setlogfilecommand.cpp

   1 /*
   2  *  setlogfilecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 4/27/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "setlogfilecommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 vector<string> SetLogFileCommand::setParameters(){
  15         try {
  16                 CommandParameter pappend("append", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pappend);
  17                 CommandParameter pname("name", "String", "", "", "", "", "","",false,true,true); parameters.push_back(pname);
  18                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  19                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  20
  21                 vector<string> myArray;
  22                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  23                 return myArray;
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "SetLogFileCommand", "setParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 string SetLogFileCommand::getHelpString(){
  32         try {
  33                 string helpString = "";
  34                 helpString += "The set.logfile command can be used to provide a specific name for your logfile and/or to append the log generated by mothur to an existing file.\n";
  35                 helpString += "The set.logfile command parameters are name and append, name is required. Append is set to false by default.\n";
  36                 helpString += "The set.logfile command should be in the following format: set.logfile(name=yourLogFileName, append=T).\n";
  37                 helpString += "Example set.logfile(name=/Users/lab/desktop/output.txt, append=T).\n";
  38                 helpString += "Note: No spaces between parameter labels (i.e. name), '=' and parameters (i.e.yourLogFileName).\n";
  39                 return helpString;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "SetLogFileCommand", "getHelpString");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47
  48 SetLogFileCommand::SetLogFileCommand(string option)  {
  49         try {
  50                 abort = false; calledHelp = false;
  51
  52                 //allow user to run help
  53                 if(option == "help") { help(); abort = true; calledHelp = true; }
  54                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  55
  56                 else {
  57                         vector<string> myArray = setParameters();
  58
  59                         OptionParser parser(option);
  60                         map<string, string> parameters = parser.getParameters();
  61
  62                         ValidParameters validParameter;
  63                         //check to make sure all parameters are valid for command
  64                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  65                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  66                         }
  67
  68                         name = validParameter.validFile(parameters, "name", false);
  69                         if (name == "not found") {  m->mothurOut("name is a required parameter for the set.logfile command."); abort = true; }
  70
  71                         string temp = validParameter.validFile(parameters, "append", false);            if (temp == "not found") {  temp = "F";  }
  72                         append = m->isTrue(temp);
  73                 }
  74         }
  75         catch(exception& e) {
  76                 m->errorOut(e, "SetLogFileCommand", "SetLogFileCommand");
  77                 exit(1);
  78         }
  79 }
  80
  81 //**********************************************************************************************************************
  82
  83 int SetLogFileCommand::execute(){
  84         try {
  85
  86                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  87
  88                 commandFactory = CommandFactory::getInstance();
  89
  90                 commandFactory->setLogfileName(name, append);
  91
  92                 return 0;
  93         }
  94         catch(exception& e) {
  95                 m->errorOut(e, "SetLogFileCommand", "execute");
  96                 exit(1);
  97         }
  98 }
  99 //**********************************************************************************************************************/