int main(int argc, char* argv[]) {
mreal::initPrecision();
mreal::initRand();
CommandParser commandParser;
initCommands(&commandParser);
CommandFactory commandFactory;
try {
int commandCode = UNKNOWN_COMMAND;
CommandParams commandParams;
commandParser.getCommandCodeAndParams(argc, argv, commandCode, commandParams);
ContextPtr pContext = Context::setup(DRY_MODE, ".3app");
CommandPtr pCommand = commandFactory.getCommand(commandCode, commandParams);
pCommand->execute();
_destroy(pCommand);
delete pContext;
}
catch(std::exception const& e) {
std::cout << e.what() << std::endl;
printSyntaxMessage();
}
}
void XMLReader::parseAction(QXmlStreamReader& xml, queue<Command*>* ListOfCommand)
{
CommandFactory cmdFactory;
if (xml.tokenType() != QXmlStreamReader::StartElement && xml.name() == "action")
return ;//ListOfCommand;
xml.readNext();
while(!(xml.tokenType() == QXmlStreamReader::EndElement && xml.name() == "action"))
{
if(xml.tokenType() == QXmlStreamReader::StartElement)
{
if(xml.name() == "type")
{
xml.readNext();
ListOfCommand->push(cmdFactory.CreateCommand(xml.text().toString().toStdString()));
//cout<<xml.text().toString().toStdString()<<endl;
}
}
xml.readNext();
}
//return ListOfCommand;
}
void ConsoleController::processInput(const CommandFactory& commandFactory)
{
std::string line;
while (std::getline(std::cin, line))
{
auto args = split(line, ' ');
if (args.size() >= 1)
{
auto command = commandFactory.getCommand(args[0]);
if (command)
{
command->execute(shared_from_this(), args);
if (args[0] == "exit")
break;
}
}
}
}
int LoadLogfileCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
m->mothurOutEndLine();
m->mothurOut("Extracting current files names..."); m->mothurOutEndLine();
m->mothurOutEndLine();
CommandFactory* cFactory;
cFactory = CommandFactory::getInstance();
ifstream in;
m->openInputFile(logfile, in);
set<string> currentTypes = m->getCurrentTypes();
map<string, string> currentFiles;
string commandName = "";
bool skip = false;
string line = "";
while (!in.eof()) {
if (m->control_pressed) { break; }
if (!skip) { line = m->getline(in); m->gobble(in); }
m->gobble(in);
//look for "mothur >"
int pos = line.find("mothur > "); //command line
int pos2 = line.find("Output File "); //indicates command completed and we can update the current file
int pos3 = line.find("/*****************");
//skipping over parts where a command runs another command
if (pos3 != string::npos) {
while (!in.eof()) {
if (m->control_pressed) { break; }
line = m->getline(in); m->gobble(in);
int posTemp = line.find("/*****************");
if (posTemp != string::npos) { break; }
}
}
if (pos != string::npos) {
skip=false;
//extract command name and option string
string input = line.substr(pos+9);
CommandOptionParser parser(input);
commandName = parser.getCommandString();
string options = parser.getOptionString();
//parse out parameters in option string
map<string,string> parameters;
OptionParser optionParser(options, parameters);
for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
if (currentTypes.count((it->first)) != 0) { //if this is a type we save
if (it->second != "current") { currentFiles[it->first] = it->second; }//save the input file name as current
}
}
}else if (pos2 != string::npos) {
//read file output file names
vector<string> theseOutputNames;
while (!in.eof()) {
if (m->control_pressed) { break; }
line = m->getline(in); m->gobble(in);
int pos = line.find("mothur > ");
if (pos != string::npos) { skip = true; break; }
else { theseOutputNames.push_back(line); }
}
//ask command for the output names for each type based on inputs
Command* command = cFactory->getCommand(commandName);
map<string, vector<string> > thisOutputTypes = command->getOutputFiles();
for (map<string, vector<string> >::iterator it = thisOutputTypes.begin(); it != thisOutputTypes.end(); it++) {
if (currentTypes.count((it->first)) != 0) { //do we save this type
//if yes whats its tag
map<string, string>::iterator itCurrentFiles = currentFiles.find(it->first);
string thisTypesCurrentFile = "";
if (itCurrentFiles != currentFiles.end()) { thisTypesCurrentFile = itCurrentFiles->second; }
//outputfilename pattern for this input type
string pattern = command->getOutputPattern(it->first);
updateCurrent(pattern, it->first, thisTypesCurrentFile, theseOutputNames, currentFiles);
//cout << "current=\n\n";
//for (map<string, string>::iterator itcc = currentFiles.begin(); itcc != currentFiles.end(); itcc++) {
// cout << itcc->first << '\t' << itcc->second << endl;
// }
}
}
}
}
in.close();
if (m->control_pressed) { return 0; }
//output results
string inputString = "";
for (map<string, string>::iterator it = currentFiles.begin(); it != currentFiles.end(); it++) { inputString += it->first + "=" + it->second + ","; }
if (inputString != "") {
inputString = inputString.substr(0, inputString.length()-1);
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: set.current(" + inputString + ")"); m->mothurOutEndLine();
m->mothurCalling = true;
Command* currentCommand = new SetCurrentCommand(inputString);
currentCommand->execute();
delete currentCommand;
m->mothurCalling = false;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "LoadLogfileCommand", "execute");
exit(1);
}
}