X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=catchallcommand.cpp;h=a914f733caef6f3535bfe88a4ff532a2989f7971;hp=1cfd4154686cd4884e275f4c3ea8c8ca3d5624d3;hb=050a3ff02473a3d4c0980964e1a9ebe52e55d6b8;hpb=f687723a8357916e86a05116978e6869b039ce36 diff --git a/catchallcommand.cpp b/catchallcommand.cpp index 1cfd415..a914f73 100644 --- a/catchallcommand.cpp +++ b/catchallcommand.cpp @@ -12,12 +12,12 @@ //********************************************************************************************************************** vector CatchAllCommand::setParameters(){ try { - CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel); + CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel); //can choose shared or sabund not both, so put them in the same chooseOnlyOneGroup - CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(pshared); - CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none",false,false); parameters.push_back(psabund); - CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); - CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); + CommandParameter pshared("shared", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(pshared); + CommandParameter psabund("sabund", "InputTypes", "", "", "catchallInputs", "catchallInputs", "none","analysis-bestanalysis-models-bubble-summary",false,false,true); parameters.push_back(psabund); + 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); } @@ -49,25 +49,24 @@ string CatchAllCommand::getHelpString(){ } } //********************************************************************************************************************** -string CatchAllCommand::getOutputFileNameTag(string type, string inputName=""){ - try { - string outputFileName = ""; - map >::iterator it; +string CatchAllCommand::getOutputPattern(string type) { + try { + string pattern = ""; - //is this a type this command creates - it = outputTypes.find(type); - if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } - else { - if (type == "csv") { outputFileName = "csv"; } - else if (type == "summary") { outputFileName = "catchall.summary"; } - else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } - } - return outputFileName; - } - catch(exception& e) { - m->errorOut(e, "CatchAllCommand", "getOutputFileNameTag"); - exit(1); - } + if (type == "analysis") { pattern = "[filename],_Analysis.csv"; } + else if (type == "bestanalysis") { pattern = "[filename],_BestModelsAnalysis.csv"; } + else if (type == "models") { pattern = "[filename],_BestModelsAnalysis.csv"; } + else if (type == "bubble") { pattern = "[filename],_BubblePlot.csv"; } + else if (type == "summary") { pattern = "[filename],catchall.summary"; } + else if (type == "sabund") { pattern = "[filename],[distance],csv"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; } + + return pattern; + } + catch(exception& e) { + m->errorOut(e, "CatchAllCommand", "getOutputPattern"); + exit(1); + } } //********************************************************************************************************************** CatchAllCommand::CatchAllCommand(){ @@ -76,8 +75,12 @@ CatchAllCommand::CatchAllCommand(){ setParameters(); //initialize outputTypes vector tempOutNames; - outputTypes["csv"] = tempOutNames; + outputTypes["analysis"] = tempOutNames; + outputTypes["bestanalysis"] = tempOutNames; + outputTypes["models"] = tempOutNames; + outputTypes["bubble"] = tempOutNames; outputTypes["summary"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; } catch(exception& e) { m->errorOut(e, "CatchAllCommand", "CatchAllCommand"); @@ -111,8 +114,13 @@ CatchAllCommand::CatchAllCommand(string option) { //initialize outputTypes vector tempOutNames; - outputTypes["csv"] = tempOutNames; - outputTypes["summary"] = tempOutNames; + outputTypes["analysis"] = tempOutNames; + outputTypes["bestanalysis"] = tempOutNames; + outputTypes["models"] = tempOutNames; + outputTypes["bubble"] = tempOutNames; + outputTypes["summary"] = tempOutNames; + outputTypes["sabund"] = tempOutNames; + //if the user changes the input directory command factory will send this info to us in the output parameter string inputDir = validParameter.validFile(parameters, "inputdir", false); @@ -231,7 +239,7 @@ int CatchAllCommand::execute() { catchAllTest = m->getFullPathName(catchAllTest); #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - catchAllCommandExe += "mono " + catchAllTest + " "; + catchAllCommandExe += "mono \"" + catchAllTest + "\" "; #else catchAllCommandExe += "\"" + catchAllTest + "\" "; #endif @@ -257,7 +265,9 @@ int CatchAllCommand::execute() { set processedLabels; set userLabels = labels; - string summaryfilename = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])) + getOutputFileNameTag("summary"); + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileNames[p])); + string summaryfilename = getOutputFileName("summary", variables); summaryfilename = m->getFullPathName(summaryfilename); if (m->debug) { m->mothurOut("[DEBUG]: Input File = " + inputFileNames[p] + ".\n[DEBUG]: inputdata address = " + toString(&input) + ".\n[DEBUG]: sabund address = " + toString(&sabund) + ".\n"); } @@ -283,12 +293,20 @@ int CatchAllCommand::execute() { //create system command string catchAllCommand = ""; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1"; + catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1"; #else - if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); } - catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1"; - //wrap entire string in "" - catchAllCommand = "\"" + catchAllCommand + "\""; + //removes extra '\\' catchall doesnt like that + vector tempNames; + string tempFilename = filename; + m->splitAtDash(tempFilename, tempNames); + tempFilename = tempNames[0]; + tempNames.clear(); + string tempOutputPath = outputPath; + m->splitAtDash(tempOutputPath, tempNames); + tempOutputPath = tempNames[0]; + if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); } + catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1"; + catchAllCommand = "\"" + catchAllCommand + "\""; #endif if (m->debug) { m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); } @@ -304,10 +322,11 @@ int CatchAllCommand::execute() { filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . if (savedOutputDir == "") { filename = m->getSimpleName(filename); } - outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); + variables["[filename]"] = filename; + outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables)); + outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables)); + outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables)); + outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables)); if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); } @@ -337,10 +356,19 @@ int CatchAllCommand::execute() { //create system command string catchAllCommand = ""; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1"; + catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1"; #else - if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); } - catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1"; + //removes extra '\\' catchall doesnt like that + vector tempNames; + string tempFilename = filename; + m->splitAtDash(tempFilename, tempNames); + tempFilename = tempNames[0]; + tempNames.clear(); + string tempOutputPath = outputPath; + m->splitAtDash(tempOutputPath, tempNames); + tempOutputPath = tempNames[0]; + if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); } + catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1"; catchAllCommand = "\"" + catchAllCommand + "\""; #endif @@ -357,10 +385,11 @@ int CatchAllCommand::execute() { filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . if (savedOutputDir == "") { filename = m->getSimpleName(filename); } - outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); + variables["[filename]"] = filename; + outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables)); + outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables)); + outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables)); + outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables)); if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); } @@ -412,11 +441,20 @@ int CatchAllCommand::execute() { //create system command string catchAllCommand = ""; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - catchAllCommand += catchAllCommandExe + filename + " " + outputPath + " 1"; + catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + + "\" 1"; #else - if (outputPath.length() > 0) { outputPath = outputPath.substr(0, outputPath.length()-1); } - catchAllCommand += catchAllCommandExe + "\"" + filename + "\" \"" + outputPath + "\" 1"; - catchAllCommand = "\"" + catchAllCommand + "\""; + //removes extra '\\' catchall doesnt like that + vector tempNames; + string tempFilename = filename; + m->splitAtDash(tempFilename, tempNames); + tempFilename = tempNames[0]; + tempNames.clear(); + string tempOutputPath = outputPath; + m->splitAtDash(tempOutputPath, tempNames); + tempOutputPath = tempNames[0]; + if (tempOutputPath.length() > 0) { tempOutputPath = tempOutputPath.substr(0, tempOutputPath.length()-1); } + catchAllCommand += catchAllCommandExe + "\"" + tempFilename + "\" \"" + tempOutputPath + "\" 1"; + catchAllCommand = "\"" + catchAllCommand + "\""; #endif if (m->debug) { m->mothurOut("[DEBUG]: catchall command = " + catchAllCommand + ". About to call system.\n"); } @@ -431,10 +469,12 @@ int CatchAllCommand::execute() { filename = m->getRootName(filename); filename = filename.substr(0, filename.length()-1); //rip off extra . if (savedOutputDir == "") { filename = m->getSimpleName(filename); } - outputNames.push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_Analysis." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsAnalysis." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BestModelsFits." + getOutputFileNameTag("csv")); - outputNames.push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); outputTypes["csv"].push_back(filename + "_BubblePlot." + getOutputFileNameTag("csv")); if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); } + variables["[filename]"] = filename; + outputNames.push_back(getOutputFileName("analysis", variables)); outputTypes["analysis"].push_back(getOutputFileName("analysis", variables)); + outputNames.push_back(getOutputFileName("bestanalysis", variables)); outputTypes["bestanalysis"].push_back(getOutputFileName("bestanalysis", variables)); + outputNames.push_back(getOutputFileName("models", variables)); outputTypes["models"].push_back(getOutputFileName("models", variables)); + outputNames.push_back(getOutputFileName("bubble", variables)); outputTypes["bubble"].push_back(getOutputFileName("bubble", variables)); + if (m->debug) { m->mothurOut("[DEBUG]: About to create summary file for: " + filename + ".\n[DEBUG]: sabund label = " + sabund->getLabel() + ".\n"); } createSummaryFile(filename + "_BestModelsAnalysis.csv", sabund->getLabel(), out); @@ -478,7 +518,10 @@ int CatchAllCommand::execute() { //********************************************************************************************************************** string CatchAllCommand::process(SAbundVector* sabund, string file1) { try { - string filename = outputDir + m->getRootName(m->getSimpleName(file1)) + sabund->getLabel() + ".csv"; + map variables; + variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(file1)); + variables["[distance]"] = sabund->getLabel(); + string filename = getOutputFileName("sabund", variables); filename = m->getFullPathName(filename); ofstream out; @@ -511,7 +554,9 @@ string CatchAllCommand::combineSummmary(vector& outputNames) { try { ofstream out; - string combineFileName = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)) + getOutputFileNameTag("summary"); + map variables; + variables["[filename]"] = savedOutputDir + m->getRootName(m->getSimpleName(sharedfile)); + string combineFileName = getOutputFileName("summary", variables); //open combined file m->openOutputFile(combineFileName, out);