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                 string tag = "";
 105 #ifdef USE_MPI
 106                 int pid;
 107                 MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are
 108
 109                 tag = toString(pid);
 110 #endif
 111
 112                 m->mothurOut("Mothur's directories:"); m->mothurOutEndLine();
 113
 114                 //redirect output
 115                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 116                 else if (output == "default") {
 117                         string exepath = m->argv;
 118                         output = exepath.substr(0, (exepath.find_last_of('m')));
 119
 120                         m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 121                         commandFactory->setOutputDirectory(output);
 122                 }else {
 123                         //add / to name if needed
 124                         string lastChar = output.substr(output.length()-1);
 125                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 126                                 if (lastChar != "/") { output += "/"; }
 127                         #else
 128                                 if (lastChar != "\\") { output += "\\"; }
 129                         #endif
 130
 131                         //test to make sure directory exists
 132                         output = m->getFullPathName(output);
 133                         string outTemp = output + tag + "temp";
 134                         ofstream out;
 135                         out.open(outTemp.c_str(), ios::trunc);
 136                         if(!out) {
 137                                 m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
 138                         }else{
 139                                 out.close();
 140                                 m->mothurRemove(outTemp);
 141                                 m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
 142                                 commandFactory->setOutputDirectory(output);
 143                         }
 144                 }
 145
 146                 //redirect input
 147                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 148                 else if (input == "default") {
 149                         string exepath = m->argv;
 150                         input = exepath.substr(0, (exepath.find_last_of('m')));
 151
 152                         m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 153                         commandFactory->setInputDirectory(input);
 154                 }else {
 155                         //add / to name if needed
 156                         string lastChar = input.substr(input.length()-1);
 157                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 158                                 if (lastChar != "/") { input += "/"; }
 159                         #else
 160                                 if (lastChar != "\\") { input += "\\"; }
 161                         #endif
 162
 163                         //test to make sure directory exists
 164                         input = m->getFullPathName(input);
 165                         string inTemp = input + tag + "temp";
 166                         ofstream in;
 167                         in.open(inTemp.c_str(), ios::trunc);
 168                         if(!in) {
 169                                 m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
 170                         }else{
 171                                 in.close();
 172                                 m->mothurRemove(inTemp);
 173                                 m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
 174                                 commandFactory->setInputDirectory(input);
 175                         }
 176                 }
 177
 178                 //set default
 179                 if (tempdefault == "clear") {
 180                         #ifdef MOTHUR_FILES
 181                                 string temp = MOTHUR_FILES;
 182                                 m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine();
 183                                 m->setDefaultPath(temp);
 184                         #else
 185                                 string temp = "";
 186                                 m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
 187                                 m->setDefaultPath(temp);
 188                         #endif
 189                 }else if (tempdefault == "") {  //do nothing
 190                 }else if (tempdefault == "default") {
 191                         string exepath = m->argv;
 192                         tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 193
 194                         m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 195                         m->setDefaultPath(tempdefault);
 196                 }else {
 197                         //add / to name if needed
 198                         string lastChar = tempdefault.substr(tempdefault.length()-1);
 199                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 200                                 if (lastChar != "/") { tempdefault += "/"; }
 201                         #else
 202                                 if (lastChar != "\\") { tempdefault += "\\"; }
 203                         #endif
 204
 205                         //test to make sure directory exists
 206                         tempdefault = m->getFullPathName(tempdefault);
 207                         string inTemp = tempdefault + tag + "temp";
 208                         ofstream in;
 209                         in.open(inTemp.c_str(), ios::trunc);
 210                         if(!in) {
 211                                 m->mothurOut(tempdefault + " directory does not exist or is not writable."); m->mothurOutEndLine();
 212                         }else{
 213                                 in.close();
 214                                 m->mothurRemove(inTemp);
 215                                 m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
 216                                 m->setDefaultPath(tempdefault);
 217                         }
 218                 }
 219
 220                 return 0;
 221         }
 222         catch(exception& e) {
 223                 m->errorOut(e, "SetDirectoryCommand", "execute");
 224                 exit(1);
 225         }
 226 }
 227 //**********************************************************************************************************************/