X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=setdircommand.cpp;h=67a1f59f8388dbfec55ae7b552f02640b5d6b93f;hb=2bb9267aa4b4ecdf8488b06605cc9f3f36fa4332;hp=001ae235dd11ff0f015ebeba76de10ee3bcb2dbf;hpb=0b99c6b6ea875e13febda76903fd4d9cda7add7d;p=mothur.git diff --git a/setdircommand.cpp b/setdircommand.cpp index 001ae23..67a1f59 100644 --- a/setdircommand.cpp +++ b/setdircommand.cpp @@ -9,19 +9,60 @@ #include "setdircommand.h" +//********************************************************************************************************************** +vector SetDirectoryCommand::setParameters(){ + try { + CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "",false,false); parameters.push_back(ptempdefault); + CommandParameter pinput("input", "String", "", "", "", "", "",false,false); parameters.push_back(pinput); + CommandParameter poutput("output", "String", "", "", "", "", "",false,false); parameters.push_back(poutput); + CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); + CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + + vector myArray; + for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); } + return myArray; + } + catch(exception& e) { + m->errorOut(e, "SetDirectoryCommand", "setParameters"); + exit(1); + } +} +//********************************************************************************************************************** +string SetDirectoryCommand::getHelpString(){ + try { + string helpString = ""; + 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"; + helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n"; + 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"; + helpString += "The set.dir command parameters are input, output and tempdefault and one is required.\n"; + helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n"; + helpString += "To return the input to the current working directory you may enter: input=clear.\n"; + helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n"; + helpString += "To set the input to the directory where mothur.exe is located you may enter: input=default.\n"; + helpString += "To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n"; + helpString += "To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n"; + helpString += "The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n"; + helpString += "Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n"; + helpString += "Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n"; + return helpString; + } + catch(exception& e) { + m->errorOut(e, "SetDirectoryCommand", "getHelpString"); + exit(1); + } +} //********************************************************************************************************************** SetDirectoryCommand::SetDirectoryCommand(string option) { try { - abort = false; + abort = false; calledHelp = false; //allow user to run help - if(option == "help") { help(); abort = true; } + if(option == "help") { help(); abort = true; calledHelp = true; } + else if(option == "citation") { citation(); abort = true; calledHelp = true;} else { - //valid paramters for this command - string Array[] = {"output","input","tempdefault","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); + vector myArray = setParameters(); OptionParser parser(option); map parameters = parser.getParameters(); @@ -53,40 +94,32 @@ SetDirectoryCommand::SetDirectoryCommand(string option) { } //********************************************************************************************************************** -void SetDirectoryCommand::help(){ - try { - 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"); - 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"); - 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"); - m->mothurOut("The set.dir command parameters are input, output and tempdefault and one is required.\n"); - m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n"); - m->mothurOut("To return the input to the same directory as the mothur.exe you may enter: input=clear.\n"); - m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n"); - m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n"); - m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n"); - m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n"); - } - catch(exception& e) { - m->errorOut(e, "SetDirectoryCommand", "help"); - exit(1); - } -} -//********************************************************************************************************************** - -SetDirectoryCommand::~SetDirectoryCommand(){} - -//********************************************************************************************************************** - int SetDirectoryCommand::execute(){ try { - if (abort == true) { return 0; } + if (abort == true) { if (calledHelp) { return 0; } return 2; } commandFactory = CommandFactory::getInstance(); + string tag = ""; +#ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); //find out who we are + + tag = toString(pid); +#endif + + m->mothurOut("Mothur's directories:"); m->mothurOutEndLine(); + //redirect output if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); } - else { + else if (output == "default") { + string exepath = m->argv; + output = exepath.substr(0, (exepath.find_last_of('m'))); + + m->mothurOut("outputDir=" + output); m->mothurOutEndLine(); + commandFactory->setOutputDirectory(output); + }else { //add / to name if needed string lastChar = output.substr(output.length()-1); #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) @@ -96,23 +129,29 @@ int SetDirectoryCommand::execute(){ #endif //test to make sure directory exists - output = getFullPathName(output); - string outTemp = output + "temp"; + output = m->getFullPathName(output); + string outTemp = output + tag + "temp"; ofstream out; out.open(outTemp.c_str(), ios::trunc); if(!out) { m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine(); }else{ out.close(); - remove(outTemp.c_str()); - m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine(); + m->mothurRemove(outTemp); + m->mothurOut("outputDir=" + output); m->mothurOutEndLine(); commandFactory->setOutputDirectory(output); } } //redirect input if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); } - else { + else if (input == "default") { + string exepath = m->argv; + input = exepath.substr(0, (exepath.find_last_of('m'))); + + m->mothurOut("inputDir=" + input); m->mothurOutEndLine(); + commandFactory->setInputDirectory(input); + }else { //add / to name if needed string lastChar = input.substr(input.length()-1); #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) @@ -122,16 +161,16 @@ int SetDirectoryCommand::execute(){ #endif //test to make sure directory exists - input = getFullPathName(input); - string inTemp = input + "temp"; + input = m->getFullPathName(input); + string inTemp = input + tag + "temp"; ofstream in; in.open(inTemp.c_str(), ios::trunc); if(!in) { m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine(); }else{ in.close(); - remove(inTemp.c_str()); - m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine(); + m->mothurRemove(inTemp); + m->mothurOut("inputDir=" + input); m->mothurOutEndLine(); commandFactory->setInputDirectory(input); } } @@ -140,7 +179,7 @@ int SetDirectoryCommand::execute(){ if (tempdefault == "clear") { #ifdef MOTHUR_FILES string temp = MOTHUR_FILES; - m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine(); + m->mothurOut("tempDefault=" + temp); m->mothurOutEndLine(); m->setDefaultPath(temp); #else string temp = ""; @@ -148,6 +187,12 @@ int SetDirectoryCommand::execute(){ m->setDefaultPath(temp); #endif }else if (tempdefault == "") { //do nothing + }else if (tempdefault == "default") { + string exepath = m->argv; + tempdefault = exepath.substr(0, (exepath.find_last_of('m'))); + + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); + m->setDefaultPath(tempdefault); }else { //add / to name if needed string lastChar = tempdefault.substr(tempdefault.length()-1); @@ -157,8 +202,19 @@ int SetDirectoryCommand::execute(){ if (lastChar != "\\") { tempdefault += "\\"; } #endif - m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine(); - m->setDefaultPath(tempdefault); + //test to make sure directory exists + tempdefault = m->getFullPathName(tempdefault); + string inTemp = tempdefault + tag + "temp"; + ofstream in; + in.open(inTemp.c_str(), ios::trunc); + if(!in) { + m->mothurOut(tempdefault + " directory does not exist or is not writable."); m->mothurOutEndLine(); + }else{ + in.close(); + m->mothurRemove(inTemp); + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); + m->setDefaultPath(tempdefault); + } } return 0;