std::string toString<stringmap>(const stringmap &v)
{
std::ostringstream oss;
oss << "std::map( ";
for (stringmap::const_iterator it = v.begin(); it != v.end(); ++it) {
oss << it->first << " = " << it->second;
stringmap::const_iterator jt(it);
if (++jt != v.end()) oss << ", ";
}
oss << " )";
return oss.str();
}
std::vector<std::string> extract_keys_from_string_map
(stringmap const& keyword_dictionary
)
{
std::vector<std::string> keywords;
stringmap_iterator i_keyword_dictionary = keyword_dictionary.begin();
for
(
;i_keyword_dictionary != keyword_dictionary.end()
;++i_keyword_dictionary
)
{
keywords.push_back((*i_keyword_dictionary).first);
}
return keywords;
}
// second version - reverse
bool takeRoute_2(string start, vector<string> & modesList, d_stringmap & UniqueRoutes, int modeIndex, stringmap & result, string end) {
if (modesList[modeIndex] == "stop")
{
if (result.count(start) == 0)
{
result.insert({start,0}) ;
}
return true ;
}
if (allCitiesPossible(UniqueRoutes,result))
{
return true ;
}
int modeID = getModeID(modesList[modeIndex]) ;
}
void insert_element(stringmap &map, const Node &node, pthread_rwlock_t *lock, ofstream &fout){
bool to_write = false;
string key;
try{
string name = node["package"].as<string>();
string version = node["version"].as<string>();
key = name + version;
}catch(...){
return;
}
pthread_rwlock_rdlock(lock);
if(map.find(key) == map.end()){
to_write = true;
}
pthread_rwlock_unlock(lock);
if(to_write){
string name = node["package"].as<string>();
string version = node["version"].as<string>();
string key = name + version;
pthread_rwlock_wrlock(lock);
map.insert(make_pair(key, ""));
Emitter out;
out << BeginSeq;
out << node;
out << EndSeq;
fout << out.c_str() << endl;
if(node["status"].as<string>() != "ok"){
broken++;
}
total++;
pthread_rwlock_unlock(lock);
}
}
void
show
(
const std::string & tag,
const stringmap<VALUETYPE> & container
)
{
fprintf
(
stdout,
"- xpc::stringmap '%s':\n"
"- Name: '%s'\n"
"- Size: %d\n"
,
tag.c_str(),
container.name().c_str(),
int(container.size())
);
std::for_each(container.begin(), container.end(), show_pair<VALUETYPE>);
}
bool allCitiesPossible(d_stringmap & UniqueRoutes, stringmap & result) {
bool notFound = false ;
for (d_stringmap::iterator kt = UniqueRoutes.begin(); kt != UniqueRoutes.end(); ++kt)
{
if (result.count(kt->first) == 0)
{
return false ;
//cout << "ALL CITIES NOT POSSIBLE!" << endl ;
}
}
//cout << "ALL CITIES POSSIBLE!!!" << endl ;
return true ;
}
stringmap merge(stringmap a, stringmap b)
{
stringmap tmp(a);
tmp.insert(b.begin(),b.end());
return tmp;
}
void insert_element(stringmap &map, const Node &node, pthread_rwlock_t *lock, ofstream &fout, string date){
bool to_write = false;
string key;
try{
string name = node["package"].as<string>();
string version = node["version"].as<string>();
key = name + version;
}catch(...){
return;
}
pthread_rwlock_rdlock(lock);
if(map.find(key) == map.end()){
to_write = true;
}
pthread_rwlock_unlock(lock);
if(to_write){
string name = node["package"].as<string>();
string version = node["version"].as<string>();
string number = node["number"].as<string>();
string key = name + version;
string status = node["status"].as<string>();
string set;
if(status == "ok"){
ostringstream out_set;
out_set << "[";
auto install = node["installationset"];
for(size_t i = 0; i < install.size(); i++){
out_set << "{";
out_set << "\"" << install[i]["package"] << "\"" << ":" << "\"" << install[i]["version"] << "\"";
out_set << "}";
if(i + 1 != install.size()){
out_set << ",";
}
}
out_set << "]";
set = out_set.str();
}else{
ostringstream out_set;
auto reasons = node["reasons"];
out_set << "[";
for(size_t i = 0; i < reasons.size(); i++){
out_set << "{";
auto missing = reasons[i]["missing"];
auto pkg = missing["pkg"];
//YAML::Emitter out;
//out << node["reasons"];
//cout << out.c_str() << endl;
//exit(-1);
//}
auto depchains = missing["depchains"];
string unsat = pkg["unsat-dependency"].as<string>();
string version_unsat = pkg["version"].as<string>();
out_set << "\"unsat\": \"" << unsat << "\", ";
out_set << "\"version\": \"" << version_unsat << "\"";
out_set << "}";
if(i + 1 != reasons.size()){
out_set << ",";
}
}
out_set << "]";
set = out_set.str();
}
//- reasons:
//- missing:
//pkg:
//unsat-dependency: system.collections.generic (>= 1)
//version: 2
//package: windows.applicationmodel.datatransfer
//depchains:
//- depchain:
//- version: 1
//depends: windows.graphics.printing (>= 1)
//package: windows.graphics.printing.optiondetails
//- depends: windows.applicationmodel.datatransfer (>= 1)
//version: 2
//package: windows.graphics.printing
//reasons:
//- missing:
//pkg:
//version: 18
//unsat-dependency: node-authorizenet (>= 1)
//package: 42-cent
string str_status;
if(status == "ok"){
str_status = "true";
}else{
str_status = "false";
}
ostringstream out;
out << "{\"name\": " << "\"" << name << "\"";
out << ", \"version\": " << "\"" << version << "\"";
out << ", \"number\": " << "\"" << number << "\"";
out << ", \"status\": " << "\"" << str_status << "\"";
out << ", \"date\": " << "{ $date: \"" << date << "T00:00:00Z" << "\"}";
out << ", \"set\": " << set << "}";
pthread_rwlock_wrlock(lock);
fout << out.str() << endl;
if(status != "ok"){
broken++;
}
total++;
map.insert(make_pair(key, ""));
pthread_rwlock_unlock(lock);
}
}
///' Calculate the intermediate network properties in the discovery dataset
///'
///' These properties are need at every permutation: so they will be computed
///' once.
///'
///' @details
///' \subsection{Input expectations:}{
///' Note that this function expects all inputs to be sensible, as checked by
///' the R function 'checkUserInput' and processed by 'modulePreservation'.
///'
///' These requirements are:
///' \itemize{
///' \item{The ordering of node names across 'dData', 'dCorr', and 'dNet' is
///' consistent.}
///' \item{The columns of 'dData' are the nodes.}
///' \item{'dData' has been scaled by 'Scale'.}
///' \item{'dCorr' and 'dNet' are square matrices, and their rownames are
///' identical to their column names.}
///' \item{'moduleAssigments' is a named character vector, where the names
///' represent node labels found in the discovery dataset (e.g. 'dNet').}
///' }
///' }
///'
///' @param dData scaled data matrix from the \emph{discovery} dataset.
///' @param dCorr matrix of correlation coefficients between all pairs of
///' variables/nodes in the \emph{discovery} dataset.
///' @param dNet adjacency matrix of network edge weights between all pairs of
///' nodes in the \emph{discovery} dataset.
///' @param tNodeNames a character vector of node names in the test dataset
///' @param moduleAssignments a named character vector containing the module
///' each node belongs to in the discovery dataset.
///' @param modules a character vector of modules for which to calculate the
///' module preservation statistics.
///'
///' @return a list containing three lists: a list of weighted degree vectors,
///' a list of correlation coefficient vectors, and a list of node
///' contribution vectors. There is one vector for each module in each list.
///'
///' @keywords internal
// [[Rcpp::export]]
Rcpp::List IntermediateProperties (
Rcpp::NumericMatrix dData, Rcpp::NumericMatrix dCorr, Rcpp::NumericMatrix dNet,
Rcpp::CharacterVector tNodeNames, Rcpp::CharacterVector moduleAssignments,
Rcpp::CharacterVector modules
) {
// First, scale the matrix data
unsigned int nSamples = dData.nrow();
unsigned int nNodes = dData.ncol();
R_CheckUserInterrupt();
// convert the colnames / rownames to C++ equivalents
const std::vector<std::string> dNames (Rcpp::as<std::vector<std::string>>(colnames(dNet)));
const std::vector<std::string> tNames (Rcpp::as<std::vector<std::string>>(tNodeNames));
/* Next, we need to create three mappings:
* - From node IDs to indices in the discovery dataset.
* - From modules to all node IDs.
* - From modules to just node IDs present in the test dataset.
*/
const namemap dIdxMap = MakeIdxMap(dNames);
const stringmap modNodeMap = MakeModMap(moduleAssignments);
const namemap tIdxMap = MakeIdxMap(tNames);
const stringmap modNodePresentMap = MakeModMap(moduleAssignments, tIdxMap);
// What modules do we actually want to analyse?
const std::vector<std::string> mods (Rcpp::as<std::vector<std::string>>(modules));
// We only need to iterate through modules which have nodes in the test
// dataset
std::vector<std::string> modsPresent;
for (auto it = mods.begin(); it != mods.end(); ++it) {
if (modNodePresentMap.count(*it) > 0) {
modsPresent.push_back(*it);
}
}
R_CheckUserInterrupt();
Rcpp::List degree;
Rcpp::List corr;
Rcpp::List contribution;
// Calculate the network properties in the discovery dataset.
std::string mod;
unsigned int mNodes;
arma::uvec dIdx, dRank;
arma::vec dSP, dWD, dCV, dNC;
for (auto mi = modsPresent.begin(); mi != modsPresent.end(); ++mi) {
// Get the node indices in the discovery dataset for this module
mod = *mi;
dIdx = GetNodeIdx(mod, modNodePresentMap, dIdxMap);
mNodes = dIdx.n_elem;
R_CheckUserInterrupt();
// Calculate the network properties and insert into their storage containers
dCV = CorrVector(dCorr.begin(), nNodes, dIdx.memptr(), mNodes);
R_CheckUserInterrupt();
// Sort node indices for sequential memory access
dRank = SortNodes(dIdx.memptr(), mNodes);
dWD = WeightedDegree(dNet.begin(), nNodes, dIdx.memptr(), mNodes);
dWD = dWD(dRank); // reorder
R_CheckUserInterrupt();
dSP = SummaryProfile(dData.begin(), nSamples, nNodes, dIdx.memptr(), mNodes);
R_CheckUserInterrupt();
dNC = NodeContribution(dData.begin(), nSamples, nNodes,
dIdx.memptr(), mNodes, dSP.memptr());
dNC = dNC(dRank); // reorder results
R_CheckUserInterrupt();
// Cast to R-vectors and add to results lists
corr.push_back(Rcpp::NumericVector(dCV.begin(), dCV.end()));
degree.push_back(Rcpp::NumericVector(dWD.begin(), dWD.end()));
contribution.push_back(Rcpp::NumericVector(dNC.begin(), dNC.end()));
}
degree.names() = modsPresent;
corr.names() = modsPresent;
contribution.names() = modsPresent;
return Rcpp::List::create(
Rcpp::Named("degree") = degree,
Rcpp::Named("corr") = corr,
Rcpp::Named("contribution") = contribution
);
}
bool takeRoute(string start, vector<string> & modesList, d_stringmap & UniqueRoutes, int modeIndex, stringmap & result) {
//cout << "TEST NO takeRoute" << endl ; // TESTDEBUG
//cout << "At " << start << " travelled " << modeIndex << " modes by " << modesList[modeIndex] << endl;
// at the final stop we...
if (modesList[modeIndex] == "stop")
{
if (result.count(start) == 0)
{
result.insert({start,0}) ;
}
// cout << " found!" << endl ;
return true ;
}
if (allCitiesPossible(UniqueRoutes,result))
{
return true ;
}
// Part 1
//cout << "Part 1" << endl ; // testing
bool notImpossible = false ;
int modeID = getModeID(modesList[modeIndex]) ;
//cout << "Part 1.5" << endl ; // testing
string nextStart ;
//cout << "Part 2" << endl ; //testing
//cout << endl << "Possible Routes at " << start << " mode " << modesList[modeIndex] << " are "; // testing
//cout << UniqueRoutes[start][modeID].size() << endl ; // testing
//cout << "They are: " << endl ; // testing
if (UniqueRoutes[start][modeID].size() == 0)
{
//cout << "No route found from " << start << " for " << modesList[modeIndex] << endl;
return false;
}
// for testing, printing out all possible routes,
// for (int i = 0; i < UniqueRoutes[start][modeID].size(); ++i)
// {
// cout << UniqueRoutes[start][modeID][i] << ", " ;
// }
// cout << endl << endl ; // testing
for (int i = 0; i < UniqueRoutes[start][modeID].size(); ++i)
{
// cout << "In this loop " << i << endl ;
nextStart = UniqueRoutes[start][modeID][i];
//cout << "After nextStart " << nextStart << " with modeIndex " << modeIndex << endl ;
if (takeRoute(nextStart, modesList, UniqueRoutes, modeIndex+1, result))
{
notImpossible = true ;
//cout << notImpossible << "Setting notImpossible to true at " << start << endl ;
}
// cout << "Back from " << nextStart << " route. " << notImpossible << endl ;
}
if (notImpossible == true)
{
//cout << "Not Impossible, returning true." << endl ;
return true ;
}
// cout << "Failed, returning false at " << start << endl ;
return false;
}