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systemcommand.cpp
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systemcommand.cpp
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/*
* systemcommand.cpp
* Mothur
*
* Created by Sarah Westcott on 7/8/09.
* Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
*
*/
#include "systemcommand.h"
//**********************************************************************************************************************
vector<string> SystemCommand::setParameters(){
try {
CommandParameter pcommand("command", "String", "", "", "", "", "",false,false); parameters.push_back(pcommand);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "SystemCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
SystemCommand::SystemCommand(string option) {
try {
abort = false; calledHelp = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string, string> parameters = parser.getParameters();
map<string, string>::iterator it;
ValidParameters validParameter;
//check for optional parameter and set defaults
// ...at some point should added some additional type checking...
string commandOption = validParameter.validFile(parameters, "command", false);
if (commandOption == "not found") { commandOption = ""; }
else { command = commandOption; }
if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
else if (commandOption == "") {
//check for outputdir and inputdir parameters
int commaPos = option.find_first_of(',');
//if there is a comma then grab string up to that pos
if (commaPos != option.npos) {
option = option.substr(0, commaPos);
}
command = option;
}
}
}
catch(exception& e) {
m->errorOut(e, "SystemCommand", "SystemCommand");
exit(1);
}
}
//**********************************************************************************************************************
string SystemCommand::getHelpString(){
try {
string helpString = "";
helpString += "The system command allows you to execute a system command from within mothur.\n";
helpString += "The system has no parameters.\n";
helpString += "The system command should be in the following format: system(yourCommand).\n";
helpString += "Example system(clear).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "SystemCommand", "help");
exit(1);
}
}
//**********************************************************************************************************************
int SystemCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//if command contains a redirect don't add the redirect
bool usedRedirect = false;
if ((command.find('>')) == string::npos) {
command += " > ./commandScreen.output 2>&1";
usedRedirect = true;
}
system(command.c_str());
if (usedRedirect) {
ifstream in;
string filename = "./commandScreen.output";
m->openInputFile(filename, in, "no error");
string output = "";
while(char c = in.get()){
if(in.eof()) { break; }
else { output += c; }
}
in.close();
m->mothurOut(output); m->mothurOutEndLine();
m->mothurRemove(filename);
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SystemCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************