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 pdebug("debug", "Boolean", "", "F", "", "", "",false,false); parameters.push_back(pdebug);
  17                 CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput);
  18                 CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput);
  19                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  21
  22                 vector<string> myArray;
  23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  24                 return myArray;
  25         }
  26         catch(exception& e) {
  27                 m->errorOut(e, "SetDirectoryCommand", "setParameters");
  28                 exit(1);
  29         }
  30 }
  31 //**********************************************************************************************************************
  32 string SetDirectoryCommand::getHelpString(){
  33         try {
  34                 string helpString = "";
  35                 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";
  36                 helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
  37                 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";
  38         helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
  39                 helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n";
  40         helpString += "To run mothur in debug mode set debug=true. Default debug=false.\n";
  41                 helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
  42                 helpString += "To return the input to the current working directory you may enter: input=clear.\n";
  43                 helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n";
  44                 helpString += "To set the input to the directory where mothur.exe is located you may enter: input=default.\n";
  45                 helpString += "To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n";
  46                 helpString += "To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n";
  47                 helpString += "The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n";
  48                 helpString += "Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n";
  49                 helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n";
  50                 return helpString;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "SetDirectoryCommand", "getHelpString");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58
  59 SetDirectoryCommand::SetDirectoryCommand(string option)  {
  60         try {
  61                 abort = false; calledHelp = false;
  62
  63                 //allow user to run help
  64                 if(option == "help") { help(); abort = true; calledHelp = true; }
  65                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  66
  67                 else {
  68                         vector<string> myArray = setParameters();
  69
  70                         OptionParser parser(option);
  71                         map<string, string> parameters = parser.getParameters();
  72
  73                         ValidParameters validParameter;
  74                         //check to make sure all parameters are valid for command
  75                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  76                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  77                         }
  78
  79                         output = validParameter.validFile(parameters, "output", false);
  80                         if (output == "not found") {  output = "";  }
  81
  82                         input = validParameter.validFile(parameters, "input", false);
  83                         if (input == "not found") {  input = "";  }
  84
  85                         tempdefault = validParameter.validFile(parameters, "tempdefault", false);
  86                         if (tempdefault == "not found") {  tempdefault = "";  }
  87
  88             bool debug = false;
  89             bool nodebug = false;
  90             debugOnly = false;
  91             string temp = validParameter.validFile(parameters, "debug", false);
  92                         if (temp == "not found") {  debug = false;  nodebug=true; }
  93             else {  debug = m->isTrue(temp); }
  94             m->debug = debug;
  95
  96                         if ((input == "") && (output == "") && (tempdefault == "") && nodebug) {
  97                                 m->mothurOut("You must provide either an input, output, tempdefault or debug for the set.outdir command."); m->mothurOutEndLine(); abort = true;
  98                         }else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; }
  99                 }
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
 103                 exit(1);
 104         }
 105 }
 106 //**********************************************************************************************************************
 107
 108 int SetDirectoryCommand::execute(){
 109         try {
 110
 111                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 112
 113         if (debugOnly) { return 0; }
 114
 115                 commandFactory = CommandFactory::getInstance();
 116
 117                 m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
 118
 119                 //redirect output
 120                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 121                 else if (output == "default") {
 122                         string exepath = m->argv;
 123                         output = exepath.substr(0, (exepath.find_last_of('m')));
 124
 125                         m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 126                         commandFactory->setOutputDirectory(output);
 127                 }else {
 128             if (m->dirCheck(output)) {
 129                 m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 130                                 commandFactory->setOutputDirectory(output);
 131             }
 132                 }
 133
 134                 //redirect input
 135                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 136                 else if (input == "default") {
 137                         string exepath = m->argv;
 138                         input = exepath.substr(0, (exepath.find_last_of('m')));
 139
 140                         m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 141                         commandFactory->setInputDirectory(input);
 142                 }else {
 143             if (m->dirCheck(input)) {
 144                 m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 145                                 commandFactory->setInputDirectory(input);
 146             }
 147         }
 148
 149                 //set default
 150                 if (tempdefault == "clear") {
 151                         #ifdef MOTHUR_FILES
 152                                 string temp = MOTHUR_FILES;
 153                                 m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
 154                                 m->setDefaultPath(temp);
 155                         #else
 156                                 string temp = "";
 157                                 m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
 158                                 m->setDefaultPath(temp);
 159                         #endif
 160                 }else if (tempdefault == "") {  //do nothing
 161                 }else if (tempdefault == "default") {
 162                         string exepath = m->argv;
 163                         tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 164
 165                         m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 166                         m->setDefaultPath(tempdefault);
 167                 }else {
 168             if (m->dirCheck(tempdefault)) {
 169                 m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 170                                 m->setDefaultPath(tempdefault);
 171             }
 172         }
 173
 174                 return 0;
 175         }
 176         catch(exception& e) {
 177                 m->errorOut(e, "SetDirectoryCommand", "execute");
 178                 exit(1);
 179         }
 180 }
 181 //**********************************************************************************************************************/