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
  63                 else {
  64                         vector<string> myArray = setParameters();
  65
  66                         OptionParser parser(option);
  67                         map<string, string> parameters = parser.getParameters();
  68
  69                         ValidParameters validParameter;
  70                         //check to make sure all parameters are valid for command
  71                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  72                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  73                         }
  74
  75                         output = validParameter.validFile(parameters, "output", false);
  76                         if (output == "not found") {  output = "";  }
  77
  78                         input = validParameter.validFile(parameters, "input", false);
  79                         if (input == "not found") {  input = "";  }
  80
  81                         tempdefault = validParameter.validFile(parameters, "tempdefault", false);
  82                         if (tempdefault == "not found") {  tempdefault = "";  }
  83
  84                         if ((input == "") && (output == "") && (tempdefault == "")) {
  85                                 m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
  86                         }
  87                 }
  88         }
  89         catch(exception& e) {
  90                 m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
  91                 exit(1);
  92         }
  93 }
  94 //**********************************************************************************************************************
  95
  96 int SetDirectoryCommand::execute(){
  97         try {
  98
  99                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 100
 101                 commandFactory = CommandFactory::getInstance();
 102
 103                 m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
 104
 105                 //redirect output
 106                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 107                 else if (output == "default") {
 108                         string exepath = m->argv;
 109                         output = exepath.substr(0, (exepath.find_last_of('m')));
 110
 111                         m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 112                         commandFactory->setOutputDirectory(output);
 113                 }else {
 114                         //add / to name if needed
 115                         string lastChar = output.substr(output.length()-1);
 116                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 117                                 if (lastChar != "/") { output += "/"; }
 118                         #else
 119                                 if (lastChar != "\\") { output += "\\"; }
 120                         #endif
 121
 122                         //test to make sure directory exists
 123                         output = m->getFullPathName(output);
 124                         string outTemp = output + "temp";
 125                         ofstream out;
 126                         out.open(outTemp.c_str(), ios::trunc);
 127                         if(!out) {
 128                                 m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
 129                         }else{
 130                                 out.close();
 131                                 remove(outTemp.c_str());
 132                                 m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 133                                 commandFactory->setOutputDirectory(output);
 134                         }
 135                 }
 136
 137                 //redirect input
 138                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 139                 else if (input == "default") {
 140                         string exepath = m->argv;
 141                         input = exepath.substr(0, (exepath.find_last_of('m')));
 142
 143                         m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 144                         commandFactory->setInputDirectory(input);
 145                 }else {
 146                         //add / to name if needed
 147                         string lastChar = input.substr(input.length()-1);
 148                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 149                                 if (lastChar != "/") { input += "/"; }
 150                         #else
 151                                 if (lastChar != "\\") { input += "\\"; }
 152                         #endif
 153
 154                         //test to make sure directory exists
 155                         input = m->getFullPathName(input);
 156                         string inTemp = input + "temp";
 157                         ofstream in;
 158                         in.open(inTemp.c_str(), ios::trunc);
 159                         if(!in) {
 160                                 m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
 161                         }else{
 162                                 in.close();
 163                                 remove(inTemp.c_str());
 164                                 m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 165                                 commandFactory->setInputDirectory(input);
 166                         }
 167                 }
 168
 169                 //set default
 170                 if (tempdefault == "clear") {
 171                         #ifdef MOTHUR_FILES
 172                                 string temp = MOTHUR_FILES;
 173                                 m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
 174                                 m->setDefaultPath(temp);
 175                         #else
 176                                 string temp = "";
 177                                 m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
 178                                 m->setDefaultPath(temp);
 179                         #endif
 180                 }else if (tempdefault == "") {  //do nothing
 181                 }else if (tempdefault == "default") {
 182                         string exepath = m->argv;
 183                         tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 184
 185                         m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 186                         m->setDefaultPath(tempdefault);
 187                 }else {
 188                         //add / to name if needed
 189                         string lastChar = tempdefault.substr(tempdefault.length()-1);
 190                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 191                                 if (lastChar != "/") { tempdefault += "/"; }
 192                         #else
 193                                 if (lastChar != "\\") { tempdefault += "\\"; }
 194                         #endif
 195
 196                         m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 197                         m->setDefaultPath(tempdefault);
 198                 }
 199
 200                 return 0;
 201         }
 202         catch(exception& e) {
 203                 m->errorOut(e, "SetDirectoryCommand", "execute");
 204                 exit(1);
 205         }
 206 }
 207 //**********************************************************************************************************************/