Examples with Entity org.molgenis.data.Entity used on opensource projects

Example 16 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class EntityUtilsTest method getIsNullValueMockEntity.

private Entity getIsNullValueMockEntity() {
    Entity entity = mock(Entity.class);
    when(entity.toString()).thenReturn("entity");
    return entity;
}

Example 17 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class AnnotationJobFactory method createJob.

@RunAsSystem
public AnnotationJob createJob(AnnotationJobExecution metaData) {
    dataService.add(ANNOTATION_JOB_EXECUTION, metaData);
    String annotatorNames = metaData.getAnnotators();
    String targetName = metaData.getTargetName();
    String username = metaData.getUser();
    // create an authentication to run as the user that is listed as the owner of the job
    RunAsUserToken runAsAuthentication = new RunAsUserToken("Job Execution", username, null, userDetailsService.loadUserByUsername(username).getAuthorities(), null);
    Repository<Entity> repository = dataService.getRepository(targetName);
    List<RepositoryAnnotator> availableAnnotators = annotationService.getAllAnnotators().stream().filter(RepositoryAnnotator::annotationDataExists).collect(toList());
    List<RepositoryAnnotator> requestedAnnotators = Arrays.stream(annotatorNames.split(",")).map(annotationService::getAnnotatorByName).collect(toList());
    AnnotatorDependencyOrderResolver resolver = new AnnotatorDependencyOrderResolver();
    List<RepositoryAnnotator> annotators = Lists.newArrayList(resolver.getAnnotatorSelectionDependencyList(availableAnnotators, requestedAnnotators, repository, entityTypeFactory));
    return new AnnotationJob(crudRepositoryAnnotator, username, annotators, repository, new ProgressImpl(metaData, jobExecutionUpdater, mailSender), runAsAuthentication, new TransactionTemplate(transactionManager));
}

Example 18 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class NegotiatorControllerTest method testValidateNegotiatorExport.

@Test
public void testValidateNegotiatorExport() {
    NegotiatorRequest request = NegotiatorRequest.create("http://molgenis.org", "molgenis_id_1", "*=q=MOLGENIS", "a nice molgenis query", "Sjfg03Msmdp92Md82103FNskas9H735F");
    Entity entity = mock(Entity.class);
    String entityOneLabel = "Entity One";
    when(entity.getLabelValue()).thenReturn(entityOneLabel);
    when(entity.get("enabled")).thenReturn(true);
    when(dataService.findAll("molgenis_id_1", molgenisQuery)).thenReturn(Stream.of(entity));
    when(jsMagmaScriptEvaluator.eval("$(enabled).value()", entity)).thenReturn(TRUE);
    ExportValidationResponse actual = negotiatorController.validateNegotiatorExport(request);
    List<String> enabledCollections = Collections.singletonList(entityOneLabel);
    ExportValidationResponse expected = ExportValidationResponse.create(true, "", enabledCollections, emptyList());
    assertEquals(actual, expected);
}

Example 19 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class NegotiatorControllerTest method testValidateNegotiatorExportEmptyCollections.

@Test
public void testValidateNegotiatorExportEmptyCollections() {
    NegotiatorRequest request = NegotiatorRequest.create("http://molgenis.org", "molgenis_id_1", "*=q=MOLGENIS", "a nice molgenis query", "Sjfg03Msmdp92Md82103FNskas9H735F");
    Entity entity = mock(Entity.class);
    when(entity.getLabelValue()).thenReturn("Entity One");
    when(entity.get("enabled")).thenReturn(true);
    when(dataService.findAll("molgenis_id_1", molgenisQuery)).thenReturn(Stream.empty());
    ExportValidationResponse actual = negotiatorController.validateNegotiatorExport(request);
    ExportValidationResponse expected = ExportValidationResponse.create(false, "Please make sure your selection contains at least 1 row that supports the negotiator.");
    assertEquals(actual, expected);
}

Example 20 with Entity

use of org.molgenis.data.Entity in project molgenis by molgenis.

the class NegotiatorControllerTest method testValidateNegotiatorExportAllCollectionsAreDisabled.

@Test
public void testValidateNegotiatorExportAllCollectionsAreDisabled() {
    NegotiatorRequest request = NegotiatorRequest.create("http://molgenis.org", "molgenis_id_1", "*=q=MOLGENIS", "a nice molgenis query", "Sjfg03Msmdp92Md82103FNskas9H735F");
    Entity entityDisabled = mock(Entity.class);
    String entityDisabledLabel = "Entity Disabled";
    when(entityDisabled.getLabelValue()).thenReturn(entityDisabledLabel);
    when(entityDisabled.get("enabled")).thenReturn(false);
    when(dataService.findAll("molgenis_id_1", molgenisQuery)).thenReturn(Stream.of(entityDisabled));
    when(jsMagmaScriptEvaluator.eval("$(enabled).value()", entityDisabled)).thenReturn(FALSE);
    ExportValidationResponse actual = negotiatorController.validateNegotiatorExport(request);
    List<String> disabledCollections = Collections.singletonList(entityDisabledLabel);
    ExportValidationResponse expected = ExportValidationResponse.create(false, "Please make sure your selection contains at least 1 row that supports the negotiator.", emptyList(), disabledCollections);
    assertEquals(actual, expected);
}