END_TEST
START_TEST(test_FbcExtension_convert_and_write)
{
string file(TestDataDirectory);
file += "/fbc_ga_example.xml";
SBMLDocument* document = readSBMLFromFile(file.c_str());
document->printErrors();
fail_unless(document->getNumErrors(LIBSBML_SEV_ERROR) == 0);
fail_unless(document->getModel() != NULL);
// convert to v2
{
ConversionProperties props;
props.addOption("convert fbc v1 to fbc v2", true);
props.addOption("strict", true);
int result = document->convert(props);
// ensure that all is well with the model
fail_unless(result == LIBSBML_OPERATION_SUCCESS);
fail_unless(document->getLevel() == 3);
fail_unless(document->getVersion() == 1);
fail_unless(document->getPlugin("fbc") != NULL);
fail_unless(document->getPlugin("fbc")->getPackageVersion() == 2);
}
// ensure that all the v1 stuff is no longer there
FbcModelPlugin* mplug = dynamic_cast<FbcModelPlugin*>(
document->getModel()->getPlugin("fbc"));
fail_unless(mplug != NULL);
fail_unless(mplug->isSetStrict());
fail_unless(mplug->getNumGeneAssociations() == 0);
fail_unless(mplug->getNumFluxBounds() == 0);
delete document;
}
END_TEST
START_TEST(test_FbcExtension_parseGeneAssociation)
{
const char* model1 =
"<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns:html='http://www.w3.org/1999/xhtml' xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version1' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless'>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='R_2DGLCNRx'>"
" <gene reference='B3553'/>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
const char* model2 =
"<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version1' metaid='_1f29713d_1639_4193_9935_d6c7ec5255c6' level='3' version='1' fbc:required='false'>"
" <model metaid='meta' id='id' name='name' timeUnits='dimensionless'>"
" <notes>"
" <p xmlns='http://www.w3.org/1999/xhtml'>"
" I prevent you from reading annotations ... "
" </p>"
" </notes>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='MNXR2184_i'>"
" <or>"
" <gene reference='MCON_1478_I'/>"
" <gene reference='MCON_2528_I'/>"
" <gene reference='MCON_3321_I'/>"
" <gene reference='METACYC_GHHN_1245_MONOMER_I'/>"
" <gene reference='METACYC_GHHN_2657_MONOMER_I'/>"
" <gene reference='METACYC_GHHN_2722_MONOMER_I'/>"
" </or>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
const char* model3 =
"<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns:html='http://www.w3.org/1999/xhtml' xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version1' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless'>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='R_2DGLCNRx'>"
" <gene reference='B3553.FR1.F121312'/>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
const char* model4 =
"<?xml version='1.0' encoding='UTF-8'?>"
"<sbml xmlns:html='http://www.w3.org/1999/xhtml' xmlns='http://www.sbml.org/sbml/level3/version1/core' xmlns:fbc='http://www.sbml.org/sbml/level3/version1/fbc/version1' level='3' version='1' fbc:required='false'>"
" <model id='M' name='E' timeUnits='dimensionless'>"
" <annotation>"
" <listOfGeneAssociations xmlns='http://www.sbml.org/sbml/level3/version1/fbc/version1'>"
" <geneAssociation id='ga_1' reaction='R_2DGLCNRx'>"
" <gene reference='3.14'/>"
" </geneAssociation>"
" </listOfGeneAssociations>"
" </annotation>"
" </model>"
"</sbml>"
;
SBMLDocument* doc = readSBMLFromString(model1);
fail_unless(doc->getModel() != NULL);
FbcModelPlugin* fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
doc = readSBMLFromString(model2);
fail_unless(doc->getModel() != NULL);
fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
doc = readSBMLFromString(model3);
fail_unless(doc->getModel() != NULL);
fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
doc = readSBMLFromString(model4);
fail_unless(doc->getModel() != NULL);
fbc = dynamic_cast<FbcModelPlugin*>(doc->getModel()->getPlugin("fbc"));
fail_unless(fbc != NULL);
fail_unless(fbc->getNumGeneAssociations() == 1);
SBMLDocument_free(doc);
Association* test = Association::parseInfixAssociation("F1.F2.F3 OR F2.f3.f4");
fail_unless(test != NULL);
fail_unless(test->toInfix() == "(F1.F2.F3 or F2.f3.f4)");
test = Association::parseInfixAssociation("3.1 or 3.2");
fail_unless(test != NULL);
fail_unless(test->toInfix() == "(3.1 or 3.2)");
}
