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;
}
