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.magetab; 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.AbstractCaarrayTest; import gov.nih.nci.caarray.domain.project.ExperimentOntologyCategory; import gov.nih.nci.caarray.magetab.idf.ExperimentalFactor; import gov.nih.nci.caarray.magetab.idf.IdfDocument; import gov.nih.nci.caarray.magetab.idf.Investigation; import gov.nih.nci.caarray.magetab.idf.Person; import gov.nih.nci.caarray.magetab.idf.Publication; import gov.nih.nci.caarray.magetab.io.JavaIOFileRef; import gov.nih.nci.caarray.magetab.sdrf.AbstractBioMaterial; import gov.nih.nci.caarray.magetab.sdrf.ArrayDataFile; import gov.nih.nci.caarray.magetab.sdrf.ArrayDesign; import gov.nih.nci.caarray.magetab.sdrf.DerivedArrayDataFile; import gov.nih.nci.caarray.magetab.sdrf.Hybridization; import gov.nih.nci.caarray.magetab.sdrf.LabeledExtract; import gov.nih.nci.caarray.magetab.sdrf.Sample; import gov.nih.nci.caarray.magetab.sdrf.SdrfColumnType; import gov.nih.nci.caarray.magetab.sdrf.SdrfDocument; import gov.nih.nci.caarray.magetab.sdrf.Source; import gov.nih.nci.caarray.test.data.magetab.MageTabDataFiles; import gov.nih.nci.caarray.validation.FileValidationResult; import gov.nih.nci.caarray.validation.InvalidDataException; import gov.nih.nci.caarray.validation.ValidationMessage; import gov.nih.nci.caarray.validation.ValidationMessage.Type; import gov.nih.nci.caarray.validation.ValidationResult; import java.util.Arrays; import java.util.Collection; import java.util.HashMap; import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; import org.apache.commons.lang.StringUtils; import org.apache.commons.lang.builder.EqualsBuilder; import org.apache.commons.lang.builder.ToStringBuilder; import org.junit.Test; /** * Tests for the MageTabParser subsystem. */ @SuppressWarnings("PMD") public class MageTabParserTest extends AbstractCaarrayTest { private static final int ONE = 1; private static final int SIX = 6; private final MageTabParser parser = MageTabParser.INSTANCE; private static final Map<String, Protocol> CAARRAY1X_EXPECTED_PROTOCOLS = new HashMap<String, Protocol>(); private static final Map<String, TermSource> CAARRAY1X_EXPECTED_TERM_SOURCES = new HashMap<String, TermSource>(); private static final Map<String, ExperimentalFactor> CAARRAY1X_EXPECTED_FACTORS = new HashMap<String, ExperimentalFactor>(); private static final Map<String, Person> CAARRAY1X_EXPECTED_PERSONS = new HashMap<String, Person>(); private static final Map<String, Publication> CAARRAY1X_EXPECTED_PUBLICATIONS = new HashMap<String, Publication>(); private static final Map<String, OntologyTerm> CAARRAY1X_EXPECTED_DESIGNS = new HashMap<String, OntologyTerm>(); private static final Map<String, OntologyTerm> CAARRAY1X_EXPECTED_QUALITY_CONTROL_TYPES = new HashMap<String, OntologyTerm>(); private static final TermSource CAARRAY1X_MO; private static final Map<String, TermSource> SPEC_EXPECTED_TERM_SOURCES = new HashMap<String, TermSource>(); static { TermSource mo = new TermSource("MO", "http://mged.sourceforge.net/ontologies/MGEDontology.php", "1.3.0.1"); final TermSource cto = new TermSource("CTO", "http://obo.sourceforge.net/cgi-bin/detail.cgi?cell", null); final TermSource ncbitax = new TermSource("ncbitax", "http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/", null); final TermSource arrayExpress = new TermSource("ArrayExpress", "http://www.ebi.ac.uk/arrayexpress/", null); SPEC_EXPECTED_TERM_SOURCES.put(mo.getName(), mo); SPEC_EXPECTED_TERM_SOURCES.put(cto.getName(), cto); SPEC_EXPECTED_TERM_SOURCES.put(ncbitax.getName(), ncbitax); SPEC_EXPECTED_TERM_SOURCES.put(arrayExpress.getName(), arrayExpress); CAARRAY1X_MO = mo = new TermSource("MO", "http://mged.sourceforge.net/ontologies/MGEDOntology1.1.8.daml", "1.1.8"); final TermSource adultMouseAnatomy = new TermSource("DB:Adult_Mouse_Anatomy"); final TermSource nciThesaurus = new TermSource("DB:NCI_Thesaurus"); final TermSource nciOrganismPartsDb = new TermSource("DB:NCI_organism_part_database"); CAARRAY1X_EXPECTED_TERM_SOURCES.put(mo.getName(), mo); CAARRAY1X_EXPECTED_TERM_SOURCES.put(adultMouseAnatomy.getName(), adultMouseAnatomy); CAARRAY1X_EXPECTED_TERM_SOURCES.put(nciOrganismPartsDb.getName(), nciOrganismPartsDb); CAARRAY1X_EXPECTED_TERM_SOURCES.put(nciThesaurus.getName(), nciThesaurus); addExpectedProtocol(CAARRAY1X_EXPECTED_PROTOCOLS, "Calvo's RNA Extraction", "Total RNA was extracted from frozen tissues using the RNeasy mini kit (Qiagen, Valencia, CA) according to the manufacturers protocol. The quality of the RNA was assessed by running aliquots on agarose gels.", "nucleic_acid_extraction", mo); addExpectedProtocol(CAARRAY1X_EXPECTED_PROTOCOLS, "Calvo's Reverse Transcription", "Briefly, 10 g of RNA from both the reference sample (Pr111) and the experimental samples were reverse transcribed for 1 h at 42C using Cyanine 3-dUTP for the reference cell line Pr111 or Cyanine 5-dUTP for the experimental samples.", "reverse_transcription", mo); addExpectedProtocol(CAARRAY1X_EXPECTED_PROTOCOLS, "Calvo's labeling", "Preparation of the cDNA-labeled probes was performed using the Micromax system (NEN Life Science Products), according to the manufactures protocol. Briefly, 10 g of RNA from both the reference sample (Pr111) and the experimental samples were reverse transcribed for 1 h at 42C using Cyanine 3-dUTP for the reference cell line Pr111 or Cyanine 5-dUTP for the experimental samples.", "labeling", mo); addExpectedProtocol(CAARRAY1X_EXPECTED_PROTOCOLS, "Calvo's Hybridization", "An equal volume of 2x hybridization solution (50% formamide, 10x SSC, and 0.2% SDS) was added to the cDNA mixture and placed onto the microarray slide for hybridization at 42C for 16 h.", "hybridization", mo); addExpectedProtocol(CAARRAY1X_EXPECTED_PROTOCOLS, "GenePix feature Extraction", "The array slides were scanned with an Axon 4000 scanner (Axon Instruments, Foster City, CA) at a resolution of 10 m.", "feature_extraction", mo); addExpectedFactor(CAARRAY1X_EXPECTED_FACTORS, "Pr117", "cell_line", mo); addExpectedFactor(CAARRAY1X_EXPECTED_FACTORS, "Pr14", "cell_line", mo); addExpectedFactor(CAARRAY1X_EXPECTED_FACTORS, "Pr14C2", "cell_line", mo); addExpectedFactor(CAARRAY1X_EXPECTED_FACTORS, "Pr14C1", "cell_line", mo); addExpectedFactor(CAARRAY1X_EXPECTED_FACTORS, "Pr111 reference", "cell_line", mo); addExpectedFactor(CAARRAY1X_EXPECTED_FACTORS, "Cell Line", "cell_line", mo); addExpectedDesignType(CAARRAY1X_EXPECTED_DESIGNS, "development_or_differentiation_design", null); addExpectedDesignType(CAARRAY1X_EXPECTED_DESIGNS, "disease_state_design", null); addExpectedDesignType(CAARRAY1X_EXPECTED_DESIGNS, "cell_type_comparison_design", null); addExpectedDesignType(CAARRAY1X_EXPECTED_DESIGNS, "cellular_process_design", null); addExpectedDesignType(CAARRAY1X_EXPECTED_DESIGNS, "reference_design", null); addExpectedQualityControlType(CAARRAY1X_EXPECTED_QUALITY_CONTROL_TYPES, "technical_replicate", mo); addExpectedPerson(CAARRAY1X_EXPECTED_PERSONS, "Jeffrey", "Green", "E", "JEGreen@nih.gov", null, null, "NCI/NIH, Behtesda, MD 20892", "Laboratory of cell regulation and carcinogenesis", mo, "investigator"); addExpectedPerson(CAARRAY1X_EXPECTED_PERSONS, "Alfonso", "Calvo", null, "jegreen@nih.gov", "(301) 435-5193", "301) 496-8395", "41 Library Drive, Bethesda, MD 20892", "Laboratory of cell regulation and carcinogenesis", mo, "submitter"); addExpectedPublication(CAARRAY1X_EXPECTED_PUBLICATIONS, "Alterations in gene expression profiles during prostate cancer progression", "12235003", null, "Calvo A, Xiao N, Kang J, Best CJ, Leiva I, Emmert-Buck MR, Jorcyk C, Green JE", "published", null); } private static void addExpectedPerson(Map<String, Person> expectedMap, String firstName, String lastName, String mi, String email, String phone, String fax, String address, String affiliation, TermSource roleTermSource, String... roles) { final Person p = new Person(); p.setFirstName(firstName); p.setLastName(lastName); p.setMidInitials(mi); p.setEmail(email); p.setPhone(phone); p.setFax(fax); p.setAffiliation(affiliation); p.setAddress(address); for (final String role : roles) { p.addToRoles(createTerm(MageTabOntologyCategory.ROLES.getCategoryName(), role, roleTermSource)); } expectedMap.put(personKey(p), p); } private static String personKey(Person person) { return person.getFirstName() + " " + person.getLastName(); } private static void addExpectedPublication(Map<String, Publication> expectedMap, String title, String pubmedId, String doi, String authorList, String status, TermSource statusTermSource) { final Publication p = new Publication(); p.setAuthorList(authorList); p.setDoi(doi); p.setPubMedId(pubmedId); p.setTitle(title); p.setStatus( createTerm(MageTabOntologyCategory.PUBLICATION_STATUS.getCategoryName(), status, statusTermSource)); expectedMap.put(publicationKey(p), p); } private static String publicationKey(Publication pub) { return pub.getTitle() + " " + pub.getPubMedId(); } private static void addExpectedProtocol(Map<String, Protocol> expectedMap, String name, String description, String type, TermSource typeTermSource) { final Protocol p = new Protocol(); p.setName(name); p.setDescription(description); p.setType(createProtocolType(type, typeTermSource)); CAARRAY1X_EXPECTED_PROTOCOLS.put(p.getName(), p); } private static void addExpectedFactor(Map<String, ExperimentalFactor> expectedMap, String name, String type, TermSource typeTermSource) { final ExperimentalFactor ef = new ExperimentalFactor(); ef.setName(name); ef.setType(createFactorType(type, typeTermSource)); expectedMap.put(ef.getName(), ef); } private static void addExpectedDesignType(Map<String, OntologyTerm> expectedMap, String typeValue, TermSource typeTermSource) { addExpectedTerm(expectedMap, MageTabOntologyCategory.EXPERIMENTAL_DESIGN_TYPE.getCategoryName(), typeValue, typeTermSource); } private static void addExpectedQualityControlType(Map<String, OntologyTerm> expectedMap, String typeValue, TermSource typeTermSource) { addExpectedTerm(expectedMap, MageTabOntologyCategory.QUALITY_CONTROL_TYPE.getCategoryName(), typeValue, typeTermSource); } private static void addExpectedTerm(Map<String, OntologyTerm> expectedMap, String termCategory, String termValue, TermSource termSource) { final OntologyTerm term = createTerm(termCategory, termValue, termSource); expectedMap.put(term.getValue(), term); } private static OntologyTerm createProtocolType(String typeValue, TermSource ts) { return createTerm(MageTabOntologyCategory.PROTOCOL_TYPE.getCategoryName(), typeValue, ts); } private static OntologyTerm createFactorType(String typeValue, TermSource ts) { return createTerm(MageTabOntologyCategory.EXPERIMENTAL_FACTOR_CATEGORY.getCategoryName(), typeValue, ts); } private static OntologyTerm createTerm(String category, String value, TermSource ts) { final OntologyTerm type = new OntologyTerm(); type.setCategory(category); type.setValue(value); type.setTermSource(ts); return type; } private ValidationResult validate(MageTabFileSet fileSet) throws MageTabParsingException { try { final MageTabDocumentSet docSet = this.parser.parse(fileSet); return docSet.getValidationResult(); } catch (final InvalidDataException e) { return e.getValidationResult(); } } @Test public void testValidate() throws MageTabParsingException { final MageTabFileSet fileSet = TestMageTabSets.MAGE_TAB_ERROR_SPECIFICATION_INPUT_SET; final ValidationResult result = validate(fileSet); System.out.println("testValidate result: " + result); assertFalse(result.isValid()); assertEquals(93, result.getMessages().size()); // check for the fix to gforge defect 12541 assertTrue(result.getMessages().toString() .contains("ERROR: Referenced Factor Name EF1 was not found in the IDF")); assertTrue( result.getMessages().toString().contains("ERROR: Experimental Factors must have a non-empty name")); assertTrue(result.getMessages().toString() .contains("Array Design File not allowed via experiment data import.")); } @Test public void testSelectRefFiles() throws MageTabParsingException, InvalidDataException { final MageTabFileSet fileSet = TestMageTabSets.MAGE_TAB_SPECIFICATION_INPUT_SET; final MageTabDocumentSet mTabDocSet = this.parser.parseDataFileNames(fileSet); assertNotNull(mTabDocSet); assertEquals(1, mTabDocSet.getSdrfDocuments().size()); } @Test public void testValidateIllegalUnitPlacement() throws MageTabParsingException { final MageTabFileSet fileSet = TestMageTabSets.MAGE_TAB_GEDP_INPUT_SET; final ValidationResult result = validate(fileSet); assertFalse(result.isValid()); assertTrue(result.getMessages().toString().contains("ERROR: Illegal Unit column")); } @Test public void testParseEmptySet() throws InvalidDataException, MageTabParsingException { final MageTabFileSet inputFileSet = new MageTabFileSet(); final MageTabDocumentSet documentSet = this.parser.parse(inputFileSet); assertNotNull(documentSet); } @Test public void testValidateMissingSdrf() throws MageTabParsingException { final MageTabFileSet inputFileSet = new MageTabFileSet(); inputFileSet.addIdf(new JavaIOFileRef(MageTabDataFiles.SPECIFICATION_EXAMPLE_IDF)); final ValidationResult result = validate(inputFileSet); assertNotNull(result); assertFalse(result.isValid()); assertEquals(1, result.getFileValidationResults().size()); final FileValidationResult fileValidationResult = result .getFileValidationResult(MageTabDataFiles.SPECIFICATION_EXAMPLE_IDF.getName()); assertNotNull(fileValidationResult); final ValidationMessage message = fileValidationResult.getMessages().get(0); assertEquals(33, message.getLine()); assertEquals(2, message.getColumn()); assertTrue(message.getMessage().startsWith("Referenced SDRF file ")); assertTrue(message.getMessage().endsWith(" was not included in the MAGE-TAB document set")); } @Test public void testValidateMissingIdf() throws MageTabParsingException { final MageTabFileSet inputFileSet = new MageTabFileSet(); inputFileSet.addSdrf(new JavaIOFileRef(MageTabDataFiles.SPECIFICATION_EXAMPLE_SDRF)); final ValidationResult result = validate(inputFileSet); assertNotNull(result); assertFalse(result.isValid()); assertEquals(1, result.getFileValidationResults().size()); final FileValidationResult fileValidationResult = result .getFileValidationResult(MageTabDataFiles.SPECIFICATION_EXAMPLE_SDRF.getName()); assertNotNull(fileValidationResult); assertEquals(1, fileValidationResult.getMessages().size()); final ValidationMessage message = fileValidationResult.getMessages().get(0); assertTrue(message.getMessage().equals("This SDRF file is not referenced by an IDF file.")); } @Test public void testValidateMissingTermSources() throws MageTabParsingException { final MageTabFileSet inputFileSet = new MageTabFileSet(); inputFileSet.addIdf(new JavaIOFileRef(MageTabDataFiles.MISSING_TERMSOURCE_IDF)); inputFileSet.addSdrf(new JavaIOFileRef(MageTabDataFiles.MISSING_TERMSOURCE_SDRF)); final ValidationResult result = validate(inputFileSet); System.out.println("Missing term sources check:\n" + result); assertTrue(result.toString().contains("Term Source not-in-IDF is not defined in the IDF document")); } @Test public void testValidateMultipleIdfs() throws MageTabParsingException { final MageTabFileSet inputFileSet = new MageTabFileSet(); inputFileSet.addIdf(new JavaIOFileRef(MageTabDataFiles.MISSING_TERMSOURCE_IDF)); inputFileSet.addSdrf(new JavaIOFileRef(MageTabDataFiles.MISSING_TERMSOURCE_SDRF)); inputFileSet.addIdf(new JavaIOFileRef(MageTabDataFiles.SPECIFICATION_EXAMPLE_IDF)); final ValidationResult result = validate(inputFileSet); System.out.println(result); assertTrue(result.toString().contains("At most one IDF document can be present in an import")); } @Test public void testValidateMissingDataFiles() throws MageTabParsingException { // Result should have a warning message, but should still pass validation. MageTabFileSet inputFileSet = new MageTabFileSet(); inputFileSet.addIdf(new JavaIOFileRef(MageTabDataFiles.SPECIFICATION_EXAMPLE_IDF)); inputFileSet.addSdrf(new JavaIOFileRef(MageTabDataFiles.SPECIFICATION_EXAMPLE_SDRF)); ValidationResult result = validate(inputFileSet); assertNotNull(result); assertTrue(result.isValid()); inputFileSet = TestMageTabSets.MAGE_TAB_SPECIFICATION_NO_DATA_MATRIX_INPUT_SET; result = validate(inputFileSet); assertNotNull(result); assertTrue(result.isValid()); } @Test public void testValidateMisplacedFactorValues() throws MageTabParsingException { final MageTabFileSet inputFileSet = TestMageTabSets.MAGE_TAB_MISPLACED_FACTOR_VALUES_INPUT_SET; final ValidationResult result = validate(inputFileSet); assertNotNull(result); assertFalse(result.isValid()); assertEquals(3, StringUtils.countMatches(result.toString(), "Factor Value columns must come after (to the right of) a Hybridization column")); assertFalse(result.toString().contains("Exception")); } @Test public void testParseTcgaBroadDocuments() throws MageTabParsingException, InvalidDataException { final MageTabFileSet fileSet = TestMageTabSets.TCGA_BROAD_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); assertNotNull(documentSet); assertEquals(1, documentSet.getIdfDocuments().size()); assertEquals(-1, documentSet.getIdfDocuments().iterator().next().getInvestigation().getDescription().indexOf("<")); assertEquals(-1, documentSet.getIdfDocuments().iterator().next().getInvestigation().getDescription().indexOf(">")); assertEquals(1, documentSet.getSdrfDocuments().size()); assertEquals(1, documentSet.getDataMatrixes().size()); assertEquals(26, documentSet.getNativeDataFiles().size()); checkSdrfTranslation(documentSet.getSdrfDocuments().iterator().next()); checkArrayDesigns(documentSet); assertTrue(documentSet.getValidationResult().isValid()); } @Test public void testDefect12537() throws MageTabParsingException, InvalidDataException { MageTabFileSet fileSet = TestMageTabSets.DEFECT_12537_ERROR_INPUT_SET; final ValidationResult validationResult = validate(fileSet); assertFalse(validationResult.isValid()); final List<ValidationMessage> errors = validationResult.getMessages(ValidationMessage.Type.ERROR); assertEquals(3, errors.size()); for (int i = 0; i < 3; i++) { assertEquals(i + 2, errors.get(i).getLine()); assertEquals(38, errors.get(i).getColumn()); assertTrue(errors.get(i).getMessage().contains("Duplicate Normalization Name")); } fileSet = TestMageTabSets.DEFECT_12537_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); assertNotNull(documentSet); assertTrue(documentSet.getValidationResult().isValid()); assertEquals(2, documentSet.getDataMatrixes().size()); assertEquals(3, documentSet.getNativeDataFiles().size()); assertEquals(1, documentSet.getIdfDocuments().size()); assertEquals(1, documentSet.getSdrfDocuments().size()); final SdrfDocument sdrfDocument = documentSet.getSdrfDocuments().iterator().next(); assertEquals(2, sdrfDocument.getAllDerivedArrayDataMatrixFiles().size()); assertEquals(3, sdrfDocument.getAllHybridizations().size()); for (final Hybridization hyb : sdrfDocument.getAllHybridizations()) { assertEquals(2, hyb.getSuccessorDerivedArrayDataMatrixFiles().size()); assertEquals(1, hyb.getSuccessorArrayDataFiles().size()); } } @Test public void testParseCarray1xDocuments() throws MageTabParsingException, InvalidDataException { final MageTabFileSet fileSet = TestMageTabSets.CAARRAY1X_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); assertNotNull(documentSet); assertTrue(documentSet.getValidationResult().isValid()); assertEquals(1, documentSet.getIdfDocuments().size()); assertEquals(1, documentSet.getSdrfDocuments().size()); assertEquals(0, documentSet.getAdfDocuments().size()); assertEquals(0, documentSet.getDataMatrixes().size()); assertEquals(19, documentSet.getNativeDataFiles().size()); assertEquals(4, documentSet.getTermSources().size()); assertEquals(5, documentSet.getProtocols().size()); final IdfDocument idfDocument = documentSet.getIdfDocuments().iterator().next(); final SdrfDocument sdrfDocument = documentSet.getSdrfDocuments().iterator().next(); assertTrue(idfDocument.getDocumentSet().getSdrfDocuments().contains(sdrfDocument)); assertEquals(idfDocument, sdrfDocument.getIdfDocument()); checkCarray1xIdfDocument(idfDocument); checkCarray1xSdrfDocument(sdrfDocument); checkTermSources(CAARRAY1X_EXPECTED_TERM_SOURCES, documentSet.getTermSources()); checkTerms(documentSet); checkProtocols(CAARRAY1X_EXPECTED_PROTOCOLS, documentSet.getProtocols()); } private void checkProtocols(Map<String, Protocol> expectedProtocols, Collection<Protocol> protocols) { assertEquals(expectedProtocols.size(), protocols.size()); for (final Protocol protocol : protocols) { final Protocol expectedProtocol = expectedProtocols.get(protocol.getName()); checkProtocolsMatch(expectedProtocol, protocol); } } private void checkProtocolsMatch(Protocol expectedProtocol, Protocol protocol) { checkTermsMatch(expectedProtocol.getType(), protocol.getType()); assertTrue( "Expected protocol " + ToStringBuilder.reflectionToString(expectedProtocol) + " differs from actual protocol " + ToStringBuilder.reflectionToString(protocol), EqualsBuilder.reflectionEquals(expectedProtocol, protocol, new String[] { "type" })); } private void checkTermSources(Map<String, TermSource> expectedTermSources, Collection<TermSource> termSources) { assertEquals(expectedTermSources.size(), termSources.size()); for (final TermSource termSource : termSources) { final TermSource expectedTermSource = expectedTermSources.get(termSource.getName()); checkTermSourcesMatch(expectedTermSource, termSource); } } private void checkTermSourcesMatch(TermSource expectedTermSource, TermSource termSource) { assertTrue( "Expected term source " + ToStringBuilder.reflectionToString(expectedTermSource) + " differs from actual term source" + ToStringBuilder.reflectionToString(termSource), EqualsBuilder.reflectionEquals(expectedTermSource, termSource)); } private void checkFactors(Map<String, ExperimentalFactor> expectedFactors, Collection<ExperimentalFactor> factors) { assertEquals(expectedFactors.size(), factors.size()); for (final ExperimentalFactor factor : factors) { final ExperimentalFactor expectedFactor = expectedFactors.get(factor.getName()); checkFactorsMatch(expectedFactor, factor); } } private void checkFactorsMatch(ExperimentalFactor expectedFactor, ExperimentalFactor factor) { checkTermsMatch(expectedFactor.getType(), factor.getType()); assertTrue( "Expected factor " + ToStringBuilder.reflectionToString(expectedFactor) + " differs from actual factor" + ToStringBuilder.reflectionToString(factor), EqualsBuilder.reflectionEquals(expectedFactor, factor, new String[] { "type" })); } private void checkPersons(Map<String, Person> expectedPersons, Collection<Person> persons) { assertEquals(expectedPersons.size(), persons.size()); for (final Person person : persons) { final Person expectedPerson = expectedPersons.get(personKey(person)); checkPersonsMatch(expectedPerson, person); } } private void checkPersonsMatch(Person expectedPerson, Person person) { assertEquals(expectedPerson.getRoles().size(), person.getRoles().size()); assertTrue( "Expected person " + ToStringBuilder.reflectionToString(expectedPerson) + " differs from actual person" + ToStringBuilder.reflectionToString(person), EqualsBuilder.reflectionEquals(expectedPerson, person, new String[] { "roles" })); } private void checkPublications(Map<String, Publication> expectedPublications, Collection<Publication> publications) { assertEquals(expectedPublications.size(), publications.size()); for (final Publication publication : publications) { final Publication expectedPublication = expectedPublications.get(publicationKey(publication)); checkPublicationsMatch(expectedPublication, publication); } } private void checkPublicationsMatch(Publication expectedPublication, Publication publication) { checkTermsMatch(expectedPublication.getStatus(), publication.getStatus()); assertTrue( "Expected publication " + ToStringBuilder.reflectionToString(expectedPublication) + " differs from actual publication" + ToStringBuilder.reflectionToString(publication), EqualsBuilder.reflectionEquals(expectedPublication, publication, new String[] { "status" })); } private void checkTerms(Map<String, OntologyTerm> expectedTerms, Collection<OntologyTerm> terms) { assertEquals(expectedTerms.size(), terms.size()); for (final OntologyTerm term : terms) { final OntologyTerm expectedTerm = expectedTerms.get(term.getValue()); checkTermsMatch(expectedTerm, term); } } private void checkTermsMatch(OntologyTerm expectedTerm, OntologyTerm term) { assertTrue( "Expected term " + ToStringBuilder.reflectionToString(expectedTerm) + " differs from actual term" + ToStringBuilder.reflectionToString(term), EqualsBuilder.reflectionEquals(expectedTerm, term)); } private void checkCarray1xSdrfDocument(SdrfDocument sdrfDocument) { assertEquals(37, sdrfDocument.getLeftmostNodes().size()); assertEquals(37, sdrfDocument.getAllSources().size()); final Source source = sdrfDocument.getAllSources().get(0); assertEquals("8kNew111_14_4601_m84", source.getName()); assertEquals(1, source.getProviders().size()); assertEquals("Laboratory of cell regulation and carcinogenesis", source.getProviders().get(0).getName()); assertEquals(7, source.getCharacteristics().size()); checkTermsMatch( createTerm(MageTabOntologyCategory.MATERIAL_TYPE.getCategoryName(), "organism_part", CAARRAY1X_MO), source.getMaterialType()); assertEquals(2, source.getProtocolApplications().size()); assertEquals(36, sdrfDocument.getAllSamples().size()); final Sample sample = sdrfDocument.getAllSamples().get(0); assertEquals("8kNew111_14_4601_m84 RNA", sample.getName()); assertEquals(1, sample.getPredecessors().size()); assertEquals(1, sample.getProtocolApplications().size()); assertEquals("Calvo's labeling", sample.getProtocolApplications().get(0).getProtocol().getName()); assertEquals("Calvo, Alfonso", sample.getProtocolApplications().get(0).getPerformer()); checkTermsMatch( createTerm(MageTabOntologyCategory.MATERIAL_TYPE.getCategoryName(), "synthetic_RNA", CAARRAY1X_MO), sample.getMaterialType()); assertEquals(38, sdrfDocument.getAllLabeledExtracts().size()); final LabeledExtract le = sdrfDocument.getAllLabeledExtracts().get(0); assertEquals("Cy3 labeled Pr111 reference_8kNew111_14_4601_m84", le.getName()); checkTermsMatch( createTerm(MageTabOntologyCategory.MATERIAL_TYPE.getCategoryName(), "synthetic_RNA", CAARRAY1X_MO), le.getMaterialType()); checkTermsMatch(createTerm(MageTabOntologyCategory.LABEL_COMPOUND.getCategoryName(), "Cy3", null), le.getLabel()); assertEquals(1, le.getProtocolApplications().size()); assertEquals("Calvo's Hybridization", le.getProtocolApplications().get(0).getProtocol().getName()); assertEquals("Calvo, Alfonso", le.getProtocolApplications().get(0).getPerformer()); assertEquals(19, sdrfDocument.getAllHybridizations().size()); final Hybridization hyb = sdrfDocument.getAllHybridizations().get(0); assertEquals("GenePix feature Extraction", hyb.getProtocolApplications().get(0).getProtocol().getName()); assertEquals("Calvo, Alfonso", hyb.getProtocolApplications().get(0).getPerformer()); assertEquals(1, hyb.getProtocolApplications().size()); assertEquals(2, hyb.getPredecessors().size()); assertEquals(0, hyb.getSuccessorArrayDataFiles().size()); assertEquals(0, hyb.getSuccessorArrayDataMatrixFiles().size()); assertEquals(0, hyb.getSuccessorDerivedArrayDataMatrixFiles().size()); assertEquals(1, hyb.getSuccessorDerivedArrayDataFiles().size()); final DerivedArrayDataFile arrayDataFile = hyb.getSuccessorDerivedArrayDataFiles().iterator().next(); assertNotNull(arrayDataFile); assertEquals("8kNew111_14_4601_m84.gpr", arrayDataFile.getName()); assertEquals(12, hyb.getFactorValues().size()); assertEquals("URN:LSID:caarray.nci.nih.gov:domain:Mm-Incyte-v1px_16Bx24Cx23R", hyb.getArrayDesign().getValue()); } private void checkCarray1xIdfDocument(IdfDocument idfDoc) { assertEquals("Alterations in Gene Expression Profiles during Prostate Cancer Progression", idfDoc.getInvestigation().getTitle()); assertEquals( "To identify molecular changes that occur during prostate tumor progression, we have characterized a series of prostate cancer cell lines isolated at different stages of tumorigenesis from C3(1)/Tag transgenic mice.", idfDoc.getInvestigation().getDescription()); assertEquals(6, idfDoc.getInvestigation().getFactors().size()); checkFactors(CAARRAY1X_EXPECTED_FACTORS, idfDoc.getInvestigation().getFactors()); assertEquals(5, idfDoc.getInvestigation().getDesigns().size()); checkTerms(CAARRAY1X_EXPECTED_DESIGNS, idfDoc.getInvestigation().getDesigns()); assertEquals(2, idfDoc.getInvestigation().getPersons().size()); checkPersons(CAARRAY1X_EXPECTED_PERSONS, idfDoc.getInvestigation().getPersons()); assertEquals(1, idfDoc.getInvestigation().getQualityControlTypes().size()); checkTerms(CAARRAY1X_EXPECTED_QUALITY_CONTROL_TYPES, idfDoc.getInvestigation().getQualityControlTypes()); assertEquals(0, idfDoc.getInvestigation().getNormalizationTypes().size()); assertEquals(0, idfDoc.getInvestigation().getReplicateTypes().size()); assertEquals(1, idfDoc.getInvestigation().getPublications().size()); checkPublications(CAARRAY1X_EXPECTED_PUBLICATIONS, idfDoc.getInvestigation().getPublications()); } private void checkSdrfTranslation(SdrfDocument document) { final List<Hybridization> hybridizations = document.getAllHybridizations(); assertEquals(26, hybridizations.size()); for (final Hybridization hybridization : hybridizations) { assertEquals(1, hybridization.getSuccessorArrayDataFiles().size()); } final List<ArrayDataFile> arrayDataFiles = document.getAllArrayDataFiles(); assertEquals(26, arrayDataFiles.size()); } private void checkArrayDesigns(MageTabDocumentSet documentSet) { final SdrfDocument sdrfDocument = documentSet.getSdrfDocuments().iterator().next(); assertEquals(1, sdrfDocument.getAllArrayDesigns().size()); final ArrayDesign arrayDesign = sdrfDocument.getAllArrayDesigns().get(0); for (final Hybridization hybridization : sdrfDocument.getAllHybridizations()) { assertEquals(arrayDesign, hybridization.getArrayDesign()); } } @Test public void testSourceDescriptionTranslation() throws InvalidDataException, MageTabParsingException { final MageTabFileSet fileSet = TestMageTabSets.MAGE_TAB_UNSUPPORTED_DATA_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); final SdrfDocument sdrfDocument = documentSet.getSdrfDocuments().iterator().next(); checkBioMaterialDescriptions(sdrfDocument.getAllSources(), "Source description "); checkBioMaterialDescriptions(sdrfDocument.getAllSamples(), "Sample description "); checkBioMaterialDescriptions(sdrfDocument.getAllExtracts(), "Extract description "); checkBioMaterialDescriptions(sdrfDocument.getAllLabeledExtracts(), "LabeledExtract description "); } private void checkBioMaterialDescriptions(List<? extends AbstractBioMaterial> materials, String description) { for (int i = 0; i < materials.size(); i++) { assertEquals(description + (i + 1), materials.get(i).getDescription()); } } @Test public void testParseSpecificationDocuments() throws MageTabParsingException, InvalidDataException { final MageTabFileSet fileSet = TestMageTabSets.MAGE_TAB_SPECIFICATION_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); assertNotNull(documentSet); checkTermSources(SPEC_EXPECTED_TERM_SOURCES, documentSet.getTermSources()); checkTerms(documentSet); assertEquals(1, documentSet.getIdfDocuments().size()); final IdfDocument idfDocument = documentSet .getIdfDocument(MageTabDataFiles.SPECIFICATION_EXAMPLE_IDF.getName()); final Investigation investigation = idfDocument.getInvestigation(); assertEquals(3, investigation.getProtocols().size()); assertEquals("submitter", investigation.getPersons().get(0).getRoles().get(0).getValue()); assertEquals(2, investigation.getPersons().get(0).getRoles().size()); assertEquals("http://mged.sourceforge.net/ontologies/MGEDontology.php", investigation.getProtocols().get(0).getType().getTermSource().getFile()); assertEquals("University of Heidelberg H sapiens TK6", investigation.getTitle()); final SdrfDocument sdrfDocument = documentSet.getSdrfDocuments().iterator().next(); assertNotNull(sdrfDocument); assertEquals(ONE, documentSet.getSdrfDocuments().size()); assertTrue(idfDocument.getDocumentSet().getSdrfDocuments().contains(sdrfDocument)); assertEquals(idfDocument, sdrfDocument.getIdfDocument()); assertEquals(6, sdrfDocument.getLeftmostNodes().size()); assertEquals(SIX, sdrfDocument.getAllSources().size()); final Source firstSource = sdrfDocument.getAllSources().get(0); assertEquals(-1, firstSource.getName().indexOf("<")); assertEquals(-1, firstSource.getName().indexOf(">")); // check issue 16421 - skip blank characteristics assertNull(firstSource.getCharacteristic("CellType")); assertEquals("B_lymphoblast", sdrfDocument.getAllSources().get(1).getCharacteristic("CellType").getTerm().getValue()); assertEquals(SIX, sdrfDocument.getAllSamples().size()); assertEquals(SIX, sdrfDocument.getAllExtracts().size()); assertEquals(SIX, sdrfDocument.getAllHybridizations().size()); assertEquals(SIX, sdrfDocument.getAllLabeledExtracts().size()); final Hybridization firstHybridization = sdrfDocument.getAllHybridizations().get(0); final Set<ArrayDataFile> rawDataFiles = firstHybridization.getSuccessorArrayDataFiles(); assertEquals(2, rawDataFiles.size()); final Iterator<ArrayDataFile> rawDataIterator = rawDataFiles.iterator(); ArrayDataFile arrayDataFile = rawDataIterator.next(); assertNotNull(arrayDataFile); if ("H_TK6 replicate 3.CEL".equals(arrayDataFile.getName())) { assertEquals(1, arrayDataFile.getSuccessorDerivedArrayDataMatrixFiles().size()); arrayDataFile = rawDataIterator.next(); assertEquals("H_TK6 replicate 1.CEL", arrayDataFile.getName()); assertEquals(0, arrayDataFile.getSuccessorDerivedArrayDataMatrixFiles().size()); } else { assertEquals(0, arrayDataFile.getSuccessorDerivedArrayDataMatrixFiles().size()); arrayDataFile = rawDataIterator.next(); assertEquals("H_TK6 replicate 3.CEL", arrayDataFile.getName()); assertEquals(1, arrayDataFile.getSuccessorDerivedArrayDataMatrixFiles().size()); } } /** * Tests to make sure derived data is properly associated with the source of that data (defect 13010). */ @Test public void testParseDerivedData() throws Exception { final MageTabFileSet fileSet = TestMageTabSets.DERIVED_DATA_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); assertNotNull(documentSet); final SdrfDocument sdrfDocument = documentSet.getSdrfDocuments().iterator().next(); assertEquals(1, sdrfDocument.getAllArrayDataFiles().size()); final ArrayDataFile arrayDataFile = sdrfDocument.getAllArrayDataFiles().get(0); final List<DerivedArrayDataFile> derivedDataFiles = sdrfDocument.getAllDerivedArrayDataFiles(); assertEquals(2, derivedDataFiles.size()); // make sure the first derived data file is derived from the raw data final DerivedArrayDataFile derivedArrayDataFile = derivedDataFiles.get(0); final Set<ArrayDataFile> predecessorArrayDataFiles = derivedArrayDataFile.getPredecessorArrayDataFiles(); assertEquals(1, predecessorArrayDataFiles.size()); assertTrue(predecessorArrayDataFiles.contains(arrayDataFile)); assertEquals(0, derivedArrayDataFile.getPredecessorDerivedArrayDataFiles().size()); // make sure the second derived data file is derived from the first derived data final DerivedArrayDataFile derivedArrayDataFile2 = derivedDataFiles.get(1); final Set<DerivedArrayDataFile> predecessorDerivedArrayDataFiles = derivedArrayDataFile2 .getPredecessorDerivedArrayDataFiles(); assertEquals(0, derivedArrayDataFile2.getPredecessorArrayDataFiles().size()); assertEquals(1, predecessorDerivedArrayDataFiles.size()); assertTrue(predecessorDerivedArrayDataFiles.contains(derivedArrayDataFile)); } private void checkTerms(MageTabDocumentSet documentSet) { for (final OntologyTerm term : documentSet.getTerms()) { assertNotNull("null value for term", term.getValue()); } } @Test public void testFeature13141() throws Exception { final MageTabFileSet fileSet = TestMageTabSets.VALID_FEATURE_13141_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); assertNotNull(documentSet); assertEquals(2, documentSet.getSdrfDocuments().size()); SdrfDocument sdrfDocument = documentSet.getSdrfDocument(MageTabDataFiles.FEATURE_13141_SDRF.getName()); assertNotNull(sdrfDocument); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(0), "Sample A", "123"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(1), "Sample B", "234"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(2), "Sample C", "345"); sdrfDocument = documentSet.getSdrfDocument(MageTabDataFiles.FEATURE_13141_SDRF2.getName()); assertNotNull(sdrfDocument); verifyFeature13141Source(sdrfDocument.getAllSources().get(0), "Source D", "ext1"); verifyFeature13141Source(sdrfDocument.getAllSources().get(1), "Source E", "ext2"); verifyFeature13141Source(sdrfDocument.getAllSources().get(2), "Source F", "ext3"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(0), "Sample D", "456"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(1), "Sample E", "567"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(2), "Sample F", "678"); } private void verifyFeature13141Sample(Sample s1, String expectedSampleName, String expectedTermValue) { assertEquals(expectedSampleName, s1.getName()); assertEquals(1, s1.getCharacteristics().size()); assertEquals(ExperimentOntologyCategory.EXTERNAL_SAMPLE_ID.getCategoryName(), s1.getCharacteristics().get(0).getCategory()); assertEquals(expectedTermValue, s1.getCharacteristics().get(0).getValue()); assertEquals(null, s1.getCharacteristics().get(0).getTerm()); } private void verifyFeature13141Source(Source s1, String expectedName, String expectedValue) { assertEquals(expectedName, s1.getName()); assertEquals(1, s1.getCharacteristics().size()); assertEquals(ExperimentOntologyCategory.EXTERNAL_ID.getCategoryName(), s1.getCharacteristics().get(0).getCategory()); assertEquals(expectedValue, s1.getCharacteristics().get(0).getValue()); assertEquals(null, s1.getCharacteristics().get(0).getTerm()); } @Test public void testFeature13141VerifyCanParsesInvalidSdrf() throws Exception { final MageTabFileSet fileSet = TestMageTabSets.INVALID_FEATURE_13141_INPUT_SET; final MageTabDocumentSet documentSet = this.parser.parse(fileSet); assertNotNull(documentSet); assertEquals(2, documentSet.getSdrfDocuments().size()); SdrfDocument sdrfDocument = documentSet .getSdrfDocument(MageTabDataFiles.FEATURE_13141_INVALID_SDRF.getName()); assertNotNull(sdrfDocument); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(0), "Sample A", "123"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(1), "Sample B", "234"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(2), "Sample C", "345"); sdrfDocument = documentSet.getSdrfDocument(MageTabDataFiles.FEATURE_13141_INVALID_SDRF2.getName()); assertNotNull(sdrfDocument); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(0), "Sample D", "123"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(1), "Sample E", "234"); verifyFeature13141Sample(sdrfDocument.getAllSamples().get(2), "Sample F", "345"); } @Test public void testDefect16421() throws Exception { final MageTabFileSet fileSet = TestMageTabSets.DEFECT_16421; final ValidationResult validationResult = validate(fileSet); assertTrue(validationResult.isValid()); final MageTabFileSet fileSet2 = TestMageTabSets.DEFECT_16421_2; final ValidationResult validationResult2 = validate(fileSet2); final List<ValidationMessage> errors = validationResult2.getMessages(ValidationMessage.Type.ERROR); for (final ValidationMessage error : errors) { assertTrue(error.getMessage().contains("Term Source Ref is not preceded by valid data type")); } } @Test public void testInvalidNodeOrder() throws Exception { final MageTabFileSet fs = TestMageTabSets.INVALID_NODE_ORDER_SET; final ValidationResult vr = validate(fs); final List<ValidationMessage> errors = vr.getMessages(ValidationMessage.Type.ERROR); assertEquals(2, errors.size()); checkInvalidNodeOrderMessage(errors.get(0), SdrfColumnType.SOURCE_NAME, 4); checkInvalidNodeOrderMessage(errors.get(1), SdrfColumnType.ARRAY_DATA_FILE, 9); } private void checkInvalidNodeOrderMessage(ValidationMessage message, SdrfColumnType type, int column) { assertEquals("Column " + type.getDisplayName() + " is not valid at this location", message.getMessage()); assertEquals(Type.ERROR, message.getType()); assertEquals(0, message.getLine()); assertEquals(column, message.getColumn()); } @Test public void testMissingColumns() throws Exception { for (final MageTabFileSet fs : Arrays.asList(TestMageTabSets.NO_BIOMATERIAL_SET, TestMageTabSets.NO_HYBRIDIZATION_SET, TestMageTabSets.NO_DATA_FILE_SET)) { final ValidationResult vr = validate(fs); final List<ValidationMessage> errors = vr.getMessages(ValidationMessage.Type.ERROR); assertEquals(1, errors.size()); assertEquals( "SDRF file does not have the minimum number of columns (a biomaterial, Hybridization, and a data file)", errors.get(0).getMessage()); } } /** * Tests for the refactored factor value / parameter value / characteristic data model. */ @Test public void testExtendedFactorValues() throws Exception { final MageTabFileSet fileSet = TestMageTabSets.EXTENDED_FACTOR_VALUES_INPUT_SET; try { final MageTabDocumentSet documentSet = this.parser.parse(fileSet); System.out.println("Parse result for extended values: \n" + documentSet.getValidationResult()); assertNotNull(documentSet); assertEquals(1, documentSet.getSdrfDocuments().size()); final SdrfDocument sdrfDocument = documentSet.getSdrfDocuments().iterator().next(); assertEquals(3, sdrfDocument.getAllSamples().size()); verifyExtendedFactorValuesSampleChars(sdrfDocument.getAllSamples().get(0), "Sample A", "123", "5", "years", "tissue", "MO"); verifyExtendedFactorValuesSampleChars(sdrfDocument.getAllSamples().get(1), "Sample B", "234", "a lot", "months", "tissue", "MO"); verifyExtendedFactorValuesSampleChars(sdrfDocument.getAllSamples().get(2), "Sample C", "345", "2.2", "days", "unknown", null); verifyExtendedFactorValuesSampleParams(sdrfDocument.getAllSamples().get(0), "Sample A", "foo", "planting", "MO", "4", "kg"); verifyExtendedFactorValuesSampleParams(sdrfDocument.getAllSamples().get(1), "Sample B", "baz", "planting", "MO", "4", null); verifyExtendedFactorValuesSampleParams(sdrfDocument.getAllSamples().get(2), "Sample C", "foo", "nothing", null, "less", "mg"); assertEquals(3, sdrfDocument.getAllHybridizations().size()); verifyExtendedFactorValuesHyb(sdrfDocument.getAllHybridizations().get(0), "Hyb A", "123", "5", "years", "tissue", "MO"); verifyExtendedFactorValuesHyb(sdrfDocument.getAllHybridizations().get(1), "Hyb B", "234", "a lot", "months", "tissue", "MO"); verifyExtendedFactorValuesHyb(sdrfDocument.getAllHybridizations().get(2), "Hyb C", "345", "2.2", null, "unknown", null); } catch (final InvalidDataException e) { fail("Could not parse magetab: " + e.getValidationResult().toString()); } } private void verifyExtendedFactorValuesHyb(Hybridization hyb, String hybName, String fv1Value, String fv2Value, String fv2Unit, String fv3Value, String fv3ts) { assertEquals(hybName, hyb.getName()); assertEquals(3, hyb.getFactorValues().size()); assertEquals("ExternalSampleId", hyb.getFactorValues().get(0).getFactor().getName()); assertEquals(fv1Value, hyb.getFactorValues().get(0).getValue()); assertNull(hyb.getFactorValues().get(0).getTerm()); assertNull(hyb.getFactorValues().get(0).getUnit()); assertEquals("Age", hyb.getFactorValues().get(1).getFactor().getName()); assertEquals(fv2Value, hyb.getFactorValues().get(1).getValue()); assertNull(hyb.getFactorValues().get(1).getTerm()); if (fv2Unit == null) { assertNull(hyb.getFactorValues().get(1).getUnit()); } else { assertEquals(fv2Unit, hyb.getFactorValues().get(1).getUnit().getValue()); assertEquals("MO", hyb.getFactorValues().get(1).getUnit().getTermSource().getName()); assertEquals("time", hyb.getFactorValues().get(1).getUnit().getCategory()); } assertEquals("MaterialType", hyb.getFactorValues().get(2).getFactor().getName()); if (fv3ts != null) { assertEquals(fv3ts, hyb.getFactorValues().get(2).getTerm().getTermSource().getName()); assertEquals(fv3Value, hyb.getFactorValues().get(2).getTerm().getValue()); assertNull(hyb.getFactorValues().get(2).getValue()); } else { assertEquals(fv3Value, hyb.getFactorValues().get(2).getValue()); assertNull(hyb.getFactorValues().get(2).getTerm()); } assertNull(hyb.getFactorValues().get(2).getUnit()); } private void verifyExtendedFactorValuesSampleChars(Sample sample, String sampleName, String c1Value, String c2Value, String c2Unit, String c3Value, String c3ts) { assertEquals(sampleName, sample.getName()); assertEquals(3, sample.getCharacteristics().size()); assertEquals(ExperimentOntologyCategory.EXTERNAL_SAMPLE_ID.getCategoryName(), sample.getCharacteristics().get(0).getCategory()); assertEquals(c1Value, sample.getCharacteristics().get(0).getValue()); assertNull(sample.getCharacteristics().get(0).getTerm()); assertNull(sample.getCharacteristics().get(0).getUnit()); assertEquals("Age", sample.getCharacteristics().get(1).getCategory()); assertEquals(c2Value, sample.getCharacteristics().get(1).getValue()); assertNull(sample.getCharacteristics().get(1).getTerm()); assertEquals(c2Unit, sample.getCharacteristics().get(1).getUnit().getValue()); assertEquals("MO", sample.getCharacteristics().get(1).getUnit().getTermSource().getName()); assertEquals("time", sample.getCharacteristics().get(1).getUnit().getCategory()); assertEquals("MaterialType", sample.getCharacteristics().get(2).getCategory()); if (c3ts != null) { assertEquals(c3Value, sample.getCharacteristics().get(2).getTerm().getValue()); assertEquals(c3ts, sample.getCharacteristics().get(2).getTerm().getTermSource().getName()); assertNull(sample.getCharacteristics().get(2).getValue()); } else { assertEquals(c3Value, sample.getCharacteristics().get(2).getValue()); assertNull(sample.getCharacteristics().get(2).getTerm()); } assertNull(sample.getCharacteristics().get(2).getUnit()); } private void verifyExtendedFactorValuesSampleParams(Sample sample, String sampleName, String pv1Value, String pv2Value, String pv2ts, String pv3Value, String pv3Unit) { assertEquals(sampleName, sample.getName()); assertEquals(1, sample.getProtocolApplications().size()); final ProtocolApplication pa = sample.getProtocolApplications().get(0); assertEquals("Dan1", pa.getProtocol().getName()); assertEquals(3, pa.getParameterValues().size()); assertEquals("p1", pa.getParameterValues().get(0).getParameter().getName()); assertEquals(pv1Value, pa.getParameterValues().get(0).getValue()); assertNull(pa.getParameterValues().get(0).getTerm()); assertNull(pa.getParameterValues().get(0).getUnit()); assertEquals("p2", pa.getParameterValues().get(1).getParameter().getName()); if (pv2ts != null) { assertEquals(pv2ts, pa.getParameterValues().get(1).getTerm().getTermSource().getName()); assertEquals(pv2Value, pa.getParameterValues().get(1).getTerm().getValue()); assertNull(pa.getParameterValues().get(1).getValue()); } else { assertEquals(pv2Value, pa.getParameterValues().get(1).getValue()); assertNull(pa.getParameterValues().get(1).getTerm()); } assertNull(pa.getParameterValues().get(1).getUnit()); assertEquals("p3", pa.getParameterValues().get(2).getParameter().getName()); assertEquals(pv3Value, pa.getParameterValues().get(2).getValue()); assertNull(pa.getParameterValues().get(2).getTerm()); assertEquals(pv3Unit, pv3Unit == null ? pa.getParameterValues().get(2).getUnit() : pa.getParameterValues().get(2).getUnit().getValue()); if (pv3Unit != null) { assertEquals("MO", pa.getParameterValues().get(2).getUnit().getTermSource().getName()); assertEquals("weight", pa.getParameterValues().get(2).getUnit().getCategory()); } } }