Examples with Beacon org.molgenis.beacon.config.Beacon used on opensource projects

Example 1 with Beacon

use of org.molgenis.beacon.config.Beacon in project molgenis by molgenis.

the class BeaconQueryServiceImpl method searchBeaconForQueryString.

private boolean searchBeaconForQueryString(String referenceName, Long start, String referenceBases, String alternateBases, String beaconId) {
    boolean exists = false;
    Beacon beacon = dataService.findOneById(BeaconMetadata.BEACON, beaconId, Beacon.class);
    if (beacon != null) {
        for (BeaconDataset beaconDataset : beacon.getDataSets()) {
            exists = queryBeaconDataset(beaconDataset, referenceName, start, referenceBases, alternateBases);
        }
    } else {
        throw new UnknownBeaconException(beaconId, BeaconAlleleRequest.create(referenceName, start, referenceBases, alternateBases));
    }
    return exists;
}

Example 2 with Beacon

use of org.molgenis.beacon.config.Beacon in project molgenis by molgenis.

the class BeaconQueryServiceTest method getQueryExistsTest.

@Test
public void getQueryExistsTest() {
    Beacon beacon = mock(Beacon.class);
    when(beacon.getDataSets()).thenReturn(Lists.newArrayList(dataset1, dataset2));
    when(dataService.findOneById(BeaconMetadata.BEACON, BEACON_ID, Beacon.class)).thenReturn(beacon);
    doReturn(0L).when(dataService).count("dataset1", query1);
    doReturn(1L).when(dataService).count("dataset2", query2);
    BeaconAlleleRequest request = BeaconAlleleRequest.create("1", 100L, "A", "T");
    BeaconAlleleResponse actualResponse = beaconQueryService.query("1", 100L, "A", "T", BEACON_ID);
    BeaconAlleleResponse expectedResponse = BeaconAlleleResponse.create(BEACON_ID, true, null, request);
    assertEquals(actualResponse, expectedResponse);
}

Example 3 with Beacon

use of org.molgenis.beacon.config.Beacon in project molgenis by molgenis.

the class BeaconQueryServiceTest method postQueryExistsTest.

@Test
public void postQueryExistsTest() {
    Beacon beacon = mock(Beacon.class);
    when(beacon.getDataSets()).thenReturn(Lists.newArrayList(dataset1, dataset2));
    when(dataService.findOneById(BeaconMetadata.BEACON, BEACON_ID, Beacon.class)).thenReturn(beacon);
    doReturn(0L).when(dataService).count("dataset1", query1);
    doReturn(1L).when(dataService).count("dataset2", query2);
    BeaconAlleleRequest request = BeaconAlleleRequest.create("1", 100L, "A", "T");
    BeaconAlleleResponse actualResponse = beaconQueryService.query(BEACON_ID, request);
    BeaconAlleleResponse expectedResponse = BeaconAlleleResponse.create(BEACON_ID, true, null, request);
    assertEquals(actualResponse, expectedResponse);
}

Example 4 with Beacon

use of org.molgenis.beacon.config.Beacon in project molgenis by molgenis.

the class BeaconQueryServiceTest method queryNotExistsTest.

@Test
public void queryNotExistsTest() {
    Beacon beacon = mock(Beacon.class);
    when(beacon.getDataSets()).thenReturn(Lists.newArrayList(dataset1, dataset2));
    when(dataService.findOneById(BeaconMetadata.BEACON, BEACON_ID, Beacon.class)).thenReturn(beacon);
    doReturn(0L).when(dataService).count("dataset1", query1);
    doReturn(0L).when(dataService).count("dataset2", query2);
    BeaconAlleleRequest request = BeaconAlleleRequest.create("1", 100L, "A", "T");
    BeaconAlleleResponse actualResponse = beaconQueryService.query(BEACON_ID, request);
    BeaconAlleleResponse expectedResponse = BeaconAlleleResponse.create(BEACON_ID, false, null, request);
    assertEquals(actualResponse, expectedResponse);
}

Example 5 with Beacon

use of org.molgenis.beacon.config.Beacon in project molgenis by molgenis.

the class BeaconInfoServiceTest method infoTest.

@Test
public void infoTest() {
    List<BeaconDatasetResponse> beaconDatasets = newArrayList(BeaconDatasetResponse.create("dataset", "DATA", ""));
    BeaconResponse beaconResponse = BeaconResponse.create("beacon", "My Beacon", "0.3.0", null, "", "", "", beaconDatasets);
    Beacon beacon = mock(Beacon.class);
    when(beacon.toBeaconResponse()).thenReturn(beaconResponse);
    when(dataService.findOneById(BEACON, "beacon", Beacon.class)).thenReturn(beacon);
    assertEquals(beaconInfoService.info("beacon"), beaconResponse);
}