#include "systemcommand.h"
//**********************************************************************************************************************
-
-SystemCommand::SystemCommand(string option){
+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;
+ abort = false; calledHelp = false;
//allow user to run help
- if(option == "help") { help(); abort = true; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
- else { command = option; }
+ 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) {
- errorOut(e, "SystemCommand", "SystemCommand");
+ m->errorOut(e, "SystemCommand", "SystemCommand");
exit(1);
}
}
//**********************************************************************************************************************
-void SystemCommand::help(){
+string SystemCommand::getHelpString(){
try {
- mothurOut("The system command allows you to execute a system command from within mothur.\n");
- mothurOut("The system has no parameters.\n");
- mothurOut("The system command should be in the following format: system(yourCommand).\n");
- mothurOut("Example system(clear).\n");
+ 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) {
- errorOut(e, "SystemCommand", "help");
+ m->errorOut(e, "SystemCommand", "help");
exit(1);
}
}
int SystemCommand::execute(){
try {
- if (abort == true) { return 0; }
+ if (abort == true) { if (calledHelp) { return 0; } return 2; }
+ command += " > ./commandScreen.output 2>&1";
system(command.c_str());
+ 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) {
- errorOut(e, "SystemCommand", "execute");
+ m->errorOut(e, "SystemCommand", "execute");
exit(1);
}
}