List of usage examples for org.apache.commons.collections CollectionUtils find
public static Object find(Collection collection, Predicate predicate)
From source file:uk.ac.ebi.bioinvindex.persistence.PropertyValuePersistenceTest.java
@Test public void testPersistValue() throws Exception { out.println(/*from w w w.j a v a 2 s .co m*/ "\n\n\n _______________ PropertyValuePersistanceTest, Basic Test ____________________________\n"); Characteristic prop = new Characteristic("Foo Property", 0); // New OE ReferenceSource source = new ReferenceSource("My fancy test ontology 2"); source.setAcc("bii:tests:MY-SRC-2"); OntologyTerm oe1 = new OntologyTerm("biionto:101", "test OE", source); prop.addOntologyTerm(oe1); // Existing OE source = new ReferenceSource("TEST ONTOLOGY"); source.setAcc("BII-1"); OntologyTerm oe2 = new OntologyTerm("OBI-EO1", "organism", source); prop.addOntologyTerm(oe2); // The Value CharacteristicValue value = new CharacteristicValue("Foo Value", prop); // Let's persist CharacteristicValue valueNew = persister.persist(value); transaction.commit(); assertNotNull("Uh! Oh! Persister returns null!", valueNew); assertTrue("Ouch! Cannot find the persisted value in the DB!", entityManager.contains(valueNew)); assertTrue("Argh! The persisted value and the original one should be the same!", value == valueNew); assertNotNull("Burp! The persisted value should have an ID!", valueNew.getId()); Characteristic typeNew = valueNew.getType(); assertNotNull("Urp! Saved Value has no type!", typeNew); assertNotNull("Urp! Type of Saved Value should have an ID!", typeNew.getId()); assertEquals("Urp! Type of Saved Value has wrong value", "Foo Property", typeNew.getValue()); Collection<OntologyTerm> oes = typeNew.getOntologyTerms(); assertNotNull("Oh no! The persisted value does not return OEs!", oes); assertEquals("Oh no! The persisted value does not return correct no. of OEs !", 2, oes.size()); OntologyTerm oeDB1 = (OntologyTerm) CollectionUtils.find(oes, new OESelector(oe1)); assertNotNull("Urp! The term " + oe1 + "was not persisted with the value!", oeDB1); assertNotNull("The term: " + oeDB1 + "should have an ID!", oeDB1); OntologyTerm oeDB2 = (OntologyTerm) CollectionUtils.find(oes, new OESelector(oe2)); assertNotNull("Urp! The term " + oe2 + "was not persisted with the value!", oeDB2); assertEquals("Wrong retrieved ID for the term : " + oeDB2 + "!", new Long(501), oeDB2.getId()); out.println("Saved Value:" + valueNew); out.println( "\n _______________ /end: PropertyValuePersistanceTest, Basic Test ____________________________\n\n"); }
From source file:uk.ac.ebi.bioinvindex.persistence.ProtocolPersistenceTest.java
@Test public void testPersistNew() throws Exception { out.println(//from w ww .j a va2 s. c o m "\n\n\n _______________ ProtocolPersistanceTest, Testing new Protocol ____________________________\n"); ReferenceSource source = new ReferenceSource("My fancy test ontology 2"); source.setAcc("bii:tests:MY-SRC-2"); ProtocolType type = new ProtocolType("proto:type:999", "My Test Proto Type", source); Protocol protocol = new Protocol("A-NEW-PROTO-99", type); protocol.setAcc(protocol.getName()); transaction.commit(); // Let's attach few parameters // Parameter param1 = new Parameter("Time Before Killing the Operator", 0); ReferenceSource sourceOE1 = new ReferenceSource("My fancy test ontology 3"); sourceOE1.setAcc("bii:tests:MY-SRC-3"); OntologyTerm oe1 = new OntologyTerm("biionto:101", "test OE", source); param1.addOntologyTerm(oe1); protocol.addParameter(param1); Parameter param2 = new Parameter("Time To get rid of the corpse", 1); ReferenceSource sourceOE2 = new ReferenceSource("101 Ontology"); sourceOE2.setAcc("BII-101"); OntologyTerm oe2 = new OntologyTerm("test:101", "Time", sourceOE2); param2.addOntologyTerm(oe2); protocol.addParameter(param2); // Let's attach few components // ProtocolComponent comp1 = new ProtocolComponent("Chain saw"); ReferenceSource sourceOE3 = new ReferenceSource("My fancy test ontology 3"); sourceOE3.setAcc("bii:tests:MY-SRC-33"); OntologyTerm oe3 = new OntologyTerm("biionto:303", "test OE", source); comp1.addOntologyTerm(oe3); protocol.addComponent(comp1); ProtocolComponent comp2 = new ProtocolComponent("Chain saw"); comp2.addOntologyTerm(oe2); protocol.addComponent(comp2); transaction.begin(); Protocol protocolDB = persister.persist(protocol); transaction.commit(); assertNotNull("Uh! No object returned by the persister!", protocolDB); assertEquals("Gosh! The persister should return the same persisted object!", protocol, protocolDB); assertNotNull("Argh! The persisted protocol should have a non null ID", protocol.getId()); assertTrue("Uhm... The returned object apparently is not in the DB", entityManager.contains(protocolDB)); assertNotNull("The New Protocol should have a non null accession!", protocolDB.getAcc()); // Type // ProtocolType typeDB = protocolDB.getType(); assertNotNull("Urp! No type persisted for the protocol!", protocolDB); assertNotNull("Ouch! The persisted protocol type should have a non null ID", type.getId()); assertTrue("Ouch! The protocol type is not in the DB!", entityManager.contains(typeDB)); assertEquals("Argh! The persisted type should be == the initial one", type, typeDB); ReferenceSource typeSrcDB = typeDB.getSource(); assertNotNull("Argh! Persisted protocol type has not a source!", typeSrcDB); assertTrue("Ouch! The protocol type is not in the DB!", entityManager.contains(typeDB)); assertEquals("Urp! Persisted protocol type has bad source", source.getName(), typeSrcDB.getName()); // Parameters // Collection<Parameter> params = protocolDB.getParameters(); assertNotNull("Oh no! No parameter from the persisted protocol!", params); assertEquals("Oh no! The persisted protocol does not return correct no. of params !", 2, params.size()); // Param 1 FreeTextTerm param1DB = (FreeTextTerm) CollectionUtils.find(params, new FreeTextSelector(param1)); assertNotNull("Urp! The param " + param1 + " was not persisted with the protocol!", param1DB); assertNotNull("The term: " + param1DB + "should have an ID!", param1DB); Collection<OntologyTerm> oes1 = param1DB.getOntologyTerms(); assertNotNull("Oh no! The persisted parameter" + param1DB + " does not return OEs!", oes1); assertEquals("Oh no! The persisted parameter does not return correct no. of OEs !", 1, oes1.size()); // Param 2 FreeTextTerm param2DB = (FreeTextTerm) CollectionUtils.find(params, new FreeTextSelector(param2)); assertNotNull("Urp! The param " + param2 + " was not persisted with the protocol!", param2DB); assertNotNull("The term: " + param2DB + "should have an ID!", param2DB.getId()); Collection<OntologyTerm> oes2 = param2DB.getOntologyTerms(); assertNotNull("Oh no! The persisted parameter" + param2DB + " does not return OEs!", oes2); assertEquals("Oh no! The persisted parameter" + param2DB + " does not return correct no. of OEs !", 1, oes2.size()); OntologyTerm oeDB2 = oes2.iterator().next(); assertEquals("Urp! The term " + oe2 + "was not persisted with the Parameter!", oe2.getAcc(), oeDB2.getAcc()); assertEquals("Wrong retrieved ID for the term : " + oeDB2 + "!", new Long(507), oeDB2.getId()); // Components // Collection<ProtocolComponent> comps = protocolDB.getComponents(); assertNotNull("Oh no! No component from the persisted protocol!", comps); assertEquals("Oh no! The persisted protocol does not return correct no. of components!", 2, comps.size()); // Component 1 FreeTextTerm comp1DB = (FreeTextTerm) CollectionUtils.find(comps, new FreeTextSelector(comp1)); assertNotNull("Urp! The component " + comp1 + " was not persisted with the protocol!", comp1DB); assertNotNull("The term: " + param1DB + "should have an ID!", comp1DB); Collection<OntologyTerm> coes1 = comp1DB.getOntologyTerms(); assertNotNull("Oh no! The persisted parameter" + comp1DB + " does not return OEs!", coes1); assertEquals("Oh no! The persisted component does not return correct no. of OEs !", 1, coes1.size()); // Component 2 FreeTextTerm comp2DB = (FreeTextTerm) CollectionUtils.find(comps, new FreeTextSelector(comp2)); assertNotNull("Urp! The param " + param2 + "was not persisted with the protocol!", comp2DB); assertNotNull("The term: " + comp2DB + "should have an ID!", comp2DB.getId()); Collection<OntologyTerm> coes2 = param2DB.getOntologyTerms(); assertNotNull("Oh no! The persisted parameter" + comp2DB + " does not return OEs!", coes2); assertEquals("Oh no! The persisted parameter" + comp2DB + " does not return correct no. of OEs !", 1, coes2.size()); OntologyTerm coeDB2 = coes2.iterator().next(); assertEquals("Urp! The term " + oe2 + "was not persisted with the Component!", oe2.getAcc(), oeDB2.getAcc()); assertEquals("Wrong retrieved ID for the component term : " + coeDB2 + "!", new Long(507), coeDB2.getId()); out.println( "\n _______________ /end: ProtocolPersistanceTest, Testing new Protocol ____________________________\n\n"); }
From source file:uk.ac.ebi.bioinvindex.persistence.ProtocolPersistenceTest.java
@Test public void testPersistExisting() throws Exception { out.println(//from w w w . java 2 s . com "\n\n\n _______________ ProtocolPersistanceTest, Testing existing Protocol ____________________________\n"); Protocol protocol = new Protocol(null, null); protocol.setAcc("bii:proto:999"); Protocol protocolDB = persister.persist(protocol); transaction.commit(); assertNotNull("Uh! No object returned by the persister!", protocolDB); assertTrue("Gosh! The persister should return a different existing protocol!", protocol != protocolDB); assertEquals("Argh! Bad ID for the persisted protocol", new Long(-10), protocolDB.getId()); assertTrue("Uhm... The returned object apparently is not in the DB", entityManager.contains(protocolDB)); // Type ProtocolType typeDB = protocolDB.getType(); assertNotNull("Urp! No type persisted for the protocol!", protocolDB); assertEquals("Ouch! Bad ID for the persisted Protocol Type", new Long(506), typeDB.getId()); assertTrue("Ouch! The protocol type is not in the DB!", entityManager.contains(typeDB)); // Parameters // Collection<Parameter> params = protocolDB.getParameters(); assertNotNull("Oh no! No param types from the persisted protocol!", params); assertEquals("Oh no! The persisted protocol does not return correct no. of params !", 2, params.size()); // Param 1 Parameter param1 = new Parameter(null, 0); param1.setId(new Long(-1)); FreeTextTerm param1DB = (FreeTextTerm) CollectionUtils.find(params, new FreeTextSelector(param1)); assertNotNull("Urp! The existing protocol should have parameter " + param1 + "!", param1DB); Collection<OntologyTerm> oes1 = param1DB.getOntologyTerms(); assertNotNull("Oh no! The persisted parameter" + param1DB + " does not return OEs!", oes1); assertEquals("Oh no! The persisted FreeTextTerm does not return correct no. of OEs !", 1, oes1.size()); OntologyTerm oeDB1 = oes1.iterator().next(); assertEquals("Wrong retrieved ID for the term : " + oeDB1 + "!", new Long(-2), oeDB1.getId()); // Param 2 Parameter param2 = new Parameter(null, 0); param2.setId(new Long(-2)); FreeTextTerm param2DB = (FreeTextTerm) CollectionUtils.find(params, new FreeTextSelector(param2)); assertNotNull("Urp! The param " + param2 + "was not persisted with the protocol!", param2DB); Collection<OntologyTerm> oes2 = param2DB.getOntologyTerms(); assertNotNull("Oh no! The persisted parameter" + param2DB + " does not return OEs!", oes2); assertEquals("Oh no! The persisted parameter" + param2DB + " does not return correct no. of OEs !", 1, oes2.size()); OntologyTerm oeDB2 = oes2.iterator().next(); assertEquals("Wrong retrieved ID for the term : " + oeDB2 + "!", new Long(507), oeDB2.getId()); out.println( "\n _______________ /end: ProtocolPersistanceTest, Testing existing Protocol ____________________________\n\n"); }
From source file:uk.ac.ebi.bioinvindex.persistence.StudyPersistenceTest.java
@Test public void testPersistBasic() throws Exception { out.println(//www .j av a2 s . c o m "\n\n\n _______________ StudyPersistanceTest, Testing new Study ____________________________\n"); Study study = new Study("My super-scientific experiment"); Design design = new Design("Whip the operator to see its performance improves"); ReferenceSource designSource = new ReferenceSource("TEST ONTOLOGY"); designSource.setAcc("BII-1"); OntologyTerm oe = new OntologyTerm("biionto:OperatorPerturbationDesign", "Operator Perturbation Design", designSource); design.addOntologyTerm(oe); study.addDesign(design); design = new Design("Whip the PI too if nothing changes"); study.addDesign(design); // Protocol 1 (does not exist) ReferenceSource source = new ReferenceSource("My fancy test ontology 2"); source.setAcc("bii:tests:MY-SRC-2"); ProtocolType type = new ProtocolType("proto:type:999", "My Test Proto Type", source); Protocol protocol1 = new Protocol("My New Protocol", type); protocol1.setAcc("A-NEW-PROTO-99"); // Let's attach some parameters Parameter param1 = new Parameter("Time Before Killing the Operator", 0); ReferenceSource sourceOE1 = new ReferenceSource("My fancy test ontology 3"); sourceOE1.setAcc("bii:tests:MY-SRC-3"); OntologyTerm oe1 = new OntologyTerm("biionto:101", "test OE", source); param1.addOntologyTerm(oe1); protocol1.addParameter(param1); Parameter param2 = new Parameter("Time To get rid of the corpse", 1); ReferenceSource sourceOE2 = new ReferenceSource("101 Ontology"); sourceOE2.setAcc("BII-101"); OntologyTerm oe2 = new OntologyTerm("test:101", "Time", sourceOE2); param2.addOntologyTerm(oe2); protocol1.addParameter(param2); study.addProtocol(protocol1); // Protocol 2 (exists) Protocol protocol2 = new Protocol(null, null); protocol2.setAcc("bii:proto:999"); study.addProtocol(protocol2); // Contacts Contact contact = new Contact("Mr", null, "Foo", "someone@somewhere.net"); ReferenceSource roleSrc = new ReferenceSource(null); roleSrc.setAcc("BII-1"); ContactRole contactRole = new ContactRole("bii:fooContactRole", "My Contact Role", roleSrc); contact.addRole(contactRole); contactRole = new ContactRole("bii:fooContactRole1", "My Contact Role 1", roleSrc); contact.addRole(contactRole); study.addContact(contact); // TODO: publications, needs role persistence // Let's go with the persistence job! // Study studyDB = persister.persist(study); transaction.commit(); assertNotNull("Oh! No study returned by the persister!", studyDB); assertEquals("Ouch! The study rerturned by the persister should be the original one!", study, studyDB); assertTrue("Argh! Cannot find the persisted study in the DB!", entityManager.contains(studyDB)); assertNotNull("Urp! The study should have an ID", studyDB.getId()); Collection<Design> designsDB = studyDB.getDesigns(); assertNotNull("Ops! The retuned study has no a design!", designsDB); assertEquals("Oh no! Bad no. of designs persisted!", 2, designsDB.size()); for (Design designDB : designsDB) assertNotNull("Urp! The study design should have an ID", designDB.getId()); final String dval = "Whip the operator to see its performance improves"; Design designDB = (Design) CollectionUtils.find(designsDB, new Predicate() { public boolean evaluate(Object object) { return dval.equals(((Design) object).getValue()); } }); assertNotNull("Arg! I cannot find a design which shoulb have been persisted ('" + dval + "')", designDB); Collection<OntologyTerm> oesDesign = designDB.getOntologyTerms(); assertNotNull("Oh no! The persisted parameter" + designDB + " does not return OEs!", oesDesign); assertEquals("Oh no! The persisted FreeTextTerm does not return correct no. of OEs !", 1, oesDesign.size()); OntologyTerm oeDB1 = oesDesign.iterator().next(); assertEquals("Wrong retrieved ID for the term : " + oeDB1 + "!", new Long(-3), oeDB1.getId()); assertEquals("Oh no! The retrieved study design's OE has bad accession!", "biionto:OperatorPerturbationDesign", oeDB1.getAcc()); final String dval1 = "Whip the PI too if nothing changes"; designDB = (Design) CollectionUtils.find(designsDB, new Predicate() { public boolean evaluate(Object object) { return dval1.equals(((Design) object).getValue()); } }); assertNotNull("Arg! I cannot find a design which shoulb have been persisted ('" + dval1 + "')", designDB); // Protocols // Collection<Protocol> protocols = study.getProtocols(); assertNotNull("Ugh! No protocols from the study!", protocols); assertEquals("Urgh! Wrong no. of protocols returned for the study!", 2, protocols.size()); // Protocol 1 // Protocol protocol1DB = (Protocol) CollectionUtils.find(protocols, new Predicate() { public boolean evaluate(Object object) { return "A-NEW-PROTO-99".equals(((Protocol) object).getAcc()); } }); assertNotNull("Ough! Cannot find the protocol A-NEW-PROTO-99 in the study!", protocol1DB); // Parameters // Collection<Parameter> params1 = protocol1DB.getParameters(); assertNotNull("Oh no! No param types from the persisted protocol!", params1); assertEquals("Oh no! The persisted protocol does not return correct no. of params !", 2, params1.size()); // Protocol 2 // Protocol protocol2DB = (Protocol) CollectionUtils.find(protocols, new Predicate() { public boolean evaluate(Object object) { return "bii:proto:999".equals(((Protocol) object).getAcc()); } }); assertNotNull("Ough! Cannot find the protocol bii:proto:999 in the study!", protocol2DB); // Params // Collection<Parameter> params2 = protocol2DB.getParameters(); assertNotNull("Oh no! No param types from the persisted protocol!", params2); assertEquals("Oh no! The persisted protocol does not return correct no. of params !", 2, params2.size()); // Contact Collection<Contact> contactsDB = studyDB.getContacts(); assertEquals("Arg! Wrong no. of contacts persisted!", 1, contactsDB.size()); Contact contactDB = contactsDB.iterator().next(); assertNotNull("Oh no! Persisted contact has not an ID!", contactDB.getId()); assertEquals("Oh no! Persisted contact has wrong email", "someone@somewhere.net", contactDB.getEmail()); Collection<ContactRole> rolesDB = contactDB.getRoles(); assertEquals("Argh! Bad no. of contact roles persisted", 2, rolesDB.size()); Iterator<ContactRole> rolesItr = rolesDB.iterator(); ContactRole roleDB = rolesItr.next(); Long id = roleDB.getId(); assertTrue("Arg! Wrong role #0 for the persisted contact", id != null); ReferenceSource roleSrcDB = roleDB.getSource(); assertEquals("Arg! Wrong role source for the persisted contact", (long) 100, roleSrcDB.getId().longValue()); roleDB = rolesItr.next(); Long id1 = roleDB.getId(); assertNotNull("Arg! Wrong role #1 for the persisted contact", id1 != null || (id == -7 || id1 == -7)); roleSrcDB = roleDB.getSource(); assertEquals("Arg! Wrong role source for the persisted contact", (long) 100, roleSrcDB.getId().longValue()); out.println("\n\nPersisted study: " + studyDB); out.println( "\n\n\n _______________ /end: StudyPersistanceTest, Testing new Study ____________________________\n"); }
From source file:uk.ac.ebi.bioinvindex.persistence.StudyPersistenceTest.java
@Test public void testPersistStudyAndInvestigation() throws Exception { out.println(/*ww w.j a va 2s . co m*/ "\n\n\n _______________ StudyPersistanceTest, Testing Study/Investigation _____________________\n"); Study study = new Study("My super-scientific experiment"); study.setDescription("A new fantastic study used for tests"); Design design = new Design("Whip the operator to see its performance improves"); ReferenceSource designSource = new ReferenceSource(null); designSource.setAcc("BII-1"); OntologyTerm oe = new OntologyTerm("biionto:OperatorPerturbationDesign", null, designSource); design.addOntologyTerm(oe); study.addDesign(design); Investigation investigation1 = new Investigation("The New Test Investigation"); investigation1.setDescription("The Investigation used for testing"); study.addInvestigation(investigation1); Investigation investigation2 = new Investigation(""); investigation2.setAcc("bii:test:inv:01"); study.addInvestigation(investigation2); Study studyDB = persister.persist(study); transaction.commit(); assertNotNull("Arg! No study returned by the persister!", studyDB); assertEquals("Ouch! The study retuned by the persister should be == the original one", studyDB, study); assertNotNull("Ops! null ID for the persisted study", studyDB.getId()); assertTrue("Oh! The study is not in the DB!", entityManager.contains(studyDB)); Collection<Investigation> investigationsDB = studyDB.getInvestigations(); assertEquals("Gosh! Wrong # of investigations associated to the persisted study!", 2, investigationsDB.size()); final String title1 = investigation1.getTitle(); Investigation investigation1DB = (Investigation) CollectionUtils.find(investigationsDB, new Predicate() { public boolean evaluate(Object object) { return title1.equals(((Investigation) object).getTitle()); } }); assertNotNull("Urp! The investigation \"" + title1 + "\" was not persisted!", investigation1DB); assertNotNull("Argh! The investigation \"" + title1 + "\" should have an ID", investigation1DB.getId()); assertNotNull("Urp! The investigation \"" + title1 + "\" should have an accession", investigation1DB.getAcc()); assertTrue("Oh! The investigation \"" + title1 + "\" is not in the DB!", entityManager.contains(investigation1DB)); assertTrue("Urgh! The investigation " + title1 + "doesn't contain the persisted study!", investigation1DB.getStudies().contains(studyDB)); final String acc2 = investigation2.getAcc(); Investigation investigation2DB = (Investigation) CollectionUtils.find(investigationsDB, new Predicate() { public boolean evaluate(Object object) { return acc2.equals(((Investigation) object).getAcc()); } }); assertNotNull("Urp! The investigation \"" + acc2 + "\" was not persisted!", investigation2DB); assertNotNull("Argh! The investigation \"" + acc2 + "\" should have an ID", investigation2DB.getId()); assertNotNull("Urp! The investigation \"" + acc2 + "\" should have an accession", investigation2DB.getAcc()); assertTrue("Oh! The investigation \"" + acc2 + "\" is not in the DB!", entityManager.contains(investigation2DB)); assertTrue("Urgh! The investigation " + acc2 + "doesn't contain the persisted study!", investigation2DB.getStudies().contains(studyDB)); out.println("\n\nPersisted study: " + studyDB); out.println("\n\nAnd its investigations:"); for (Investigation investigation : studyDB.getInvestigations()) out.println(investigation); out.println( "\n\n\n _______________ StudyPersistanceTest, Testing Study/Investigation _____________________\n"); }