setdircommand.cpp

   1 /*
   2  *  setoutdircommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 1/21/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "setdircommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> SetDirectoryCommand::setParameters(){
  14         try {
  15                 CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault);
  16                 CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
  17                 CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
  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, "SetDirectoryCommand", "setParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 string SetDirectoryCommand::getHelpString(){
  32         try {
  33                 string helpString = "";
  34                 helpString += "The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n";
  35                 helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
  36                 helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
  37                 helpString += "The set.dir command parameters are input, output and tempdefault and one is required.\n";
  38                 helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
  39                 helpString += "To return the input to the current working directory you may enter: input=clear.\n";
  40                 helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n";
  41                 helpString += "To set the input to the directory where mothur.exe is located you may enter: input=default.\n";
  42                 helpString += "To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n";
  43                 helpString += "To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n";
  44                 helpString += "The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n";
  45                 helpString += "Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n";
  46                 helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n";
  47                 return helpString;
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "SetDirectoryCommand", "getHelpString");
  51                 exit(1);
  52         }
  53 }
  54 //**********************************************************************************************************************
  55
  56 SetDirectoryCommand::SetDirectoryCommand(string option)  {
  57         try {
  58                 abort = false; calledHelp = false;
  59
  60                 //allow user to run help
  61                 if(option == "help") { help(); abort = true; calledHelp = true; }
  62                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  63
  64                 else {
  65                         vector<string> myArray = setParameters();
  66
  67                         OptionParser parser(option);
  68                         map<string, string> parameters = parser.getParameters();
  69
  70                         ValidParameters validParameter;
  71                         //check to make sure all parameters are valid for command
  72                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  73                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  74                         }
  75
  76                         output = validParameter.validFile(parameters, "output", false);
  77                         if (output == "not found") {  output = "";  }
  78
  79                         input = validParameter.validFile(parameters, "input", false);
  80                         if (input == "not found") {  input = "";  }
  81
  82                         tempdefault = validParameter.validFile(parameters, "tempdefault", false);
  83                         if (tempdefault == "not found") {  tempdefault = "";  }
  84
  85                         if ((input == "") && (output == "") && (tempdefault == "")) {
  86                                 m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
  87                         }
  88                 }
  89         }
  90         catch(exception& e) {
  91                 m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
  92                 exit(1);
  93         }
  94 }
  95 //**********************************************************************************************************************
  96
  97 int SetDirectoryCommand::execute(){
  98         try {
  99
 100                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 101
 102                 commandFactory = CommandFactory::getInstance();
 103
 104                 m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
 105
 106                 //redirect output
 107                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 108                 else if (output == "default") {
 109                         string exepath = m->argv;
 110                         output = exepath.substr(0, (exepath.find_last_of('m')));
 111
 112                         m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 113                         commandFactory->setOutputDirectory(output);
 114                 }else {
 115             if (m->dirCheck(output)) {
 116                 m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 117                                 commandFactory->setOutputDirectory(output);
 118             }
 119                 }
 120
 121                 //redirect input
 122                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 123                 else if (input == "default") {
 124                         string exepath = m->argv;
 125                         input = exepath.substr(0, (exepath.find_last_of('m')));
 126
 127                         m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 128                         commandFactory->setInputDirectory(input);
 129                 }else {
 130             if (m->dirCheck(input)) {
 131                 m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 132                                 commandFactory->setInputDirectory(input);
 133             }
 134         }
 135
 136                 //set default
 137                 if (tempdefault == "clear") {
 138                         #ifdef MOTHUR_FILES
 139                                 string temp = MOTHUR_FILES;
 140                                 m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
 141                                 m->setDefaultPath(temp);
 142                         #else
 143                                 string temp = "";
 144                                 m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
 145                                 m->setDefaultPath(temp);
 146                         #endif
 147                 }else if (tempdefault == "") {  //do nothing
 148                 }else if (tempdefault == "default") {
 149                         string exepath = m->argv;
 150                         tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 151
 152                         m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 153                         m->setDefaultPath(tempdefault);
 154                 }else {
 155             if (m->dirCheck(tempdefault)) {
 156                 m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 157                                 m->setDefaultPath(tempdefault);
 158             }
 159         }
 160
 161                 return 0;
 162         }
 163         catch(exception& e) {
 164                 m->errorOut(e, "SetDirectoryCommand", "execute");
 165                 exit(1);
 166         }
 167 }
 168 //**********************************************************************************************************************/