TransformationModelLinear::TransformationModelLinear(
const TransformationModel::DataPoints & data, const Param & params)
{
params_ = params;
data_given_ = !data.empty();
if (!data_given_ && params.exists("slope") && (params.exists("intercept")))
{
// don't estimate parameters, use given values
slope_ = params.getValue("slope");
intercept_ = params.getValue("intercept");
}
else // estimate parameters from data
{
Param defaults;
getDefaultParameters(defaults);
params_.setDefaults(defaults);
symmetric_ = params_.getValue("symmetric_regression") == "true";
size_t size = data.size();
if (size == 0) // no data
{
throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
"no data points for 'linear' model");
}
else if (size == 1) // degenerate case, but we can still do something
{
slope_ = 1.0;
intercept_ = data[0].second - data[0].first;
}
else // compute least-squares fit
{
vector<double> x(size), y(size);
for (size_t i = 0; i < size; ++i)
{
if (symmetric_)
{
x[i] = data[i].second + data[i].first;
y[i] = data[i].second - data[i].first;
}
else
{
x[i] = data[i].first;
y[i] = data[i].second;
}
}
double cov00, cov01, cov11, sumsq; // covariance values, sum of squares
double * x_start = &(x[0]), * y_start = &(y[0]);
gsl_fit_linear(x_start, 1, y_start, 1, size, &intercept_, &slope_,
&cov00, &cov01, &cov11, &sumsq);
if (symmetric_) // undo coordinate transformation:
{
slope_ = (1.0 + slope_) / (1.0 - slope_);
intercept_ = intercept_ * 1.41421356237309504880; // 1.41... = sqrt(2)
}
}
}
}
Param File::getSystemParameters()
{
String filename = String(QDir::homePath()) + "/.OpenMS/OpenMS.ini";
Param p;
if (!File::readable(filename)) // create file
{
p = getSystemParameterDefaults_();
String dirname = String(QDir::homePath()) + "/.OpenMS";
QDir dir(dirname.toQString());
if (!dir.exists())
{
if (!File::writable(dirname))
{
LOG_WARN << "Warning: Cannot create folder '.OpenMS' in user home directory. Please check your environment!" << std::endl;
LOG_WARN << " Home directory determined is: " << QDir::homePath().toStdString() << "." << std::endl;
return p;
}
dir.mkpath(".");
}
if (!File::writable(filename))
{
LOG_WARN << "Warning: Cannot create '.OpenMS/OpenMS.ini' in user home directory. Please check your environment!" << std::endl;
LOG_WARN << " Home directory determined is: " << QDir::homePath().toStdString() << "." << std::endl;
return p;
}
ParamXMLFile paramFile;
paramFile.store(filename, p);
}
else
{
ParamXMLFile paramFile;
paramFile.load(filename, p);
// check version
if (!p.exists("version") || (p.getValue("version") != VersionInfo::getVersion()))
{
if (!p.exists("version"))
{
LOG_WARN << "Broken file '" << filename << "' discovered. The 'version' tag is missing." << std::endl;
}
else // old version
{
LOG_WARN << "File '" << filename << "' is deprecated." << std::endl;
}
LOG_WARN << "Updating missing/wrong entries in '" << filename << "' with defaults!" << std::endl;
Param p_new = getSystemParameterDefaults_();
p.setValue("version", VersionInfo::getVersion()); // update old version, such that p_new:version does not get overwritten during update()
p_new.update(p);
paramFile.store(filename, p_new);
}
}
return p;
}
TransformationModelLinear::TransformationModelLinear(const TransformationModel::DataPoints& data, const Param& params) :
TransformationModel(data, params) // initializes model
{
data_given_ = !data.empty();
if (!data_given_ && params.exists("slope") && params.exists("intercept"))
{
// don't estimate parameters, use given values
slope_ = params.getValue("slope");
intercept_ = params.getValue("intercept");
}
else // estimate parameters from data
{
Param defaults;
getDefaultParameters(defaults);
params_.setDefaults(defaults);
symmetric_ = params_.getValue("symmetric_regression") == "true";
// weight the data (if weighting is specified)
TransformationModel::DataPoints data_weighted = data;
if ((params.exists("x_weight") && params.getValue("x_weight") != "") || (params.exists("y_weight") && params.getValue("y_weight") != ""))
{
weightData(data_weighted);
}
size_t size = data_weighted.size();
std::vector<Wm5::Vector2d> points;
if (size == 0) // no data
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"no data points for 'linear' model");
}
else if (size == 1) // degenerate case, but we can still do something
{
slope_ = 1.0;
intercept_ = data_weighted[0].second - data_weighted[0].first;
}
else // compute least-squares fit
{
for (size_t i = 0; i < size; ++i)
{
points.push_back(Wm5::Vector2d(data_weighted[i].first, data_weighted[i].second));
}
if (!Wm5::HeightLineFit2<double>(static_cast<int>(size), &points.front(), slope_, intercept_))
{
throw Exception::UnableToFit(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "TransformationModelLinear", "Unable to fit linear transformation to data points.");
}
}
// update params
params_.setValue("slope", slope_);
params_.setValue("intercept", intercept_);
}
}
String File::getTempDirectory()
{
Param p = getSystemParameters();
if (p.exists("temp_dir") && String(p.getValue("temp_dir")).trim() != "")
{
return p.getValue("temp_dir");
}
return String(QDir::tempPath());
}
//there is only one parameter at the moment
Param getSubsectionDefaults_(const String& /*section*/) const
{
Param p = PosteriorErrorProbabilityModel().getParameters();
if (p.exists("out_plot"))
{ // hide from user -- we have a top-level param for that
p.remove("out_plot");
}
else
{
throw Exception::Precondition(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "INTERNAL ERROR: Param 'out_plot' was removed from fit-algorithm. Please update param handling internally!");
}
return p;
}
/// The current OpenMS user data path (for result files)
String File::getUserDirectory()
{
Param p = getSystemParameters();
String dir;
if (p.exists("home_dir") && String(p.getValue("home_dir")).trim() != "")
{
dir = p.getValue("home_dir");
}
else
{
dir = String(QDir::homePath());
}
dir.ensureLastChar('/');
return dir;
}
int main(int argc, const char** argv)
{
//list of all the valid options
Map<String, String> valid_options, valid_flags, option_lists;
valid_flags["--help"] = "help";
valid_options["-ini"] = "ini";
Param param;
param.parseCommandLine(argc, argv, valid_options, valid_flags, option_lists);
// '--help' given
if (param.exists("help"))
{
print_usage();
return 0;
}
// test if unknown options were given
if (param.exists("unknown"))
{
// if TOPPView is packed as Mac OS X bundle it will get a -psn_.. parameter by default from the OS
// if this is the only unknown option it will be ignored .. maybe this should be solved directly
// in Param.h
if (!(param.getValue("unknown").toString().hasSubstring("-psn") && !param.getValue("unknown").toString().hasSubstring(", ")))
{
cout << "Unknown option(s) '" << param.getValue("unknown").toString() << "' given. Aborting!" << endl;
print_usage();
return 1;
}
}
try
{
QApplicationTOPP a(argc, const_cast<char**>(argv));
a.connect(&a, SIGNAL(lastWindowClosed()), &a, SLOT(quit()));
TOPPViewBase* mw = new TOPPViewBase();
a.connect(&a, SIGNAL(fileOpen(QString)), mw, SLOT(loadFile(QString)));
mw->show();
// Create the splashscreen that is displayed while the application loads
QSplashScreen* splash_screen = new QSplashScreen(QPixmap(":/TOPPView_Splashscreen.png"));
splash_screen->show();
splash_screen->showMessage("Loading parameters");
QApplication::processEvents();
StopWatch stop_watch;
stop_watch.start();
if (param.exists("ini"))
{
mw->loadPreferences((String)param.getValue("ini"));
}
//load command line files
if (param.exists("misc"))
{
mw->loadFiles(param.getValue("misc"), splash_screen);
}
// We are about to show the application.
// Proper time to remove the splashscreen, if at least 1.5 seconds have passed...
while (stop_watch.getClockTime() < 1.5) /*wait*/
{
}
stop_watch.stop();
splash_screen->close();
delete splash_screen;
#ifdef OPENMS_WINDOWSPLATFORM
FreeConsole(); // get rid of console window at this point (we will not see any console output from this point on)
AttachConsole(-1); // if the parent is a console, reattach to it - so we can see debug output - a normal user will usually not use cmd.exe to start a GUI)
#endif
int result = a.exec();
delete(mw);
return result;
}
//######################## ERROR HANDLING #################################
catch (Exception::UnableToCreateFile& e)
{
cout << String("Error: Unable to write file (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::FileNotFound& e)
{
cout << String("Error: File not found (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::FileNotReadable& e)
{
cout << String("Error: File not readable (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::FileEmpty& e)
{
cout << String("Error: File empty (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::ParseError& e)
{
cout << String("Error: Unable to read file (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::InvalidValue& e)
{
cout << String("Error: Invalid value (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::BaseException& e)
{
cout << String("Error: Unexpected error (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
return 1;
}
void updateINI(const String& infile, const String& outfile)
{
Int this_instance = getIntOption_("instance");
INIUpdater updater;
String tmp_ini_file = File::getTempDirectory() + "/" + File::getUniqueName() + "_INIUpdater.ini";
tmp_files_.push_back(tmp_ini_file);
String path = File::getExecutablePath();
Param p;
ParamXMLFile paramFile;
paramFile.load(infile, p);
// get sections (usually there is only one - or the user has merged INI files manually)
StringList sections = updater.getToolNamesFromINI(p);
if (sections.empty())
{
writeLog_("Update for file " + infile + " failed because tool section does not exist. Check INI file for corruption!");
failed_.push_back(infile);
return;
}
// get version of first section
String version_old = "Unknown";
if (!p.exists(sections[0] + ":version"))
{
writeLog_("No OpenMS version information found in file " + infile + "! Cannot update!");
failed_.push_back(infile);
return;
}
else
{
version_old = p.getValue(sections[0] + ":version");
// TODO: return on newer version?!
}
// update sections
writeDebug_("Section names: " + ListUtils::concatenate(sections, ", "), 1);
bool update_success = true;
for (Size s = 0; s < sections.size(); ++s)
{
String sec_inst = sections[s] + ":" + String(this_instance) + ":";
// check for default instance
if (!p.exists(sec_inst + "debug"))
{
writeLog_("Update for file '" + infile + "' failed because the instance section '" + sec_inst + "' does not exist. Use -instance or check INI file for corruption!");
update_success = false;
break;
}
String new_tool;
String ttype;
// find mapping to new tool (might be the same name)
if (p.exists(sec_inst + "type")) ttype = p.getValue(sec_inst + "type");
if (!updater.getNewToolName(sections[s], ttype, new_tool))
{
String type_text = ((ttype == "") ? "" : " with type '" + ttype + "' ");
writeLog_("Update for file '" + infile + "' failed because the tool '" + sections[s] + "'" + type_text + "is unknown. TOPPAS file seems to be corrupted!");
update_success = false;
break;
}
// get defaults of new tool by calling it
QProcess pr;
QStringList arguments;
arguments << "-write_ini";
arguments << tmp_ini_file.toQString();
arguments << "-instance";
arguments << String(this_instance).toQString();
pr.start((path + "/" + new_tool).toQString(), arguments);
if (!pr.waitForFinished(-1))
{
writeLog_("Update for file '" + infile + "' failed because the tool '" + new_tool + "' returned with an error! Check if the tool works properly.");
update_success = false;
break;
}
// update defaults with old values
Param new_param;
paramFile.load(tmp_ini_file, new_param);
new_param = new_param.copy(new_tool, true);
Param old_param = p.copy(sections[s], true);
new_param.update(old_param);
// push back changes
p.remove(sections[s] + ":");
p.insert(new_tool, new_param);
}
if (!update_success)
{
failed_.push_back(infile);
return;
}
// STORE
if (outfile.empty()) // create a backup
{
QFileInfo fi(infile.toQString());
String backup_filename = String(fi.path()) + "/" + fi.completeBaseName() + "_v" + version_old + ".ini";
QFile::rename(infile.toQString(), backup_filename.toQString());
std::cout << "Backup of input file created: " << backup_filename << std::endl;
// write updated/new file
paramFile.store(infile, p);
}
else
{
paramFile.store(outfile, p);
}
}
void updateTOPPAS(const String& infile, const String& outfile)
{
Int this_instance = getIntOption_("instance");
INIUpdater updater;
String tmp_ini_file = File::getTempDirectory() + "/" + File::getUniqueName() + "_INIUpdater.ini";
tmp_files_.push_back(tmp_ini_file);
String path = File::getExecutablePath();
ParamXMLFile paramFile;
Param p;
paramFile.load(infile, p);
// get version of TOPPAS file
String version = "Unknown";
if (!p.exists("info:version"))
{
writeLog_("No OpenMS version information found in file " + infile + "! Assuming OpenMS 1.8 and below.");
version = "1.8.0";
}
else
{
version = p.getValue("info:version");
// TODO: return on newer version?!
}
Int vertices = p.getValue("info:num_vertices");
// update sections
writeDebug_("#Vertices: " + String(vertices), 1);
bool update_success = true;
for (Int v = 0; v < vertices; ++v)
{
String sec_inst = "vertices:" + String(v) + ":";
// check for default instance
if (!p.exists(sec_inst + "toppas_type"))
{
writeLog_("Update for file " + infile + " failed because the vertex #" + String(v) + " does not have a 'toppas_type' node. Check INI file for corruption!");
update_success = false;
break;
}
if (p.getValue(sec_inst + "toppas_type") != "tool") // not a tool (but input/output/merge node)
{
continue;
}
if (!p.exists(sec_inst + "tool_name"))
{
writeLog_("Update for file " + infile + " failed because the vertex #" + String(v) + " does not have a 'tool_name' node. Check INI file for corruption!");
update_success = false;
break;
}
String old_name = p.getValue(sec_inst + "tool_name");
String new_tool;
String ttype;
// find mapping to new tool (might be the same name)
if (p.exists(sec_inst + "tool_type")) ttype = p.getValue(sec_inst + "tool_type");
if (!updater.getNewToolName(old_name, ttype, new_tool))
{
String type_text = ((ttype == "") ? "" : " with type '" + ttype + "' ");
writeLog_("Update for file " + infile + " failed because the tool '" + old_name + "'" + type_text + "is unknown. TOPPAS file seems to be corrupted!");
update_success = false;
break;
}
// set new tool name
p.setValue(sec_inst + "tool_name", new_tool);
// delete TOPPAS type
if (new_tool != "GenericWrapper")
{
p.setValue(sec_inst + "tool_type", "");
}
// get defaults of new tool by calling it
QProcess pr;
QStringList arguments;
arguments << "-write_ini";
arguments << tmp_ini_file.toQString();
arguments << "-instance";
arguments << String(this_instance).toQString();
pr.start((path + "/" + new_tool).toQString(), arguments);
if (!pr.waitForFinished(-1))
{
writeLog_("Update for file " + infile + " failed because the tool '" + new_tool + "' returned with an error! Check if the tool works properly.");
update_success = false;
break;
}
// update defaults with old values
Param new_param;
paramFile.load(tmp_ini_file, new_param);
new_param = new_param.copy(new_tool + ":1", true);
Param old_param = p.copy(sec_inst + "parameters", true);
new_param.update(old_param);
// push back changes
p.remove(sec_inst + "parameters:");
p.insert(sec_inst + "parameters", new_param);
}
if (!update_success)
{
failed_.push_back(infile);
return;
}
paramFile.store(tmp_ini_file, p);
// update internal structure (e.g. edges format changed from 1.8 to 1.9)
int argc = 1;
const char* c = "IniUpdater";
const char** argv = &c;
QApplication app(argc, const_cast<char**>(argv), false);
String tmp_dir = File::getTempDirectory() + "/" + File::getUniqueName();
QDir d;
d.mkpath(tmp_dir.toQString());
TOPPASScene ts(nullptr, tmp_dir.toQString(), false);
paramFile.store(tmp_ini_file, p);
ts.load(tmp_ini_file);
ts.store(tmp_ini_file);
paramFile.load(tmp_ini_file, p);
// STORE
if (outfile.empty()) // create a backup
{
QFileInfo fi(infile.toQString());
String new_name = String(fi.path()) + "/" + fi.completeBaseName() + "_v" + version + ".toppas";
QFile::rename(infile.toQString(), new_name.toQString());
// write new file
paramFile.store(infile, p);
}
else
{
paramFile.store(outfile, p);
}
}
ExitCodes main_(int, const char **)
{
// find the config for the tool:
String type = getStringOption_("type");
Param tool_param = this->getParam_();
// check required parameters (TOPPBase does not do this as we did not use registerInputFile_(...) etc)
Param p = tool_param.copy("ETool:", true);
for (Param::ParamIterator it = p.begin(); it != p.end(); ++it)
{
if ((it->tags).count("required") > 0)
{
if (it->value.toString().trim().empty()) // any required parameter should have a value
{
LOG_ERROR << "The INI-parameter '" + it->name + "' is required, but was not given! Aborting ...";
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
else if ((it->tags).count("input file") > 0) // any required input file should exist
{
if (!File::exists(it->value))
{
LOG_ERROR << "Input file '" + String(it->value) + "' does not exist! Aborting ...";
return wrapExit(INPUT_FILE_NOT_FOUND);
}
}
}
}
Internal::ToolDescription gw = ToolHandler::getTOPPToolList(true)[toolName_()];
for (Size i = 0; i < gw.types.size(); ++i)
{
if (type == gw.types[i])
{
tde_ = gw.external_details[i];
if (tde_.working_directory.trim() == "") tde_.working_directory = ".";
break;
}
}
LOG_INFO << tde_.text_startup << "\n";
String command_args = tde_.commandline;
// check for double spaces and warn
if (command_args.hasSubstring(" "))
{
LOG_WARN << "Commandline contains double spaces, which is not allowed. Condensing...\n";
while (command_args.hasSubstring(" "))
{
command_args.substitute(" ", " ");
}
LOG_WARN << "result: " << command_args << std::endl;
}
writeDebug_("CommandLine from ttd (unprocessed): " + command_args, 1);
// do "pre" moves (e.g. if the wrapped tool works on its data in-place (overwrites) it - we need to make a copy first
// - we copy the file
// - we set the value of the affected parameter to the copied tmp file, such that subsequent calls target the tmp file
for (Size i = 0; i < tde_.tr_table.pre_moves.size(); ++i)
{
const Internal::FileMapping & fm = tde_.tr_table.pre_moves[i];
// find target param:
Param p = tool_param.copy("ETool:", true);
String target = fm.target;
if (!p.exists(target)) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Cannot find target parameter '" + target + "' being mapped from external tools output!", target);
String tmp_location = fm.location;
// fragment's placeholder evaluation:
createFragment_(tmp_location, p);
// check if target already exists:
String target_file = (String)p.getValue(target);
if (File::exists(tmp_location))
{
if (!File::remove(tmp_location))
{
LOG_ERROR << "While writing a tmp file: Cannot remove conflicting file '" + tmp_location + "'. Check permissions! Aborting ...";
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
}
// create the temp file tmp_location target_file
writeDebug_(String("Copying '") + target_file + "' to '" + tmp_location + "'", 1);
bool move_ok = QFile::copy(target_file.toQString(), tmp_location.toQString());
if (!move_ok)
{
LOG_ERROR << "Copying the target file '" + tmp_location + "' from '" + target_file + "' failed! Aborting ...";
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
// set the input file's value to the temp file
tool_param.setValue(String("ETool:") + target, tmp_location);
}
///// construct the command line:
// go through mappings (reverse because replacing %10 must come before %1):
for (std::map<Int, String>::reverse_iterator it = tde_.tr_table.mapping.rbegin(); it != tde_.tr_table.mapping.rend(); ++it)
{
//std::cout << "mapping #" << it->first << "\n";
String fragment = it->second;
// fragment's placeholder evaluation:
createFragment_(fragment, tool_param.copy("ETool:", true));
// replace fragment in cl
//std::cout << "replace : " << "%"+String(it->first) << " with '" << fragment << "\n";
command_args.substitute("%" + String(it->first), fragment);
}
QProcess builder;
builder.setProcessChannelMode(QProcess::MergedChannels);
String call = tde_.path + " " + command_args;
writeDebug_("call command: " + call, 1);
builder.setWorkingDirectory(tde_.working_directory.toQString());
builder.start(call.toQString());
if (!builder.waitForFinished(-1) || builder.exitStatus() != 0 || builder.exitCode() != 0)
{
LOG_ERROR << ("External tool returned with non-zero exit code (" + String(builder.exitCode()) + "), exit status (" + String(builder.exitStatus()) + ") or timed out. Aborting ...\n");
LOG_ERROR << ("External tool output:\n" + String(QString(builder.readAll())));
return wrapExit(EXTERNAL_PROGRAM_ERROR);
}
LOG_INFO << ("External tool output:\n" + String(QString(builder.readAll())));
// post processing (file moving via 'file' command)
for (Size i = 0; i < tde_.tr_table.post_moves.size(); ++i)
{
const Internal::FileMapping & fm = tde_.tr_table.post_moves[i];
// find target param:
Param p = tool_param.copy("ETool:", true);
String target = fm.target;
if (!p.exists(target)) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Cannot find target parameter '" + target + "' being mapped from external tools output!", target);
String source = fm.location;
// fragment's placeholder evaluation:
createFragment_(source, p);
// check if target already exists:
String target_file = (String)p.getValue(target);
if (target_file.trim().empty()) // if target was not given, we skip the copying step (usually for optional parameters)
{
LOG_INFO << "Parameter '" + target + "' not given. Skipping forwarding of files.\n";
continue;
}
if (File::exists(target_file))
{
if (!File::remove(target_file))
{
LOG_ERROR << "Cannot remove conflicting file '" + target_file + "'. Check permissions! Aborting ..." << std::endl;
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
}
// move to target
writeDebug_(String("moving '") + source + "' to '" + target_file + "'", 1);
bool move_ok = QFile::rename(source.toQString(), target_file.toQString());
if (!move_ok)
{
LOG_ERROR << "Moving the target file '" + target_file + "' from '" + source + "' failed! Aborting ..." << std::endl;
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
}
LOG_INFO << tde_.text_finish << "\n";
return wrapExit(EXECUTION_OK);
}
ExitCodes main_(int, const char **) override
{
// find the config for the tool:
String type = getStringOption_("type");
Param tool_param = this->getParam_();
// check required parameters (TOPPBase does not do this as we did not use registerInputFile_(...) etc)
Param p = tool_param.copy("ETool:", true);
for (Param::ParamIterator it = p.begin(); it != p.end(); ++it)
{
if ((it->tags).count("required") > 0)
{
String in = it->value.toString().trim(); // will give '[]' for empty lists (hack, but DataValue class does not offer a convenient query)
if (in.empty() || in == "[]") // any required parameter should have a value
{
LOG_ERROR << "The INI-parameter 'ETool:" << it->name << "' is required, but was not given! Aborting ..." << std::endl;
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
else if ((it->tags).count("input file") > 0) // any required input file should exist
{
StringList ifs;
switch (it->value.valueType())
{
case DataValue::STRING_VALUE:
ifs.push_back(it->value);
break;
case DataValue::STRING_LIST:
ifs = it->value;
break;
default:
LOG_ERROR << "The INI-parameter 'ETool:" << it->name << "' is tagged as input file and thus must be a string! Aborting ...";
return wrapExit(ILLEGAL_PARAMETERS);
}
for (StringList::const_iterator itf = ifs.begin(); itf != ifs.end(); ++itf)
{
if (!File::exists(*itf))
{
LOG_ERROR << "Input file '" << *itf << "' does not exist! Aborting ...";
return wrapExit(INPUT_FILE_NOT_FOUND);
}
}
}
}
}
Internal::ToolDescription gw = ToolHandler::getTOPPToolList(true)[toolName_()];
for (Size i = 0; i < gw.types.size(); ++i)
{
if (type == gw.types[i])
{
tde_ = gw.external_details[i];
if (tde_.working_directory.trim() == "") tde_.working_directory = ".";
break;
}
}
LOG_INFO << tde_.text_startup << "\n";
String command_args = tde_.commandline;
// check for double spaces and warn
if (command_args.hasSubstring(" "))
{
LOG_WARN << "Command line contains double spaces, which is not allowed. Condensing...\n";
while (command_args.hasSubstring(" "))
{
command_args.substitute(" ", " ");
}
LOG_WARN << "result: " << command_args << std::endl;
}
writeDebug_("CommandLine from ttd (unprocessed): " + command_args, 1);
// do "pre" moves (e.g. if the wrapped tool works on its data in-place (overwrites) it - we need to make a copy first
// - we copy the file
// - we set the value of the affected parameter to the copied tmp file, such that subsequent calls target the tmp file
for (Size i = 0; i < tde_.tr_table.pre_moves.size(); ++i)
{
const Internal::FileMapping & fm = tde_.tr_table.pre_moves[i];
// find target param:
Param p = tool_param.copy("ETool:", true);
String target = fm.target;
if (!p.exists(target)) throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Cannot find target parameter '" + target + "' being mapped from external tools output!", target);
String tmp_location = fm.location;
// fragment's placeholder evaluation:
createFragment_(tmp_location, p);
// check if target already exists:
String target_file = (String)p.getValue(target);
if (File::exists(tmp_location))
{
if (!File::remove(tmp_location))
{
LOG_ERROR << "While writing a tmp file: Cannot remove conflicting file '" + tmp_location + "'. Check permissions! Aborting ...";
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
}
// create the temp file tmp_location target_file
writeDebug_(String("Copying '") + target_file + "' to '" + tmp_location + "'", 1);
bool move_ok = QFile::copy(target_file.toQString(), tmp_location.toQString());
if (!move_ok)
{
LOG_ERROR << "Copying the target file '" + tmp_location + "' from '" + target_file + "' failed! Aborting ...";
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
// set the input file's value to the temp file
tool_param.setValue(String("ETool:") + target, tmp_location);
}
///// construct the command line:
std::map<int, std::string> mappings; // remember the values for each mapping (for file_post substitution later on)
// go through mappings (reverse because replacing %10 must come before %1):
for (std::map<Int, String>::reverse_iterator it = tde_.tr_table.mapping.rbegin(); it != tde_.tr_table.mapping.rend(); ++it)
{
//std::cout << "mapping #" << it->first << "\n";
String fragment = it->second;
// fragment's placeholder evaluation:
createFragment_(fragment, tool_param.copy("ETool:", true));
// replace fragment in cl
//std::cout << "replace : " << "%"+String(it->first) << " with '" << fragment << "\n";
command_args.substitute("%" + String(it->first), fragment);
// cache mapping
mappings[it->first] = fragment;
}
QProcess builder;
builder.setProcessChannelMode(QProcess::MergedChannels);
String call = tde_.path + " " + command_args;
writeDebug_("call command: " + call, 1);
builder.setWorkingDirectory(tde_.working_directory.toQString());
builder.start(call.toQString());
if (!builder.waitForFinished(-1) || builder.exitStatus() != 0 || builder.exitCode() != 0)
{
LOG_ERROR << ("External tool returned with exit code (" + String(builder.exitCode()) + "), exit status (" + String(builder.exitStatus()) + ") or timed out. Aborting ...\n");
LOG_ERROR << ("External tool output:\n" + String(QString(builder.readAll())));
return wrapExit(EXTERNAL_PROGRAM_ERROR);
}
LOG_INFO << ("External tool output:\n" + String(QString(builder.readAll())));
// post processing (file moving via 'file_post' command)
for (Size i = 0; i < tde_.tr_table.post_moves.size(); ++i)
{
const Internal::FileMapping & fm = tde_.tr_table.post_moves[i];
// find target param:
Param p = tool_param.copy("ETool:", true);
String source_file = fm.location;
// fragment's placeholder evaluation:
createFragment_(source_file, p, mappings);
// check if target already exists:
String target = fm.target;
if (!p.exists(target)) throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Cannot find target parameter '" + target + "' being mapped from external tools output!", target);
String target_file = (String)p.getValue(target);
if (target_file.trim().empty()) // if target was not given, we skip the copying step (usually for optional parameters)
{
LOG_INFO << "Parameter '" + target + "' not given. Skipping forwarding of files.\n";
continue;
}
// check if the target exists already (should not; if yes, delete it before overwriting it)
if (File::exists(target_file))
{
if (!File::remove(target_file))
{
LOG_ERROR << "Cannot remove conflicting file '" + target_file + "'. Check permissions! Aborting ..." << std::endl;
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
}
// move to target
writeDebug_(String("<file_post>: moving '") + source_file + "' to '" + target_file + "'", 1);
if (!File::exists(source_file))
{
LOG_ERROR << "Moving the source file '" + source_file + "' during <file_post> failed, since it does not exist!\n"
<< "Make sure the external program created the file and its filename is either\n"
<< "unique or you only run one GenericWrapper at a time to avoid overwriting of files!\n"
<< "Ideally, (if the external program allows to specify output filenames directly) avoid <file_post>\n"
<< "in the TTD and request the output file directly. Aborting ..." << std::endl;
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
bool move_ok = QFile::rename(source_file.toQString(), target_file.toQString());
if (!move_ok)
{
LOG_ERROR << "Moving the target file '" + target_file + "' from '" + source_file + "' failed!\n"
<< "This file exists, but is either currently open for writing or otherwise blocked (concurrent process?). Aborting ..." << std::endl;
return wrapExit(CANNOT_WRITE_OUTPUT_FILE);
}
}
LOG_INFO << tde_.text_finish << "\n";
return wrapExit(EXECUTION_OK);
}
int main(int argc, const char** argv)
{
// list of all the valid options
Map<String, String> valid_options, valid_flags, option_lists;
valid_flags["--help"] = "help";
valid_flags["--debug"] = "debug";
valid_options["-ini"] = "ini";
// invalid, but keep for now in order to inform users where to find this functionality now
valid_options["-execute"] = "execute";
valid_options["-out_dir"] = "out_dir";
Param param;
param.parseCommandLine(argc, argv, valid_options, valid_flags, option_lists);
// '--help' given
if (param.exists("help"))
{
print_usage();
return 0;
}
// '-debug' given
if (param.exists("debug"))
{
LOG_INFO << "Debug flag provided. Enabling 'LOG_DEBUG' ..." << std::endl;
Log_debug.insert(cout); // allows to use LOG_DEBUG << "something" << std::endl;
}
// test if unknown options were given
if (param.exists("unknown"))
{
// if TOPPAS is packed as Mac OS X bundle it will get a -psn_.. parameter by default from the OS
// if this is the only unknown option it will be ignored .. maybe this should be solved directly
// in Param.h
if (!(param.getValue("unknown").toString().hasSubstring("-psn") && !param.getValue("unknown").toString().hasSubstring(", ")))
{
LOG_ERROR << "Unknown option(s) '" << param.getValue("unknown").toString() << "' given. Aborting!" << endl;
print_usage(Log_error);
return 1;
}
}
try
{
if (param.exists("execute") || param.exists("out_dir"))
{
LOG_ERROR << "The parameters '-execute' and '-out_dir' are not valid anymore. This functionality has been moved to the ExecutePipeline tool." << endl;
return 1;
}
QApplicationTOPP a(argc, const_cast<char**>(argv));
a.connect(&a, SIGNAL(lastWindowClosed()), &a, SLOT(quit()));
TOPPASBase* mw = new TOPPASBase();
mw->show();
a.connect(&a, SIGNAL(fileOpen(QString)), mw, SLOT(openToppasFile(QString)));
// Create the splashscreen that is displayed while the application loads (version is drawn dynamically)
QPixmap qpm(":/TOPPAS_Splashscreen.png");
QPainter pt_ver(&qpm);
pt_ver.setFont(QFont("Helvetica [Cronyx]", 15, 2, true));
pt_ver.setPen(QColor(44, 50, 152));
pt_ver.drawText(490, 84, VersionInfo::getVersion().toQString());
QSplashScreen* splash_screen = new QSplashScreen(qpm);
splash_screen->show();
QApplication::processEvents();
StopWatch stop_watch;
stop_watch.start();
if (param.exists("ini"))
{
mw->loadPreferences((String)param.getValue("ini"));
}
if (param.exists("misc"))
{
mw->loadFiles(param.getValue("misc"), splash_screen);
}
else // remember this new window as obsolete once a real workflow is loaded without this window being touched
{ // if this is not desired, simply call newPipeline() without arguments
mw->newPipeline(mw->IDINITIALUNTITLED);
}
// We are about to show the application.
// Proper time to remove the splash screen, if at least 1.5 seconds have passed...
while (stop_watch.getClockTime() < 1.5) /*wait*/
{
}
stop_watch.stop();
splash_screen->close();
delete splash_screen;
#ifdef OPENMS_WINDOWSPLATFORM
FreeConsole(); // get rid of console window at this point (we will not see any console output from this point on)
AttachConsole(-1); // if the parent is a console, reattach to it - so we can see debug output - a normal user will usually not use cmd.exe to start a GUI)
#endif
int result = a.exec();
delete(mw);
return result;
}
//######################## ERROR HANDLING #################################
catch (Exception::UnableToCreateFile& e)
{
cout << String("Error: Unable to write file (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::FileNotFound& e)
{
cout << String("Error: File not found (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::FileNotReadable& e)
{
cout << String("Error: File not readable (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::FileEmpty& e)
{
cout << String("Error: File empty (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::ParseError& e)
{
cout << String("Error: Unable to read file (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::InvalidValue& e)
{
cout << String("Error: Invalid value (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
catch (Exception::BaseException& e)
{
cout << String("Error: Unexpected error (") << e.what() << ")" << endl << "Code location: " << e.getFile() << ":" << e.getLine() << endl;
}
return 1;
}
int main(int argc, const char** argv)
{
#if defined(__APPLE__)
// we do not want to load plugins as this leads to serious problems
// when shipping on mac os x
QApplication::setLibraryPaths(QStringList());
#endif
// ensure correct encoding of paths
QTextCodec::setCodecForCStrings(QTextCodec::codecForName("UTF-8"));
Map<String, String> option_lists;
Map<String, String> options;
options["-print"] = "print";
Map<String, String> flags;
flags["--help"] = "help";
Param param;
param.parseCommandLine(argc, argv, options, flags, option_lists);
//catch command line errors
if (param.exists("help") //help requested
|| argc > 3 //too many arguments
|| (argc == 3 && !param.exists("print")) //three argument but no -print
|| (param.exists("print") && param.getValue("print") == "") //-print but no file given
)
{
cerr << endl
<< "INIFileEditor -- An editor for OpenMS configuration files." << endl
<< endl
<< "Usage:" << endl
<< " INIFileEditor [options] [file]" << endl
<< endl
<< "Options are:" << endl
<< " --help Shows this help and exits" << endl
<< " -print <file> Prints the content of the file to the command line and exits" << endl
<< endl;
return 0;
}
//print a ini file as text
if (param.exists("print"))
{
Param data;
ParamXMLFile paramFile;
try
{
paramFile.load(param.getValue("print"), data);
for (Param::ParamIterator it = data.begin(); it != data.end(); ++it)
{
cout << it.getName() << " = " << it->value << endl;
}
}
catch (Exception::BaseException& e)
{
LOG_ERROR << "Error while parsing file '" << param.getValue("print") << "'\n";
LOG_ERROR << e << "\n";
}
return 0;
}
//Create window
QApplicationTOPP app(argc, const_cast<char**>(argv));
//set plastique style unless windows / mac style is available
if (QStyleFactory::keys().contains("windowsxp", Qt::CaseInsensitive))
{
app.setStyle("windowsxp");
}
else if (QStyleFactory::keys().contains("macintosh", Qt::CaseInsensitive))
{
app.setStyle("macintosh");
}
else if (QStyleFactory::keys().contains("plastique", Qt::CaseInsensitive))
{
app.setStyle("plastique");
}
INIFileEditorWindow editor_window;
//Open passed file
if (argc == 2)
{
//cout << "OPEN: " << argv[1] << endl;
editor_window.openFile(argv[1]);
}
#ifdef OPENMS_WINDOWSPLATFORM
FreeConsole(); // get rid of console window at this point (we will not see any console output from this point on)
AttachConsole(-1); // if the parent is a console, reattach to it - so we can see debug output - a normal user will usually not use cmd.exe to start a GUI)
#endif
editor_window.show();
return app.exec();
}