END_TEST
START_TEST (test_comp_deletion_metaid)
{
const char *name = "delMetaId";
fail_unless( !SBase_isSetMetaId(P) );
SBase_setMetaId(P, name);
const char* getmetaid = SBase_getMetaId(P);
fail_unless( !strcmp(getmetaid, name) );
fail_unless( SBase_isSetMetaId(P) );
if (getmetaid == name)
{
fail("SBase_setMetaId(...) did not make a copy of string.");
}
SBase_unsetMetaId(P);
fail_unless( !SBase_isSetMetaId(P) );
if (SBase_getMetaId(P) != NULL)
{
fail("Deletion_unsetName(P) did not clear string.");
}
}
END_TEST
START_TEST (test_SBMLConvertStrict_convertToL1)
{
SBMLDocument_t *d = SBMLDocument_createWithLevelAndVersion(2, 4);
/* create model with metaid */
Model_t * m = SBMLDocument_createModel(d);
SBase_setMetaId((SBase_t *) (m), "_m");
/* create a compartment with sbo*/
Compartment_t * c = Model_createCompartment(m);
Compartment_setId(c, "c");
SBase_setSBOTerm((SBase_t *) (c), 240);
/* create a species with hasOnlySubstanceUnits = true*/
Species_t *s = Model_createSpecies(m);
Species_setId(s, "s");
Species_setCompartment(s, "c");
Species_setHasOnlySubstanceUnits(s, 1);
fail_unless( SBMLDocument_setLevelAndVersionStrict(d, 1, 2) == 1 );
fail_unless( SBMLDocument_getLevel (d) == 1, NULL );
fail_unless( SBMLDocument_getVersion(d) == 2, NULL );
///* check that attributes that are no longer valid have been removed */
Model_t * m1 = SBMLDocument_getModel(d);
fail_unless (SBase_getMetaId((SBase_t *) (m1)) == NULL);
Compartment_t *c1 = Model_getCompartment(m1, 0);
fail_unless (SBase_getSBOTerm((SBase_t *) (c1)) == -1, NULL );
Species_t *s1 = Model_getSpecies(m1, 0);
fail_unless (Species_getHasOnlySubstanceUnits(s1) == 0);
SBMLDocument_free(d);
}
END_TEST
START_TEST (test_L3_Species_ModelHistory)
{
ModelHistory_t * history = ModelHistory_create();
SBase_setMetaId((SBase_t *)(S), "_3");
int i = SBase_setModelHistory((SBase_t *)(S), history);
fail_unless( i == LIBSBML_INVALID_OBJECT );
fail_unless( !SBase_isSetModelHistory((SBase_t *)(S)) );
ModelCreator_t * mc = ModelCreator_create();
Date_t * date =
Date_createFromValues(2005, 12, 30, 12, 15, 45, 1, 2, 0);
ModelCreator_setFamilyName(mc, "Keating");
ModelCreator_setGivenName(mc, "Sarah");
ModelCreator_setEmail(mc, "*****@*****.**");
ModelCreator_setOrganisation(mc, "UH");
ModelHistory_addCreator(history, mc);
ModelHistory_setCreatedDate(history, date);
ModelHistory_setModifiedDate(history, date);
i = SBase_setModelHistory((SBase_t *)(S), history);
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( SBase_isSetModelHistory((SBase_t *)(S)) );
i = SBase_unsetModelHistory((SBase_t *)(S));
fail_unless( i == LIBSBML_OPERATION_SUCCESS );
fail_unless( !SBase_isSetModelHistory((SBase_t *)(S)) );
fail_unless( SBase_getModelHistory((SBase_t *)(S)) == NULL );
ModelHistory_free(history);
ModelCreator_free(mc);
Date_free(date);
}
int
main (int argc, char *argv[])
{
SBMLDocument_t* d;
Model_t* m;
unsigned int errors, n;
Reaction_t *r;
if (argc != 3)
{
printf("\n"
" usage: addingEvidenceCodes_1 <input-filename> <output-filename>\n"
" Adds controlled vocabulary term to a reaction\n"
"\n");
return 2;
}
d = readSBML(argv[1]);
errors = SBMLDocument_getNumErrors(d);
if (errors > 0)
{
printf("Read Error(s):\n");
SBMLDocument_printErrors(d, stdout);
printf("Correct the above and re-run.\n");
}
else
{
m = SBMLDocument_getModel(d);
n = Model_getNumReactions(m);
if (n <= 0)
{
printf( "Model has no reactions.\n Cannot add CV terms\n");
}
else
{
CVTerm_t *cv1, *cv2;
r = Model_getReaction(m, 0);
/* check that the reaction has a metaid
* no CVTerms will be added if there is no metaid to reference
*/
if (SBase_isSetMetaId((SBase_t*)r))
SBase_setMetaId((SBase_t*)r, "metaid_0000052");
cv1 = CVTerm_createWithQualifierType(BIOLOGICAL_QUALIFIER);
CVTerm_setBiologicalQualifierType(cv1, BQB_IS_DESCRIBED_BY);
CVTerm_addResource(cv1, "urn:miriam:obo.eco:ECO%3A0000183");
SBase_addCVTerm((SBase_t*)r, cv1);
cv2 = CVTerm_createWithQualifierType(BIOLOGICAL_QUALIFIER);
CVTerm_setBiologicalQualifierType(cv2, BQB_IS);
CVTerm_addResource(cv2, "urn:miriam:kegg.reaction:R00756");
CVTerm_addResource(cv2, "urn:miriam:reactome:REACT_736");
SBase_addCVTerm((SBase_t*)r, cv2);
writeSBML(d, argv[2]);
}
}
SBMLDocument_free(d);
return errors;
}
