void ResidueDB::readResiduesFromFile_(const String& file_name)
{
String file = File::find(file_name);
Param param;
ParamXMLFile paramFile;
paramFile.load(file, param);
if (!param.begin().getName().hasPrefix("Residues"))
{
throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", "");
}
try
{
vector<String> split;
param.begin().getName().split(':', split);
String prefix = split[0] + split[1];
Residue* res_ptr = nullptr;
Map<String, String> values;
for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
{
it.getName().split(':', split);
if (prefix != split[0] + split[1])
{
// add residue
res_ptr = parseResidue_(values);
values.clear();
residues_.insert(res_ptr);
const_residues_.insert(res_ptr);
prefix = split[0] + split[1];
}
String value = it->value;
String key = it.getName();
values[key] = value;
}
// add last residue
res_ptr = parseResidue_(values);
residues_.insert(res_ptr);
const_residues_.insert(res_ptr);
}
catch (Exception::BaseException& e)
{
throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, e.what(), "");
}
}
void EnzymesDB::readEnzymesFromFile_(const String& file_name)
{
String file = File::find(file_name);
Param param;
ParamXMLFile paramFile;
paramFile.load(file, param);
if (!param.begin().getName().hasPrefix("Enzymes"))
{
throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "", "");
}
try
{
vector<String> split;
param.begin().getName().split(':', split);
String prefix = split[0] + split[1];
Map<String, String> values;
for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
{
it.getName().split(':', split);
if (prefix != split[0] + split[1])
{
// add enzyme
addEnzyme_(parseEnzyme_(values));
prefix = split[0] + split[1];
values.clear();
}
values[it.getName()] = it->value;
}
// add last enzyme
addEnzyme_(parseEnzyme_(values));
}
catch (Exception::BaseException& e)
{
throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, e.what(), "");
}
}
StringList INIUpdater::getToolNamesFromINI(const Param & ini) const
{
StringList tool_names;
for (Param::ParamIterator it = ini.begin(); it != ini.end(); ++it)
{
if (it.getName().toQString().count(':') == 1 && it.getName().hasSuffix(":version"))
{
tool_names.push_back(it.getName().prefix(':'));
}
}
return tool_names;
}
void ElementDB::readFromFile_(const String& file_name)
{
String file = File::find(file_name);
// load elements into param object
Param param;
ParamXMLFile paramFile;
paramFile.load(file, param);
UInt an(0);
String name, symbol;
// determine prefix
vector<String> split;
param.begin().getName().split(':', split);
String prefix("");
for (Size i = 0; i < split.size() - 1; ++i)
{
prefix += split[i] + ":";
}
//cout << "first element prefix=" << prefix << endl;
Map<UInt, double> Z_to_abundancy;
Map<UInt, double> Z_to_mass;
for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
{
// new element started?
if (!it.getName().hasPrefix(prefix))
{
// update prefix
it.getName().split(':', split);
prefix = "";
for (Size i = 0; i < split.size() - 1; ++i)
{
prefix += split[i] + ":";
}
// cout << "new element prefix=" << prefix << endl;
// Parsing of previous element is finished. Now store data in Element object
IsotopeDistribution isotopes = parseIsotopeDistribution_(Z_to_abundancy);
double avg_weight = calculateAvgWeight_(Z_to_abundancy, Z_to_mass);
double mono_weight = calculateMonoWeight_(Z_to_mass);
/*
// print information about elements
cout << "Name: " << name << " AtomicNumber: " << an << " Symbol: " << symbol << " AvgWeight: " << avg_weight
<< " MonoWeight: " << mono_weight << " NIsotopes: " << isotopes.size() << endl;
*/
Element* e = new Element(name, symbol, an, avg_weight, mono_weight, isotopes);
names_[name] = e;
symbols_[symbol] = e;
atomic_numbers_[an] = e;
// add all the individual isotopes as separat elements
for (IsotopeDistribution::ConstIterator iit = isotopes.begin(); iit != isotopes.end(); ++iit)
{
String iso_name = "(" + String(iit->first) + ")" + name;
String iso_symbol = "(" + String(iit->first) + ")" + symbol;
// set avg and mono to same value for isotopes (old hack...)
DoubleReal iso_avg_weight = Z_to_mass[(UInt) iit->first];
DoubleReal iso_mono_weight = iso_avg_weight;
IsotopeDistribution iso_isotopes;
vector<pair<Size, double> > iso_container;
iso_container.push_back(make_pair(iit->first, 1.0));
iso_isotopes.set(iso_container);
/*
// print name, symbal and atomic mass of the current isotope
cout << "Isotope Name: " << iso_name << " Symbol: " << iso_symbol << " AtomicMass: " << iso_mono_weight << endl;
*/
Element* iso_e = new Element(iso_name, iso_symbol, an, iso_avg_weight, iso_mono_weight, iso_isotopes);
names_[iso_name] = iso_e;
names_[iso_symbol] = iso_e;
}
Z_to_abundancy.clear();
Z_to_mass.clear();
}
// top level: read the contents of the element section
it.getName().split(':', split);
String key = split[2];
String value = it->value;
value.trim();
// cout << "Key=" << key << endl;
if (key == "AtomicNumber")
{
an = (UInt)value.toInt();
}
else
{
if (key == "Isotopes")
{
UInt Z = UInt(split[3].toInt());
String item = split[4];
if (item == "RelativeAbundance")
{
Z_to_abundancy[Z] = double(value.toDouble() / 100.0);
}
else if (item == "AtomicMass")
{
Z_to_mass[Z] = double(value.toDouble());
}
else
{
cerr << "read unknown item in Isotopes: " << item << endl;
}
}
else
{
if (key == "Name")
{
name = value;
}
else
{
if (key == "Symbol")
{
symbol = value;
}
else
{
cerr << "read unknown tag: " << key << endl;
}
}
}
}
}
// build last element
double avg_weight(0), mono_weight(0);
IsotopeDistribution isotopes = parseIsotopeDistribution_(Z_to_abundancy);
Element* e = new Element(name, symbol, an, avg_weight, mono_weight, isotopes);
names_[name] = e;
symbols_[symbol] = e;
atomic_numbers_[an] = e;
}
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);
}
void createFragment_(String & fragment, const Param & param)
{
//std::cerr << "FRAGMENT: " << fragment << "\n\n";
// e.g.: -input %BASENAME[%%in].mzML
// we have to make this little detour param -> vector<String>
// to sort the param names by length, otherwise we have a
// problem with parameter substitution
// i.e., if A is a prefix of B and gets replaced first, the
// suffix of B remains and will cause trouble!
vector<String> param_names;
param_names.reserve(param.size());
for (Param::ParamIterator it = param.begin(); it != param.end(); ++it)
{
param_names.push_back(it->name);
}
// sort by length
std::sort(param_names.begin(), param_names.end(), reverseComparator(StringSizeLess()));
// iterate through all input params and replace with values:
SignedSize allowed_percent(0); // filenames might contain '%', which are allowed to remain there (and even must remain)
for (vector<String>::iterator it = param_names.begin(); it != param_names.end(); ++it)
{
if (!fragment.hasSubstring("%%" + *it)) continue;
String s_new = paramToString_(param.getEntry(*it));
allowed_percent += s_new.length() - String(s_new).substitute("%", "").length();
//std::cerr << "IN: " << s_new << "(" << allowed_percent << "\n";
fragment.substitute("%%" + *it, s_new);
}
if (fragment.hasSubstring("%%")) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Invalid '%%' found in '" + fragment + "' after replacing all parameters!", fragment);
// %TMP replace:
fragment.substitute("%TMP", File::getTempDirectory());
// %RND replace:
fragment.substitute("%RND", String(UniqueIdGenerator::getUniqueId()));
// %WORKINGDIR replace:
fragment.substitute("%WORKINGDIR", tde_.working_directory);
// %DIR% replace
{
QRegExp rx("%DIR\\[(.*)\\]");
rx.setMinimal(true);
int pos = 0;
QString t_tmp = fragment.toQString();
//std::cout << "fragment is:" << fragment << std::endl;
while ((pos = rx.indexIn(t_tmp, pos)) != -1)
{
String value = rx.cap(1); // param name (hopefully)
// replace in fragment:
QFileInfo qfi(value.toQString());
//std::cout << "match @ " << pos << " " << value << " --> " << qfi.canonicalPath() << "\n";
t_tmp = t_tmp.replace(String("%DIR[" + value + "]").toQString(), qfi.canonicalPath());
}
fragment = String(t_tmp);
//std::cout << "NEW fragment is:" << fragment << std::endl;
}
// %BASENAME% replace
{
QRegExp rx("%BASENAME\\[(.*)\\]");
rx.setMinimal(true);
int pos = 0, count = 0;
QString t_tmp = fragment.toQString();
while ((pos = rx.indexIn(t_tmp, pos)) != -1)
{
//std::cout << "match @ " << pos << "\n";
String value = rx.cap(1); // param name (hopefully)
// replace in fragment:
QFileInfo qfi(value.toQString());
//std::cout << "match @ " << pos << " " << value << " --> " << qfi.completeBaseName() << "\n";
t_tmp = t_tmp.replace(String("%BASENAME[" + value + "]").toQString(), qfi.completeBaseName());
++count;
}
// update expected count of valid '%'
allowed_percent -= (fragment.length() - String(fragment).substitute("%", "").length()) // original # of %
- (t_tmp.length() - String(t_tmp).substitute("%", "").length()) // new # of %
- count; // expected # of % due to %BASENAME
fragment = String(t_tmp);
}
SignedSize diff = (fragment.length() - String(fragment).substitute("%", "").length()) - allowed_percent;
//std::cerr << "allowed: " << allowed_percent << "\n" << "diff: " << diff << " in: " << fragment << "\n";
if (diff > 0) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Mapping still contains '%' after substitution! Did you use % instead of %%?", fragment);
else if (diff < 0) throw Exception::InvalidValue(__FILE__, __LINE__, __PRETTY_FUNCTION__, "Error: '%' from a filename where accidentally considered command tags! "
"This is a bug! Remove '%' from input filesnames to fix, but please report this as well!", fragment);
//std::cout << fragment << "'\n";
}
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)
{
#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();
}
void convertINI2HTML(const Param & p, ostream & os)
{
// the .css file is included via the Header.html (see doc/doxygen/common/Header.html)
os << "<div class=\"ini_global\">\n";
os << "<div class=\"legend\">\n";
os << "<b>Legend:</b><br>\n";
os << " <div class=\"item item_required\">required parameter</div>\n";
os << " <div class=\"item item_advanced\">advanced parameter</div>\n";
os << "</div>\n";
Param::ParamIterator it = p.begin();
String indentation = " ";
while (it != p.end())
{
string key = it.getName();
//write opened/closed nodes
const std::vector<Param::ParamIterator::TraceInfo> & trace = it.getTrace();
for (std::vector<Param::ParamIterator::TraceInfo>::const_iterator it2 = trace.begin(); it2 != trace.end(); ++it2)
{
if (it2->opened) //opened node
{
String d = it2->description;
d.substitute("\n", "<br>");
os << indentation << "<div class=\"node\"><span class=\"node_name\">" << (String().fillLeft('+', (UInt) indentation.size() / 2) + it2->name) << "</span><span class=\"node_description\">" << (d) << "</span></div>" << "\n";
indentation += " ";
}
else //closed node
{
indentation.resize(indentation.size() - 2);
//os << indentation << "</div>" << "\n";
}
}
//write item
String s_attr;
String s_req;
if (it->tags.find("advanced") != it->tags.end())
s_attr += " item_advanced"; // optionally add advanced class
if (it->tags.find("required") != it->tags.end())
s_req += " item_required"; // optionally add required class
DataValue::DataType value_type = it->value.valueType();
//write opening tag
os << indentation << "<div class=\"item" + s_attr + "\"><span class=\"item_name" + s_req + "\" style=\"padding-left:" << indentation.size() * 4 << "px;\">" << (it->name) << "</span><span class=\"item_value\">" << it->value.toString() << "</span>" << "\n";
//replace all critical characters in description
String d = it->description;
d.substitute("\n", "<br>");
os << "<span class=\"item_description\">" << (d) << "</span>";
//tags
String list;
for (set<String>::const_iterator tag_it = it->tags.begin(); tag_it != it->tags.end(); ++tag_it)
{
if (*tag_it == "advanced")
continue; // do not list "advanced" or "required" (this is done by color coding)
if (*tag_it == "required")
continue;
if (!list.empty())
list += ",";
list += *tag_it;
}
os << "<span class=\"item_tags\">" << (list) << "</span>";
//restrictions
String restrictions = "";
bool escape_restrictions(true);
switch (value_type)
{
case DataValue::INT_VALUE:
case DataValue::INT_LIST:
{
bool min_set = (it->min_int != -numeric_limits<Int>::max());
bool max_set = (it->max_int != numeric_limits<Int>::max());
if (max_set || min_set)
{
if (min_set)
restrictions += String(it->min_int);
else
restrictions += "-∞"; // infinity symbol
restrictions += ':';
if (max_set)
restrictions += String(it->max_int);
else
restrictions += "∞";
}
escape_restrictions = false; // prevent html escape of infinity symbol
}
break;
case DataValue::DOUBLE_VALUE:
case DataValue::DOUBLE_LIST:
{
bool min_set = (it->min_float != -numeric_limits<DoubleReal>::max());
bool max_set = (it->max_float != numeric_limits<DoubleReal>::max());
if (max_set || min_set)
{
if (min_set)
restrictions += String(it->min_float);
else
restrictions += "-∞"; // infinity symbol
restrictions += ':';
if (max_set)
restrictions += String(it->max_float);
else
restrictions += "∞";
}
escape_restrictions = false; // prevent html escape of infinity symbol
}
break;
case DataValue::STRING_VALUE:
case DataValue::STRING_LIST:
if (it->valid_strings.size() != 0)
{
restrictions.concatenate(it->valid_strings.begin(), it->valid_strings.end(), ",");
}
break;
default:
break;
}
if (restrictions.empty())
restrictions = " "; // create content, such that the cell gets an underline
os << "<span class=\"item_restrictions\">" << restrictions << "</span>";
os << "</div>"; // end div item
++it;
}
os << "</div>\n"; // end global div
}