systemcommand.cpp

   1 /*
   2  *  systemcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 7/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "systemcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SystemCommand::setParameters(){
  14         try {
  15                 CommandParameter pcommand("command", "String", "", "", "", "", "",false,false); parameters.push_back(pcommand);
  16
  17                 vector<string> myArray;
  18                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  19                 return myArray;
  20         }
  21         catch(exception& e) {
  22                 m->errorOut(e, "SystemCommand", "setParameters");
  23                 exit(1);
  24         }
  25 }
  26 //**********************************************************************************************************************
  27 SystemCommand::SystemCommand(string option)  {
  28         try {
  29                 abort = false; calledHelp = false;
  30
  31                 //allow user to run help
  32                 if(option == "help") { help(); abort = true; calledHelp = true; }
  33
  34                 else {
  35                         vector<string> myArray = setParameters();
  36
  37                         OptionParser parser(option);
  38                         map<string, string> parameters = parser.getParameters();
  39                         map<string, string>::iterator it;
  40
  41                         ValidParameters validParameter;
  42
  43                         //check for optional parameter and set defaults
  44                         // ...at some point should added some additional type checking...
  45                         string commandOption = validParameter.validFile(parameters, "command", false);
  46                         if (commandOption == "not found") { commandOption = ""; }
  47                         else { command = commandOption; }
  48
  49                         if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
  50                         else if (commandOption == "") {
  51                                 //check for outputdir and inputdir parameters
  52                                 int commaPos = option.find_first_of(',');
  53
  54                                 //if there is a comma then grab string up to that pos
  55                                 if (commaPos != option.npos) {
  56                                         option = option.substr(0, commaPos);
  57                                 }
  58
  59                                 command = option;
  60                         }
  61                 }
  62
  63         }
  64         catch(exception& e) {
  65                 m->errorOut(e, "SystemCommand", "SystemCommand");
  66                 exit(1);
  67         }
  68 }
  69 //**********************************************************************************************************************
  70
  71 string SystemCommand::getHelpString(){
  72         try {
  73                 string helpString = "";
  74                 helpString += "The system command allows you to execute a system command from within mothur.\n";
  75                 helpString += "The system has no parameters.\n";
  76                 helpString += "The system command should be in the following format: system(yourCommand).\n";
  77                 helpString += "Example system(clear).\n";
  78                 return helpString;
  79         }
  80         catch(exception& e) {
  81                 m->errorOut(e, "SystemCommand", "help");
  82                 exit(1);
  83         }
  84 }
  85
  86 //**********************************************************************************************************************
  87
  88 int SystemCommand::execute(){
  89         try {
  90
  91                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  92
  93                 system(command.c_str());
  94
  95                 return 0;
  96         }
  97
  98         catch(exception& e) {
  99                 m->errorOut(e, "SystemCommand", "execute");
 100                 exit(1);
 101         }
 102 }
 103
 104 //**********************************************************************************************************************