X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=setdircommand.cpp;h=3e50f4a508d2608ef1b51b9445fd3a388d1f4dec;hp=214bd172e80208f246bede7978ad69329f6e23db;hb=df7e3ff9f68ef157b0328a2d353c3258c5d45d89;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281 diff --git a/setdircommand.cpp b/setdircommand.cpp index 214bd17..3e50f4a 100644 --- a/setdircommand.cpp +++ b/setdircommand.cpp @@ -10,36 +10,49 @@ #include "setdircommand.h" //********************************************************************************************************************** -vector SetDirectoryCommand::getValidParameters(){ - try { - string Array[] = {"output","input","tempdefault","outputdir","inputdir"}; - vector myArray (Array, Array+(sizeof(Array)/sizeof(string))); - return myArray; - } - catch(exception& e) { - m->errorOut(e, "SetDirectoryCommand", "getValidParameters"); - exit(1); - } -} -//********************************************************************************************************************** -vector SetDirectoryCommand::getRequiredParameters(){ +vector SetDirectoryCommand::setParameters(){ try { + CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault); + CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug); + CommandParameter pmodnames("modifynames", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmodnames); + CommandParameter pinput("input", "String", "", "", "", "", "","",false,false,true); parameters.push_back(pinput); + CommandParameter poutput("output", "String", "", "", "", "", "","",false,false,true); 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", "getRequiredParameters"); + m->errorOut(e, "SetDirectoryCommand", "setParameters"); exit(1); } } //********************************************************************************************************************** -vector SetDirectoryCommand::getRequiredFiles(){ +string SetDirectoryCommand::getHelpString(){ try { - vector myArray; - return myArray; + 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 can also be used to run mothur in debug mode.\n"; + helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees. modifynames=F will leave sequence names as they are.\n"; + helpString += "The set.dir command parameters are input, output, tempdefault and debug and one is required.\n"; + helpString += "To run mothur in debug mode set debug=true. Default debug=false.\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", "getRequiredFiles"); + m->errorOut(e, "SetDirectoryCommand", "getHelpString"); exit(1); } } @@ -47,15 +60,14 @@ vector SetDirectoryCommand::getRequiredFiles(){ 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(); @@ -74,10 +86,27 @@ SetDirectoryCommand::SetDirectoryCommand(string option) { tempdefault = validParameter.validFile(parameters, "tempdefault", false); if (tempdefault == "not found") { tempdefault = ""; } + + bool debug = false; + bool nodebug = false; + debugOnly = false; + string temp = validParameter.validFile(parameters, "debug", false); + if (temp == "not found") { debug = false; nodebug=true; } + else { debug = m->isTrue(temp); } + m->debug = debug; + + bool nomod = false; + temp = validParameter.validFile(parameters, "modifynames", false); + if (temp == "not found") { modifyNames = true; nomod=true; } + else { modifyNames = m->isTrue(temp); } + m->modifyNames = modifyNames; + + if (debug) { m->mothurOut("Setting [DEBUG] flag.\n"); } + - if ((input == "") && (output == "") && (tempdefault == "")) { - m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true; - } + if ((input == "") && (output == "") && (tempdefault == "") && nodebug && nomod) { + m->mothurOut("You must provide either an input, output, tempdefault, debug or modifynames for the set.outdir command."); m->mothurOutEndLine(); abort = true; + }else if((input == "") && (output == "") && (tempdefault == "")) { debugOnly = true; } } } catch(exception& e) { @@ -87,111 +116,52 @@ 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 current working directory you may enter: input=clear.\n"); - m->mothurOut("To set the output to the directory where mothur.exe is located you may enter: output=default.\n"); - m->mothurOut("To set the input to the directory where mothur.exe is located you may enter: input=default.\n"); - m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n"); - m->mothurOut("To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\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; } + if (debugOnly) { return 0; } + commandFactory = CommandFactory::getInstance(); + m->mothurOut("Mothur's directories:"); m->mothurOutEndLine(); + //redirect output if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); } else if (output == "default") { - GlobalData* globaldata = GlobalData::getInstance(); - string exepath = globaldata->argv; + string exepath = m->argv; output = exepath.substr(0, (exepath.find_last_of('m'))); - m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine(); + 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) - if (lastChar != "/") { output += "/"; } - #else - if (lastChar != "\\") { output += "\\"; } - #endif - - //test to make sure directory exists - output = m->getFullPathName(output); - string outTemp = output + "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(); + if (m->dirCheck(output)) { + m->mothurOut("outputDir=" + output); m->mothurOutEndLine(); commandFactory->setOutputDirectory(output); - } + } } //redirect input if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); } else if (input == "default") { - GlobalData* globaldata = GlobalData::getInstance(); - string exepath = globaldata->argv; + string exepath = m->argv; input = exepath.substr(0, (exepath.find_last_of('m'))); - m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine(); + 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) - if (lastChar != "/") { input += "/"; } - #else - if (lastChar != "\\") { input += "\\"; } - #endif - - //test to make sure directory exists - input = m->getFullPathName(input); - string inTemp = input + "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(); + if (m->dirCheck(input)) { + m->mothurOut("inputDir=" + input); m->mothurOutEndLine(); commandFactory->setInputDirectory(input); - } - } + } + } //set default 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 = ""; @@ -200,24 +170,17 @@ int SetDirectoryCommand::execute(){ #endif }else if (tempdefault == "") { //do nothing }else if (tempdefault == "default") { - GlobalData* globaldata = GlobalData::getInstance(); - string exepath = globaldata->argv; + string exepath = m->argv; tempdefault = exepath.substr(0, (exepath.find_last_of('m'))); - m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine(); + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); m->setDefaultPath(tempdefault); }else { - //add / to name if needed - string lastChar = tempdefault.substr(tempdefault.length()-1); - #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) - if (lastChar != "/") { tempdefault += "/"; } - #else - if (lastChar != "\\") { tempdefault += "\\"; } - #endif - - m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine(); - m->setDefaultPath(tempdefault); - } + if (m->dirCheck(tempdefault)) { + m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine(); + m->setDefaultPath(tempdefault); + } + } return 0; }