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

Example 1 with GenomeBrowserTrack

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

the class DataExplorerController method getTracksJson.

/**
 * Get readable genome entities
 */
private List<JSONObject> getTracksJson(Map<String, GenomeBrowserTrack> entityTracks) {
    Map<String, GenomeBrowserTrack> allTracks = new HashMap<>();
    allTracks.putAll(entityTracks);
    for (GenomeBrowserTrack track : entityTracks.values()) {
        allTracks.putAll(genomeBrowserService.getReferenceTracks(track));
    }
    return allTracks.values().stream().map(track -> track.toTrackJson()).collect(Collectors.toList());
}

Example 2 with GenomeBrowserTrack

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

the class DataExplorerController method getModule.

@GetMapping("/module/{moduleId}")
public String getModule(@PathVariable("moduleId") String moduleId, @RequestParam("entity") String entityTypeId, Model model) {
    EntityType selectedEntityType;
    Map<String, GenomeBrowserTrack> entityTracks;
    switch(moduleId) {
        case MOD_DATA:
            selectedEntityType = dataService.getMeta().getEntityTypeById(entityTypeId);
            entityTracks = genomeBrowserService.getGenomeBrowserTracks(selectedEntityType);
            model.addAttribute("genomeTracks", getTracksJson(entityTracks));
            // if multiple tracks are available we assume chrom and pos attribute are the same
            if (!entityTracks.isEmpty()) {
                // FIXME: how to do this cleaner
                GenomeBrowserTrack track = entityTracks.entrySet().iterator().next().getValue();
                model.addAttribute("pos_attr", track.getGenomeBrowserAttrs().getPos());
                model.addAttribute("chrom_attr", track.getGenomeBrowserAttrs().getChrom());
            }
            model.addAttribute("showDirectoryButton", directoryController.showDirectoryButton(entityTypeId));
            model.addAttribute("NegotiatorEnabled", directoryController.showDirectoryButton(entityTypeId));
            break;
        case MOD_ENTITIESREPORT:
            // TODO: figure out if we need to know pos and chrom attrs here
            selectedEntityType = dataService.getMeta().getEntityTypeById(entityTypeId);
            entityTracks = genomeBrowserService.getGenomeBrowserTracks(selectedEntityType);
            model.addAttribute("genomeTracks", getTracksJson(entityTracks));
            model.addAttribute("showDirectoryButton", directoryController.showDirectoryButton(entityTypeId));
            model.addAttribute("NegotiatorEnabled", directoryController.showDirectoryButton(entityTypeId));
            model.addAttribute("datasetRepository", dataService.getRepository(entityTypeId));
            model.addAttribute("viewName", dataExplorerSettings.getEntityReport(entityTypeId));
            break;
        case MOD_ANNOTATORS:
            // self-explanatory
            if (!permissionService.hasPermission(new EntityTypeIdentity(entityTypeId), EntityTypePermission.WRITEMETA)) {
                throw new MolgenisDataAccessException("No " + Permission.WRITEMETA + " permission on entity [" + entityTypeId + "], this permission is necessary run the annotators.");
            }
            Entity annotationRun = dataService.findOne(ANNOTATION_JOB_EXECUTION, new QueryImpl<>().eq(AnnotationJobExecutionMetaData.TARGET_NAME, entityTypeId).sort(new Sort(JobExecutionMetaData.START_DATE, Sort.Direction.DESC)));
            model.addAttribute("annotationRun", annotationRun);
            model.addAttribute("entityTypeId", entityTypeId);
            break;
    }
    // TODO bad request in case of invalid module id
    return "view-dataexplorer-mod-" + moduleId;
}

Example 3 with GenomeBrowserTrack

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

the class GenomeBrowserService method getGenomeBrowserTracks.

public Map<String, GenomeBrowserTrack> getGenomeBrowserTracks(EntityType entityType, List<GenomeBrowserAttributes> defaultGenomeBrowserAttributes) {
    Map<String, GenomeBrowserTrack> settings = new HashMap<>();
    dataService.findAll(GENOMEBROWSERSETTINGS, new QueryImpl<GenomeBrowserSettings>().eq(GenomeBrowserSettingsMetadata.ENTITY, entityType.getIdValue()), GenomeBrowserSettings.class).forEach(referenceSettings -> settings.put(referenceSettings.getIdentifier(), GenomeBrowserTrack.create(referenceSettings)));
    if (settings.isEmpty()) {
        // if not check if attrs match any default config
        Collections.sort(defaultGenomeBrowserAttributes);
        for (GenomeBrowserAttributes genomeBrowserAttributes : defaultGenomeBrowserAttributes) {
            List<String> attributeNames = Lists.newArrayList(entityType.getAttributeNames());
            if (areAllAttributeAvailable(genomeBrowserAttributes, attributeNames)) {
                GenomeBrowserTrack genomeBrowserTrack = getDefaultGenomeBrowserSettingsEntity(entityType, genomeBrowserAttributes);
                settings.put(genomeBrowserTrack.getId(), genomeBrowserTrack);
                break;
            }
        }
    }
    return settings;
}

Example 4 with GenomeBrowserTrack

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

the class GenomeBrowserServiceTest method testGetReferenceTracks.

@Test
public void testGetReferenceTracks() {
    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.ALL, genomeBrowserAttributes, null, null, null, null);
    EntityType molgenisEntity = mock(EntityType.class);
    GenomeBrowserTrack track = GenomeBrowserTrack.create("id", "label", "entityLabel", molgenisEntity, GenomeBrowserSettings.TrackType.VARIANT, Collections.singletonList(reference), GenomeBrowserSettings.MolgenisReferenceMode.CONFIGURED, genomeBrowserAttributes, "alert(\"test\")", "attr 1:attr1,reference attribute:REF,position on genome:POS", null, null);
    Map<String, GenomeBrowserTrack> result = genomeBrowserService.getReferenceTracks(track);
    assertEquals(result.size(), 1);
    assertEquals(result.get("ref_id"), reference);
}

Example 5 with GenomeBrowserTrack

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

the class GenomeBrowserServiceTest method testGetReferenceTracksNone.

@Test
public void testGetReferenceTracksNone() {
    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);
    GenomeBrowserTrack track = GenomeBrowserTrack.create("id", "label", "entityLabel", molgenisEntity, GenomeBrowserSettings.TrackType.VARIANT, Collections.singletonList(reference), GenomeBrowserSettings.MolgenisReferenceMode.NONE, genomeBrowserAttributes, "alert(\"test\")", "attr 1:attr1,reference attribute:REF,position on genome:POS", null, null);
    Map<String, GenomeBrowserTrack> result = genomeBrowserService.getReferenceTracks(track);
    assertEquals(result.size(), 0);
    verify(dataService, never()).getMeta();
}