public void test_XMLOutputStream_CharacterReference()
{
OStringStream oss = new OStringStream();
XMLOutputStream stream = new XMLOutputStream(oss,"",false);
stream.startElement( "testcr");
stream.writeAttribute( "chars", "one" );
stream.writeAttribute( "amp", "&" );
stream.writeAttribute( "deccr", "¨" );
stream.writeAttribute( "hexcr", "¨");
stream.writeAttribute( "lhexcr", "¨");
stream.writeAttribute( "nodeccr1", "ژ" );
stream.writeAttribute( "nodeccr2", "&#;" );
stream.writeAttribute( "nodeccr3", "�a8;" );
stream.writeAttribute( "nodeccr4", "�A8;" );
stream.writeAttribute( "nohexcr1", "&#x;" );
stream.writeAttribute( "nohexcr2", "ꯍ" );
stream.endElement( "testcr");
string expected = "<testcr chars=\"one\" amp=\"&\" deccr=\"¨\" hexcr=\"¨\" " +
"lhexcr=\"¨\" nodeccr1=\"&#01688\" nodeccr2=\"&#;\" " +
"nodeccr3=\"&#00a8;\" nodeccr4=\"&#00A8;\" " +
"nohexcr1=\"&#x;\" nohexcr2=\"&#xABCD\"/>";
string s = oss.str();
assertTrue(( expected == s ));
stream = null;
}
private static int Main(string[] args)
{
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Define the external model definitions
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var extmod = compdoc.createExternalModelDefinition();
extmod.setId("ExtMod1");
extmod.setSource("enzyme_model.xml");
extmod.setModelRef("enzyme");
// create the main Model
var model = document.createModel();
// Set the submodels
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("A");
submod1.setModelRef("ExtMod1");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("ExtMod1");
// create a replacement compartment
var comp = model.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
//Tell the model that this compartment replaces both of the inside ones.
var compartplug = (CompSBasePlugin)(comp.getPlugin("comp"));
var re = new ReplacedElement();
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug.addReplacedElement(re);
re.setSubmodelRef("B");
compartplug.addReplacedElement(re);
// create a replacement species
var spec = model.createSpecies();
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
//Tell the model that this species replaces both of the inside ones.
var spp = (CompSBasePlugin)(spec.getPlugin("comp"));
re.setIdRef("S");
re.setSubmodelRef("A");
spp.addReplacedElement(re);
re.setSubmodelRef("B");
spp.addReplacedElement(re);
libsbml.writeSBMLToFile(document, "spec_example2.xml");
document = libsbml.readSBMLFromFile("spec_example2.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
return -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
return -1;
}
libsbml.writeSBMLToFile(document, "spec_example2_rt.xml");
}
return 0;
}
public static int Main(string[] args)
{
int retval = 0;
SBMLNamespaces sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
SBMLDocument document = new SBMLDocument(sbmlns);
// create the Model
Model model = document.createModel();
// create a replacement parameter
Parameter parameter = model.createParameter();
parameter.setId("x");
parameter.setConstant(true);
// create a parameter to be a conversion factor
Parameter param2 = model.createParameter();
param2.setId("x_conv");
param2.setMetaId("_110013");
param2.setConstant(true);
// create a parameter to be a conversion factor
Parameter param3 = model.createParameter();
param3.setId("lcf");
param3.setConstant(true);
// Convert parameter to the plugin version so we can add the new attributes and replacements to it.
CompSBasePlugin splugin = (CompSBasePlugin) (parameter.getPlugin("comp"));
// Add a replaced element.
ReplacedElement rep1 = splugin.createReplacedElement();
int rv = rep1.setSubmodelRef("submod1");
rv = rep1.setConversionFactor("x_conv");
rv = rep1.setIdRef("param1");
// Add a second replaced element in a different way.
ReplacedElement rep2 = new ReplacedElement();
rv = rep2.setSubmodelRef("submod2");
rv = rep2.setDeletion("del1");
rv = splugin.addReplacedElement(rep2);
//Now create a replaced element that points into a submodel.
rep2.unsetDeletion();
rep2.setIdRef("submod2");
SBaseRef sbr5 = rep2.createSBaseRef();
sbr5.setIdRef("submodelG");
SBaseRef sbr6 = sbr5.createSBaseRef();
sbr6.setIdRef("buriedElement");
splugin.addReplacedElement(rep2);
// Create a submodel
CompModelPlugin mplugin = (CompModelPlugin) (model.getPlugin("comp"));
CompSBMLDocumentPlugin compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp"));
compdoc.setRequired(true);
ModelDefinition moddef1 = compdoc.createModelDefinition();
moddef1.setId("Mod1");
Parameter m1param1 = moddef1.createParameter();
m1param1.setId("param1");
m1param1.setConstant(true);
Parameter m1param2 = moddef1.createParameter();
m1param2.setId("param2");
m1param2.setConstant(false);
m1param2.setValue(3.2);
ModelDefinition moddef2 = new ModelDefinition();
moddef2.setId("Mod2");
Parameter subparam2 = moddef2.createParameter();
subparam2.setId("subparam2");
subparam2.setConstant(false);
compdoc.addModelDefinition(moddef2);
ExternalModelDefinition extmod1 = compdoc.createExternalModelDefinition();
extmod1.setId("ExtMod1");
extmod1.setSource("urn:miriam:biomodels.db:BIOMD0000000127");
ExternalModelDefinition extmod2 = new ExternalModelDefinition();
extmod2.setId("ExtMod2");
extmod2.setSource("otherfile.xml");
extmod2.setModelRef("modelnamethere");
extmod2.setMd5("406022s908ge74sklj");
compdoc.addExternalModelDefinition(extmod2);
Submodel submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("Mod1");
Deletion del1 = submod1.createDeletion();
del1.setId("deletionA");
del1.setIdRef("param2");
Submodel submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("ExtMod1");
submod2.setSubstanceConversionFactor("subcf");
submod2.setTimeConversionFactor("tcf");
submod2.setExtentConversionFactor("xtf");
Deletion del2 = new Deletion();
del2.setId("deletionB");
del2.setMetaIdRef("_0010110");
rv = submod2.addDeletion(del2);
del2.setId("deletionC");
del2.unsetMetaIdRef();
del2.setPortRef("port2");
rv = submod2.addDeletion(del2);
del2.unsetId();
del2.unsetPortRef();
del2.setUnitRef("mph");
rv = submod2.addDeletion(del2);
del2.unsetUnitRef();
del2.setIdRef("submodG");
SBaseRef sbr = del2.createSBaseRef();
sbr.setIdRef("element5");
rv = submod2.addDeletion(del2);
Deletion del3 = new Deletion();
del3.setIdRef("submodG");
SBaseRef sbr2 = new SBaseRef();
sbr2.setIdRef("subsubmodQ");
SBaseRef subsbr = sbr2.createSBaseRef();
subsbr.setPortRef("toBdel");
del3.setSBaseRef(sbr2);
submod2.addDeletion(del3);
mplugin.addSubmodel(submod2);
Port port1 = mplugin.createPort();
port1.setId("port1");
port1.setMetaIdRef("_110013");
Port port2 = new Port();
port2.setId("port2");
port2.setIdRef("x");
mplugin.addPort(port2);
port2.setId("port3");
port2.setIdRef("submod2");
port2.setSBaseRef(sbr2);
mplugin.addPort(port2);
libsbml.writeSBMLToFile(document, "comp_example1.xml");
document = libsbml.readSBMLFromFile("comp_example1.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
OStringStream stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "comp_example1_rt.xml");
}
return retval;
}
public static void validate(string inputFile)
{
if ( ! File.Exists(inputFile) )
{
Console.WriteLine("[Error] {0} : No such file.", inputFile);
++NumInvalid;
return;
}
SBMLDocument sbmlDoc;
long start, stop;
double timeRead;
start = System.DateTime.UtcNow.ToFileTimeUtc();
sbmlDoc = libsbml.readSBML(inputFile);
stop = System.DateTime.UtcNow.ToFileTimeUtc();
timeRead = (double)(stop - start)/10000;
long errors = sbmlDoc.getNumErrors();
FileInfo fi = new FileInfo(inputFile);
bool seriousErrors = false;
long numReadErrors = 0;
long numReadWarnings = 0;
string errMsgRead = "";
if (errors > 0 )
{
for (int i = 0; i < errors; i++)
{
long severity = sbmlDoc.getError(i).getSeverity();
if (severity == libsbml.LIBSBML_SEV_ERROR || severity == libsbml.LIBSBML_SEV_FATAL )
{
seriousErrors = true;
++numReadErrors;
}
else {
++numReadWarnings;
}
}
OStringStream oss = new OStringStream();
sbmlDoc.printErrors(oss);
errMsgRead = oss.str();
}
// If serious errors are encountered while reading an SBML document, it
// does not make sense to go on and do full consistency checking because
// the model may be nonsense in the first place.
long numCCErrors = 0;
long numCCWarnings = 0;
string errMsgCC = "";
bool skipCC = false;
double timeCC = 0.0;
if (seriousErrors)
{
skipCC = true;
errMsgRead += "Further consistency checking and validation aborted.";
++NumInvalid;
}
else
{
long failures;
sbmlDoc.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, enableUnitCCheck);
start = System.DateTime.UtcNow.ToFileTimeUtc();
failures = sbmlDoc.checkConsistency();
stop = System.DateTime.UtcNow.ToFileTimeUtc();
timeCC = (double)(stop - start)/10000;
bool isInvalid = false;
if (failures > 0)
{
for (int i = 0; i < failures; i++)
{
long severity = sbmlDoc.getError(i).getSeverity();
if (severity == libsbml.LIBSBML_SEV_ERROR || severity == libsbml.LIBSBML_SEV_FATAL )
{
++numCCErrors;
isInvalid = true;
}
else {
++numCCWarnings;
}
}
if ( isInvalid)
{
++NumInvalid;
}
OStringStream oss = new OStringStream();
sbmlDoc.printErrors(oss);
errMsgCC = oss.str();
}
}
//
// print results
//
Console.WriteLine(" filename : {0}", inputFile);
Console.WriteLine(" file size (byte) : {0}", fi.Length);
Console.WriteLine(" read time (ms) : {0}", timeRead );
Console.WriteLine(" c-check time (ms) : {0}", ( skipCC ? "skipped" : timeCC.ToString() ));
Console.WriteLine(" validation error(s) : {0}", numReadErrors + numCCErrors );
Console.WriteLine(" (consistency error(s)): {0}", ( skipCC ? "skipped" : numCCErrors.ToString() ));
Console.WriteLine(" validation warning(s) : {0}", numReadWarnings + numCCWarnings);
Console.WriteLine("(consistency warning(s)): {0}", ( skipCC ? "skipped" : numCCWarnings.ToString() ));
if ( errMsgRead != "" || errMsgCC != "")
{
Console.WriteLine("\n===== validation error/warning messages =====\n");
if ( errMsgRead != "")
{
Console.WriteLine(errMsgRead);
}
if ( errMsgCC != "")
{
Console.WriteLine("*** consistency check ***\n");
Console.WriteLine(errMsgCC);
}
}
}
private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Define the external model definition
var compdoc = (CompSBMLDocumentPlugin)(document.getPlugin("comp"));
compdoc.setRequired(true);
var extmod = compdoc.createExternalModelDefinition();
extmod.setId("ExtMod1");
extmod.setSource("enzyme_model.xml");
extmod.setModelRef("enzyme");
//Define the 'simple' model
var mod1 = compdoc.createModelDefinition();
mod1.setId("simple");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(sbmlns);
//We have to construct it this way because we get the comp plugin from it later.
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
spec.setInitialConcentration(5);
mod1.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
rxn.setId("J0");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("D");
rxn.addProduct(sr);
mod1.addReaction(rxn);
var mod1plug = (CompModelPlugin)(mod1.getPlugin("comp"));
var port = new Port();
port.setId("S_port");
port.setIdRef("S");
mod1plug.addPort(port);
var port2 = mod1plug.createPort();
port2.setId("D_port");
port2.setIdRef("D");
port.setId("comp_port");
port.setIdRef("comp");
mod1plug.addPort(port);
port.setId("J0_port");
port.setIdRef("J0");
mod1plug.addPort(port);
// create the Model
var model = document.createModel();
model.setId("complexified");
// Set the submodels
var mplugin = (CompModelPlugin)(model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("A");
submod1.setModelRef("ExtMod1");
var submod2 = mplugin.createSubmodel();
submod2.setId("B");
submod2.setModelRef("simple");
var del = submod2.createDeletion();
del.setPortRef("J0_port");
// Synchronize the compartments
var mcomp = model.createCompartment();
mcomp.setSpatialDimensions(3);
mcomp.setConstant(true);
mcomp.setId("comp");
mcomp.setSize(1L);
var compartplug = (CompSBasePlugin)(mcomp.getPlugin("comp"));
var re = new ReplacedElement();
re.setIdRef("comp");
re.setSubmodelRef("A");
compartplug.addReplacedElement(re);
re.setSubmodelRef("B");
re.unsetIdRef();
re.setPortRef("comp_port");
compartplug.addReplacedElement(re);
//Synchronize the species
spec.setId("S");
spec.setInitialConcentration(5);
var specplug = (CompSBasePlugin)(spec.getPlugin("comp"));
var sre = specplug.createReplacedElement();
sre.setSubmodelRef("A");
sre.setIdRef("S");
var sre2 = specplug.createReplacedElement();
sre2.setSubmodelRef("B");
sre2.setPortRef("S_port");
model.addSpecies(spec);
spec.setId("D");
spec.setInitialConcentration(10);
sre.setIdRef("D");
sre2.setPortRef("D_port");
model.addSpecies(spec);
libsbml.writeSBMLToFile(document, "spec_example3.xml");
document = libsbml.readSBMLFromFile("spec_example3.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "spec_example3_rt.xml");
}
return retval;
}
public void test_XMLOutputStream_createStringWithProgramInfo()
{
string expected = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n";
OStringStream oss = new OStringStream();
XMLOutputStream stream = new XMLOutputStream(oss,"UTF-8",true, "", "");
assertTrue( stream != null );
string str = oss.str();
assertTrue(( expected == str ));
stream = null;
}
public void test_XMLOutputStream_startEnd()
{
OStringStream oss = new OStringStream();
XMLOutputStream stream = new XMLOutputStream(oss,"",false);
assertTrue( stream != null );
stream.startEndElement( "id");
string str = oss.str();
assertTrue(( "<id/>" == str ));
stream = null;
}
public void test_XMLOutputStream_PredefinedEntity()
{
OStringStream oss = new OStringStream();
XMLOutputStream stream = new XMLOutputStream(oss,"",false);
stream.startElement( "testpde");
stream.writeAttribute( "amp", "&" );
stream.writeAttribute( "apos", "'" );
stream.writeAttribute( "gt", ">" );
stream.writeAttribute( "lt", "<" );
stream.writeAttribute( "quot", "\"" );
stream.writeAttribute( "pdeamp", "&" );
stream.writeAttribute( "pdeapos", "'");
stream.writeAttribute( "pdegt", ">" );
stream.writeAttribute( "pdelt", "<" );
stream.writeAttribute( "pdequot", """);
stream.endElement( "testpde");
string expected = "<testpde amp=\"&\" apos=\"'\" gt=\">\" lt=\"<\" " +
"quot=\""\" pdeamp=\"&\" pdeapos=\"'\" pdegt=\">\" " + "pdelt=\"<\" pdequot=\""\"/>";
string s = oss.str();
assertTrue(( expected == s ));
stream = null;
}
public void test_XMLOutputStream_Elements()
{
double d = 2.4;
long l = 123456789;
long ui = 5;
int i = -3;
OStringStream oss = new OStringStream();
XMLOutputStream stream = new XMLOutputStream(oss,"",false);
stream.startElement( "fred");
stream.writeAttribute( "chars", "two");
stream.writeAttribute( "bool",true);
stream.writeAttribute( "double",d);
stream.writeAttribute( "long",l);
stream.writeAttribute( "uint",ui);
stream.writeAttribute( "int",i);
stream.endElement( "fred");
string expected = "<fred chars=\"two\" bool=\"true\" double=\"2.4\" long=\"123456789\" uint=\"5\" int=\"-3\"/>";
string s = oss.str();
assertTrue(( expected == s ));
stream = null;
}
private static int Main(string[] args)
{
var retval = 0;
var sbmlns = new SBMLNamespaces(3, 1, "comp", 1);
// create the document
var document = new SBMLDocument(sbmlns);
//Create our submodel
var compdoc = (CompSBMLDocumentPlugin) (document.getPlugin("comp"));
compdoc.setRequired(true);
var mod1 = compdoc.createModelDefinition();
mod1.setId("enzyme");
mod1.setName("enzyme");
var comp = mod1.createCompartment();
comp.setSpatialDimensions(3);
comp.setConstant(true);
comp.setId("comp");
comp.setSize(1L);
var spec = new Species(3, 1);
spec.setCompartment("comp");
spec.setHasOnlySubstanceUnits(false);
spec.setConstant(false);
spec.setBoundaryCondition(false);
spec.setId("S");
mod1.addSpecies(spec);
spec.setId("E");
mod1.addSpecies(spec);
spec.setId("D");
mod1.addSpecies(spec);
spec.setId("ES");
mod1.addSpecies(spec);
var rxn = new Reaction(3, 1);
rxn.setReversible(true);
rxn.setFast(false);
var rxn2 = new Reaction(rxn);
rxn.setId("J0");
rxn2.setId("J1");
var sr = new SpeciesReference(3, 1);
sr.setConstant(true);
sr.setStoichiometry(1);
sr.setSpecies("S");
rxn.addReactant(sr);
sr.setSpecies("E");
rxn.addReactant(sr);
rxn2.addProduct(sr);
sr.setSpecies("ES");
rxn.addProduct(sr);
rxn2.addReactant(sr);
sr.setSpecies("D");
rxn2.addProduct(sr);
mod1.addReaction(rxn);
mod1.addReaction(rxn2);
// create the Model
var model = document.createModel();
model.setId("aggregate");
// Create a submodel
var mplugin = (CompModelPlugin) (model.getPlugin("comp"));
var submod1 = mplugin.createSubmodel();
submod1.setId("submod1");
submod1.setModelRef("enzyme");
var submod2 = new Submodel();
submod2.setId("submod2");
submod2.setModelRef("enzyme");
mplugin.addSubmodel(submod2);
libsbml.writeSBMLToFile(document, "enzyme_model.xml");
document = libsbml.readSBMLFromFile("enzyme_model.xml");
if (document == null)
{
Console.WriteLine("Error reading back in file.");
retval = -1;
}
else
{
document.setConsistencyChecks(libsbml.LIBSBML_CAT_UNITS_CONSISTENCY, false);
document.checkConsistency();
if (document.getErrorLog().getNumFailsWithSeverity(2) > 0 ||
document.getErrorLog().getNumFailsWithSeverity(3) > 0)
{
var stream = new OStringStream();
document.printErrors(stream);
Console.WriteLine("Errors encoutered when round-tripping SBML file: \n" +
stream.str());
retval = -1;
}
libsbml.writeSBMLToFile(document, "enzyme_model_rt.xml");
}
return retval;
}
