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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  34
  35                 else {
  36                         vector<string> myArray = setParameters();
  37
  38                         OptionParser parser(option);
  39                         map<string, string> parameters = parser.getParameters();
  40                         map<string, string>::iterator it;
  41
  42                         ValidParameters validParameter;
  43
  44                         //check for optional parameter and set defaults
  45                         // ...at some point should added some additional type checking...
  46                         string commandOption = validParameter.validFile(parameters, "command", false);
  47                         if (commandOption == "not found") { commandOption = ""; }
  48                         else { command = commandOption; }
  49
  50                         if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
  51                         else if (commandOption == "") {
  52                                 //check for outputdir and inputdir parameters
  53                                 int commaPos = option.find_first_of(',');
  54
  55                                 //if there is a comma then grab string up to that pos
  56                                 if (commaPos != option.npos) {
  57                                         option = option.substr(0, commaPos);
  58                                 }
  59
  60                                 command = option;
  61                         }
  62                 }
  63
  64         }
  65         catch(exception& e) {
  66                 m->errorOut(e, "SystemCommand", "SystemCommand");
  67                 exit(1);
  68         }
  69 }
  70 //**********************************************************************************************************************
  71
  72 string SystemCommand::getHelpString(){
  73         try {
  74                 string helpString = "";
  75                 helpString += "The system command allows you to execute a system command from within mothur.\n";
  76                 helpString += "The system has no parameters.\n";
  77                 helpString += "The system command should be in the following format: system(yourCommand).\n";
  78                 helpString += "Example system(clear).\n";
  79                 return helpString;
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "SystemCommand", "help");
  83                 exit(1);
  84         }
  85 }
  86
  87 //**********************************************************************************************************************
  88
  89 int SystemCommand::execute(){
  90         try {
  91
  92                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  93
  94                 //if command contains a redirect don't add the redirect
  95                 bool usedRedirect = false;
  96                 if ((command.find('>')) == string::npos) {
  97                         command += " > ./commandScreen.output 2>&1";
  98                         usedRedirect = true;
  99                 }
 100
 101                 system(command.c_str());
 102
 103                 if (usedRedirect) {
 104                         ifstream in;
 105                         string filename = "./commandScreen.output";
 106                         m->openInputFile(filename, in, "no error");
 107
 108                         string output = "";
 109                         while(char c = in.get()){
 110                                 if(in.eof())            {       break;                  }
 111                                 else                            {       output += c;    }
 112                         }
 113                         in.close();
 114
 115                         m->mothurOut(output); m->mothurOutEndLine();
 116                         m->mothurRemove(filename);
 117                 }
 118
 119                 return 0;
 120         }
 121
 122         catch(exception& e) {
 123                 m->errorOut(e, "SystemCommand", "execute");
 124                 exit(1);
 125         }
 126 }
 127
 128 //**********************************************************************************************************************