21 #include "utilities.hpp"
27 #include "sbml/SBMLDocument.h"
28 #include "sbml/Model.h"
29 #include "sbml/Species.h"
54 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
56 CPPUNIT_ASSERT(pDocument == NULL);
57 std::string sbmlString;
66 CPPUNIT_ASSERT(
false);
69 CPPUNIT_ASSERT(!sbmlString.empty());
72 CPPUNIT_ASSERT(pDocument != NULL);
73 const Model* pModel = pDocument->getModel();
74 CPPUNIT_ASSERT(pModel != NULL);
75 unsigned int iMax = pModel->getListOfCompartments()->size();
76 CPPUNIT_ASSERT(iMax == 3);
78 const Compartment* pCompartment = pModel->getCompartment(
"compartment_1");
79 CPPUNIT_ASSERT(pCompartment != NULL);
80 CPPUNIT_ASSERT(pCompartment->getName() ==
"compartment_2");
83 iMax = pModel->getListOfSpecies()->size();
84 CPPUNIT_ASSERT(iMax == 3);
86 const Species* pSpecies = pModel->getSpecies(
"species_1");
87 CPPUNIT_ASSERT(pSpecies != NULL);
88 CPPUNIT_ASSERT(pSpecies->getName() ==
"species_2");
91 iMax = pModel->getListOfParameters()->size();
92 CPPUNIT_ASSERT(iMax == 3);
94 const Parameter* pParameter = pModel->getParameter(
"parameter_1");
95 CPPUNIT_ASSERT(pParameter != NULL);
96 CPPUNIT_ASSERT(pParameter->getName() ==
"quantity_2");
99 iMax = pModel->getListOfReactions()->size();
100 CPPUNIT_ASSERT(iMax == 3);
102 const Reaction* pReaction = pModel->getReaction(
"reaction_1");
103 CPPUNIT_ASSERT(pReaction != NULL);
104 CPPUNIT_ASSERT(pReaction->getName() ==
"reaction_2");
108 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
109 "<!-- generated with COPASI 4.5.30 (Debug) (http://www.copasi.org) at 2009-05-07 08:59:15 UTC -->\n"
110 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"30\">\n"
111 " <ListOfFunctions>\n"
112 " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
114 " k1*PRODUCT<substrate_i>\n"
116 " <ListOfParameterDescriptions>\n"
117 " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
118 " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
119 " </ListOfParameterDescriptions>\n"
121 " </ListOfFunctions>\n"
122 " <Model key=\"Model_1\" name=\"Model_1\" timeUnit=\"s\" volumeUnit=\"ml\" quantityUnit=\"mmol\" type=\"deterministic\">\n"
124 " <html xmlns=\"http://www.w3.org/1999/xhtml\">\n"
126 " <meta name=\"qrichtext\" content=\"1\"/>\n"
128 " <body style=\"font-size:13pt;font-family:Lucida Grande\">\n"
129 " <p>This is a test model for Bug 1205</p>\n"
134 " <ListOfCompartments>\n"
135 " <Compartment key=\"Compartment_0\" name=\"compartment\" simulationType=\"fixed\">\n"
137 " <Compartment key=\"Compartment_1\" name=\"compartment_1\" simulationType=\"fixed\">\n"
139 " <Compartment key=\"Compartment_2\" name=\"compartment_2\" simulationType=\"fixed\">\n"
141 " </ListOfCompartments>\n"
142 " <ListOfMetabolites>\n"
143 " <Metabolite key=\"Metabolite_0\" name=\"species\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
145 " <Metabolite key=\"Metabolite_1\" name=\"species_1\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
147 " <Metabolite key=\"Metabolite_2\" name=\"species_2\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
149 " </ListOfMetabolites>\n"
150 " <ListOfModelValues>\n"
151 " <ModelValue key=\"ModelValue_0\" name=\"quantity\" simulationType=\"fixed\">\n"
153 " <ModelValue key=\"ModelValue_1\" name=\"quantity_1\" simulationType=\"fixed\">\n"
155 " <ModelValue key=\"ModelValue_2\" name=\"quantity_2\" simulationType=\"fixed\">\n"
157 " </ListOfModelValues>\n"
158 " <ListOfReactions>\n"
159 " <Reaction key=\"Reaction_1\" name=\"reaction\" reversible=\"false\">\n"
160 " <ListOfSubstrates>\n"
161 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
162 " </ListOfSubstrates>\n"
163 " <ListOfConstants>\n"
164 " <Constant key=\"Parameter_79\" name=\"k1\" value=\"0.1\"/>\n"
165 " </ListOfConstants>\n"
166 " <KineticLaw function=\"Function_13\">\n"
167 " <ListOfCallParameters>\n"
168 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
169 " <SourceParameter reference=\"Parameter_79\"/>\n"
170 " </CallParameter>\n"
171 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
172 " <SourceParameter reference=\"Metabolite_0\"/>\n"
173 " </CallParameter>\n"
174 " </ListOfCallParameters>\n"
177 " <Reaction key=\"Reaction_0\" name=\"reaction_1\" reversible=\"false\">\n"
178 " <ListOfSubstrates>\n"
179 " <Substrate metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
180 " </ListOfSubstrates>\n"
181 " <ListOfConstants>\n"
182 " <Constant key=\"Parameter_80\" name=\"k1\" value=\"0.1\"/>\n"
183 " </ListOfConstants>\n"
184 " <KineticLaw function=\"Function_13\">\n"
185 " <ListOfCallParameters>\n"
186 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
187 " <SourceParameter reference=\"Parameter_80\"/>\n"
188 " </CallParameter>\n"
189 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
190 " <SourceParameter reference=\"Metabolite_1\"/>\n"
191 " </CallParameter>\n"
192 " </ListOfCallParameters>\n"
195 " <Reaction key=\"Reaction_2\" name=\"reaction_2\" reversible=\"false\">\n"
196 " <ListOfSubstrates>\n"
197 " <Substrate metabolite=\"Metabolite_2\" stoichiometry=\"1\"/>\n"
198 " </ListOfSubstrates>\n"
199 " <ListOfConstants>\n"
200 " <Constant key=\"Parameter_507\" name=\"k1\" value=\"0.1\"/>\n"
201 " </ListOfConstants>\n"
202 " <KineticLaw function=\"Function_13\">\n"
203 " <ListOfCallParameters>\n"
204 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
205 " <SourceParameter reference=\"Parameter_507\"/>\n"
206 " </CallParameter>\n"
207 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
208 " <SourceParameter reference=\"Metabolite_2\"/>\n"
209 " </CallParameter>\n"
210 " </ListOfCallParameters>\n"
213 " </ListOfReactions>\n"
215 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
216 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
217 " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
218 " <StateTemplateVariable objectReference=\"Metabolite_2\"/>\n"
219 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
220 " <StateTemplateVariable objectReference=\"ModelValue_1\"/>\n"
221 " <StateTemplateVariable objectReference=\"ModelValue_2\"/>\n"
222 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
223 " <StateTemplateVariable objectReference=\"Compartment_1\"/>\n"
224 " <StateTemplateVariable objectReference=\"Compartment_2\"/>\n"
225 " </StateTemplate>\n"
226 " <InitialState type=\"initialState\">\n"
227 " 0 6.022141500000001e+20 6.022141500000001e+20 6.022141500000001e+20 0 0 0 1 1 1\n"
232 " <SBMLReference file=\"bug1205.xml\">\n"
233 " <SBMLMap SBMLid=\"compartment_1\" COPASIkey=\"Compartment_2\"/>\n"
234 " <SBMLMap SBMLid=\"parameter_1\" COPASIkey=\"ModelValue_2\"/>\n"
235 " <SBMLMap SBMLid=\"reaction_1\" COPASIkey=\"Reaction_2\"/>\n"
236 " <SBMLMap SBMLid=\"species_1\" COPASIkey=\"Metabolite_2\"/>\n"
237 " </SBMLReference>\n"
SBMLDocument * getCurrentSBMLDocument()
static const char * MODEL_STRING1
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
static CCopasiDataModel * pCOPASIDATAMODEL
bool load_cps_model_from_stream(std::istream &is, CCopasiDataModel &dataModel)
static CCopasiDataModel * addDatamodel()
static void init(int argc, char *argv[], const bool &withGui=false)