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::getValidParameters(){
  14         try {
  15                 string Array[] =  {"output","input","tempdefault","outputdir","inputdir"};
  16                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  17                 return myArray;
  18         }
  19         catch(exception& e) {
  20                 m->errorOut(e, "SetDirectoryCommand", "getValidParameters");
  21                 exit(1);
  22         }
  23 }
  24 //**********************************************************************************************************************
  25 vector<string> SetDirectoryCommand::getRequiredParameters(){
  26         try {
  27                 vector<string> myArray;
  28                 return myArray;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "SetDirectoryCommand", "getRequiredParameters");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 vector<string> SetDirectoryCommand::getRequiredFiles(){
  37         try {
  38                 vector<string> myArray;
  39                 return myArray;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "SetDirectoryCommand", "getRequiredFiles");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47
  48 SetDirectoryCommand::SetDirectoryCommand(string option)  {
  49         try {
  50                 abort = false;
  51
  52                 //allow user to run help
  53                 if(option == "help") { help(); abort = true; }
  54
  55                 else {
  56                         //valid paramters for this command
  57                         string Array[] =  {"output","input","tempdefault","outputdir","inputdir"};
  58                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  59
  60                         OptionParser parser(option);
  61                         map<string, string> parameters = parser.getParameters();
  62
  63                         ValidParameters validParameter;
  64                         //check to make sure all parameters are valid for command
  65                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  66                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  67                         }
  68
  69                         output = validParameter.validFile(parameters, "output", false);
  70                         if (output == "not found") {  output = "";  }
  71
  72                         input = validParameter.validFile(parameters, "input", false);
  73                         if (input == "not found") {  input = "";  }
  74
  75                         tempdefault = validParameter.validFile(parameters, "tempdefault", false);
  76                         if (tempdefault == "not found") {  tempdefault = "";  }
  77
  78                         if ((input == "") && (output == "") && (tempdefault == "")) {
  79                                 m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
  80                         }
  81                 }
  82         }
  83         catch(exception& e) {
  84                 m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
  85                 exit(1);
  86         }
  87 }
  88 //**********************************************************************************************************************
  89
  90 void SetDirectoryCommand::help(){
  91         try {
  92                 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");
  93                 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");
  94                 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");
  95                 m->mothurOut("The set.dir command parameters are input, output and tempdefault and one is required.\n");
  96                 m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
  97                 m->mothurOut("To return the input to the current working directory you may enter: input=clear.\n");
  98                 m->mothurOut("To set the output to the directory where mothur.exe is located you may enter: output=default.\n");
  99                 m->mothurOut("To set the input to the directory where mothur.exe is located you may enter: input=default.\n");
 100                 m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n");
 101                 m->mothurOut("To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n");
 102                 m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n");
 103                 m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
 104                 m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
 105         }
 106         catch(exception& e) {
 107                 m->errorOut(e, "SetDirectoryCommand", "help");
 108                 exit(1);
 109         }
 110 }
 111 //**********************************************************************************************************************
 112
 113 SetDirectoryCommand::~SetDirectoryCommand(){}
 114
 115 //**********************************************************************************************************************
 116
 117 int SetDirectoryCommand::execute(){
 118         try {
 119
 120                 if (abort == true) { return 0; }
 121
 122                 commandFactory = CommandFactory::getInstance();
 123
 124                 //redirect output
 125                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
 126                 else if (output == "default") {
 127                         GlobalData* globaldata = GlobalData::getInstance();
 128                         string exepath = globaldata->argv;
 129                         output = exepath.substr(0, (exepath.find_last_of('m')));
 130
 131                         m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
 132                         commandFactory->setOutputDirectory(output);
 133                 }else {
 134                         //add / to name if needed
 135                         string lastChar = output.substr(output.length()-1);
 136                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 137                                 if (lastChar != "/") { output += "/"; }
 138                         #else
 139                                 if (lastChar != "\\") { output += "\\"; }
 140                         #endif
 141
 142                         //test to make sure directory exists
 143                         output = m->getFullPathName(output);
 144                         string outTemp = output + "temp";
 145                         ofstream out;
 146                         out.open(outTemp.c_str(), ios::trunc);
 147                         if(!out) {
 148                                 m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
 149                         }else{
 150                                 out.close();
 151                                 remove(outTemp.c_str());
 152                                 m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
 153                                 commandFactory->setOutputDirectory(output);
 154                         }
 155                 }
 156
 157                 //redirect input
 158                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 159                 else if (input == "default") {
 160                         GlobalData* globaldata = GlobalData::getInstance();
 161                         string exepath = globaldata->argv;
 162                         input = exepath.substr(0, (exepath.find_last_of('m')));
 163
 164                         m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
 165                         commandFactory->setInputDirectory(input);
 166                 }else {
 167                         //add / to name if needed
 168                         string lastChar = input.substr(input.length()-1);
 169                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 170                                 if (lastChar != "/") { input += "/"; }
 171                         #else
 172                                 if (lastChar != "\\") { input += "\\"; }
 173                         #endif
 174
 175                         //test to make sure directory exists
 176                         input = m->getFullPathName(input);
 177                         string inTemp = input + "temp";
 178                         ofstream in;
 179                         in.open(inTemp.c_str(), ios::trunc);
 180                         if(!in) {
 181                                 m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
 182                         }else{
 183                                 in.close();
 184                                 remove(inTemp.c_str());
 185                                 m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
 186                                 commandFactory->setInputDirectory(input);
 187                         }
 188                 }
 189
 190                 //set default
 191                 if (tempdefault == "clear") {
 192                         #ifdef MOTHUR_FILES
 193                                 string temp = MOTHUR_FILES;
 194                                 m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();
 195                                 m->setDefaultPath(temp);
 196                         #else
 197                                 string temp = "";
 198                                 m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
 199                                 m->setDefaultPath(temp);
 200                         #endif
 201                 }else if (tempdefault == "") {  //do nothing
 202                 }else if (tempdefault == "default") {
 203                         GlobalData* globaldata = GlobalData::getInstance();
 204                         string exepath = globaldata->argv;
 205                         tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 206
 207                         m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
 208                         m->setDefaultPath(tempdefault);
 209                 }else {
 210                         //add / to name if needed
 211                         string lastChar = tempdefault.substr(tempdefault.length()-1);
 212                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 213                                 if (lastChar != "/") { tempdefault += "/"; }
 214                         #else
 215                                 if (lastChar != "\\") { tempdefault += "\\"; }
 216                         #endif
 217
 218                         m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
 219                         m->setDefaultPath(tempdefault);
 220                 }
 221
 222                 return 0;
 223         }
 224         catch(exception& e) {
 225                 m->errorOut(e, "SetDirectoryCommand", "execute");
 226                 exit(1);
 227         }
 228 }
 229 //**********************************************************************************************************************/