19 #include "test000010.hpp"
22 #include "utilities.hpp"
25 #include "sbml/SBMLDocument.h"
26 #include "sbml/Model.h"
27 #include "sbml/Rule.h"
28 #include "sbml/Species.h"
29 #include "sbml/Parameter.h"
30 #include "sbml/math/ASTNode.h"
36 void test000010::setUp()
44 void test000010::tearDown()
49 void test000010::test_references_to_species()
55 std::istringstream iss(test000010::MODEL_STRING);
57 CPPUNIT_ASSERT(pDataModel->
getModel() != NULL);
60 CPPUNIT_ASSERT(pDocument != NULL);
61 Model* pModel = pDocument->getModel();
62 CPPUNIT_ASSERT(pModel != NULL);
65 CPPUNIT_ASSERT(pModel->getNumCompartments() == 1);
66 Compartment* pCompartment = pModel->getCompartment(0);
67 CPPUNIT_ASSERT(pCompartment->getConstant() ==
false);
68 CPPUNIT_ASSERT(pModel->getNumSpecies() == 2);
69 Species* pSpecies = pModel->getSpecies(1);
70 CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() ==
true);
71 pSpecies = pModel->getSpecies(0);
72 std::string idSpeciesA = pSpecies->getId();
73 CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() ==
true);
74 CPPUNIT_ASSERT(pModel->getNumRules() == 2);
77 AssignmentRule* pRule =
dynamic_cast<AssignmentRule*
>(pModel->getRule(0));
78 AssignmentRule* pOtherRule =
dynamic_cast<AssignmentRule*
>(pModel->getRule(1));
79 CPPUNIT_ASSERT(pRule != NULL);
80 CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
81 Parameter* pParameter = pModel->getParameter(0);
82 CPPUNIT_ASSERT(pParameter != NULL);
84 if (pRule->getVariable() != pCompartment->getId())
86 pRule =
dynamic_cast<AssignmentRule*
>(pModel->getRule(1));
87 pOtherRule =
dynamic_cast<AssignmentRule*
>(pModel->getRule(0));
90 CPPUNIT_ASSERT(pRule->getVariable() == pCompartment->getId());
91 CPPUNIT_ASSERT(pOtherRule != NULL);
92 CPPUNIT_ASSERT(pOtherRule->getVariable() == pParameter->getId());
93 const ASTNode* pMath = pOtherRule->getMath();
94 CPPUNIT_ASSERT(pMath != NULL);
96 CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
97 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
98 CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
99 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
100 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pSpecies->getId());
101 CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
102 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
103 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
104 CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
105 Reaction* pReaction = pModel->getReaction(0);
107 CPPUNIT_ASSERT(pReaction != NULL);
108 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
109 CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
115 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
116 KineticLaw* pLaw = pReaction->getKineticLaw();
117 CPPUNIT_ASSERT(pLaw != NULL);
118 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
119 pMath = pLaw->getMath();
120 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
121 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
122 CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
123 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
124 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string(
"k1"));
125 CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
126 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
127 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == idSpeciesA);
129 pReaction = pModel->getReaction(1);
131 CPPUNIT_ASSERT(pReaction != NULL);
132 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
133 CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
138 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
139 pLaw = pReaction->getKineticLaw();
140 CPPUNIT_ASSERT(pLaw != NULL);
141 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
142 pMath = pLaw->getMath();
143 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
144 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
145 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
146 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
147 pMath = pMath->getChild(1);
148 CPPUNIT_ASSERT(pMath != NULL);
149 CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
150 CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
151 pMath = pMath->getChild(0);
152 CPPUNIT_ASSERT(pMath != NULL);
153 CPPUNIT_ASSERT(pMath->getType() == AST_DIVIDE);
154 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
155 CPPUNIT_ASSERT(pMath->getChild(0) != NULL);
156 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
157 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == idSpeciesA);
158 CPPUNIT_ASSERT(pMath->getChild(1) != NULL);
159 CPPUNIT_ASSERT(pMath->getChild(1)->getType() == AST_NAME);
160 CPPUNIT_ASSERT(pMath->getChild(1)->getName() == pCompartment->getId());
163 const char* test000010::MODEL_STRING =
164 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
165 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-02-15 10:01:28 UTC -->\n"
166 "<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"
167 " <ListOfFunctions>\n"
168 " <Function key=\"Function_8\" name=\"Henri-Michaelis-Menten (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
170 " V*substrate/(Km+substrate)\n"
172 " <ListOfParameterDescriptions>\n"
173 " <ParameterDescription key=\"FunctionParameter_41\" name=\"substrate\" order=\"0\" role=\"substrate\"/>\n"
174 " <ParameterDescription key=\"FunctionParameter_30\" name=\"Km\" order=\"1\" role=\"constant\"/>\n"
175 " <ParameterDescription key=\"FunctionParameter_45\" name=\"V\" order=\"2\" role=\"constant\"/>\n"
176 " </ListOfParameterDescriptions>\n"
178 " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
180 " k1*PRODUCT<substrate_i>\n"
182 " <ListOfParameterDescriptions>\n"
183 " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
184 " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
185 " </ListOfParameterDescriptions>\n"
187 " </ListOfFunctions>\n"
188 " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"s\" volumeUnit=\"ml\" quantityUnit=\"#\" type=\"deterministic\">\n"
190 " <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"
191 "<p>Model with variable volume compartment,# quantity units and a reference to the species transient concentration.</p>\n"
192 "<p>On export this should create an SBML file with the hasOnlySubstanceUnits flag on the species set. </p>\n"
193 "<p>The reference in the rule should be divided by the volume. The references in the reactions should be divided by the volume.</p>\n"
196 " <ListOfCompartments>\n"
197 " <Compartment key=\"Compartment_0\" name=\"compartment\" simulationType=\"assignment\">\n"
202 " </ListOfCompartments>\n"
203 " <ListOfMetabolites>\n"
204 " <Metabolite key=\"Metabolite_0\" name=\"A\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
206 " <Metabolite key=\"Metabolite_1\" name=\"S\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
208 " </ListOfMetabolites>\n"
209 " <ListOfModelValues>\n"
210 " <ModelValue key=\"ModelValue_0\" name=\"K\" simulationType=\"assignment\">\n"
212 " <CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=Concentration>\n"
215 " </ListOfModelValues>\n"
216 " <ListOfReactions>\n"
217 " <Reaction key=\"Reaction_0\" name=\"reaction\" reversible=\"false\">\n"
218 " <ListOfSubstrates>\n"
219 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
220 " </ListOfSubstrates>\n"
221 " <ListOfConstants>\n"
222 " <Constant key=\"Parameter_93\" name=\"k1\" value=\"0.1\"/>\n"
223 " </ListOfConstants>\n"
224 " <KineticLaw function=\"Function_13\">\n"
225 " <ListOfCallParameters>\n"
226 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
227 " <SourceParameter reference=\"Parameter_93\"/>\n"
228 " </CallParameter>\n"
229 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
230 " <SourceParameter reference=\"Metabolite_0\"/>\n"
231 " </CallParameter>\n"
232 " </ListOfCallParameters>\n"
235 " <Reaction key=\"Reaction_1\" name=\"reaction_1\" reversible=\"false\">\n"
236 " <ListOfSubstrates>\n"
237 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
238 " </ListOfSubstrates>\n"
239 " <ListOfProducts>\n"
240 " <Product metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
241 " </ListOfProducts>\n"
242 " <ListOfConstants>\n"
243 " <Constant key=\"Parameter_92\" name=\"Km\" value=\"0.1\"/>\n"
244 " <Constant key=\"Parameter_91\" name=\"V\" value=\"0.1\"/>\n"
245 " </ListOfConstants>\n"
246 " <KineticLaw function=\"Function_8\">\n"
247 " <ListOfCallParameters>\n"
248 " <CallParameter functionParameter=\"FunctionParameter_41\">\n"
249 " <SourceParameter reference=\"Metabolite_0\"/>\n"
250 " </CallParameter>\n"
251 " <CallParameter functionParameter=\"FunctionParameter_30\">\n"
252 " <SourceParameter reference=\"Parameter_92\"/>\n"
253 " </CallParameter>\n"
254 " <CallParameter functionParameter=\"FunctionParameter_45\">\n"
255 " <SourceParameter reference=\"Parameter_91\"/>\n"
256 " </CallParameter>\n"
257 " </ListOfCallParameters>\n"
260 " </ListOfReactions>\n"
262 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
263 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
264 " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
265 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
266 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
267 " </StateTemplate>\n"
268 " <InitialState type=\"initialState\">\n"
269 " 0 7 0.7000000000000002 7 1\n"
SBMLDocument * getCurrentSBMLDocument()
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
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)