Examples with BioSamplesClient uk.ac.ebi.biosamples.client.BioSamplesClient used on opensource projects

Example 1 with BioSamplesClient

use of uk.ac.ebi.biosamples.client.BioSamplesClient in project biosamples-v4 by EBIBioSamples.

the class NcbiElementCallableTest method should_extract_double_organism_if_organism_is_in_description_with_null_amr_map.

@Test
public void should_extract_double_organism_if_organism_is_in_description_with_null_amr_map() throws Exception {
    ArgumentCaptor<Sample> generatedSample = ArgumentCaptor.forClass(Sample.class);
    when(bioSamplesClient.persistSampleResource(generatedSample.capture())).thenReturn(null);
    NcbiSampleConversionService ncbiSampleConversionService = new NcbiSampleConversionService(taxonService);
    NcbiElementCallable callable = new NcbiElementCallable(ncbiSampleConversionService, bioSamplesClient, sample, "test", null);
    callable.call();
    Sample sample = generatedSample.getValue();
    List<Attribute> organisms = sample.getAttributes().stream().filter(attr -> attr.getType().equalsIgnoreCase("organism")).collect(Collectors.toList());
    assertThat(organisms).hasSize(2);
    assertThat(organisms.stream().anyMatch(organism -> organism.getValue().equals("Oryza sativa Japonica Group")));
    assertThat(organisms.stream().anyMatch(organism -> organism.getValue().equals("Oryza sativa")));
}

Example 2 with BioSamplesClient

use of uk.ac.ebi.biosamples.client.BioSamplesClient in project biosamples-v4 by EBIBioSamples.

the class NcbiElementCallableTest method should_extract_double_organism_if_organism_is_in_description.

@Test
public void should_extract_double_organism_if_organism_is_in_description() throws Exception {
    ArgumentCaptor<Sample> generatedSample = ArgumentCaptor.forClass(Sample.class);
    when(bioSamplesClient.persistSampleResource(generatedSample.capture())).thenReturn(null);
    NcbiSampleConversionService ncbiSampleConversionService = new NcbiSampleConversionService(taxonService);
    NcbiElementCallable callable = new NcbiElementCallable(ncbiSampleConversionService, bioSamplesClient, sample, "test", new HashMap<>());
    callable.call();
    Sample sample = generatedSample.getValue();
    List<Attribute> organisms = sample.getAttributes().stream().filter(attr -> attr.getType().equalsIgnoreCase("organism")).collect(Collectors.toList());
    assertThat(organisms).hasSize(2);
    assertThat(organisms.stream().anyMatch(organism -> organism.getValue().equals("Oryza sativa Japonica Group")));
    assertThat(organisms.stream().anyMatch(organism -> organism.getValue().equals("Oryza sativa")));
}