List of usage examples for org.apache.commons.lang StringUtils center
public static String center(String str, int size, String padStr)
Centers a String in a larger String of size size.
From source file:org.isatools.isatab_v1.validator.ValidatorTest.java
@Test public void testValidatorDupeFiles() throws Exception { out.println("\n\n" + StringUtils.center("Testing validator for the dupe files case", 120, "-") + "\n"); String baseDir = System.getProperty("basedir"); String subDir = baseDir + "/target/test-classes/test-data/isatab/isatab_bii/JCastrillo-BII-I-1_duped_files"; GUIISATABValidator validator = new GUIISATABValidator(); GUIInvokerResult result = validator.validate(subDir); assertEquals("Validation should have failed!", GUIInvokerResult.ERROR, result); out.println("\n" + StringUtils.center("/end:Testing validator for the dupe files case", 120, "-") + "\n\n"); }
From source file:org.isatools.isatab_v1.validator.ValidatorTest.java
@Test public void testValidatorFieldOrder() throws Exception { out.println(// www .j a va2 s . com "\n\n" + StringUtils.center("Testing validator for the wrong field order case", 120, "-") + "\n"); String baseDir = System.getProperty("basedir"); String subDir = baseDir + "/target/test-classes/test-data/isatab/isatab_bii/JCastrillo-BII-I-1_wrong_field_order"; GUIISATABValidator validator = new GUIISATABValidator(); GUIInvokerResult result = validator.validate(subDir); assertEquals("Validation should have failed!", GUIInvokerResult.ERROR, result); out.println("\n" + StringUtils.center("/end:Testing validator for the wrong field order case", 120, "-") + "\n\n"); }
From source file:org.isatools.tablib.utils.logging.TabAppenderTest.java
@Test @SuppressWarnings("static-access") public void testTabAppender() { out.println("\n" + StringUtils.center(" Testing TabAppender ", 120, "-")); Logger log = Logger.getLogger(TabAppenderTest.class); // This is necessary in order to override external config. log.setLevel(Level.ALL);// w w w.j av a2s . c o m ListTabAppender app = new ListTabAppender(); final String APP_NAME = "testTabAppender"; app.setName(APP_NAME); app.setLayout(new PatternLayout("%d {%x} [%-5p] (%C{1},%L): %m%n")); app.setThreshold(Level.ALL); Logger rootLog = log.getRootLogger(); rootLog.setLevel(Level.ALL); rootLog.addAppender(app); TabNDC ndc = TabNDC.getInstance(); int ct = 0; ndc.pushFormat("fooFormat", "A Foo Test Format", "some/path"); log.debug("A debug message"); ct++; log.info("An info message"); ct++; Study study = new Study("Test Study"); study.setAcc("TEST:S:01"); ndc.pushObject(study); log.warn("A warn message "); ct++; log.warn("Another warn message"); ct++; ndc.popObject(); log.trace("Debug message, one step back in the NDC"); ct++; ndc.popTabDescriptor(); ListTabAppender app1 = (ListTabAppender) log.getRootLogger().getAppender(APP_NAME); assertTrue("log4j is not returing the correct appender!", app1 == app); List<TabLoggingEventWrapper> tlog = app1.getOutput(); for (TabLoggingEventWrapper tevent : tlog) { out.println("TAB CONTEXT: " + tevent.getTabDescriptors()); out.println("OBJECTS: " + TabNDC.getObjectDescriptions(tevent.getObjects())); out.println(tevent.getFormattedMessage()); out.println(StringUtils.repeat("-", 120) + "\n"); } assertEquals("Wrong no of recorded messages!", ct, tlog.size()); out.println(StringUtils.center(" /end:Testing TabAppender ", 120, "-") + "\n\n"); }
From source file:uk.ac.ebi.bioinvindex.unloading.PipelineUnloadingTest.java
@Test public void testBasics() { out.println("\n\n" + StringUtils.center(" Testing ISATAB unloader, basiscs ", 120, "-") + "\n"); SimplePipelineModel pip = new SimplePipelineModel(); Timestamp ts = new Timestamp(System.currentTimeMillis()); StudyPersister studyPersister = new StudyPersister(daoFactory, ts); AssayMaterialPersister assayMaterialPersister = new AssayMaterialPersister(daoFactory, ts); studyPersister.persist(pip.study);// w w w .j a v a 2 s .c o m assayMaterialPersister.persist(pip.assayMaterial1); commitTansaction(); session.flush(); AccessibleDAO<Accessible> adao = daoFactory.getAccessibleDAO(Accessible.class); OntologyEntryDAO<OntologyEntry> oedao = daoFactory.getOntologyEntryDAO(); assertNotNull("Ops! nsrc1 not saved!", adao.getByAcc(pip.nsrc1.getAcc())); assertNotNull("Ops! nsrc2 not saved!", adao.getByAcc(pip.nsrc2.getAcc())); assertNotNull("Ops! p1 not saved!", adao.getByAcc(pip.p1.getAcc())); assertNotNull("Ops! nas1 not saved!", adao.getByAcc(pip.nas1.getAcc())); assertNotNull("Ops! p2 not saved!", adao.getByAcc(pip.p2.getAcc())); assertNotNull("Ops! nar1 not saved!", adao.getByAcc(pip.nar1.getAcc())); assertNotNull("Ops! src1 not saved!", adao.getByAcc(pip.src1.getAcc())); assertNotNull("Ops! src2 not saved!", adao.getByAcc(pip.src2.getAcc())); assertNotNull("Ops! assay1 not saved!", adao.getByAcc(pip.assayMaterial1.getAcc())); assertNotNull("Ops! dt1 not saved!", adao.getByAcc(pip.dt1.getAcc())); assertNotNull("Ops! dt2 not saved!", adao.getByAcc(pip.dt2.getAcc())); assertNotNull("Ops! cv1 not saved!", pip.cv1.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv1.getClass()).getById(pip.cv1.getId())); assertNotNull("Ops! cv2 not saved!", pip.cv2.getId()); assertNotNull("Ops! cv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2.getClass()).getById(pip.cv2.getId())); assertNotNull("Ops! fv1 not saved!", pip.fv1.getId()); assertNotNull("Ops! fv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv1.getClass()).getById(pip.fv1.getId())); assertNotNull("Ops! fv2 not saved!", pip.fv2.getId()); assertNotNull("Ops! fv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv2.getClass()).getById(pip.fv2.getId())); assertNotNull("Ops! c1 not saved!", pip.c1.getId()); assertNotNull("Ops! c1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c1.getClass()).getById(pip.c1.getId())); assertNotNull("Ops! c2 not saved!", pip.c2.getId()); assertNotNull("Ops! c2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c2.getClass()).getById(pip.c2.getId())); assertNotNull("Ops! fact1 not saved!", pip.fact1.getId()); assertNotNull("Ops! fact1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact1.getClass()).getById(pip.fact1.getId())); assertNotNull("Ops! fact2 not saved!", pip.fact2.getId()); assertNotNull("Ops! fact2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact2.getClass()).getById(pip.fact2.getId())); assertNotNull("Ops! cv2UnitVal not saved!", pip.cv2UnitVal.getId()); assertNotNull("Ops! cv2UnitVal not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2UnitVal.getClass()).getById(pip.cv2UnitVal.getId())); assertNotNull("Ops! cv2Unit not saved!", pip.cv2Unit.getId()); assertNotNull("Ops! cv2Unit not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2Unit.getClass()).getById(pip.cv2Unit.getId())); ReferenceSource fooOntoDB = (ReferenceSource) adao.getByAcc(pip.fooOnto.getAcc()); assertNotNull("Ops! fooOnto not saved!", fooOntoDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, fooOntoDB.getId().longValue()); assertNotNull("Ops! srcRole not saved!", oedao.getByAcc(pip.srcRole.getAcc())); assertNotNull("Ops! assayRole not saved!", oedao.getByAcc(pip.assayRole.getAcc())); assertNotNull("Ops! dataType not saved!", oedao.getByAcc(pip.dataType.getAcc())); OntologyEntry c1OtDB = oedao.getByAcc(pip.c1Ot.getAcc()); assertNotNull("Ops! fooOnto not saved!", c1OtDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, c1OtDB.getId().longValue()); transaction.begin(); UnloadManager unloaderMgr = new UnloadManager(DaoFactory.getInstance(entityManager), ts); StudyUnloader unloader = (StudyUnloader) unloaderMgr.getUnloader(Study.class); unloader.queueByAcc(pip.study.getAcc()); unloaderMgr.delete(); transaction.commit(); session.flush(); out.println("\n ====> Unloading done, Warnings/Errors: " + unloaderMgr.getMessages()); checkAllUnloaded(ts); out.println("\n" + StringUtils.center(" /end: Testing ISATAB unloader, basiscs ", 120, "-") + "\n"); }
From source file:uk.ac.ebi.bioinvindex.unloading.PipelineUnloadingTest.java
@Test public void testWithProtocols() { out.println("\n\n" + StringUtils.center(" Testing ISATAB unloader, study+protocols ", 120, "-") + "\n"); ProtocolEquippedModel pip = new ProtocolEquippedModel(); Timestamp ts = new Timestamp(System.currentTimeMillis()); StudyPersister studyPersister = new StudyPersister(daoFactory, ts); AssayMaterialPersister assayMaterialPersister = new AssayMaterialPersister(daoFactory, ts); studyPersister.persist(pip.study);/*from www .j av a2s . c o m*/ assayMaterialPersister.persist(pip.assayMaterial1); commitTansaction(); session.flush(); AccessibleDAO<Accessible> adao = daoFactory.getAccessibleDAO(Accessible.class); OntologyEntryDAO<OntologyEntry> oedao = daoFactory.getOntologyEntryDAO(); assertNotNull("Ops! nsrc1 not saved!", adao.getByAcc(pip.nsrc1.getAcc())); assertNotNull("Ops! nsrc2 not saved!", adao.getByAcc(pip.nsrc2.getAcc())); assertNotNull("Ops! p1 not saved!", adao.getByAcc(pip.p1.getAcc())); assertNotNull("Ops! nas1 not saved!", adao.getByAcc(pip.nas1.getAcc())); assertNotNull("Ops! p2 not saved!", adao.getByAcc(pip.p2.getAcc())); assertNotNull("Ops! nar1 not saved!", adao.getByAcc(pip.nar1.getAcc())); assertNotNull("Ops! src1 not saved!", adao.getByAcc(pip.src1.getAcc())); assertNotNull("Ops! src2 not saved!", adao.getByAcc(pip.src2.getAcc())); assertNotNull("Ops! assay1 not saved!", adao.getByAcc(pip.assayMaterial1.getAcc())); assertNotNull("Ops! dt1 not saved!", adao.getByAcc(pip.dt1.getAcc())); assertNotNull("Ops! dt2 not saved!", adao.getByAcc(pip.dt2.getAcc())); assertNotNull("Ops! cv1 not saved!", pip.cv1.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv1.getClass()).getById(pip.cv1.getId())); assertNotNull("Ops! cv2 not saved!", pip.cv2.getId()); assertNotNull("Ops! cv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2.getClass()).getById(pip.cv2.getId())); assertNotNull("Ops! fv1 not saved!", pip.fv1.getId()); assertNotNull("Ops! fv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv1.getClass()).getById(pip.fv1.getId())); assertNotNull("Ops! fv2 not saved!", pip.fv2.getId()); assertNotNull("Ops! fv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv2.getClass()).getById(pip.fv2.getId())); assertNotNull("Ops! c1 not saved!", pip.c1.getId()); assertNotNull("Ops! c1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c1.getClass()).getById(pip.c1.getId())); assertNotNull("Ops! c2 not saved!", pip.c2.getId()); assertNotNull("Ops! c2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c2.getClass()).getById(pip.c2.getId())); assertNotNull("Ops! fact1 not saved!", pip.fact1.getId()); assertNotNull("Ops! fact1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact1.getClass()).getById(pip.fact1.getId())); assertNotNull("Ops! fact2 not saved!", pip.fact2.getId()); assertNotNull("Ops! fact2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact2.getClass()).getById(pip.fact2.getId())); assertNotNull("Ops! cv2UnitVal not saved!", pip.cv2UnitVal.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2UnitVal.getClass()).getById(pip.cv2UnitVal.getId())); assertNotNull("Ops! cv2Unit not saved!", pip.cv2Unit.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2Unit.getClass()).getById(pip.cv2Unit.getId())); assertNotNull("Ops! paramv1 not saved!", pip.paramv1.getId()); assertNotNull("Ops! paramv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv1.getClass()).getById(pip.paramv1.getId())); assertNotNull("Ops! paramv2 not saved!", pip.paramv2.getId()); assertNotNull("Ops! paramv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv2.getClass()).getById(pip.paramv2.getId())); assertNotNull("Ops! param1 not saved!", pip.param1.getId()); assertNotNull("Ops! param1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.param1.getClass()).getById(pip.param1.getId())); assertNotNull("Ops! param2 not saved!", pip.param2.getId()); assertNotNull("Ops! param2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.param2.getClass()).getById(pip.param2.getId())); assertNotNull("Ops! paramv2UnitVal not saved!", pip.paramv2UnitVal.getId()); assertNotNull("Ops! paramv2UnitVal not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv2UnitVal.getClass()).getById(pip.paramv2UnitVal.getId())); assertNotNull("Ops! paramv2Unit not saved!", pip.paramv2Unit.getId()); assertNotNull("Ops! paramv2Unit not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv2Unit.getClass()).getById(pip.paramv2Unit.getId())); assertNotNull("Ops! proto1 not saved!", adao.getByAcc(pip.proto1.getAcc())); assertNotNull("Ops! proto2 not saved!", adao.getByAcc(pip.proto2.getAcc())); ReferenceSource fooOntoDB = (ReferenceSource) adao.getByAcc(pip.fooOnto.getAcc()); assertNotNull("Ops! fooOnto not saved!", fooOntoDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, fooOntoDB.getId().longValue()); assertNotNull("Ops! srcRole not saved!", oedao.getByAcc(pip.srcRole.getAcc())); assertNotNull("Ops! assayRole not saved!", oedao.getByAcc(pip.assayRole.getAcc())); assertNotNull("Ops! dataType not saved!", oedao.getByAcc(pip.dataType.getAcc())); OntologyEntry c1OtDB = oedao.getByAcc(pip.c1Ot.getAcc()); assertNotNull("Ops! fooOnto not saved!", c1OtDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, c1OtDB.getId().longValue()); transaction.begin(); UnloadManager unloaderMgr = new UnloadManager(DaoFactory.getInstance(entityManager), ts); StudyUnloader unloader = (StudyUnloader) unloaderMgr.getUnloader(Study.class); unloader.queueByAcc(pip.study.getAcc()); unloaderMgr.delete(); transaction.commit(); session.flush(); out.println("\n ====> Unloading done, Warnings/Errors: " + unloaderMgr.getMessages()); checkAllUnloaded(ts); out.println("\n" + StringUtils.center(" /end: Testing ISATAB unloader, study+protocols ", 120, "-") + "\n"); }
From source file:uk.ac.ebi.bioinvindex.unloading.PipelineUnloadingTest.java
@Test public void testFullStudy() { out.println("\n\n" + StringUtils.center(" Testing ISATAB unloader, study+protocols+assays+ARs ", 120, "-") + "\n"); FullStudyPipelineModel pip = new FullStudyPipelineModel(); Timestamp ts = new Timestamp(System.currentTimeMillis()); StudyPersister studyPersister = new StudyPersister(daoFactory, ts); studyPersister.persist(pip.study);/*from w ww . j a v a2s .c o m*/ commitTansaction(); session.flush(); AccessibleDAO<Accessible> adao = daoFactory.getAccessibleDAO(Accessible.class); OntologyEntryDAO<OntologyEntry> oedao = daoFactory.getOntologyEntryDAO(); assertNotNull("Ops! nsrc1 not saved!", adao.getByAcc(pip.nsrc1.getAcc())); assertNotNull("Ops! nsrc2 not saved!", adao.getByAcc(pip.nsrc2.getAcc())); assertNotNull("Ops! p1 not saved!", adao.getByAcc(pip.p1.getAcc())); assertNotNull("Ops! nas1 not saved!", adao.getByAcc(pip.nas1.getAcc())); assertNotNull("Ops! p2 not saved!", adao.getByAcc(pip.p2.getAcc())); assertNotNull("Ops! nar1 not saved!", adao.getByAcc(pip.nar1.getAcc())); assertNotNull("Ops! src1 not saved!", adao.getByAcc(pip.src1.getAcc())); assertNotNull("Ops! src2 not saved!", adao.getByAcc(pip.src2.getAcc())); assertNotNull("Ops! assay1 not saved!", adao.getByAcc(pip.assayMaterial1.getAcc())); assertNotNull("Ops! dt1 not saved!", adao.getByAcc(pip.dt1.getAcc())); assertNotNull("Ops! dt2 not saved!", adao.getByAcc(pip.dt2.getAcc())); assertNotNull("Ops! cv1 not saved!", pip.cv1.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv1.getClass()).getById(pip.cv1.getId())); assertNotNull("Ops! cv2 not saved!", pip.cv2.getId()); assertNotNull("Ops! cv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2.getClass()).getById(pip.cv2.getId())); assertNotNull("Ops! fv1 not saved!", pip.fv1.getId()); assertNotNull("Ops! fv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv1.getClass()).getById(pip.fv1.getId())); assertNotNull("Ops! fv2 not saved!", pip.fv2.getId()); assertNotNull("Ops! fv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv2.getClass()).getById(pip.fv2.getId())); assertNotNull("Ops! c1 not saved!", pip.c1.getId()); assertNotNull("Ops! c1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c1.getClass()).getById(pip.c1.getId())); assertNotNull("Ops! c2 not saved!", pip.c2.getId()); assertNotNull("Ops! c2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c2.getClass()).getById(pip.c2.getId())); assertNotNull("Ops! fact1 not saved!", pip.fact1.getId()); assertNotNull("Ops! fact1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact1.getClass()).getById(pip.fact1.getId())); assertNotNull("Ops! fact2 not saved!", pip.fact2.getId()); assertNotNull("Ops! fact2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact2.getClass()).getById(pip.fact2.getId())); assertNotNull("Ops! cv2UnitVal not saved!", pip.cv2UnitVal.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2UnitVal.getClass()).getById(pip.cv2UnitVal.getId())); assertNotNull("Ops! cv2Unit not saved!", pip.cv2Unit.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2Unit.getClass()).getById(pip.cv2Unit.getId())); assertNotNull("Ops! paramv1 not saved!", pip.paramv1.getId()); assertNotNull("Ops! paramv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv1.getClass()).getById(pip.paramv1.getId())); assertNotNull("Ops! paramv2 not saved!", pip.paramv2.getId()); assertNotNull("Ops! paramv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv2.getClass()).getById(pip.paramv2.getId())); assertNotNull("Ops! param1 not saved!", pip.param1.getId()); assertNotNull("Ops! param1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.param1.getClass()).getById(pip.param1.getId())); assertNotNull("Ops! param2 not saved!", pip.param2.getId()); assertNotNull("Ops! param2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.param2.getClass()).getById(pip.param2.getId())); assertNotNull("Ops! paramv2UnitVal not saved!", pip.paramv2UnitVal.getId()); assertNotNull("Ops! paramv2UnitVal not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv2UnitVal.getClass()).getById(pip.paramv2UnitVal.getId())); assertNotNull("Ops! paramv2Unit not saved!", pip.paramv2Unit.getId()); assertNotNull("Ops! paramv2Unit not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.paramv2Unit.getClass()).getById(pip.paramv2Unit.getId())); assertNotNull("Ops! proto1 not saved!", adao.getByAcc(pip.proto1.getAcc())); assertNotNull("Ops! proto2 not saved!", adao.getByAcc(pip.proto2.getAcc())); ReferenceSource fooOntoDB = (ReferenceSource) adao.getByAcc(pip.fooOnto.getAcc()); assertNotNull("Ops! fooOnto not saved!", fooOntoDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, fooOntoDB.getId().longValue()); assertNotNull("Ops! srcRole not saved!", oedao.getByAcc(pip.srcRole.getAcc())); assertNotNull("Ops! assayRole not saved!", oedao.getByAcc(pip.assayRole.getAcc())); assertNotNull("Ops! dataType not saved!", oedao.getByAcc(pip.dataType.getAcc())); OntologyEntry c1OtDB = (OntologyEntry) oedao.getByAcc(pip.c1Ot.getAcc()); assertNotNull("Ops! fooOnto not saved!", c1OtDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, c1OtDB.getId().longValue()); assertNotNull("Ops! as1 not saved!", adao.getByAcc(pip.as1.getAcc())); assertNotNull("Ops! ar1 not saved!", pip.ar1.getId()); assertNotNull("Ops! ar1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.ar1.getClass()).getById(pip.ar1.getId())); assertNotNull("Ops! ar2 not saved!", pip.ar2.getId()); assertNotNull("Ops! ar2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.ar2.getClass()).getById(pip.ar2.getId())); for (PropertyValue<?> pv : pip.ar1.getCascadedPropertyValues()) { assertNotNull("Ops! pv not saved!", pv.getId()); assertNotNull("Ops! pv not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pv.getClass()).getById(pv.getId())); } for (PropertyValue<?> pv : pip.ar2.getCascadedPropertyValues()) { assertNotNull("Ops! pv not saved!", pv.getId()); assertNotNull("Ops! pv not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pv.getClass()).getById(pv.getId())); } assertTrue("Ops! ar1 does not contain fv1", pip.ar1.getCascadedPropertyValues().contains(pip.fv1)); assertTrue("Ops! ar1 does not contain fv2", pip.ar1.getCascadedPropertyValues().contains(pip.fv2)); transaction.begin(); UnloadManager unloaderMgr = new UnloadManager(DaoFactory.getInstance(entityManager), ts); StudyUnloader unloader = (StudyUnloader) unloaderMgr.getUnloader(Study.class); unloader.queueByAcc(pip.study.getAcc()); unloaderMgr.delete(); transaction.commit(); session.flush(); out.println("\n ====> Unloading done, Warnings/Errors: " + unloaderMgr.getMessages()); checkAllUnloaded(ts); out.println( "\n" + StringUtils.center(" /end: Testing ISATAB unloader, study+protocols+assays+ARs ", 120, "-") + "\n"); }
From source file:uk.ac.ebi.bioinvindex.unloading.PipelineUnloadingTest.java
@Test public void testLightPersistence() { out.println("\n\n" + StringUtils.center(" Testing ISATAB unloader, Light Persistence ", 120, "-") + "\n"); System.setProperty(Persister.LIGHT_PERSISTENCE_PROPERTY, "true"); FullStudyPipelineModel pip = new FullStudyPipelineModel(); Timestamp ts = new Timestamp(System.currentTimeMillis()); StudyPersister studyPersister = new StudyPersister(daoFactory, ts); studyPersister.persist(pip.study);/* w w w.j av a 2 s. c o m*/ commitTansaction(); session.flush(); AccessibleDAO<Accessible> adao = daoFactory.getAccessibleDAO(Accessible.class); OntologyEntryDAO<OntologyEntry> oedao = daoFactory.getOntologyEntryDAO(); assertNotNull("Ops! cv1 not saved!", pip.cv1.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv1.getClass()).getById(pip.cv1.getId())); assertNotNull("Ops! cv2 not saved!", pip.cv2.getId()); assertNotNull("Ops! cv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2.getClass()).getById(pip.cv2.getId())); assertNotNull("Ops! fv1 not saved!", pip.fv1.getId()); assertNotNull("Ops! fv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv1.getClass()).getById(pip.fv1.getId())); assertNotNull("Ops! fv2 not saved!", pip.fv2.getId()); assertNotNull("Ops! fv2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fv2.getClass()).getById(pip.fv2.getId())); assertNotNull("Ops! c1 not saved!", pip.c1.getId()); assertNotNull("Ops! c1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c1.getClass()).getById(pip.c1.getId())); assertNotNull("Ops! c2 not saved!", pip.c2.getId()); assertNotNull("Ops! c2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.c2.getClass()).getById(pip.c2.getId())); assertNotNull("Ops! fact1 not saved!", pip.fact1.getId()); assertNotNull("Ops! fact1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact1.getClass()).getById(pip.fact1.getId())); assertNotNull("Ops! fact2 not saved!", pip.fact2.getId()); assertNotNull("Ops! fact2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.fact2.getClass()).getById(pip.fact2.getId())); assertNotNull("Ops! cv2UnitVal not saved!", pip.cv2UnitVal.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2UnitVal.getClass()).getById(pip.cv2UnitVal.getId())); assertNotNull("Ops! cv2Unit not saved!", pip.cv2Unit.getId()); assertNotNull("Ops! cv1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.cv2Unit.getClass()).getById(pip.cv2Unit.getId())); assertNotNull("Ops! proto1 not saved!", adao.getByAcc(pip.proto1.getAcc())); assertNotNull("Ops! proto2 not saved!", adao.getByAcc(pip.proto2.getAcc())); ReferenceSource fooOntoDB = (ReferenceSource) adao.getByAcc(pip.fooOnto.getAcc()); assertNotNull("Ops! fooOnto not saved!", fooOntoDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, fooOntoDB.getId().longValue()); OntologyEntry c1OtDB = (OntologyEntry) oedao.getByAcc(pip.c1Ot.getAcc()); assertNotNull("Ops! fooOnto not saved!", c1OtDB); assertEquals("Ops! fooOnto #ID is wrong!", -1L, c1OtDB.getId().longValue()); assertNotNull("Ops! as1 not saved!", adao.getByAcc(pip.as1.getAcc())); assertNotNull("Ops! ar1 not saved!", pip.ar1.getId()); assertNotNull("Ops! ar1 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.ar1.getClass()).getById(pip.ar1.getId())); assertNotNull("Ops! ar2 not saved!", pip.ar2.getId()); assertNotNull("Ops! ar2 not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pip.ar2.getClass()).getById(pip.ar2.getId())); for (PropertyValue<?> pv : pip.ar1.getCascadedPropertyValues()) { assertNotNull("Ops! pv not saved!", pv.getId()); assertNotNull("Ops! pv not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pv.getClass()).getById(pv.getId())); } for (PropertyValue<?> pv : pip.ar2.getCascadedPropertyValues()) { assertNotNull("Ops! pv not saved!", pv.getId()); assertNotNull("Ops! pv not saved (retrieval test)!", daoFactory.getIdentifiableDAO(pv.getClass()).getById(pv.getId())); } assertTrue("Ops! ar1 does not contain fv1", pip.ar1.getCascadedPropertyValues().contains(pip.fv1)); assertTrue("Ops! ar1 does not contain fv2", pip.ar1.getCascadedPropertyValues().contains(pip.fv2)); transaction.begin(); UnloadManager unloaderMgr = new UnloadManager(DaoFactory.getInstance(entityManager), ts); StudyUnloader unloader = (StudyUnloader) unloaderMgr.getUnloader(Study.class); unloader.queueByAcc(pip.study.getAcc()); unloaderMgr.delete(); transaction.commit(); session.flush(); out.println("\n ====> Unloading done, Warnings/Errors: " + unloaderMgr.getMessages()); checkAllUnloaded(ts); out.println( "\n" + StringUtils.center(" /end: Testing ISATAB unloader, study+protocols+assays+ARs ", 120, "-") + "\n"); }