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
  14 SystemCommand::SystemCommand(string option){
  15         try {
  16                 abort = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; }
  20
  21                 else {
  22                         //valid paramters for this command
  23                         string Array[] =  {"command"};
  24                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  25
  26                         OptionParser parser(option);
  27                         map<string,string> parameters = parser.getParameters();
  28
  29                         ValidParameters validParameter;
  30
  31                         //check to make sure all parameters are valid for command
  32                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  33                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  34                         }
  35
  36                         //check for required parameters
  37                         command = validParameter.validFile(parameters, "command", false);
  38                         if (command == "not found") { mothurOut("command is a required parameter."); mothurOutEndLine(); abort = true; }
  39                 }
  40
  41         }
  42         catch(exception& e) {
  43                 errorOut(e, "SystemCommand", "SystemCommand");
  44                 exit(1);
  45         }
  46 }
  47 //**********************************************************************************************************************
  48
  49 void SystemCommand::help(){
  50         try {
  51                 mothurOut("The system command allows you to execute a system command from within mothur.\n");
  52                 mothurOut("The system command parameter is command and it is required.\n");
  53                 mothurOut("The system command should be in the following format: system(command=yourCommand).\n");
  54                 mothurOut("Example system(command=clear).\n");
  55                 mothurOut("Note: No spaces between parameter labels (i.e. command), '=' and parameters (i.e.yourCommand).\n\n");
  56         }
  57         catch(exception& e) {
  58                 errorOut(e, "SystemCommand", "help");
  59                 exit(1);
  60         }
  61 }
  62
  63 //**********************************************************************************************************************
  64
  65 int SystemCommand::execute(){
  66         try {
  67
  68                 if (abort == true) { return 0; }
  69
  70                 system(command.c_str());
  71
  72                 return 0;
  73         }
  74
  75         catch(exception& e) {
  76                 errorOut(e, "SystemCommand", "execute");
  77                 exit(1);
  78         }
  79 }
  80
  81 //**********************************************************************************************************************