Java tutorial
//====================================================================================== // Copyright 5AM Solutions Inc, Yale University // // Distributed under the OSI-approved BSD 3-Clause License. // See http://ncip.github.com/caarray/LICENSE.txt for details. //====================================================================================== package gov.nih.nci.caarray.web.action.project; import static org.junit.Assert.assertEquals; import static org.junit.Assert.assertFalse; import static org.junit.Assert.assertNotNull; import static org.junit.Assert.assertNull; import static org.junit.Assert.assertTrue; import static org.junit.Assert.fail; import gov.nih.nci.caarray.application.GenericDataService; import gov.nih.nci.caarray.application.GenericDataServiceStub; import gov.nih.nci.caarray.application.project.ProjectManagementService; import gov.nih.nci.caarray.application.project.ProjectManagementServiceStub; import gov.nih.nci.caarray.application.vocabulary.VocabularyService; import gov.nih.nci.caarray.application.vocabulary.VocabularyServiceStub; import gov.nih.nci.caarray.domain.data.DerivedArrayData; import gov.nih.nci.caarray.domain.data.RawArrayData; import gov.nih.nci.caarray.domain.file.CaArrayFile; import gov.nih.nci.caarray.domain.hybridization.Hybridization; import gov.nih.nci.caarray.domain.project.Project; import gov.nih.nci.caarray.domain.sample.Extract; import gov.nih.nci.caarray.domain.sample.LabeledExtract; import gov.nih.nci.caarray.security.PermissionDeniedException; import gov.nih.nci.caarray.test.data.magetab.MageTabDataFiles; import gov.nih.nci.caarray.util.j2ee.ServiceLocatorStub; import gov.nih.nci.caarray.web.AbstractDownloadTest; import gov.nih.nci.caarray.web.helper.DownloadHelper; import java.io.ByteArrayInputStream; import java.util.ArrayList; import java.util.Collections; import java.util.List; import java.util.zip.ZipEntry; import java.util.zip.ZipInputStream; import org.apache.commons.io.IOUtils; import org.junit.Before; import org.junit.Test; import com.fiveamsolutions.nci.commons.data.persistent.PersistentObject; import com.fiveamsolutions.nci.commons.web.struts2.action.ActionHelper; /** * @author Winston Cheng * */ public class ProjectLabeledExtractsActionTest extends AbstractDownloadTest { private final ProjectLabeledExtractsAction action = new ProjectLabeledExtractsAction(); private static LabeledExtract DUMMY_LABELED_EXTRACT = new LabeledExtract(); private static Extract DUMMY_EXTRACT = new Extract(); @SuppressWarnings("deprecation") @Before public void setUp() throws Exception { final ServiceLocatorStub locatorStub = ServiceLocatorStub.registerEmptyLocator(); locatorStub.addLookup(GenericDataService.JNDI_NAME, new LocalGenericDataService()); locatorStub.addLookup(ProjectManagementService.JNDI_NAME, new ProjectManagementServiceStub()); locatorStub.addLookup(VocabularyService.JNDI_NAME, new VocabularyServiceStub()); DUMMY_LABELED_EXTRACT.setId(1L); } @SuppressWarnings("deprecation") @Test public void testPrepare() throws Exception { // no current extract id this.action.prepare(); assertNull(this.action.getCurrentLabeledExtract().getId()); // valid current extract id LabeledExtract extract = new LabeledExtract(); extract.setId(1L); this.action.setCurrentLabeledExtract(extract); this.action.prepare(); assertEquals(DUMMY_LABELED_EXTRACT, this.action.getCurrentLabeledExtract()); // invalid current extract id extract = new LabeledExtract(); extract.setId(2L); this.action.setCurrentLabeledExtract(extract); try { this.action.prepare(); fail("Expected PermissionDeniedException"); } catch (final PermissionDeniedException pde) { } } @Test public void testCopy() { this.action.setCurrentLabeledExtract(DUMMY_LABELED_EXTRACT); assertEquals("list", this.action.copy()); } @Test public void testDelete() { DUMMY_EXTRACT.getLabeledExtracts().add(DUMMY_LABELED_EXTRACT); DUMMY_LABELED_EXTRACT.getExtracts().add(DUMMY_EXTRACT); this.action.setCurrentLabeledExtract(DUMMY_LABELED_EXTRACT); assertEquals("list", this.action.delete()); assertFalse(DUMMY_EXTRACT.getLabeledExtracts().contains(DUMMY_LABELED_EXTRACT)); DUMMY_LABELED_EXTRACT.getHybridizations().add(new Hybridization()); this.action.setCurrentLabeledExtract(DUMMY_LABELED_EXTRACT); assertEquals("list", this.action.delete()); assertTrue(ActionHelper.getMessages().contains("experiment.annotations.cantdelete")); } @Test public void testDownload() throws Exception { assertEquals("noLabeledExtractData", this.action.download()); final CaArrayFile rawFile = this.fasStub.add(MageTabDataFiles.MISSING_TERMSOURCE_IDF); final CaArrayFile derivedFile = this.fasStub.add(MageTabDataFiles.MISSING_TERMSOURCE_SDRF); final Project p = new Project(); p.getExperiment().setPublicIdentifier("test"); final LabeledExtract le = new LabeledExtract(); final Hybridization h1 = new Hybridization(); le.getHybridizations().add(h1); final Hybridization h2 = new Hybridization(); le.getHybridizations().add(h2); final RawArrayData raw = new RawArrayData(); h1.addArrayData(raw); final DerivedArrayData derived = new DerivedArrayData(); h2.getDerivedDataCollection().add(derived); raw.setDataFile(rawFile); derived.setDataFile(derivedFile); this.action.setCurrentLabeledExtract(le); this.action.setProject(p); final List<CaArrayFile> files = new ArrayList<CaArrayFile>(le.getAllDataFiles()); Collections.sort(files, DownloadHelper.CAARRAYFILE_NAME_COMPARATOR_INSTANCE); assertEquals(2, files.size()); assertEquals("missing_term_source.idf", files.get(0).getName()); assertEquals("missing_term_source.sdrf", files.get(1).getName()); this.action.download(); assertEquals("application/zip", this.mockResponse.getContentType()); assertEquals("filename=\"caArray_test_files.zip\"", this.mockResponse.getHeader("Content-disposition")); final ZipInputStream zis = new ZipInputStream( new ByteArrayInputStream(this.mockResponse.getContentAsByteArray())); ZipEntry ze = zis.getNextEntry(); assertNotNull(ze); assertEquals("missing_term_source.idf", ze.getName()); ze = zis.getNextEntry(); assertNotNull(ze); assertEquals("missing_term_source.sdrf", ze.getName()); assertNull(zis.getNextEntry()); IOUtils.closeQuietly(zis); } @Test public void testSave() { final Extract toAdd = new Extract(); final List<Extract> addList = new ArrayList<Extract>(); addList.add(toAdd); this.action.setItemsToAssociate(addList); final Extract toRemove = new Extract(); toRemove.getLabeledExtracts().add(DUMMY_LABELED_EXTRACT); final List<Extract> removeList = new ArrayList<Extract>(); removeList.add(toRemove); this.action.setItemsToRemove(removeList); this.action.setCurrentLabeledExtract(DUMMY_LABELED_EXTRACT); assertEquals(ProjectTabAction.RELOAD_PROJECT_RESULT, this.action.save()); assertTrue(ActionHelper.getMessages().contains("experiment.items.updated")); assertTrue(toAdd.getLabeledExtracts().contains(DUMMY_LABELED_EXTRACT)); assertFalse(toRemove.getLabeledExtracts().contains(DUMMY_LABELED_EXTRACT)); } private static class LocalGenericDataService extends GenericDataServiceStub { @SuppressWarnings("unchecked") @Override public <T extends PersistentObject> T getPersistentObject(Class<T> entityClass, Long entityId) { if (entityClass.equals(LabeledExtract.class) && entityId.equals(1L)) { return (T) DUMMY_LABELED_EXTRACT; } return null; } } }