Examples with GenomeBrowserTrack org.molgenis.genomebrowser.GenomeBrowserTrack used on opensource projects

Example 6 with GenomeBrowserTrack

use of org.molgenis.genomebrowser.GenomeBrowserTrack in project molgenis by molgenis.

the class GenomeBrowserServiceTest method testGetReferenceTracksAll.

@Test
public void testGetReferenceTracksAll() {
    EntityType entity = mock(EntityType.class);
    when(entity.getLabel()).thenReturn("label");
    GenomeBrowserAttributes genomeBrowserAttributes = getGenomeBrowserAttributes("postion", "chrom", "normal", "mutant");
    GenomeBrowserTrack reference = GenomeBrowserTrack.create("ref_id", "label", "ref_label", entity, GenomeBrowserSettings.TrackType.VARIANT, null, GenomeBrowserSettings.MolgenisReferenceMode.NONE, genomeBrowserAttributes, null, null, null, null);
    EntityType molgenisEntity = mock(EntityType.class);
    when(molgenisEntity.getLabel()).thenReturn("label");
    GenomeBrowserTrack track = GenomeBrowserTrack.create("id", "label", "entityLabel", molgenisEntity, GenomeBrowserSettings.TrackType.VARIANT, Collections.singletonList(reference), GenomeBrowserSettings.MolgenisReferenceMode.ALL, genomeBrowserAttributes, "alert(\"test\")", "attr 1:attr1,reference attribute:REF,position on genome:POS", null, null);
    GenomeBrowserAttributes attrs1 = getGenomeBrowserAttributes("pos", "chr", "ref", "alt");
    GenomeBrowserAttributes attrs2 = getGenomeBrowserAttributes("POS", "CHROM", null, null);
    when(dataService.findAll(GenomeBrowserAttributesMetadata.GENOMEBROWSERATTRIBUTES, new QueryImpl<GenomeBrowserAttributes>().eq(GenomeBrowserAttributesMetadata.DEFAULT, true), GenomeBrowserAttributes.class)).thenReturn(Stream.of(attrs1, attrs2));
    EntityType type1 = mock(EntityType.class);
    EntityType type2 = mock(EntityType.class);
    EntityType type3 = mock(EntityType.class);
    Attribute labelAttr = mock(Attribute.class);
    when(labelAttr.getName()).thenReturn("refLabel");
    List<EntityType> types = new ArrayList<>();
    types.add(type1);
    when(type1.getIdValue()).thenReturn("type1");
    when(type1.getLabel()).thenReturn("label1");
    when(type1.getAttributeNames()).thenReturn(Arrays.asList("POS", "CHROM", "AAP", "NOOT", "MIES"));
    when(type1.getLabelAttribute()).thenReturn(labelAttr);
    types.add(type2);
    when(type2.getIdValue()).thenReturn("type2");
    when(type2.getLabel()).thenReturn("label2");
    when(type2.getAttributeNames()).thenReturn(Arrays.asList("pos", "chr", "ref", "alt", "aap"));
    when(type2.getLabelAttribute()).thenReturn(labelAttr);
    types.add(type3);
    when(type3.getIdValue()).thenReturn("type3");
    when(type3.getLabel()).thenReturn("label3");
    when(type3.getAttributeNames()).thenReturn(Arrays.asList("pos", "chr", "ref", "alternative", "monkey"));
    when(type3.getLabelAttribute()).thenReturn(labelAttr);
    MetaDataService metaDataService = mock(MetaDataService.class);
    when(dataService.getMeta()).thenReturn(metaDataService);
    when(metaDataService.getEntityTypes()).thenReturn(types.stream());
    Map<String, GenomeBrowserTrack> result = genomeBrowserService.getReferenceTracks(track);
    assertEquals(result.size(), 2);
    assertEquals(result.get("type2"), GenomeBrowserTrack.create("type2", "label2", "refLabel", type2, GenomeBrowserSettings.TrackType.VARIANT, Collections.emptyList(), GenomeBrowserSettings.MolgenisReferenceMode.ALL, attrs1, null, null, null, null));
    assertEquals(result.get("type1"), GenomeBrowserTrack.create("type1", "label1", "refLabel", type1, GenomeBrowserSettings.TrackType.VARIANT, Collections.emptyList(), GenomeBrowserSettings.MolgenisReferenceMode.ALL, attrs2, null, null, null, null));
}