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Fix rules engine treating behavior/signal synonyms as separate entries #423

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Fix rules engine treating behavior/signal synonyms as separate entries #423

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53 changes: 36 additions & 17 deletions core/PhysiCell_rules.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -250,8 +250,9 @@ void Hypothesis_Rule::English_display_HTML( std::ostream& os )

void Hypothesis_Rule::add_signal( std::string signal , double half_max , double hill_power , std::string response )
{
int signal_index = find_signal_index(signal);
// check: is this a valid signal? (is it in the dictionary?)
if( find_signal_index(signal) < 0 )
if( signal_index < 0 )
{
std::cout << "Error! Attempted to add signal " << signal << " which is not in the dictionary." << std::endl;
std::cout << "Either fix your model or add the missing signal to the simulation." << std::endl;
Expand All @@ -261,6 +262,9 @@ void Hypothesis_Rule::add_signal( std::string signal , double half_max , double
exit(-1);
}

// canonicalize the name so that synonyms of the same signal are treated as one signal
signal = signal_name( signal_index );

// check to see if the signal and response already there
int n = find_signal(signal);
bool bResponse = false; // true if up-regulate, false if down
Expand All @@ -278,8 +282,8 @@ void Hypothesis_Rule::add_signal( std::string signal , double half_max , double
exit(-1);
}

// add the signal;
signals_map[signal] = signals_map.size();
// add the signal;
signals_map[signal] = signals.size();

signals.push_back( signal );
half_maxes.push_back( half_max );
Expand Down Expand Up @@ -411,6 +415,11 @@ void Hypothesis_Rule::sync_to_cell_definition( std::string cell_name )

int Hypothesis_Rule::find_signal( std::string name )
{
int index = find_signal_index( name );
if( index < 0 )
{ return -1; }
name = signal_name( index );

auto search = signals_map.find(name);

if( search == signals_map.end() )
Expand All @@ -420,7 +429,11 @@ int Hypothesis_Rule::find_signal( std::string name )
}

void Hypothesis_Rule::set_half_max( std::string name , double hm )
{
{
int index = find_signal_index( name );
if( index >= 0 )
{ name = signal_name( index ); }

int n = find_signal( name );
if( n < 0 )
{ return; }
Expand Down Expand Up @@ -448,6 +461,10 @@ void Hypothesis_Rule::set_half_max( std::string name , double hm )

void Hypothesis_Rule::set_hill_power( std::string name , double hp )
{
int index = find_signal_index( name );
if( index >= 0 )
{ name = signal_name( index ); }

int n = find_signal( name );
if( n < 0 )
{ return; }
Expand All @@ -474,6 +491,10 @@ void Hypothesis_Rule::set_hill_power( std::string name , double hp )

void Hypothesis_Rule::set_response( std::string name , std::string response )
{
int index = find_signal_index( name );
if( index >= 0 )
{ name = signal_name( index ); }

int n = find_signal( name );
if( n < 0 )
{ return; }
Expand Down Expand Up @@ -757,7 +778,8 @@ void Hypothesis_Ruleset::sync_to_cell_definition( Cell_Definition* pCD )
Hypothesis_Rule* Hypothesis_Ruleset::add_behavior( std::string behavior , double min_behavior, double max_behavior )
{
// check: is this a valid signal? (is it in the dictionary?)
if( find_behavior_index(behavior) < 0 )
int behavior_index = find_behavior_index(behavior);
if( behavior_index < 0 )
{
std::cout << "Warning! Attempted to add behavior " << behavior << " which is not in the dictionary." << std::endl;
std::cout << "Either fix your model or add the missing behavior to the simulation." << std::endl;
Expand All @@ -767,6 +789,10 @@ Hypothesis_Rule* Hypothesis_Ruleset::add_behavior( std::string behavior , double
exit(-1);
}

// canonicalize the name so that synonyms of the same behavior share a single rule
// (and hence a single multivariate Hill response) instead of one overwriting another
behavior = behavior_name( behavior_index );

// first, check. Is there already a ruleset?
auto search = rules_map.find( behavior );

Expand Down Expand Up @@ -812,6 +838,11 @@ void Hypothesis_Ruleset::sync_to_cell_definition( std::string cell_name )

Hypothesis_Rule* Hypothesis_Ruleset::find_behavior( std::string name )
{
int index = find_behavior_index( name );
if( index < 0 )
{ return NULL; }
name = behavior_name( index );

auto search = rules_map.find( name);
if( search == rules_map.end() )
{
Expand Down Expand Up @@ -903,12 +934,6 @@ void add_rule( std::string cell_type, std::string signal, std::string behavior ,
exit(-1);
}

if( pHRS->find_behavior(behavior) )
{
if( (*pHRS)[behavior].behavior != behavior )
{ (*pHRS)[behavior].behavior = behavior; std::cout << "wha?" << std::endl; }
}

pHRS->add_behavior(behavior);

(*pHRS)[behavior].add_signal(signal,response);
Expand All @@ -934,12 +959,6 @@ void add_rule( std::string cell_type, std::string signal, std::string behavior ,
exit(-1);
}

if( pHRS->find_behavior(behavior) )
{
if( (*pHRS)[behavior].behavior != behavior )
{ (*pHRS)[behavior].behavior = behavior; std::cout << "wha?" << std::endl; }
}

pHRS->add_behavior(behavior);

(*pHRS)[behavior].add_signal(signal,response);
Expand Down
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