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//
// loadlogfilecommand.cpp
// Mothur
//
// Created by Sarah Westcott on 6/13/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "loadlogfilecommand.h"
#include "commandoptionparser.hpp"
#include "commandfactory.hpp"
#include "setcurrentcommand.h"
//**********************************************************************************************************************
vector<string> LoadLogfileCommand::setParameters(){
try {
CommandParameter plogfile("logfile", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(plogfile);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "LoadLogfileCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string LoadLogfileCommand::getHelpString(){
try {
string helpString = "";
helpString += "The load.logfile command extracts the current file names from a logfile.\n";
helpString += "The load.logfile parameter is logfile, and it is required.\n";
helpString += "The load.logfile command should be in the following format: \n";
helpString += "load.logfile(logfile=yourLogFile)\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "LoadLogfileCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
LoadLogfileCommand::LoadLogfileCommand(){
try {
abort = true; calledHelp = true;
setParameters();
}
catch(exception& e) {
m->errorOut(e, "LoadLogfileCommand", "LoadLogfileCommand");
exit(1);
}
}
//**********************************************************************************************************************
LoadLogfileCommand::LoadLogfileCommand(string option) {
try {
abort = false; calledHelp = false;
//allow user to run help
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else {
//valid paramters for this command
vector<string> myArray = setParameters();
OptionParser parser(option);
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
map<string,string>::iterator it;
//check to make sure all parameters are valid for command
for (it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//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);
if (inputDir == "not found"){ inputDir = ""; }
else {
string path;
it = parameters.find("logfile");
//user has given a template file
if(it != parameters.end()){
path = m->hasPath(it->second);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["logfile"] = inputDir + it->second; }
}
}
//get shared file, it is required
logfile = validParameter.validFile(parameters, "logfile", true);
if (logfile == "not open") { logfile = ""; abort = true; }
else if (logfile == "not found") { m->mothurOut("The logfile parameter is required."); m->mothurOutEndLine();abort = true; }
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){
outputDir = m->hasPath(logfile); //if user entered a file with a path then preserve it
}
}
}
catch(exception& e) {
m->errorOut(e, "NewCommand", "NewCommand");
exit(1);
}
}
//**********************************************************************************************************************
int LoadLogfileCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
m->mothurOutEndLine();
m->mothurOut("Extracting current files names..."); m->mothurOutEndLine();
m->mothurOutEndLine();
CommandFactory* cFactory;
cFactory = CommandFactory::getInstance();
ifstream in;
m->openInputFile(logfile, in);
set<string> currentTypes = m->getCurrentTypes();
map<string, string> currentFiles;
string commandName = "";
bool skip = false;
string line = "";
while (!in.eof()) {
if (m->control_pressed) { break; }
if (!skip) { line = m->getline(in); m->gobble(in); }
m->gobble(in);
//look for "mothur >"
int pos = line.find("mothur > "); //command line
int pos2 = line.find("Output File "); //indicates command completed and we can update the current file
int pos3 = line.find("/*****************");
//skipping over parts where a command runs another command
if (pos3 != string::npos) {
while (!in.eof()) {
if (m->control_pressed) { break; }
line = m->getline(in); m->gobble(in);
int posTemp = line.find("/*****************");
if (posTemp != string::npos) { break; }
}
}
if (pos != string::npos) {
skip=false;
//extract command name and option string
string input = line.substr(pos+9);
CommandOptionParser parser(input);
commandName = parser.getCommandString();
string options = parser.getOptionString();
//parse out parameters in option string
map<string,string> parameters;
OptionParser optionParser(options, parameters);
for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
if (currentTypes.count((it->first)) != 0) { //if this is a type we save
if (it->second != "current") { currentFiles[it->first] = it->second; }//save the input file name as current
}
}
}else if (pos2 != string::npos) {
//read file output file names
vector<string> theseOutputNames;
while (!in.eof()) {
if (m->control_pressed) { break; }
line = m->getline(in); m->gobble(in);
int pos = line.find("mothur > ");
if (pos != string::npos) { skip = true; break; }
else { theseOutputNames.push_back(line); }
}
//ask command for the output names for each type based on inputs
Command* command = cFactory->getCommand(commandName);
map<string, vector<string> > thisOutputTypes = command->getOutputFiles();
for (map<string, vector<string> >::iterator it = thisOutputTypes.begin(); it != thisOutputTypes.end(); it++) {
if (currentTypes.count((it->first)) != 0) { //do we save this type
//if yes whats its tag
map<string, string>::iterator itCurrentFiles = currentFiles.find(it->first);
string thisTypesCurrentFile = "";
if (itCurrentFiles != currentFiles.end()) { thisTypesCurrentFile = itCurrentFiles->second; }
//outputfilename pattern for this input type
string pattern = command->getOutputPattern(it->first);
updateCurrent(pattern, it->first, thisTypesCurrentFile, theseOutputNames, currentFiles);
//cout << "current=\n\n";
//for (map<string, string>::iterator itcc = currentFiles.begin(); itcc != currentFiles.end(); itcc++) {
// cout << itcc->first << '\t' << itcc->second << endl;
// }
}
}
}
}
in.close();
if (m->control_pressed) { return 0; }
//output results
string inputString = "";
for (map<string, string>::iterator it = currentFiles.begin(); it != currentFiles.end(); it++) { inputString += it->first + "=" + it->second + ","; }
if (inputString != "") {
inputString = inputString.substr(0, inputString.length()-1);
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
m->mothurOut("Running command: set.current(" + inputString + ")"); m->mothurOutEndLine();
m->mothurCalling = true;
Command* currentCommand = new SetCurrentCommand(inputString);
currentCommand->execute();
delete currentCommand;
m->mothurCalling = false;
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "LoadLogfileCommand", "execute");
exit(1);
}
}
//**********************************************************************************************************************
int LoadLogfileCommand::updateCurrent(string pattern, string type, string thisTypesCurrentFile, vector<string> filenames, map<string, string>& currentFiles){
try {
vector<string> patterns; m->splitAtChar(pattern, patterns, '-');
for (int i = 0; i < patterns.size(); i++) {
vector<string> peices; m->splitAtChar(patterns[i], peices, ',');
//cout << "patterns i = " << patterns[i] << endl;
if (peices.size() != 0) {
string tag = peices[peices.size()-1];
//cout << "tag = " << tag << endl;
if (peices[peices.size()-1] == "[extension]") { tag = m->getExtension(thisTypesCurrentFile); }
//search for the tag in the list of output files
for (int h = 0; h < filenames.size(); h++) {
if (m->control_pressed) { return 0; }
//cout << "filename h = " << filenames[h]<< endl;
string ending = filenames[h].substr(filenames[h].length()-tag.length(), tag.length());
if (ending == tag) { //if it's there and this is a type we save a current version of, save it
if ((type == "column") || (type == "phylip")) { //check for format
string RippedName = "";
bool foundDot = false;
for (int i = filenames[h].length()-1; i >= 0; i--) {
if (foundDot && (filenames[h][i] != '.')) { RippedName = filenames[h][i] + RippedName; }
else if (foundDot && (filenames[h][i] == '.')) { break; }
else if (!foundDot && (filenames[h][i] == '.')) { foundDot = true; }
}
if ((RippedName == "phylip") || (RippedName == "lt") || (RippedName == "square")) { currentFiles["phylip"] = filenames[h]; }
else { currentFiles["column"] = filenames[h]; }
}else { currentFiles[type] = filenames[h]; }
break;
}
}
}
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "LoadLogfileCommand", "updateCurrent");
exit(1);
}
}
//**********************************************************************************************************************
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