#include "systemcommand.h"
//**********************************************************************************************************************
-
-SystemCommand::SystemCommand(string option){
+vector<string> SystemCommand::setParameters(){
try {
- abort = false;
+ 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; }
+ if(option == "help") { help(); abort = true; calledHelp = true; }
+ else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
- //valid paramters for this command
- string Array[] = {"command"};
- vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
+ vector<string> myArray = setParameters();
OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
+ map<string, string> parameters = parser.getParameters();
+ map<string, string>::iterator it;
ValidParameters validParameter;
- //check to make sure all parameters are valid for command
- for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
+ //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; }
- //check for required parameters
- command = validParameter.validFile(parameters, "command", false);
- if (command == "not found") { mothurOut("command is a required parameter."); mothurOutEndLine(); abort = true; }
+ 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 command parameter is command and it is required.\n");
- mothurOut("The system command should be in the following format: system(command=yourCommand).\n");
- mothurOut("Example system(command=clear).\n");
- mothurOut("Note: No spaces between parameter labels (i.e. command), '=' and parameters (i.e.yourCommand).\n\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; }
system(command.c_str());
}
catch(exception& e) {
- errorOut(e, "SystemCommand", "execute");
+ m->errorOut(e, "SystemCommand", "execute");
exit(1);
}
}