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eva-server/src/test/java/uk/ac/ebi/eva/server/contigalias/ContigAliasServiceTest.java
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| package uk.ac.ebi.eva.server.contigalias; | ||
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| import org.junit.Before; | ||
| import org.junit.Test; | ||
| import org.mockito.InjectMocks; | ||
| import org.mockito.Mock; | ||
| import org.mockito.MockitoAnnotations; | ||
| import org.springframework.web.client.RestTemplate; | ||
| import uk.ac.ebi.eva.commons.core.models.Annotation; | ||
| import uk.ac.ebi.eva.commons.core.models.FeatureCoordinates; | ||
| import uk.ac.ebi.eva.commons.core.models.contigalias.ContigAliasChromosome; | ||
| import uk.ac.ebi.eva.commons.core.models.contigalias.ContigAliasEmbedded; | ||
| import uk.ac.ebi.eva.commons.core.models.contigalias.ContigAliasResponse; | ||
| import uk.ac.ebi.eva.commons.core.models.contigalias.ContigNamingConvention; | ||
| import uk.ac.ebi.eva.commons.core.models.ws.VariantWithSamplesAndAnnotation; | ||
| import uk.ac.ebi.eva.server.ws.contigalias.ContigAliasService; | ||
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| import java.util.Arrays; | ||
| import java.util.List; | ||
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| import static org.junit.Assert.assertEquals; | ||
| import static org.junit.Assert.assertFalse; | ||
| import static org.junit.Assert.assertTrue; | ||
| import static org.mockito.Mockito.anyString; | ||
| import static org.mockito.Mockito.eq; | ||
| import static org.mockito.Mockito.when; | ||
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| public class ContigAliasServiceTest { | ||
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| @Mock | ||
| private RestTemplate restTemplate; | ||
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| @InjectMocks | ||
| private ContigAliasService contigAliasService; | ||
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| private final String contigAliasUrl = "http://example.com"; | ||
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| @Before | ||
| public void setup() { | ||
| MockitoAnnotations.initMocks(this); | ||
| contigAliasService = new ContigAliasService(restTemplate, contigAliasUrl); | ||
| } | ||
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| @Test | ||
| public void testSkipContigTranslation() { | ||
| assertTrue(contigAliasService.skipContigTranslation(null)); | ||
| assertTrue(contigAliasService.skipContigTranslation(ContigNamingConvention.INSDC)); | ||
| assertTrue(contigAliasService.skipContigTranslation(ContigNamingConvention.NO_REPLACEMENT)); | ||
| assertFalse(contigAliasService.skipContigTranslation(ContigNamingConvention.UCSC)); | ||
| assertFalse(contigAliasService.skipContigTranslation(ContigNamingConvention.ENA_SEQUENCE_NAME)); | ||
| assertFalse(contigAliasService.skipContigTranslation(ContigNamingConvention.REFSEQ)); | ||
| } | ||
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| @Test | ||
| public void testGetVariantsWithTranslatedContig() { | ||
| List<VariantWithSamplesAndAnnotation> variantsList = Arrays.asList(new VariantWithSamplesAndAnnotation("1", 1000, 1005, | ||
| "A", "T", "rs1")); | ||
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| // skip translation | ||
| List<VariantWithSamplesAndAnnotation> result = contigAliasService | ||
| .getVariantsWithTranslatedContig(variantsList, ContigNamingConvention.INSDC); | ||
| assertEquals("1", result.get(0).getChromosome()); | ||
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| // no translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))) | ||
| .thenReturn(new ContigAliasResponse()); | ||
| result = contigAliasService | ||
| .getVariantsWithTranslatedContig(variantsList, ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("1", result.get(0).getChromosome()); | ||
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| // with translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))) | ||
| .thenReturn(getContigAliasResponse(ContigNamingConvention.ENA_SEQUENCE_NAME, "chr1")); | ||
| result = contigAliasService | ||
| .getVariantsWithTranslatedContig(variantsList, ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("chr1", result.get(0).getChromosome()); | ||
| } | ||
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| @Test | ||
| public void testGetFeatureCoordinatesWithTranslatedContig() { | ||
| List<FeatureCoordinates> featureCoordinatesList = Arrays.asList(new FeatureCoordinates("id", "fbx02", "feature", "1", 0, 1)); | ||
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| // skip translation | ||
| List<FeatureCoordinates> result = contigAliasService | ||
| .getFeatureCoordinatesWithTranslatedContig(featureCoordinatesList, ContigNamingConvention.INSDC); | ||
| assertEquals("1", result.get(0).getChromosome()); | ||
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| // no translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))).thenReturn(new ContigAliasResponse()); | ||
| result = contigAliasService.getFeatureCoordinatesWithTranslatedContig(featureCoordinatesList, ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("1", result.get(0).getChromosome()); | ||
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| // with translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))) | ||
| .thenReturn(getContigAliasResponse(ContigNamingConvention.ENA_SEQUENCE_NAME, "chr1")); | ||
| result = contigAliasService.getFeatureCoordinatesWithTranslatedContig(featureCoordinatesList, ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("chr1", result.get(0).getChromosome()); | ||
| } | ||
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| @Test | ||
| public void testGetAnnotationWithTranslatedContig() { | ||
| Annotation annotation = new Annotation("1", 0, 0, null, null, null, null); | ||
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| // skip translation | ||
| Annotation result = contigAliasService | ||
| .getAnnotationWithTranslatedContig(annotation, ContigNamingConvention.INSDC); | ||
| assertEquals("1", result.getChromosome()); | ||
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| // no translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))).thenReturn(new ContigAliasResponse()); | ||
| result = contigAliasService.getAnnotationWithTranslatedContig(annotation, ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("1", result.getChromosome()); | ||
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| // with translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))) | ||
| .thenReturn(getContigAliasResponse(ContigNamingConvention.ENA_SEQUENCE_NAME, "chr1")); | ||
| result = contigAliasService.getAnnotationWithTranslatedContig(annotation, ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("chr1", result.getChromosome()); | ||
| } | ||
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| @Test | ||
| public void testTranslateContigFromInsdc() { | ||
| // no translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))).thenReturn(new ContigAliasResponse()); | ||
| String translatedContig = contigAliasService.translateContigFromInsdc("1", ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("", translatedContig); | ||
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| // with translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))) | ||
| .thenReturn(getContigAliasResponse(ContigNamingConvention.ENA_SEQUENCE_NAME, "chr1")); | ||
| translatedContig = contigAliasService.translateContigFromInsdc("1", ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("chr1", translatedContig); | ||
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| } | ||
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| @Test | ||
| public void testTranslateContigToInsdc() { | ||
| // no translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))).thenReturn(new ContigAliasResponse()); | ||
| String translatedContig = contigAliasService.translateContigToInsdc("1", "asm1", null); | ||
| assertEquals("1", translatedContig); | ||
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| // with refseq translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))) | ||
| .thenReturn(getContigAliasResponse(ContigNamingConvention.INSDC, "chr1")); | ||
| translatedContig = contigAliasService.translateContigToInsdc("1", "asm1", ContigNamingConvention.REFSEQ); | ||
| assertEquals("chr1", translatedContig); | ||
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| // with ena_seq_name translation | ||
| when(restTemplate.getForObject(anyString(), eq(ContigAliasResponse.class))) | ||
| .thenReturn(getContigAliasResponse(ContigNamingConvention.INSDC, "chr1")); | ||
| translatedContig = contigAliasService.translateContigToInsdc("1", "asm1", ContigNamingConvention.ENA_SEQUENCE_NAME); | ||
| assertEquals("chr1", translatedContig); | ||
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| } | ||
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| private ContigAliasResponse getContigAliasResponse(ContigNamingConvention contigNamingConvention, String chromosome) { | ||
| ContigAliasChromosome contigAliasChromosome = new ContigAliasChromosome(); | ||
| switch (contigNamingConvention) { | ||
| case GENBANK_SEQUENCE_NAME: | ||
| contigAliasChromosome.setGenbankSequenceName(chromosome); | ||
| break; | ||
| case REFSEQ: | ||
| contigAliasChromosome.setRefseq(chromosome); | ||
| break; | ||
| case UCSC: | ||
| contigAliasChromosome.setUcscName(chromosome); | ||
| break; | ||
| case ENA_SEQUENCE_NAME: | ||
| contigAliasChromosome.setEnaSequenceName(chromosome); | ||
| break; | ||
| case INSDC: | ||
| contigAliasChromosome.setInsdcAccession(chromosome); | ||
| break; | ||
| } | ||
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| ContigAliasEmbedded contigAliasEmbedded = new ContigAliasEmbedded(); | ||
| contigAliasEmbedded.setContigAliasChromosomes(Arrays.asList(contigAliasChromosome)); | ||
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| ContigAliasResponse contigAliasResponse = new ContigAliasResponse(); | ||
| contigAliasResponse.setEmbedded(contigAliasEmbedded); | ||
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| return contigAliasResponse; | ||
| } | ||
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| } |