19 #include "test000003.hpp"
22 #include "utilities.hpp"
26 #include "sbml/SBMLDocument.h"
27 #include "sbml/Model.h"
28 #include "sbml/Rule.h"
29 #include "sbml/Species.h"
30 #include "sbml/Parameter.h"
31 #include "sbml/math/ASTNode.h"
37 void test000003::setUp()
45 void test000003::tearDown()
50 void test000003::test_references_to_species()
56 std::istringstream iss(test000003::MODEL_STRING);
58 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
61 CPPUNIT_ASSERT(pDocument != NULL);
62 Model* pModel = pDocument->getModel();
63 CPPUNIT_ASSERT(pModel != NULL);
66 CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
67 Compartment* pCompartment = pModel->getCompartment(0);
68 CPPUNIT_ASSERT(pCompartment->getConstant() ==
true);
69 CPPUNIT_ASSERT(pModel->getNumSpecies() == 2);
70 Species* pSpecies = pModel->getSpecies(1);
71 CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() ==
false);
72 pSpecies = pModel->getSpecies(0);
73 std::string idSpeciesA = pSpecies->getId();
74 CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() ==
false);
75 CPPUNIT_ASSERT(pModel->getNumRules() == 1);
76 AssignmentRule* pRule =
dynamic_cast<AssignmentRule*
>(pModel->getRule(0));
77 CPPUNIT_ASSERT(pRule != NULL);
78 CPPUNIT_ASSERT(pModel->getNumParameters() == 2);
79 Parameter* pParameter = pModel->getParameter(0);
80 CPPUNIT_ASSERT(pParameter != NULL);
81 Parameter* pFactor = pModel->getParameter(1);
82 CPPUNIT_ASSERT(pFactor != NULL);
84 CPPUNIT_ASSERT(pRule->getVariable() == pParameter->getId());
85 const ASTNode* pMath = pRule->getMath();
86 CPPUNIT_ASSERT(pMath != NULL);
89 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
90 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
91 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
92 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
93 pMath = pMath->getChild(0);
94 CPPUNIT_ASSERT(pMath != NULL);
95 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
96 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
97 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
98 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pSpecies->getId());
100 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
101 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pFactor->getId());
102 CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
103 Reaction* pReaction = pModel->getReaction(0);
105 CPPUNIT_ASSERT(pReaction != NULL);
106 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
107 CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
113 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
114 KineticLaw* pLaw = pReaction->getKineticLaw();
115 CPPUNIT_ASSERT(pLaw != NULL);
116 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
117 pMath = pLaw->getMath();
118 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
119 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
120 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
121 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
122 pMath = pMath->getChild(1);
123 CPPUNIT_ASSERT(pMath != NULL);
124 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
125 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
126 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
127 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string(
"k1"));
128 pMath = pMath->getChild(1);
129 CPPUNIT_ASSERT(pMath != NULL);
130 CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
131 CPPUNIT_ASSERT(pMath->getName() == idSpeciesA);
133 pReaction = pModel->getReaction(1);
135 CPPUNIT_ASSERT(pReaction != NULL);
136 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
137 CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
142 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
143 pLaw = pReaction->getKineticLaw();
144 CPPUNIT_ASSERT(pLaw != NULL);
145 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
146 pMath = pLaw->getMath();
147 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
148 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
149 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
150 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
151 pMath = pMath->getChild(1);
152 CPPUNIT_ASSERT(pMath != NULL);
153 CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
154 CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
155 pMath = pMath->getChild(0);
156 CPPUNIT_ASSERT(pMath != NULL);
157 CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
158 CPPUNIT_ASSERT(pMath->getName() == idSpeciesA);
161 const char* test000003::MODEL_STRING =
162 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
163 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-02-15 09:28:38 UTC -->\n"
164 "<COPASI xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xsi:noNamespaceSchemaLocation=\"http://www.copasi.org/static/schema.xsd\" versionMajor=\"1\" versionMinor=\"0\" versionDevel=\"25\">\n"
165 " <ListOfFunctions>\n"
166 " <Function key=\"Function_8\" name=\"Henri-Michaelis-Menten (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
168 " V*substrate/(Km+substrate)\n"
170 " <ListOfParameterDescriptions>\n"
171 " <ParameterDescription key=\"FunctionParameter_41\" name=\"substrate\" order=\"0\" role=\"substrate\"/>\n"
172 " <ParameterDescription key=\"FunctionParameter_30\" name=\"Km\" order=\"1\" role=\"constant\"/>\n"
173 " <ParameterDescription key=\"FunctionParameter_45\" name=\"V\" order=\"2\" role=\"constant\"/>\n"
174 " </ListOfParameterDescriptions>\n"
176 " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
178 " k1*PRODUCT<substrate_i>\n"
180 " <ListOfParameterDescriptions>\n"
181 " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
182 " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
183 " </ListOfParameterDescriptions>\n"
185 " </ListOfFunctions>\n"
186 " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"s\" volumeUnit=\"ml\" quantityUnit=\"mmol\" type=\"deterministic\">\n"
188 " <html xmlns=\"http://www.w3.org/1999/xhtml\"><head><meta name=\"qrichtext\" content=\"1\" /></head><body style=\"font-size:13pt;font-family:Lucida Grande\">\n"
189 "<p>Model with constant volume compartment,mmol quantity units and a reference to the species transient amount.</p>\n"
190 "<p>On export this should create an SBML file with the hasOnlySubstanceUnits flag on the species unset. </p>\n"
191 "<p>The reference to the species in the rule should be multiplied by a factor (6.023e20) as well as by the volume of the compartment</p>\n"
194 " <ListOfCompartments>\n"
195 " <Compartment key=\"Compartment_0\" name=\"compartment\" simulationType=\"fixed\">\n"
197 " </ListOfCompartments>\n"
198 " <ListOfMetabolites>\n"
199 " <Metabolite key=\"Metabolite_0\" name=\"A\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
201 " <Metabolite key=\"Metabolite_1\" name=\"S\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
203 " </ListOfMetabolites>\n"
204 " <ListOfModelValues>\n"
205 " <ModelValue key=\"ModelValue_0\" name=\"K\" simulationType=\"assignment\">\n"
207 " <CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=ParticleNumber>\n"
210 " </ListOfModelValues>\n"
211 " <ListOfReactions>\n"
212 " <Reaction key=\"Reaction_0\" name=\"reaction\" reversible=\"false\">\n"
213 " <ListOfSubstrates>\n"
214 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
215 " </ListOfSubstrates>\n"
216 " <ListOfConstants>\n"
217 " <Constant key=\"Parameter_93\" name=\"k1\" value=\"0.1\"/>\n"
218 " </ListOfConstants>\n"
219 " <KineticLaw function=\"Function_13\">\n"
220 " <ListOfCallParameters>\n"
221 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
222 " <SourceParameter reference=\"Parameter_93\"/>\n"
223 " </CallParameter>\n"
224 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
225 " <SourceParameter reference=\"Metabolite_0\"/>\n"
226 " </CallParameter>\n"
227 " </ListOfCallParameters>\n"
230 " <Reaction key=\"Reaction_1\" name=\"reaction_1\" reversible=\"false\">\n"
231 " <ListOfSubstrates>\n"
232 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
233 " </ListOfSubstrates>\n"
234 " <ListOfProducts>\n"
235 " <Product metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
236 " </ListOfProducts>\n"
237 " <ListOfConstants>\n"
238 " <Constant key=\"Parameter_92\" name=\"Km\" value=\"0.1\"/>\n"
239 " <Constant key=\"Parameter_91\" name=\"V\" value=\"0.1\"/>\n"
240 " </ListOfConstants>\n"
241 " <KineticLaw function=\"Function_8\">\n"
242 " <ListOfCallParameters>\n"
243 " <CallParameter functionParameter=\"FunctionParameter_41\">\n"
244 " <SourceParameter reference=\"Metabolite_0\"/>\n"
245 " </CallParameter>\n"
246 " <CallParameter functionParameter=\"FunctionParameter_30\">\n"
247 " <SourceParameter reference=\"Parameter_92\"/>\n"
248 " </CallParameter>\n"
249 " <CallParameter functionParameter=\"FunctionParameter_45\">\n"
250 " <SourceParameter reference=\"Parameter_91\"/>\n"
251 " </CallParameter>\n"
252 " </ListOfCallParameters>\n"
255 " </ListOfReactions>\n"
257 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
258 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
259 " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
260 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
261 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
262 " </StateTemplate>\n"
263 " <InitialState type=\"initialState\">\n"
264 " 0 6.022141500000001e+20 6.022141500000001e+19 6.022141500000001e+20 1\n"
SBMLDocument * getCurrentSBMLDocument()
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
bool load_cps_model_from_stream(std::istream &is, CCopasiDataModel &dataModel)
const C_FLOAT64 & getQuantity2NumberFactor() const
static CCopasiDataModel * addDatamodel()
static void init(int argc, char *argv[], const bool &withGui=false)