiRegions(any(AllelesInMultiRegionsRequest.class)))
.thenReturn(emptyIterator);
// Call with null limit
client.selectVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, null, null
);
// Verify the request was made with limit=50 (MAX_RETURNED_ITEMS)
verify(mockBlockingStub).selectVariantsInMultiRegions(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.selectVariantsInMultiRegions(any(AllelesInMultiRegionsRequest.class)))
.thenReturn(emptyIterator);
// Call with negative limit
client.selectVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, null, -1
);
verify(mockBlockingStub).selectVariantsInMultiRegions(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.selectVariantsInMultiRegions(any(AllelesInMultiRegionsRequest.class)))
.thenReturn(emptyIterator);
// Call with over limit
client.selectVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, null, 500
);
verify(mockBlockingStub).selectVariantsInMultiRegions(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.selectVariantsInMultiRegions(any(AllelesInMultiRegionsRequest.class)))
.thenReturn(emptyIterator);
// Call with valid limit
client.selectVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, null, 25
);
verify(mockBlockingStub).selectVariantsInMultiRegions(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.selectVariantsInMultiRegions(any(AllelesInMultiRegionsRequest.class)))
.thenReturn(emptyIterator);
client.selectVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, null, 50
);
verify(mockBlockingStub).selectVariantsInMultiRegions(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.selectVariantsInMultiRegions(any(AllelesInMultiRegionsRequest.class)))
.thenReturn(emptyIterator);
client.selectVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, -10, 50
);
verify(mockBlockingStub).selectVariantsInMultiRegions(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.selectVariantsInMultiRegions(any(AllelesInMultiRegionsRequest.class)))
.thenReturn(emptyIterator);
client.selectVariants(
List.of(new GenomicRegion("1", 1000, 2000, null, null)), true, true,
NO_ANNOTATIONS, 200, 50
);
verify(mockBlockingStub).selectVariantsInMultiRegions(argThat(request ->
request.getSkip() == 200
));
}
}
// ========================================
// ALPHA MISSENSE STAT RECORD TESTS
// ========================================
@Nested
@DisplayName("AlphaMissenseAvg Record Tests")
class AlphaMissenseAvgRecordTests {
@Test
@DisplayName("AlphaMissenseAvg record holds correct values")
void testAlphaMissenseAvgRecord() {
DnaerysClient.AlphaMissenseAvg stat = new DnaerysClient.AlphaMissenseAvg(0.65, 0.12, 100);
assertThat(stat.alphaMissenseMean()).isEqualTo(0.65);
assertThat(stat.alphaMissenseDeviation()).isEqualTo(0.12);
assertThat(stat.variantCount()).isEqualTo(100);
}
@Test
@DisplayName("AlphaMissenseAvg record equality")
void testAlphaMissenseAvgEquality() {
DnaerysClient.AlphaMissenseAvg stat1 = new DnaerysClient.AlphaMissenseAvg(0.65, 0.12, 100);
DnaerysClient.AlphaMissenseAvg stat2 = new DnaerysClient.AlphaMissenseAvg(0.65, 0.12, 100);
assertThat(stat1).isEqualTo(stat2);
}
}
// ========================================
// 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
);
}
}
}
