/* declares constant = false for any L1 compartment/parameter
* assigned by a rule
*/
void
Model::addConstantAttribute()
{
unsigned int n;
// parameters and compartments are declared to have constant=true
// by default. Since in L1 the constant attribute didnt exist
// parameters/compartments that are the subjcet of rules must have
// the value changed
for ( n = 0; n < getNumParameters(); n++)
{
if (getRule(getParameter(n)->getId()) != NULL)
{
getParameter(n)->setConstant(false);
}
}
for ( n = 0; n < getNumCompartments(); n++)
{
if (getRule(getCompartment(n)->getId()) != NULL)
{
getCompartment(n)->setConstant(false);
}
}
}
bool CLuaSocketRestrictions::isAllowed(RestrictType type, const char* hostname, int port) {
const TSocketRule* rule = getRule(type, hostname, port);
if (rule==NULL) {
return false;
}
return rule->allowed;
}
L::Integrator::Status L::RuleIntegratorErr::integrate (
Integrand &f, const Hypercube &h, Index maxEval,
real reqAbsError, real reqRelError, EstErr &ee)
{
checkDimension(h, f);
checkTerminationCriteria (maxEval, reqAbsError, reqRelError, false);
std::auto_ptr<EmbeddedRule> rule (getRule(h.getDimension()));
if (maxEval < rule->getNumPoints ())
{
#ifdef HINTLIB_NO_EXCEPTIONS
ee.set (0.0, 0.0);
return ERROR;
#else
throw NoEvaluationsPossible (maxEval);
#endif
}
rule->evalError (f, h, ee);
Status status = checkRequestedError (ee, reqAbsError, reqRelError);
return (status == ERROR) ? MAX_EVAL_REACHED : status;
}
void LessAtRule::process(Stylesheet &s) {
AtRule* target = s.createAtRule(getKeyword());
target->setRule(getRule());
getLessStylesheet()->getContext()->processValue(target->getRule());
}
/* the new strict setters mean that for a conversion to L2 to
* take place the model needs to think it still l1 for
* some actions and think it is already L2 for others
*/
void
Model::removeParameterRuleUnits (bool strict)
{
if (strict == true)
{
/* in L1 a parameterRule coulkd specify units
* for a strict conversion this attribute should be unset
*/
for (unsigned int n = 0; n < getNumParameters(); n++)
{
if (getRule(getParameter(n)->getId()) != NULL)
{
getRule(getParameter(n)->getId())->unsetUnits();
}
}
}
}
void LegacyRulePlanNode::write(FileWriter &w, CPArea parentArea) const
{
PlanNode::write(w, parentArea);
// write rule identification including revision here
w.appendIdentifier(getDatabase()->getId(),'/');
w.appendIdentifier(getCube()->getId(),'/');
w.appendIdentifier(getRule()->getId(),'/');
w.appendIdentifier((IdentifierType)getDatabase()->getObjectRevision(),0); // TODO: -jj- serialize uint64_t
}
void drawFractal(char* axiom, double heading, double angle, int depth, int fractalNumber)
{
currX = 149 + (300 * fractalNumber);
currY = 299;
currH = heading;
minX = 300;
maxX = 0;
minY = 300;
maxY = 0;
int dim;
dim = depth;
if (depth == 0)
dim = 1;
char masterAxiom[MAX_RULES * dim * MAX_CHARS];
strcpy(masterAxiom, axiom);
char rule[MAX_RULES * dim * MAX_CHARS];
char after[MAX_RULES * dim * MAX_CHARS];
int i;
for (i = 0; i < depth; i++)
{
int j;
for (j = 0; j < strlen(masterAxiom); j++)
{
if ('A' <= masterAxiom[j] && masterAxiom[j] <= 'Z' ||
'a' <= masterAxiom[j] && masterAxiom[j] <= 'z')
{
if (masterAxiom[j] != 'F' &&
masterAxiom[j] != 'f')
{
strcpy(rule, getRule(masterAxiom[j]));
strcpy(after, masterAxiom+(j + 1));
strcpy(masterAxiom+j, rule);
strcpy(masterAxiom+(j + strlen(rule)), after);
j = j + strlen(rule) + 1;
}
}
}
}
scaleAxiom(masterAxiom, angle);
currX = 149 + (300 * fractalNumber);
currY = 299;
currH = heading;
stackIndex = -1;
drawAxiom(masterAxiom, angle);
}
Atlas::Objects::Root RuleTreeAdapter::getSelectedRule()
{
CEGUI::TreeItem* item = mTreeWidget.getFirstSelectedItem();
if (item) {
auto itemData = getRule(item->getText().c_str());
if (itemData.isValid()) {
return itemData;
}
}
return Atlas::Objects::Root();
}
/* converting to l1 any metaid attributes should be removed */
void
Model::removeMetaId()
{
unsigned int n, i;
unsetMetaId();
for (n = 0; n < getNumUnitDefinitions(); n++)
{
getUnitDefinition(n)->unsetMetaId();
for (i = 0; i < getUnitDefinition(n)->getNumUnits(); i++)
{
getUnitDefinition(n)->getUnit(i)->unsetMetaId();
}
}
for (n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->unsetMetaId();
}
for (n = 0; n < getNumSpecies(); n++)
{
getSpecies(n)->unsetMetaId();
}
for (n = 0; n < getNumParameters(); n++)
{
getParameter(n)->unsetMetaId();
}
for (n = 0; n < getNumRules(); n++)
{
getRule(n)->unsetMetaId();
}
for (n = 0; n < getNumReactions(); n++)
{
getReaction(n)->unsetMetaId();
for (i = 0; i < getReaction(n)->getNumReactants(); i++)
{
getReaction(n)->getReactant(i)->unsetMetaId();
}
for (i = 0; i < getReaction(n)->getNumProducts(); i++)
{
getReaction(n)->getProduct(i)->unsetMetaId();
}
if (getReaction(n)->isSetKineticLaw())
{
getReaction(n)->getKineticLaw()->unsetMetaId();
}
}
}
void CLuaSocketRestrictions::addIP(const char* hostname, const char* ip)
{
for(int i=0; i<ALL_RULES; i++) {
TStrIntMap::iterator it;
for(it = restrictions[i].begin(); it != restrictions[i].end(); ++it) {
const TSocketRule &rule = *it;
if ((rule.hostname == hostname) && (getRule((RestrictType)i, ip, rule.port) == NULL)) { //add rule with ip, when not exisitng
addRule((RestrictType)i, ip, rule.port, rule.allowed);
}
}
}
}
void RuleTreeAdapter::fetcherAllRulesReceived()
{
mRules = mFetcher->getRules();
std::string rootRule = mFetcher->getRootRule();
delete mFetcher;
mFetcher = nullptr;
const auto& root = getRule(rootRule);
if (root.isValid()) {
addToTree(root, nullptr, true);
}
EventAllRulesReceived.emit();
}
void CLuaSocketRestrictions::addRule(RestrictType type, const std::string& hostname, int port, bool allowed)
{
if ((port<=0) || (port>65535)){
LOG_L(L_ERROR, "Invalid port specified: %d", port);
return;
}
if (getRule(type, hostname.c_str(), port)!=NULL) {
LOG_L(L_ERROR, "Rule already exists: %s %d", hostname.c_str(), port);
return;
}
LOG("Adding rule %d %s:%d",type, hostname.c_str(), port);
if (!allowed) { //add deny rules to the front of the list
restrictions[type].push_front(TSocketRule(hostname, port, allowed));
} else {
restrictions[type].push_back(TSocketRule(hostname, port, allowed));
}
}
void * start_routine(void * ptr){
rule_struct * myRule= NULL;
while(queue_size(&rulesQueue) > 0){
pthread_mutex_lock(&mutex);
while((myRule = getRule()) == NULL){
if(queue_size(&rulesQueue))
pthread_cond_wait(&cond, &mutex);
else break;
}
pthread_mutex_unlock(&mutex);
//
if(myRule == NULL)
return NULL;
//
if(depsAreFiles(myRule->rule->deps)){
if(access(myRule->rule->target, F_OK) == -1){
runRule(myRule);
}
else{
struct stat stat1, stat2;
stat(myRule->rule->target, &stat1);
int i= 0;
for( ; i < queue_size(myRule->rule->deps); i++){
stat(queue_at(myRule->rule->deps, i), &stat2);
if(stat2.st_mtime > stat1.st_mtime){
runRule(myRule);
break;
}
}
}
}
else {
runRule(myRule);
}
//printf("queue_size= %d\n", queue_size(&rulesQueue));
pthread_mutex_lock(&mutex);
myRule->ready= 1;
pthread_cond_broadcast(&cond);
pthread_mutex_unlock(&mutex);
}
return NULL;
}
L::Integrator::Status L::RuleIntegrator::integrate (
Integrand &f, const Hypercube &h, Index maxEval,
real reqAbsError, real reqRelError, EstErr &ee)
{
checkDimension(h, f);
checkTerminationCriteria (maxEval, reqAbsError, reqRelError, false);
std::auto_ptr<CubatureRule> rule (getRule(h.getDimension()));
if (maxEval < rule->getNumPoints ())
{
#ifdef HINTLIB_NO_EXCEPTIONS
ee.set (0.0, 0.0);
return ERROR;
#else
throw NoEvaluationsPossible (maxEval);
#endif
}
ee.setNoErr (rule->eval(f, h));
return MAX_EVAL_REACHED;
}
void RuleTreeAdapter::addToTree(const Root& rule, CEGUI::TreeItem* parent, bool addRecursive)
{
CEGUI::TreeItem* item = ColouredTreeItem::create(rule->getId());
item->toggleIsOpen();
if (!parent) {
mTreeWidget.addItem(item);
} else {
parent->addItem(item);
}
if (addRecursive) {
std::list<std::string> children;
extractChildren(rule, children);
for (auto& child : children) {
const auto& childData = getRule(child);
if (childData.isValid()) {
addToTree(childData, item, addRecursive);
}
}
}
}
const strings_t Decision::getPredicates(string ruleName) const
{
return getRule()->find(ruleName)->second;
}
int
showRules( inStruct Sentries ) {
int n, i, j;
char ruleCondition[MAX_RULE_LENGTH];
char ruleAction[MAX_RULE_LENGTH];
char ruleRecovery[MAX_RULE_LENGTH];
char ruleHead[MAX_ACTION_SIZE];
char ruleBase[MAX_ACTION_SIZE];
char *actionArray[MAX_ACTION_IN_RULE];
char *recoveryArray[MAX_ACTION_IN_RULE];
char configDirEV[200];
char ruleSet[RULE_SET_DEF_LENGTH];
char oldRuleBase[MAX_ACTION_SIZE];
strcpy( ruleSet, "" );
strcpy( oldRuleBase, "" );
fprintf( stdout, "Content-type: text/html%c%c", 10, 10 );
fflush( stdout );
fprintf( stdout, "<HTML>\n<HEAD>\n<TITLE>iRODS Rule Administration</TITLE>\n</HEAD>\n<BODY bgcolor=#FFFFFF>\n" );
fprintf( stdout, "<CENTER> <B><FONT COLOR=#FF0000>iRODS Rule Base</FONT></B></CENTER>\n" );
fflush( stdout );
/* sprintf(configDirEV,"irodsConfigDir=/scratch/s1/sekar/irods/RODS/server/config");
sprintf(configDirEV,"irodsConfigDir=/misc/www/projects/srb-secure/cgi-bin");
putenv(configDirEV);
*/
for ( i = 0; i <= Sentries->m; i++ ) {
if ( !strcmp( Sentries->entries[i].name, "ruleSet" ) ) {
if ( strlen( Sentries->entries[i].val ) > 0 ) {
if ( ruleSet[0] != '\0' ) {
strcat( ruleSet, "," );
}
rstrcat( ruleSet, Sentries->entries[i].val, 999 );
}
}
else if ( !strcmp( Sentries->entries[i].name, "configDir" ) ) {
if ( strlen( Sentries->entries[i].val ) > 0 ) {
snprintf( configDirEV, 199, "irodsConfigDir=%s", Sentries->entries[i].val );
}
else {
sprintf( configDirEV, "irodsConfigDir=%s", MY_SERVER_CONFIG_DIR );
}
putenv( configDirEV );
}
}
if ( ruleSet[0] == '\0' ) {
strcpy( ruleSet, "core" );
}
fprintf( stdout, "<CENTER> <B><FONT COLOR=#0000FF>[%s]</FONT></B></CENTER>\n", ruleSet );
fflush( stdout );
initRuleStruct( NULL, ruleSet, "core", "core" );
fprintf( stdout, "<TABLE>\n" );
for ( j = 0 ; j < coreRuleStrct.MaxNumOfRules; j++ ) {
getRule( j + 1000 , ruleBase, ruleHead, ruleCondition, ruleAction, ruleRecovery, MAX_RULE_LENGTH );
if ( strcmp( oldRuleBase, ruleBase ) ) {
if ( strlen( oldRuleBase ) > 0 ) {
fprintf( stdout, "<TR><TD COLSPAN=6><HR NOSHADE COLOR=#00FF00 SIZE=4></TD></TR>" );
}
strcpy( oldRuleBase, ruleBase );
}
n = getActionRecoveryList( ruleAction, ruleRecovery, actionArray, recoveryArray );
fprintf( stdout, "<TR><TD><BR> %i</TD><TD><BR> <FONT COLOR=#0000FF>ON</FONT></TD><TD COLSPAN=3><BR> <FONT COLOR=#FF0000>%s.</FONT><FONT COLOR=#0000FF>%s</FONT></TD></TR>\n", j, ruleBase, ruleHead );
if ( strlen( ruleCondition ) != 0 ) {
fprintf( stdout, "<TR><TD></TD><TD></TD><TD VALIGN=TOP>IF </TD><TD COLSPAN=3 VALIGN=TOP><FONT COLOR=#FF0000>%s</FONT></TD></TR>\n", ruleCondition );
}
for ( i = 0; i < n; i++ ) {
if ( i == 0 )
fprintf( stdout, "<TR><TD></TD><TD></TD><TD VALIGN=TOP>DO </TD><TD VALIGN=TOP>%s</TD><TD NOWRAP> </TD><TD VALIGN=TOP>[%s]</TD></TR>\n",
actionArray[i], recoveryArray[i] );
else
fprintf( stdout, "<TR><TD></TD><TD></TD><TD VALIGN=TOP>AND </TD><TD VALIGN=TOP>%s</TD><TD NOWRAP> </TD><TD VALIGN=TOP>[%s]</TD></TR>\n",
actionArray[i], recoveryArray[i] );
}
}
fprintf( stdout, "</TABLE>\n" );
fprintf( stdout, "</BODY>\n</HTML>\n" );
return 0;
}
void
Model::removeDuplicateTopLevelAnnotations()
{
unsigned int i, n;
this->removeDuplicateAnnotations();
if (getNumFunctionDefinitions() > 0)
{
getListOfFunctionDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumFunctionDefinitions(); i++)
{
getFunctionDefinition(i)->removeDuplicateAnnotations();
}
}
if (getNumUnitDefinitions() > 0)
{
getListOfUnitDefinitions()->removeDuplicateAnnotations();
for (i = 0; i < getNumUnitDefinitions(); i++)
{
getUnitDefinition(i)->removeDuplicateAnnotations();
getUnitDefinition(i)->getListOfUnits()->removeDuplicateAnnotations();
for (n = 0; n < getUnitDefinition(i)->getNumUnits(); n++)
{
getUnitDefinition(i)->getUnit(n)->removeDuplicateAnnotations();
}
}
}
if (getNumCompartmentTypes() > 0)
{
getListOfCompartmentTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartmentTypes(); i++)
{
getCompartmentType(i)->removeDuplicateAnnotations();
}
}
if (getNumSpeciesTypes() > 0)
{
getListOfSpeciesTypes()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpeciesTypes(); i++)
{
getSpeciesType(i)->removeDuplicateAnnotations();
}
}
if (getNumCompartments() > 0)
{
getListOfCompartments()->removeDuplicateAnnotations();
for (i = 0; i < getNumCompartments(); i++)
{
getCompartment(i)->removeDuplicateAnnotations();
}
}
if (getNumSpecies() > 0)
{
getListOfSpecies()->removeDuplicateAnnotations();
for (i = 0; i < getNumSpecies(); i++)
{
getSpecies(i)->removeDuplicateAnnotations();
}
}
if (getNumParameters() > 0)
{
getListOfParameters()->removeDuplicateAnnotations();
for (i = 0; i < getNumParameters(); i++)
{
getParameter(i)->removeDuplicateAnnotations();
}
}
if (getNumInitialAssignments() > 0)
{
getListOfInitialAssignments()->removeDuplicateAnnotations();
for (i = 0; i < getNumInitialAssignments(); i++)
{
getInitialAssignment(i)->removeDuplicateAnnotations();
}
}
if (getNumConstraints() > 0)
{
getListOfConstraints()->removeDuplicateAnnotations();
for (i = 0; i < getNumConstraints(); i++)
{
getConstraint(i)->removeDuplicateAnnotations();
}
}
if (getNumRules() > 0)
{
getListOfRules()->removeDuplicateAnnotations();
for (i = 0; i < getNumRules(); i++)
{
getRule(i)->removeDuplicateAnnotations();
}
}
if (getNumReactions() > 0)
{
getListOfReactions()->removeDuplicateAnnotations();
for (i = 0; i < getNumReactions(); i++)
{
Reaction * r = getReaction(i);
r->removeDuplicateAnnotations();
if (r->getNumReactants() > 0)
{
r->getListOfReactants()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumReactants(); n++)
{
r->getReactant(n)->removeDuplicateAnnotations();
}
}
if (r->getNumProducts() > 0)
{
r->getListOfProducts()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumProducts(); n++)
{
r->getProduct(n)->removeDuplicateAnnotations();
}
}
if (r->getNumModifiers() > 0)
{
r->getListOfModifiers()->removeDuplicateAnnotations();
for (n = 0; n < r->getNumModifiers(); n++)
{
r->getModifier(n)->removeDuplicateAnnotations();
}
}
if (r->isSetKineticLaw())
{
r->getKineticLaw()->removeDuplicateAnnotations();
if (r->getKineticLaw()->getNumParameters() > 0)
{
r->getKineticLaw()->getListOfParameters()
->removeDuplicateAnnotations();
for (n = 0; n < r->getKineticLaw()->getNumParameters(); n++)
{
r->getKineticLaw()->getParameter(n)->removeDuplicateAnnotations();
}
}
}
}
}
if (getNumEvents() > 0)
{
getListOfEvents()->removeDuplicateAnnotations();
for (i = 0; i < getNumEvents(); i++)
{
getEvent(i)->removeDuplicateAnnotations();
if (getEvent(i)->getNumEventAssignments() > 0)
{
getEvent(i)->getListOfEventAssignments()->removeDuplicateAnnotations();
for (n = 0; n < getEvent(i)->getNumEventAssignments(); n++)
{
getEvent(i)->getEventAssignment(n)->removeDuplicateAnnotations();
}
}
}
}
}
void
Model::removeSBOTerms(bool strict)
{
unsigned int n, i;
if (strict == true)
{
unsetSBOTerm();
for (n = 0; n < getNumUnitDefinitions(); n++)
{
getUnitDefinition(n)->unsetSBOTerm();
for (i = 0; i < getUnitDefinition(n)->getNumUnits(); i++)
{
getUnitDefinition(n)->getUnit(i)->unsetSBOTerm();
}
}
for (n = 0; n < getNumCompartments(); n++)
{
getCompartment(n)->unsetSBOTerm();
}
for (n = 0; n < getNumSpecies(); n++)
{
getSpecies(n)->unsetSBOTerm();
}
for (n = 0; n < getNumParameters(); n++)
{
getParameter(n)->unsetSBOTerm();
}
for (n = 0; n < getNumRules(); n++)
{
getRule(n)->unsetSBOTerm();
}
for (n = 0; n < getNumReactions(); n++)
{
getReaction(n)->unsetSBOTerm();
for (i = 0; i < getReaction(n)->getNumReactants(); i++)
{
getReaction(n)->getReactant(i)->unsetSBOTerm();
if (getReaction(n)->getReactant(i)->isSetStoichiometryMath())
{
getReaction(n)->getReactant(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumProducts(); i++)
{
getReaction(n)->getProduct(i)->unsetSBOTerm();
if (getReaction(n)->getProduct(i)->isSetStoichiometryMath())
{
getReaction(n)->getProduct(i)->getStoichiometryMath()->unsetSBOTerm();
}
}
for (i = 0; i < getReaction(n)->getNumModifiers(); i++)
{
getReaction(n)->getModifier(i)->unsetSBOTerm();
}
if (getReaction(n)->isSetKineticLaw())
{
getReaction(n)->getKineticLaw()->unsetSBOTerm();
}
}
for (n = 0; n < getNumFunctionDefinitions(); n++)
{
getFunctionDefinition(n)->unsetSBOTerm();
}
for (n = 0; n < getNumEvents(); n++)
{
getEvent(n)->unsetSBOTerm();
for (i = 0; i < getEvent(n)->getNumEventAssignments(); i++)
{
getEvent(n)->getEventAssignment(i)->unsetSBOTerm();
}
if (getEvent(n)->isSetTrigger())
{
getEvent(n)->getTrigger()->unsetSBOTerm();
}
if (getEvent(n)->isSetDelay())
{
getEvent(n)->getDelay()->unsetSBOTerm();
}
}
}
}
int main ()
{
FILE* fp;
char il[MLEN];
char ilc[MLEN];
char ribbon[MRIBBON]; //the ribbon of calculations.
int rp = 0; // the ribbon phrase beggining
int rn = 0; // ribbon new expressions starts here.
int re = 0; // ribbon end.
char rules[MRULES]; // list of rules applicable to the case.
char * crule;
int rsize; // rule size;
int c;
char * pname;
int soffs; // input offset
printf("Ssum\n");
fp = fopen ("defs", "r");
if (fp == NULL)
{
perror("Can't open file with definitions.");
return -1;
}
c = 0;
do
{
rules[c++] = fgetc(fp);
if (rules[c-1] == '\n' ) rules[c-1] = rdel[0];
if (rules[c-1] == '\r' ) rules[c-1] = rdel[0];
}
while ( (c < MRULES) && (rules[c-1] != EOF) );
rules[c-1] = 0; // clear EOL symbol
printf("%d\n", strlen(rules));
printf("%s\n", rules );
memset((void*)il, 0, MLEN);
//read input line.
c = 0;
do
{
il[c++] = getchar();
}
while ( (c < MLEN) && (il[c-1] != '\n') );
il[c-1] = 0;
//clear trailing spaces
c--;
while (il [c-1] == ' ' && c>0) il[--c] = 0;
if (strlen (il) == 0)
{
printf("Empty input, skipping.\n");
return 0;
}
printf("%d\n", strlen(il));
printf("%s\n", il );
// normalize string and look for pattern in the definitions.
normalize(il);
// check if we have definition of the equation.
soffs = checkExpr(il, rules);
printf("Offset = %d\n", soffs);
if ( soffs >=0 )
{
rsize = getRule(soffs, rules); // extracting the rule from the list of rules
crule = strtok( &rules[rsize], rdel ); //extract full rule string
printf("crule: %s\n", crule);
if (applyRule(il, crule) >=0 ) // apply rule type of 'X Y ==' or 'Y X =='.
{
printf("Answer: %s\n", crule);
return 0;
}
}else
{
printf("Does not match any rule. Continue...\n");
}
// now the main loop of pattern search and defs application
memset(ribbon, 0, MRIBBON);
strcpy (ribbon, il);
re += strlen(il);
ribbon[re++] = edel[0];
ribbon[re++] = '\n';
printf("%s\n", ribbon);
strcpy(ilc, il); // copy input line.
// getting names from rules list.
pname = strtok (il," ");
printf("Name: %s\n", pname);
soffs = findDef(pname, rules); // looking for definition of name in the rules list.
printf("Offset = %d\n", soffs);
if ( soffs >=0 )
{
rsize = getRule(soffs, rules); // extracting the rule from the list of rules
crule = strtok( &rules[rsize], rdel ); //extract full rule string
printf("Definition: %s\n", crule);
// apply name
printf("il before: %s\n", ilc);
if ( applyName(ilc, crule, pname) >=0 )
{
printf("Converted string: %s\n", crule);
//add to ribbon
addToRibbon(ribbon, crule);
}
}else
{
printf("Definition of name is not found. Please define the name and retry.\n");
return 0;
}
printf("Ribbon: %s\n", ribbon);
// find all names in the definition.
// find all operations in rules.
close(fp);
return 0;
}
void
Model::dealWithStoichiometry()
{
unsigned int idCount = 0;
for (unsigned int i = 0; i < getNumReactions(); i++)
{
Reaction *r = getReaction(i);
unsigned int j;
for (j = 0; j < r->getNumReactants(); j++)
{
SpeciesReference *sr = r->getReactant(j);
if (sr->isSetStoichiometry() == false)
{
if (sr->isSetId() == false)
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
else
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
else
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
}
}
else
{
// stoichiometry is set
if (sr->isSetId())
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
}
// no id set - do not need to do anything
}
}
for (j = 0; j < r->getNumProducts(); j++)
{
SpeciesReference *sr = r->getProduct(j);
if (sr->isSetStoichiometry() == false)
{
if (sr->isSetId() == false)
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
else
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
else
{
createNoValueStoichMath(*this, *sr, idCount);
idCount++;
}
}
}
else
{
// stoichiometry is set
if (sr->isSetId())
{
// id is set it could be used by initialAssignment
// used by rule
// not used
if (getInitialAssignment(sr->getId()) != NULL)
{
useStoichMath(*this, *sr, false);
}
else if (getRule(sr->getId()) != NULL)
{
//assignmentRule
if (getRule(sr->getId())->getTypeCode() == SBML_ASSIGNMENT_RULE)
{
useStoichMath(*this, *sr, true);
}
else if (getRule(sr->getId())->getTypeCode() == SBML_RATE_RULE)
{
createParameterAsRateRule(*this, *sr, *(getRule(sr->getId())), idCount);
idCount++;
}
}
}
// no id set - do not need to do anything
}
}
}
}
void CSV::parse ()
{
Setting rule;
getRule(rule);
if (! rule.count())
{
QString s(tr("Empty rule"));
printStatusLogMessage(s);
downloadComplete();
return;
}
QString ts = "Rule";
QString ts2, s;
rule.getData(ts, ts2);
if (! ts2.contains("Date:"))
{
QString ss(tr("Rule missing Date field"));
printStatusLogMessage(ss);
downloadComplete();
return;
}
ts = "Delimiter";
rule.getData(ts, s);
if (! s.length())
{
QString ss(tr("Delimiter not found"));
printStatusLogMessage(ss);
downloadComplete();
return;
}
setDelimiter(s);
if (dateRange->isChecked())
{
if (sdate->date() >= edate->date() || edate->date() <= sdate->date())
{
QString ss = stringDone + " " + QDateTime::currentDateTime().toString("yyyy-MM-dd hh:mm:ss");
printStatusLogMessage(ss);
downloadComplete();
return;
}
}
QString type;
ts = "Type";
rule.getData(ts, type);
if (! type.length())
{
QString ss(tr("Type not found"));
printStatusLogMessage(ss);
downloadComplete();
return;
}
ts = "Rule";
rule.getData(ts, ts2);
QStringList fieldList = QStringList::split(",", ts2, FALSE);
if (! fieldList.count())
{
QString ss(tr("No rule found"));
printStatusLogMessage(ss);
downloadComplete();
return;
}
// get the directory path offset
ts = "Directory";
QString directory;
rule.getData(ts, directory);
if (! directory.length())
{
QString ss(tr("Directory not found"));
printStatusLogMessage(ss);
downloadComplete();
return;
}
// get the symbol filter
ts = "SymbolFilter";
rule.getData(ts, ts2);
QStringList symbolFilter = QStringList::split(",", ts2, FALSE);
// check for time field and set the tickflag
bool tickFlag = FALSE;
ts = "Rule";
rule.getData(ts, ts2);
if (ts2.contains("Time"))
tickFlag = TRUE;
else
{
if (ts2.contains("HHMMSS"))
tickFlag = TRUE;
}
QStringList list;
file->getFile(list);
int loop;
for (loop = 0; loop < (int) list.count(); loop++)
{
if (cancelFlag)
break;
QFile f(list[loop]);
if (! f.open(QIODevice::ReadOnly))
continue;
Q3TextStream stream(&f);
QString symbol = symbolOveride;
if (! symbol.length() && fieldList.findIndex("Symbol") == -1)
{
QStringList l = QStringList::split("/", list[loop], FALSE);
symbol = l[l.count() - 1];
if (symbol.right(4).contains(".txt"))
symbol.truncate(symbol.length() - 4);
if (symbol.right(4).contains(".TXT"))
symbol.truncate(symbol.length() - 4);
while (symbol.contains("_"))
symbol = symbol.remove(symbol.find("_", 0, TRUE), 1);
}
QString path;
if (! type.compare("Stocks"))
{
QString tmp = "Stocks/" + directory;
createDirectory(tmp, path);
if (! path.length())
{
QString ss(tr("CSVPlugin::Unable to create directory"));
printStatusLogMessage(ss);
downloadComplete();
f.close();
return;
}
}
else
{
if (! type.compare("Futures"))
{
QString tmp = "Futures/" + directory;
createDirectory(tmp, path);
if (! path.length())
{
QString ss(tr("CSVPlugin::Unable to create directory"));
printStatusLogMessage(ss);
downloadComplete();
f.close();
return;
}
}
}
path.append("/");
if (symbol.length())
{
QString s = path;
s.append(symbol);
if (openDb(s, symbol, type, tickFlag))
continue;
// QString ss = tr("Updating") + " " + symbol;
// printStatusLogMessage(ss);
progressBar->setProgress(loop, (int) list.count());
}
int lineCount = 0;
QFileInfo fi(f);
QString fName = fi.fileName();
while(stream.atEnd() == 0)
{
QString ts = stream.readLine();
QStringList l = QStringList::split( '\n', substituteSeparator(ts, delim, '\n'), FALSE);
lineCount++;
if (l.count() != fieldList.count())
{
QString ss = QString().sprintf(
"%s - %s - %s: %s Number of fields in file (%i) != rule format (%i)",
fName.latin1(), symbol.latin1(), tr("Line").latin1(),
QString::number(lineCount).latin1(), l.count(), fieldList.count()
);
printStatusLogMessage(ss);
continue;
}
int fieldLoop;
bool flag = FALSE;
Setting r;
for (fieldLoop = 0; fieldLoop < (int) fieldList.count(); fieldLoop++)
{
QString listItem = l[fieldLoop].stripWhiteSpace();
if (fieldList[fieldLoop].contains("Date:"))
{
QDate dt;
getDate(fieldList[fieldLoop], listItem, r, dt);
if (! dt.isValid())
{
QString ss = QString().sprintf("%s - %s - %s: %s %s: %s",
fName.latin1(), symbol.latin1(), tr("Line").latin1(), QString::number(lineCount).latin1(),
tr("Bad date").latin1(), listItem.latin1()
);
printStatusLogMessage(ss);
flag = TRUE;
break;
}
if (dateRange->isChecked())
{
if (dt < sdate->date() || dt > edate->date())
{
flag = TRUE;
break;
}
}
ts = "Date";
ts2 = dt.toString("yyyyMMdd");
r.setData(ts, ts2);
continue;
}
if (! fieldList[fieldLoop].compare("Time"))
{
getTime(listItem, s);
if (! s.length())
{
QString ss = QString().sprintf("%s - %s - %s: %s %s: %s",
fName.latin1(), symbol.latin1(), tr("Line").latin1(), QString::number(lineCount).latin1(),
tr("Bad time").latin1(), listItem.latin1()
);
printStatusLogMessage(ss);
flag = TRUE;
break;
}
ts = "Time";
r.setData(ts, s);
continue;
}
if (! fieldList[fieldLoop].compare("Symbol"))
{
if (symbolFilter.count())
{
if (symbolFilter.findIndex(listItem) == -1)
{
flag = TRUE;
break;
}
}
ts = "Symbol";
r.setData(ts, listItem);
continue;
}
if (! fieldList[fieldLoop].compare("Name"))
{
ts = "Name";
r.setData(ts, listItem);
continue;
}
if (! fieldList[fieldLoop].compare("Open") ||
! fieldList[fieldLoop].compare("High") ||
! fieldList[fieldLoop].compare("Low") ||
! fieldList[fieldLoop].compare("Close"))
{
if (setTFloat(listItem, TRUE))
{
QString ss = QString().sprintf("%s - %s - %s: %i %s: %s",
fName.latin1(), symbol.latin1(), tr("Line").latin1(), lineCount,
tr("Bad value").latin1(), tr(fieldList[fieldLoop]).latin1()
);
printStatusLogMessage(ss);
flag = TRUE;
break;
}
ts = QString::number(tfloat);
r.setData(fieldList[fieldLoop], ts);
continue;
}
if (! fieldList[fieldLoop].compare("Volume") ||
! fieldList[fieldLoop].compare("OI"))
{
if (setTFloat(listItem, FALSE))
{
QString ss = QString().sprintf("%s - %s - %s: %s %s: %s",
fName.latin1(), symbol.latin1(), tr("Line").latin1(), QString::number(lineCount).latin1(),
tr("Bad value").latin1(), tr(fieldList[fieldLoop]).latin1()
);
printStatusLogMessage(ss);
flag = TRUE;
break;
}
ts = QString::number(tfloat);
r.setData(fieldList[fieldLoop], ts);
continue;
}
}
if (flag)
continue;
ts = "Date";
r.getData(ts, s);
if (! s.length())
continue;
ts = "Time";
r.getData(ts, ts2);
if (ts2.length())
s.append(ts2);
else
s.append("000000");
Bar bar;
if (bar.setDate(s))
{
ts = "Date";
r.getData(ts, ts2);
QString ss = tr("Bad date") + " " + ts2;
printStatusLogMessage(ss);
continue;
}
bar.setTickFlag(tickFlag);
ts = "Open";
bar.setOpen(r.getDouble(ts));
ts = "High";
bar.setHigh(r.getDouble(ts));
ts = "Low";
bar.setLow(r.getDouble(ts));
ts = "Close";
bar.setClose(r.getDouble(ts));
ts = "Volume";
bar.setVolume(r.getDouble(ts));
ts = "OI";
bar.setOI(r.getInt(ts));
DBIndexItem item;
if (! symbol.length())
{
ts = "Symbol";
QString t;
r.getData(ts, t);
s = path;
s.append(t);
if (openDb(s, t, type, tickFlag))
continue;
ts = "Name";
r.getData(ts, s);
if (s.length())
{
chartIndex->getIndexItem(t, item);
item.setTitle(s);
chartIndex->setIndexItem(t, item);
}
db.setBar(bar);
ts = "Symbol";
r.getData(ts, ts2);
// QString ss = tr("Updating") + " " + ts2;
// printStatusLogMessage(ss);
config.closePlugin(type);
db.close();
emit signalWakeup();
}
else
{
ts = "Name";
r.getData(ts, s);
if (s.length())
{
chartIndex->getIndexItem(symbol, item);
item.setTitle(s);
chartIndex->setIndexItem(symbol, item);
}
db.setBar(bar);
emit signalWakeup();
}
}
db.close();
f.close();
}
progressBar->setProgress((int) list.count(), (int) list.count());
downloadComplete();
if (cancelFlag)
{
cancelFlag = FALSE;
printStatusLogMessage(stringCanceled);
}
else {
QString ss = stringDone + " " + QDateTime::currentDateTime().toString("yyyy-MM-dd hh:mm:ss");
printStatusLogMessage(ss);
}
progressBar->reset();
}