19 #include "test000006.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 test000006::setUp()
44 void test000006::tearDown()
49 void test000006::test_references_to_species()
55 std::istringstream iss(test000006::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() ==
true);
68 CPPUNIT_ASSERT(pModel->getNumSpecies() == 2);
69 Species* pSpecies = pModel->getSpecies(1);
70 CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() ==
false);
71 pSpecies = pModel->getSpecies(0);
72 std::string idSpeciesA = pSpecies->getId();
73 CPPUNIT_ASSERT(pSpecies->getHasOnlySubstanceUnits() ==
false);
74 CPPUNIT_ASSERT(pModel->getNumInitialAssignments() == 1);
75 InitialAssignment* pAssignment = pModel->getInitialAssignment(0);
76 CPPUNIT_ASSERT(pAssignment != NULL);
77 CPPUNIT_ASSERT(pModel->getNumParameters() == 1);
78 Parameter* pParameter = pModel->getParameter(0);
79 CPPUNIT_ASSERT(pParameter != NULL);
80 CPPUNIT_ASSERT(pAssignment->getSymbol() == pParameter->getId());
81 const ASTNode* pMath = pAssignment->getMath();
82 CPPUNIT_ASSERT(pMath != NULL);
85 CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
86 CPPUNIT_ASSERT(pMath->getName() == pSpecies->getId());
87 CPPUNIT_ASSERT(pModel->getNumReactions() == 2);
88 Reaction* pReaction = pModel->getReaction(0);
90 CPPUNIT_ASSERT(pReaction != NULL);
91 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
92 CPPUNIT_ASSERT(pReaction->getNumProducts() == 0);
98 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
99 KineticLaw* pLaw = pReaction->getKineticLaw();
100 CPPUNIT_ASSERT(pLaw != NULL);
101 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
102 pMath = pLaw->getMath();
103 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
104 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
105 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
106 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
107 pMath = pMath->getChild(1);
108 CPPUNIT_ASSERT(pMath != NULL);
109 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
110 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
111 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
112 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == std::string(
"k1"));
113 pMath = pMath->getChild(1);
114 CPPUNIT_ASSERT(pMath != NULL);
115 CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
116 CPPUNIT_ASSERT(pMath->getName() == idSpeciesA);
118 pReaction = pModel->getReaction(1);
120 CPPUNIT_ASSERT(pReaction != NULL);
121 CPPUNIT_ASSERT(pReaction->getNumReactants() == 1);
122 CPPUNIT_ASSERT(pReaction->getNumProducts() == 1);
127 CPPUNIT_ASSERT(pReaction->isSetKineticLaw() ==
true);
128 pLaw = pReaction->getKineticLaw();
129 CPPUNIT_ASSERT(pLaw != NULL);
130 CPPUNIT_ASSERT(pLaw->isSetMath() ==
true);
131 pMath = pLaw->getMath();
132 CPPUNIT_ASSERT(pMath->getType() == AST_TIMES);
133 CPPUNIT_ASSERT(pMath->getNumChildren() == 2);
134 CPPUNIT_ASSERT(pMath->getChild(0)->getType() == AST_NAME);
135 CPPUNIT_ASSERT(pMath->getChild(0)->getName() == pCompartment->getId());
136 pMath = pMath->getChild(1);
137 CPPUNIT_ASSERT(pMath != NULL);
138 CPPUNIT_ASSERT(pMath->getType() == AST_FUNCTION);
139 CPPUNIT_ASSERT(pMath->getNumChildren() == 3);
140 pMath = pMath->getChild(0);
141 CPPUNIT_ASSERT(pMath != NULL);
142 CPPUNIT_ASSERT(pMath->getType() == AST_NAME);
143 CPPUNIT_ASSERT(pMath->getName() == idSpeciesA);
146 const char* test000006::MODEL_STRING =
147 "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n"
148 "<!-- generated with COPASI 4.3.25 (Debug) (http://www.copasi.org) at 2008-02-15 09:31:22 UTC -->\n"
149 "<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"
150 " <ListOfFunctions>\n"
151 " <Function key=\"Function_8\" name=\"Henri-Michaelis-Menten (irreversible)\" type=\"PreDefined\" reversible=\"false\">\n"
153 " V*substrate/(Km+substrate)\n"
155 " <ListOfParameterDescriptions>\n"
156 " <ParameterDescription key=\"FunctionParameter_41\" name=\"substrate\" order=\"0\" role=\"substrate\"/>\n"
157 " <ParameterDescription key=\"FunctionParameter_30\" name=\"Km\" order=\"1\" role=\"constant\"/>\n"
158 " <ParameterDescription key=\"FunctionParameter_45\" name=\"V\" order=\"2\" role=\"constant\"/>\n"
159 " </ListOfParameterDescriptions>\n"
161 " <Function key=\"Function_13\" name=\"Mass action (irreversible)\" type=\"MassAction\" reversible=\"false\">\n"
163 " k1*PRODUCT<substrate_i>\n"
165 " <ListOfParameterDescriptions>\n"
166 " <ParameterDescription key=\"FunctionParameter_81\" name=\"k1\" order=\"0\" role=\"constant\"/>\n"
167 " <ParameterDescription key=\"FunctionParameter_79\" name=\"substrate\" order=\"1\" role=\"substrate\"/>\n"
168 " </ListOfParameterDescriptions>\n"
170 " </ListOfFunctions>\n"
171 " <Model key=\"Model_1\" name=\"New Model\" timeUnit=\"s\" volumeUnit=\"ml\" quantityUnit=\"#\" type=\"deterministic\">\n"
173 " <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"
174 "<p>Model with constant volume compartment,# quantity units and a reference to the species initial concentration.</p>\n"
175 "<p>On export this should create an SBML file with the hasOnlySubstanceUnits flag on the species unset. </p>\n"
176 "<p>All references to the species should be unmodified.</p>\n"
179 " <ListOfCompartments>\n"
180 " <Compartment key=\"Compartment_0\" name=\"compartment\" simulationType=\"fixed\">\n"
182 " </ListOfCompartments>\n"
183 " <ListOfMetabolites>\n"
184 " <Metabolite key=\"Metabolite_0\" name=\"A\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
186 " <Metabolite key=\"Metabolite_1\" name=\"S\" simulationType=\"reactions\" compartment=\"Compartment_0\">\n"
188 " </ListOfMetabolites>\n"
189 " <ListOfModelValues>\n"
190 " <ModelValue key=\"ModelValue_0\" name=\"K\" simulationType=\"fixed\">\n"
191 " <InitialExpression>\n"
192 " <CN=Root,Model=New Model,Vector=Compartments[compartment],Vector=Metabolites[A],Reference=InitialConcentration>\n"
193 " </InitialExpression>\n"
195 " </ListOfModelValues>\n"
196 " <ListOfReactions>\n"
197 " <Reaction key=\"Reaction_0\" name=\"reaction\" reversible=\"false\">\n"
198 " <ListOfSubstrates>\n"
199 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
200 " </ListOfSubstrates>\n"
201 " <ListOfConstants>\n"
202 " <Constant key=\"Parameter_93\" name=\"k1\" value=\"0.1\"/>\n"
203 " </ListOfConstants>\n"
204 " <KineticLaw function=\"Function_13\">\n"
205 " <ListOfCallParameters>\n"
206 " <CallParameter functionParameter=\"FunctionParameter_81\">\n"
207 " <SourceParameter reference=\"Parameter_93\"/>\n"
208 " </CallParameter>\n"
209 " <CallParameter functionParameter=\"FunctionParameter_79\">\n"
210 " <SourceParameter reference=\"Metabolite_0\"/>\n"
211 " </CallParameter>\n"
212 " </ListOfCallParameters>\n"
215 " <Reaction key=\"Reaction_1\" name=\"reaction_1\" reversible=\"false\">\n"
216 " <ListOfSubstrates>\n"
217 " <Substrate metabolite=\"Metabolite_0\" stoichiometry=\"1\"/>\n"
218 " </ListOfSubstrates>\n"
219 " <ListOfProducts>\n"
220 " <Product metabolite=\"Metabolite_1\" stoichiometry=\"1\"/>\n"
221 " </ListOfProducts>\n"
222 " <ListOfConstants>\n"
223 " <Constant key=\"Parameter_92\" name=\"Km\" value=\"0.1\"/>\n"
224 " <Constant key=\"Parameter_91\" name=\"V\" value=\"0.1\"/>\n"
225 " </ListOfConstants>\n"
226 " <KineticLaw function=\"Function_8\">\n"
227 " <ListOfCallParameters>\n"
228 " <CallParameter functionParameter=\"FunctionParameter_41\">\n"
229 " <SourceParameter reference=\"Metabolite_0\"/>\n"
230 " </CallParameter>\n"
231 " <CallParameter functionParameter=\"FunctionParameter_30\">\n"
232 " <SourceParameter reference=\"Parameter_92\"/>\n"
233 " </CallParameter>\n"
234 " <CallParameter functionParameter=\"FunctionParameter_45\">\n"
235 " <SourceParameter reference=\"Parameter_91\"/>\n"
236 " </CallParameter>\n"
237 " </ListOfCallParameters>\n"
240 " </ListOfReactions>\n"
242 " <StateTemplateVariable objectReference=\"Model_1\"/>\n"
243 " <StateTemplateVariable objectReference=\"Metabolite_0\"/>\n"
244 " <StateTemplateVariable objectReference=\"Metabolite_1\"/>\n"
245 " <StateTemplateVariable objectReference=\"ModelValue_0\"/>\n"
246 " <StateTemplateVariable objectReference=\"Compartment_0\"/>\n"
247 " </StateTemplate>\n"
248 " <InitialState type=\"initialState\">\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)