void MySQLConnection::connect()
{
bool reconnecting = false;
if (_myConn != nullptr) //reconnection attempt
{
if (!mysql_ping(_myConn)) //ping ok
return;
else
reconnecting = true;
}
//remove any state from previous session
this->clear();
Poco::Logger& logger = _dbEngine->getLogger();
for(;;)
{
const char* unix_socket = nullptr;
if (_unix_socket.length() > 0)
unix_socket = _unix_socket.c_str();
_myConn = mysql_real_connect(_myHandle, _host.c_str(), _user.c_str(), _password.c_str(), _database.c_str(), _port, unix_socket, CLIENT_REMEMBER_OPTIONS);
if (!_myConn)
{
const char* actionToDo = "connect";
if (reconnecting)
actionToDo = "reconnect";
unsigned int errNo = mysql_errno(_myHandle);
if (IsConnectionErrFatal(errNo))
throw SqlException(errNo,mysql_error(_myHandle),actionToDo);
static const long sleepTime = 1000;
logger.warning(Poco::format("Could not %s to MySQL database at %s: %s, retrying in %d seconds",
string(actionToDo),_host,string(mysql_error(_myHandle)),static_cast<int>(sleepTime/1000)));
Poco::Thread::sleep(sleepTime);
continue;
}
break;
}
string actionDone = (reconnecting)?string("Reconnected"):string("Connected");
poco_information(logger,Poco::format( actionDone + " to MySQL database %s:%d/%s client ver: %s server ver: %s",
_host, _port,_database,string(mysql_get_client_info()),string(mysql_get_server_info(_myConn)) ));
//Autocommit should be ON because without it, MySQL would require everything to be wrapped into a transaction
if (!mysql_autocommit(_myConn, 1))
poco_trace(logger,"Set autocommit to true");
else
poco_error(logger,"Failed to set autocommit to true");
//set connection properties to UTF8 to properly handle locales for different server configs
//core sends data in UTF8, so MySQL must expect UTF8 too
if (!mysql_set_character_set(_myConn,"utf8"))
poco_trace(logger,Poco::format("Character set changed to %s",string(mysql_character_set_name(_myConn))));
else
poco_error(logger,Poco::format("Failed to change charset, remains at %s",string(mysql_character_set_name(_myConn))));
}
Pothos::PluginModule::~PluginModule(void)
{
if (not _impl) return; //no private data
if (not _impl.unique()) return; //this is not the last copy
if (not _impl->sharedLibrary.isLoaded()) return; //module not loaded
poco_information(Poco::Logger::get("Pothos.PluginModule.unload"), _impl->sharedLibrary.getPath());
for (const auto &pluginPath : this->getPluginPaths())
{
PluginRegistry::remove(pluginPath);
}
_impl->sharedLibrary.unload();
}
void PostgreSQLConnection::connect()
{
bool reconnecting = false;
if (_pgConn != nullptr) //reconnection attempt
{
if (!_ConnectionLost())
return;
else
reconnecting = true;
}
//remove any state from previous session
this->clear();
Poco::Logger& logger = _dbEngine->getLogger();
for(;;)
{
if (reconnecting)
PQreset(_pgConn);
else
{
if (_host == ".")
_pgConn = PQsetdbLogin(nullptr, _port == "." ? nullptr : _port.c_str(), nullptr, nullptr, _database.c_str(), _user.c_str(), _password.c_str());
else
_pgConn = PQsetdbLogin(_host.c_str(), _port.c_str(), nullptr, nullptr, _database.c_str(), _user.c_str(), _password.c_str());
}
//check to see that the backend connection was successfully made
if (_ConnectionLost())
{
const char* actionToDo = "connect";
if (reconnecting)
actionToDo = "reconnect";
static const long sleepTime = 1000;
logger.warning(Poco::format("Could not %s to Postgre database at %s: %s, retrying in %d seconds",
string(actionToDo),_host,lastErrorDescr(),static_cast<int>(sleepTime/1000)));
Poco::Thread::sleep(sleepTime);
continue;
}
break;
}
string actionDone = (reconnecting)?string("Reconnected"):string("Connected");
poco_information(logger,Poco::format("%s to Postgre database %s:%s/%s server ver: %d",actionDone,_host,_port,_database,PQserverVersion(_pgConn)));
}
Pothos::PluginModule::PluginModule(const std::string &path):
_impl(new Impl())
{
_impl->path = path;
poco_information(Poco::Logger::get("Pothos.PluginModule.load"), path);
try
{
std::lock_guard<std::mutex> lock(getModuleMutex());
registrySetActiveModuleLoading(*this);
ErrorMessageDisableGuard emdg;
_impl->sharedLibrary.load(path);
registrySetActiveModuleLoading(PluginModule());
_impl->pluginPaths = ::getPluginPaths(*this);
}
catch(const Poco::LibraryLoadException &ex)
{
throw PluginModuleError("Pothos::PluginModule("+path+")", ex.displayText());
}
}
std::vector<Poco::Path> getModulePaths(const Poco::Path &path)
{
poco_information(Poco::Logger::get("Pothos.PluginLoader.load"), path.toString());
std::vector<Poco::Path> paths;
const Poco::File file(path);
if (not file.exists()) return paths;
else if (file.isFile() and (path.getExtension() == "@MODULE_EXT@"))
{
paths.push_back(path);
}
else if (file.isDirectory())
{
std::vector<std::string> files; file.list(files);
for (size_t i = 0; i < files.size(); i++)
{
auto subpaths = getModulePaths(Poco::Path(path, files[i]).absolute());
paths.insert(paths.end(), subpaths.begin(), subpaths.end());
}
}
return paths;
}
std::string MsvcCompilerSupport::compileCppModule(const Pothos::Util::CompilerArgs &compilerArgs)
{
std::vector<std::string> tempFilesToCleanup;
//create compiler bat script
const auto clBatPath = Poco::TemporaryFile::tempName() + ".bat";
tempFilesToCleanup.push_back(clBatPath);
std::ofstream clBatFile(clBatPath.c_str());
clBatFile << "call \"" << _vcvars_path << "\"" << std::endl;
clBatFile << "cl.exe %*" << std::endl;
clBatFile << "exit /b %ERRORLEVEL%" << std::endl;
clBatFile.close();
//create args
Poco::Process::Args args;
args.push_back("/LD"); //Creates a dynamic-link library
args.push_back("/MD"); //Creates a multithreaded DLL
//add libraries
for (const auto &library : compilerArgs.libraries)
{
args.push_back("\""+library+"\"");
}
//add compiler flags
for (const auto &flag : compilerArgs.flags)
{
args.push_back(flag);
}
//add include paths
for (const auto &include : compilerArgs.includes)
{
args.push_back("/I");
args.push_back("\""+include+"\"");
}
//add compiler sources
for (const auto &source : compilerArgs.sources)
{
const auto filePath = Poco::TemporaryFile::tempName() + ".cpp";
tempFilesToCleanup.push_back(filePath);
std::ofstream(filePath.c_str()).write(source.data(), source.size());
args.push_back("/Tp"); //Specifies a C++ source file
args.push_back(filePath);
}
//create temp out file
const auto outPath = Poco::TemporaryFile::tempName() + Poco::SharedLibrary::suffix();
tempFilesToCleanup.push_back(outPath);
args.push_back("/link");
args.push_back("/out:"+outPath);
//log the command
std::string cmdToLog = "cl.exe ";
for (const auto &a : args) cmdToLog += a + " ";
poco_information(Poco::Logger::get("Pothos.MsvcCompilerSupport.compileCppModule"), cmdToLog);
//launch
Poco::Pipe outPipe;
Poco::Process::Env env;
Poco::ProcessHandle ph(Poco::Process::launch(
clBatPath, args, nullptr, &outPipe, &outPipe, env));
//handle error case
if (ph.wait() != 0 or not Poco::File(outPath.c_str()).exists())
{
Poco::PipeInputStream errStream(outPipe);
const std::string errMsgBuff = std::string(
std::istreambuf_iterator<char>(errStream),
std::istreambuf_iterator<char>());
cleanupTempFiles(tempFilesToCleanup);
throw Pothos::Exception("MsvcCompilerSupport::compileCppModule", errMsgBuff);
}
//output file to string
std::ifstream outFile(outPath.c_str(), std::ios::binary);
const std::string outBuff = std::string(
std::istreambuf_iterator<char>(outFile),
std::istreambuf_iterator<char>());
cleanupTempFiles(tempFilesToCleanup);
return outBuff;
}
/**
* Stop ItemDB.
*/
void ItemDB::stopItemDB() {
DBUtils::closeBasicDB(hashDB);
DBUtils::closeBasicDB(grassDB);
poco_information(*logger, "Stop ItemDB");
}
void TagDB::stopTagDB() {
DBUtils::closeBasicDB(hashDB);
DBUtils::closeBasicDB(grassDB);
poco_information(*logger, "stopTagDB: Stop TagDB");
return;
}
void LLVMModelDataSymbols::initFloatingSpecies(const libsbml::Model* model,
bool computeAndAssignConsevationLaws)
{
const ListOfSpecies *species = model->getListOfSpecies();
list<string> indFltSpecies;
list<string> depFltSpecies;
// get the floating species and set thier compartments
ls::LibStructural structural(model);
poco_information(getLogger(),
"performed structural analysis on model: " +
structural.getAnalysisMsg());
// reorder by linearly independent first, then linearly dependent
vector<string> reorderedList = computeAndAssignConsevationLaws ?
structural.getReorderedSpecies() :
structural.getSpecies();
linearlyIndependentFloatingSpeciesSize = structural.getNumIndSpecies();
// figure out 'fully' indendent flt species -- those without rules.
for (uint i = 0; i < reorderedList.size(); ++i)
{
// just make sure its a valid species
const string& sid = reorderedList[i];
const Species *s = 0;
assert((s = species->get(sid)) && !s->getBoundaryCondition());
if (computeAndAssignConsevationLaws &&
i <= linearlyIndependentFloatingSpeciesSize &&
!isIndependentElement(sid))
{
string msg = "structural analysis determined that " + sid +
" is linearly independent, but it has has rules "
"(assignment or rate) determining its dynamics.";
throw_llvm_exception(msg);
}
if (isIndependentElement(sid))
{
indFltSpecies.push_back(sid);
}
else
{
depFltSpecies.push_back(sid);
}
}
// stuff the species in the map
for (list<string>::const_iterator i = indFltSpecies.begin();
i != indFltSpecies.end(); ++i)
{
uint si = floatingSpeciesMap.size();
floatingSpeciesMap[*i] = si;
}
for (list<string>::const_iterator i = depFltSpecies.begin();
i != depFltSpecies.end(); ++i)
{
uint si = floatingSpeciesMap.size();
floatingSpeciesMap[*i] = si;
}
// finally set how many ind species we've found
independentFloatingSpeciesSize = indFltSpecies.size();
if (Logger::PRIO_INFORMATION <= getLogger().getLevel())
{
LoggingBuffer log(Logger::PRIO_INFORMATION, __FILE__, __LINE__);
log.stream() << "found " << indFltSpecies.size()
<< " independent and " << depFltSpecies.size()
<< " dependent floating species." << endl;
log.stream() << "linearly independent species: " <<
linearlyIndependentFloatingSpeciesSize << endl;
vector<string> ids = getFloatingSpeciesIds();
for (uint i = 0; i < ids.size(); ++i)
{
log.stream() << "floating species [" << i << "] = \'" << ids[i]
<< "\'" << endl;
}
}
}
