END_TEST
START_TEST (test_conversion_inlineFD_bug)
{
std::string filename = "/inline_bug_minimal.xml";
filename = TestDataDirectory + filename;
SBMLDocument* doc = readSBMLFromFile(filename.c_str());
ConversionProperties props;
props.addOption("expandFunctionDefinitions", "true");
fail_unless(doc->getModel() != NULL);
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel()->getNumReactions() == 1);
fail_unless(doc->getModel()->getReaction(0)->isSetKineticLaw());
fail_unless(doc->getModel()->getReaction(0)->getKineticLaw()->getMath() != NULL);
// all seems good ... write it
const ASTNode * node = doc->getModel()->getReaction(0)->getKineticLaw()->getMath();
#ifndef LIBSBML_USE_LEGACY_MATH
fail_unless(node->ASTBase::isChild() == false);
#endif
std::string math = writeMathMLToString(node);
ASTNode* test = readMathMLFromString(math.c_str());
fail_unless(test != NULL);
// additional test where the node being converted is the top-level
fail_unless(doc->getModel()->getNumRules() == 1);
fail_unless(doc->getModel()->getRule(0)->isSetMath());
fail_unless(doc->getModel()->getRule(0)->getMath() != NULL);
node = doc->getModel()->getRule(0)->getMath();
#ifndef LIBSBML_USE_LEGACY_MATH
fail_unless(node->ASTBase::isChild() == false);
#endif
math = writeMathMLToString(node);
test = readMathMLFromString(math.c_str());
fail_unless(test != NULL);
delete test;
delete doc;
}
END_TEST
START_TEST (test_conversion_inlineIA_bug)
{
std::string filename = "/ia-ternary-lt.xml";
filename = TestDataDirectory + filename;
SBMLDocument* doc = readSBMLFromFile(filename.c_str());
ConversionProperties props;
props.addOption("expandInitialAssignments", "true");
fail_unless(doc->getModel() != NULL);
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel()->getNumInitialAssignments() == 0);
fail_unless(doc->getModel()->getParameter("x")->isSetValue());
fail_unless(doc->getModel()->getParameter("x")->getValue() == 3);
delete doc;
}
END_TEST
START_TEST (test_SBMLTransforms_expandFD)
{
std::string filename(TestDataDirectory);
filename += "multiple-functions.xml";
// test 1: skip expansion of 'f'
SBMLDocument *doc = readSBMLFromFile(filename.c_str());
ConversionProperties props;
props.addOption("expandFunctionDefinitions", true);
props.addOption("skipIds", "f");
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel() != NULL);
fail_unless(doc->getModel()->getNumFunctionDefinitions() == 1);
fail_unless(doc->getModel()->getFunctionDefinition("f") != NULL);
delete doc;
// test 2: expand all
doc = readSBMLFromFile(filename.c_str());
props = ConversionProperties();
props.addOption("expandFunctionDefinitions", true);
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel() != NULL);
fail_unless(doc->getModel()->getNumFunctionDefinitions() == 0);
delete doc;
// test 3: don't expand f and g
doc = readSBMLFromFile(filename.c_str());
props = ConversionProperties();
props.addOption("expandFunctionDefinitions", true);
props.addOption("skipIds", "f,g");
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel() != NULL);
fail_unless(doc->getModel()->getNumFunctionDefinitions() == 2);
delete doc;
// test 4: even though comma separated is advertized, make sure that ';' works
doc = readSBMLFromFile(filename.c_str());
props = ConversionProperties();
props.addOption("expandFunctionDefinitions", true);
props.addOption("skipIds", "f;g");
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel() != NULL);
fail_unless(doc->getModel()->getNumFunctionDefinitions() == 2);
delete doc;
// test 5: or space
doc = readSBMLFromFile(filename.c_str());
props = ConversionProperties();
props.addOption("expandFunctionDefinitions", true);
props.addOption("skipIds", "f g");
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel() != NULL);
fail_unless(doc->getModel()->getNumFunctionDefinitions() == 2);
delete doc;
// test 6: or tab
doc = readSBMLFromFile(filename.c_str());
props = ConversionProperties();
props.addOption("expandFunctionDefinitions", true);
props.addOption("skipIds", "f\tg");
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel() != NULL);
fail_unless(doc->getModel()->getNumFunctionDefinitions() == 2);
delete doc;
// test 7: or a combination
doc = readSBMLFromFile(filename.c_str());
props = ConversionProperties();
props.addOption("expandFunctionDefinitions", true);
props.addOption("skipIds", "f; g");
fail_unless(doc->convert(props) == LIBSBML_OPERATION_SUCCESS);
fail_unless(doc->getModel() != NULL);
fail_unless(doc->getModel()->getNumFunctionDefinitions() == 2);
delete doc;
}
int
main (int argc, char* argv[])
{
char *line;
char *result;
char *buffer = (char*)calloc( 1, sizeof(char) );
unsigned long len;
L3ParserSettings_t* settings;
int reading = 1;
SBMLDocument_t* doc = NULL;
printf( "\n" );
printf( "This program translates infix formulas into MathML and\n" );
printf( "vice-versa. An 'enter' or a 'return' on an empty line\n" );
printf( "triggers translation.\n" );
printf( "\n" );
settings = L3ParserSettings_create();
while (reading)
{
printf( "Enter infix formula, MathML expression, \n");
printf( "or change parsing rules with the keywords:\n");
printf( "LOG_AS_LOG10, LOG_AS_LN, LOG_AS_ERROR, EXPAND_UMINUS, ");
printf( "COLLAPSE_UMINUS, TARGETL2, TARGETL3, NO_UNITS, UNITS, ");
printf( "or FILE:<filename>\n\n\n" );
printf( "> " );
do
{
line = trim_whitespace(get_line(stdin));
len = (unsigned int)strlen(line);
if (len > 0)
{
buffer = (char *) realloc( buffer, 1 + strlen(buffer) + len );
if (strcmp(line, "LOG_AS_LOG10")==0) {
L3ParserSettings_setParseLog(settings, L3P_PARSE_LOG_AS_LOG10);
printf( "Now parsing 'log(x)' as 'log10(x)'\n\n> ");
}
else if (strcmp(line, "LOG_AS_LN")==0) {
L3ParserSettings_setParseLog(settings, L3P_PARSE_LOG_AS_LN);
printf( "Now parsing 'log(x)' as 'ln(x)'\n\n> ");
}
else if (strcmp(line, "LOG_AS_ERROR")==0) {
L3ParserSettings_setParseLog(settings, L3P_PARSE_LOG_AS_ERROR);
printf( "Now parsing 'log(x)' as an error\n\n> ");
}
else if (strcmp(line, "EXPAND_UMINUS")==0) {
L3ParserSettings_setParseCollapseMinus(settings, 0);
printf( "Will now leave multiple unary minuses expanded, ");
printf("and all negative numbers will be translated using the ");
printf("<minus> construct.\n\n> ");
}
else if (strcmp(line, "COLLAPSE_UMINUS")==0) {
L3ParserSettings_setParseCollapseMinus(settings, 1);
printf( "Will now collapse multiple unary minuses, and incorporate ");
printf("a negative sign into digits.\n\n> ");
}
else if (strcmp(line, "NO_UNITS")==0) {
L3ParserSettings_setParseUnits(settings, 0);
printf( "Will now target MathML but with no units on numbers.\n\n> ");
}
else if (strcmp(line, "UNITS")==0) {
L3ParserSettings_setParseUnits(settings, 1);
printf( "Will now target MathML but with units on numbers.\n\n> ");
}
else if (line[0] == 'F' && line[1] == 'I' && line[2]=='L'
&& line[3]=='E' && line[4]==':') {
int len = strlen(line);
char *filename = (char*) malloc(len-5+1);
strncpy(filename, line+5, len-5);
SBMLDocument_free(doc);
doc = readSBMLFromFile(filename);
if (SBMLDocument_getModel(doc)==NULL) {
printf( "File '%s' not found or no model present.", filename);
printf( "Clearing the Model parsing object.\n\n> ");
}
else {
printf( "Using model from file %s to parse infix:", filename);
printf( "all symbols present in that model will not be translated ");
printf( "as native MathML or SBML-defined elements.\n\n> ");;
}
L3ParserSettings_setModel(settings, SBMLDocument_getModel(doc));
}
else
{
strncat(buffer, line, len);
strncat(buffer, "\n", 1);
}
}
else
{
result = (buffer[0] == '<') ?
translateMathML(buffer) : translateInfix(buffer, settings);
printf("Result:\n\n%s\n\n\n", result);
free(result);
reading = 0;
}
}
while (len > 0);
}
free(line);
return 0;
}
