public static int Main(string[] args) { SBMLDocument d; int errors; if (args.Length != 2) { Console.Write(Environment.NewLine + " usage: addModelHistory <input-filename> <output-filename>" + Environment.NewLine + Environment.NewLine); return 2; } d = libsbml.readSBML(args[0]); errors = (int)d.getNumErrors(); if (errors > 0) { Console.Write("Read Error(s):" + Environment.NewLine); d.printErrors(); Console.Write("Correct the above and re-run." + Environment.NewLine); } else { ModelHistory h = new ModelHistory(); ModelCreator c = new ModelCreator(); c.setFamilyName("Keating"); c.setGivenName("Sarah"); c.setEmail("*****@*****.**"); c.setOrganization("University of Hertfordshire"); long status = h.addCreator(c); printStatus("Status for addCreator: ", status); Date date = new Date("1999-11-13T06:54:32"); Date date2 = new Date("2007-11-30T06:54:00-02:00"); status = h.setCreatedDate(date); printStatus("Set created date: ", status); status = h.setModifiedDate(date2); printStatus("Set modified date: ", status); status = d.getModel().setModelHistory(h); printStatus("Set model history: ", status); libsbml.writeSBML(d, args[1]); } return errors; }
public void test_SBase_setModelHistory_Model() { S.setMetaId("_001"); ModelHistory history = new ModelHistory(); ModelCreator mc = new ModelCreator(); Date date = new Date(2005,12,30,12,15,45,1,2,0); mc.setFamilyName( "Keating"); mc.setGivenName( "Sarah"); mc.setEmail( "*****@*****.**"); mc.setOrganisation( "UH"); history.addCreator(mc); history.setCreatedDate(date); history.setModifiedDate(date); int i = S.setModelHistory(history); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); history = null; }
public void test_SBase_setModelHistoryL3() { SBase sb = new Species(3,1); sb.setMetaId("_s"); ModelHistory mh = new ModelHistory(); ModelCreator mc = new ModelCreator(); Date date = new Date(2005,12,30,12,15,45,1,2,0); mc.setFamilyName( "Keating"); mc.setGivenName( "Sarah"); mc.setEmail( "*****@*****.**"); mc.setOrganisation( "UH"); mh.addCreator(mc); mh.setCreatedDate(date); mh.setModifiedDate(date); int i = sb.setModelHistory(mh); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( sb.isSetModelHistory() == true ); mh = sb.getModelHistory(); assertTrue( mh != null ); sb.unsetModelHistory(); mh = sb.getModelHistory(); assertTrue( sb.isSetModelHistory() == false ); assertTrue( mh == null ); mh = null; }
public void test_ModelHistory_setModifiedDate2() { ModelHistory mh = new ModelHistory(); assertTrue( mh != null ); Date date = new Date(200,13,76,56,89,90,0,0,0); int i = mh.setModifiedDate(date); assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT ); assertTrue( mh.isSetModifiedDate() == false ); date = null; mh = null; }
public void test_ModelHistory_setModifiedDate1() { ModelHistory mh = new ModelHistory(); assertTrue( mh != null ); Date date = new Date("2005-12-30T12:15:32+02:00"); int i = mh.setModifiedDate(date); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertTrue( mh.isSetModifiedDate() == true ); assertTrue( date != mh.getModifiedDate() ); string dateChar = mh.getModifiedDate().getDateAsString(); assertTrue(( "2005-12-30T12:15:32+02:00" == dateChar )); i = mh.setModifiedDate(null); assertTrue( i == libsbml.LIBSBML_OPERATION_FAILED ); assertTrue( mh.isSetModifiedDate() == true ); date = null; mh = null; }
public void test_Model_setgetModelHistory() { M.setMetaId("_001"); ModelHistory history = new ModelHistory(); ModelCreator mc = new ModelCreator(); Date date = new Date(2005,12,30,12,15,45,1,2,0); mc.setFamilyName( "Keating"); mc.setGivenName( "Sarah"); mc.setEmail( "*****@*****.**"); mc.setOrganisation( "UH"); history.addCreator(mc); history.setCreatedDate(date); history.setModifiedDate(date); assertTrue( M.isSetModelHistory() == false ); M.setModelHistory(history); assertTrue( M.isSetModelHistory() == true ); ModelCreator newMC = history.getCreator(0); assertTrue( newMC != null ); assertTrue(( "Keating" == newMC.getFamilyName() )); assertTrue(( "Sarah" == newMC.getGivenName() )); assertTrue(( "*****@*****.**" == newMC.getEmail() )); assertTrue(( "UH" == newMC.getOrganisation() )); M.unsetModelHistory(); assertTrue( M.isSetModelHistory() == false ); history = null; mc = null; }
public void test_SBase_unsetAnnotationWithModelHistory() { ModelHistory h = new ModelHistory (); ModelCreator c = new ModelCreator (); Date dc; Date dm; string annt = "<annotation>\n" + " <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" + "</annotation>"; string annt_with_modelhistory = "<annotation>\n" + " <test:test xmlns:test=\"http://test.org/test\">this is a test node</test:test>\n" + " <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" " + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\" " + "xmlns:dcterms=\"http://purl.org/dc/terms/\" " + "xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" " + "xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" " + "xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" + " <rdf:Description rdf:about=\"#_000001\">\n" + " <dc:creator>\n" + " <rdf:Bag>\n" + " <rdf:li rdf:parseType=\"Resource\">\n" + " <vCard:N rdf:parseType=\"Resource\">\n" + " <vCard:Family>Keating</vCard:Family>\n" + " <vCard:Given>Sarah</vCard:Given>\n" + " </vCard:N>\n" + " <vCard:EMAIL>[email protected]</vCard:EMAIL>\n" + " </rdf:li>\n" + " </rdf:Bag>\n" + " </dc:creator>\n" + " <dcterms:created rdf:parseType=\"Resource\">\n" + " <dcterms:W3CDTF>2005-12-29T12:15:45+02:00</dcterms:W3CDTF>\n" + " </dcterms:created>\n" + " <dcterms:modified rdf:parseType=\"Resource\">\n" + " <dcterms:W3CDTF>2005-12-30T12:15:45+02:00</dcterms:W3CDTF>\n" + " </dcterms:modified>\n" + " </rdf:Description>\n" + " </rdf:RDF>\n" + "</annotation>"; S.setAnnotation (annt); assertTrue (S.isSetAnnotation () == true); assertTrue ((annt == S.getAnnotationString ())); S.unsetAnnotation (); assertTrue (S.isSetAnnotation () == false); assertTrue (S.getAnnotation () == null); S.setAnnotation (annt); S.setMetaId ("_000001"); c.setFamilyName ("Keating"); c.setGivenName ("Sarah"); c.setEmail ("*****@*****.**"); h.addCreator (c); dc = new Date (2005, 12, 29, 12, 15, 45, 1, 2, 0); h.setCreatedDate (dc); dm = new Date (2005, 12, 30, 12, 15, 45, 1, 2, 0); h.setModifiedDate (dm); S.setModelHistory (h); assertTrue (S.isSetAnnotation () == true); assertTrue ((annt_with_modelhistory == S.getAnnotationString ())); S.unsetAnnotation (); assertTrue (S.isSetAnnotation () == false); assertTrue (S.getAnnotation () == null); c = null; h = null; }
public void test_Validation_ModelHistory3() { ModelHistory mh = new ModelHistory(); assertTrue( mh != null ); assertEquals( false, (mh.hasRequiredAttributes()) ); Date date = new Date(2007,12,30,12,15,45,1,2,0); mh.setCreatedDate(date); assertEquals( false, (mh.hasRequiredAttributes()) ); mh.setModifiedDate(date); assertEquals( false, (mh.hasRequiredAttributes()) ); ModelCreator mc = new ModelCreator(); mc.setFamilyName("Keating"); mh.addCreator(mc); assertEquals( false, (mh.hasRequiredAttributes()) ); mh = null; }
public void test_L3_Species_ModelHistory() { (S).setMetaId("_3"); ModelHistory history = new ModelHistory(); int i = (S).setModelHistory(history); assertTrue( i == libsbml.LIBSBML_INVALID_OBJECT ); assertEquals( false, (S).isSetModelHistory() ); ModelCreator mc = new ModelCreator(); Date date = new Date(2005,12,30,12,15,45,1,2,0); mc.setFamilyName( "Keating"); mc.setGivenName( "Sarah"); mc.setEmail( "*****@*****.**"); mc.setOrganisation( "UH"); history.addCreator(mc); history.setCreatedDate(date); history.setModifiedDate(date); i = (S).setModelHistory(history); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertEquals( true, (S).isSetModelHistory() ); i = (S).unsetModelHistory(); assertTrue( i == libsbml.LIBSBML_OPERATION_SUCCESS ); assertEquals( false, (S).isSetModelHistory() ); assertTrue( (S).getModelHistory() == null ); history = null; }
public void test_RDFAnnotation2_modelWithHistoryAndCVTerms() { ModelHistory h = new ModelHistory(); ModelCreator c = new ModelCreator(); c.setFamilyName("Keating"); c.setGivenName("Sarah"); h.addCreator(c); Date d = new Date(2008,11,17,18,37,0,0,0,0); h.setCreatedDate(d); h.setModifiedDate(d); m2.unsetModelHistory(); m2.setModelHistory(h); CVTerm cv = new CVTerm(); cv.setQualifierType(libsbml.BIOLOGICAL_QUALIFIER); cv.setBiologicalQualifierType(libsbml.BQB_IS_VERSION_OF); cv.addResource("http://www.geneontology.org/#GO:0005892"); m2.addCVTerm(cv); XMLNode ann = RDFAnnotationParser.parseModelHistory(m2); string expected = "<annotation>\n" + " <rdf:RDF xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" xmlns:dc=\"http://purl.org/dc/elements/1.1/\" xmlns:dcterms=\"http://purl.org/dc/terms/\" xmlns:vCard=\"http://www.w3.org/2001/vcard-rdf/3.0#\" xmlns:bqbiol=\"http://biomodels.net/biology-qualifiers/\" xmlns:bqmodel=\"http://biomodels.net/model-qualifiers/\">\n" + " <rdf:Description rdf:about=\"#_000001\">\n" + " <dc:creator rdf:parseType=\"Resource\">\n" + " <rdf:Bag>\n" + " <rdf:li rdf:parseType=\"Resource\">\n" + " <vCard:N rdf:parseType=\"Resource\">\n" + " <vCard:Family>Keating</vCard:Family>\n" + " <vCard:Given>Sarah</vCard:Given>\n" + " </vCard:N>\n" + " </rdf:li>\n" + " </rdf:Bag>\n" + " </dc:creator>\n" + " <dcterms:created rdf:parseType=\"Resource\">\n" + " <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n" + " </dcterms:created>\n" + " <dcterms:modified rdf:parseType=\"Resource\">\n" + " <dcterms:W3CDTF>2008-11-17T18:37:00Z</dcterms:W3CDTF>\n" + " </dcterms:modified>\n" + " <bqbiol:isVersionOf>\n" + " <rdf:Bag>\n" + " <rdf:li rdf:resource=\"http://www.geneontology.org/#GO:0005892\"/>\n" + " </rdf:Bag>\n" + " </bqbiol:isVersionOf>\n" + " </rdf:Description>\n" + " </rdf:RDF>\n" + "</annotation>"; if (ann != null); { assertEquals( true, equals(expected,ann.toXMLString()) ); } { } }
public void test_ModelHistory_setModifiedDate() { ModelHistory history = new ModelHistory(); assertTrue( history != null ); assertTrue( history.isSetModifiedDate() == false ); Date date = new Date(2005,12,30,12,15,45,1,2,0); history.setModifiedDate(date); date = null; assertTrue( history.isSetModifiedDate() == true ); Date newdate = history.getModifiedDate(); assertTrue( newdate.getYear() == 2005 ); assertTrue( newdate.getMonth() == 12 ); assertTrue( newdate.getDay() == 30 ); assertTrue( newdate.getHour() == 12 ); assertTrue( newdate.getMinute() == 15 ); assertTrue( newdate.getSecond() == 45 ); assertTrue( newdate.getSignOffset() == 1 ); assertTrue( newdate.getHoursOffset() == 2 ); assertTrue( newdate.getMinutesOffset() == 0 ); history = null; }