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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 {
CurrentFile* current; current = CurrentFile::getInstance();
outputdir = current->getOutputDir();
abort = false; calledHelp = false;
vector<string> myArray;
return myArray;
}
catch(exception& e) {
m->errorOut(e, "SystemCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
SystemCommand::SystemCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
setParameters();
string optionCopy = option;
string parameter = "";
//if command is used parameter=command optionCopy=cp ....
if (optionCopy.find("command=") != string::npos) { util.splitAtEquals(parameter, optionCopy); }
//ValidParameters validParameter;
if (parameter != "command") { command = option; }
else { command = optionCopy; } //command= removed
if ((command == "")) { m->mothurOut("[ERROR]: You must enter a command to run.\n"); abort = true; }
}
}
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) { if (calledHelp) { return 0; } return 2; }
if (outputdir == "") { outputdir = "./"; }
string redirectFileName = outputdir + "commandScreen.output";
//if command contains a redirect don't add the redirect
bool usedRedirect = false;
if ((command.find('>')) == string::npos) {
command += " > " + redirectFileName + " 2>&1";
usedRedirect = true;
}
//m->mothurOut("[DEBUG]: command = '" + command + "'\n");
if (m->getDebug()) { m->mothurOut("[DEBUG]: command = '" + command + "'\n"); }
system(command.c_str());
if (usedRedirect) {
ifstream in; util.openInputFile(redirectFileName, in, "no error");
string output = "";
while(char c = in.get()){
if(in.eof()) { break; }
else { output += c; }
}
in.close();
m->mothurOut(output); m->mothurOutEndLine();
util.mothurRemove(redirectFileName);
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "SystemCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
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