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
  14 SetDirectoryCommand::SetDirectoryCommand(string option)  {
  15         try {
  16                 abort = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; }
  20
  21                 else {
  22                         //valid paramters for this command
  23                         string Array[] =  {"output","input","tempdefault","outputdir","inputdir"};
  24                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  25
  26                         OptionParser parser(option);
  27                         map<string, string> parameters = parser.getParameters();
  28
  29                         ValidParameters validParameter;
  30                         //check to make sure all parameters are valid for command
  31                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  32                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  33                         }
  34
  35                         output = validParameter.validFile(parameters, "output", false);
  36                         if (output == "not found") {  output = "";  }
  37
  38                         input = validParameter.validFile(parameters, "input", false);
  39                         if (input == "not found") {  input = "";  }
  40
  41                         tempdefault = validParameter.validFile(parameters, "tempdefault", false);
  42                         if (tempdefault == "not found") {  tempdefault = "";  }
  43
  44                         if ((input == "") && (output == "") && (tempdefault == "")) {
  45                                 m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
  46                         }
  47                 }
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
  51                 exit(1);
  52         }
  53 }
  54 //**********************************************************************************************************************
  55
  56 void SetDirectoryCommand::help(){
  57         try {
  58                 m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
  59                 m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
  60                 m->mothurOut("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");
  61                 m->mothurOut("The set.dir command parameters are input, output and tempdefault and one is required.\n");
  62                 m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
  63                 m->mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n");
  64                 m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n");
  65                 m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n");
  66                 m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
  67                 m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
  68         }
  69         catch(exception& e) {
  70                 m->errorOut(e, "SetDirectoryCommand", "help");
  71                 exit(1);
  72         }
  73 }
  74 //**********************************************************************************************************************
  75
  76 SetDirectoryCommand::~SetDirectoryCommand(){}
  77
  78 //**********************************************************************************************************************
  79
  80 int SetDirectoryCommand::execute(){
  81         try {
  82
  83                 if (abort == true) { return 0; }
  84
  85                 commandFactory = CommandFactory::getInstance();
  86
  87                 //redirect output
  88                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
  89                 else {
  90                         //add / to name if needed
  91                         string lastChar = output.substr(output.length()-1);
  92                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  93                                 if (lastChar != "/") { output += "/"; }
  94                         #else
  95                                 if (lastChar != "\\") { output += "\\"; }
  96                         #endif
  97
  98                         //test to make sure directory exists
  99                         output = getFullPathName(output);
 100                         string outTemp = output + "temp";
 101                         ofstream out;
 102                         out.open(outTemp.c_str(), ios::trunc);
 103                         if(!out) {
 104                                 m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
 105                         }else{
 106                                 out.close();
 107                                 remove(outTemp.c_str());
 108                                 m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
 109                                 commandFactory->setOutputDirectory(output);
 110                         }
 111                 }
 112
 113                 //redirect input
 114                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 115                 else {
 116                         //add / to name if needed
 117                         string lastChar = input.substr(input.length()-1);
 118                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 119                                 if (lastChar != "/") { input += "/"; }
 120                         #else
 121                                 if (lastChar != "\\") { input += "\\"; }
 122                         #endif
 123
 124                         //test to make sure directory exists
 125                         input = getFullPathName(input);
 126                         string inTemp = input + "temp";
 127                         ofstream in;
 128                         in.open(inTemp.c_str(), ios::trunc);
 129                         if(!in) {
 130                                 m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
 131                         }else{
 132                                 in.close();
 133                                 remove(inTemp.c_str());
 134                                 m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
 135                                 commandFactory->setInputDirectory(input);
 136                         }
 137                 }
 138
 139                 //set default
 140                 if (tempdefault == "clear") {
 141                         #ifdef MOTHUR_FILES
 142                                 string temp = MOTHUR_FILES;
 143                                 m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();
 144                                 m->setDefaultPath(temp);
 145                         #else
 146                                 string temp = "";
 147                                 m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
 148                                 m->setDefaultPath(temp);
 149                         #endif
 150                 }else if (tempdefault == "") {  //do nothing
 151                 }else {
 152                         //add / to name if needed
 153                         string lastChar = tempdefault.substr(tempdefault.length()-1);
 154                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 155                                 if (lastChar != "/") { tempdefault += "/"; }
 156                         #else
 157                                 if (lastChar != "\\") { tempdefault += "\\"; }
 158                         #endif
 159
 160                         m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
 161                         m->setDefaultPath(tempdefault);
 162                 }
 163
 164                 return 0;
 165         }
 166         catch(exception& e) {
 167                 m->errorOut(e, "SetDirectoryCommand", "execute");
 168                 exit(1);
 169         }
 170 }
 171 //**********************************************************************************************************************/