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//
// batchengine.cpp
// Mothur
//
// Created by Sarah Westcott on 10/21/19.
// Copyright © 2019 Schloss Lab. All rights reserved.
//
#include "batchengine.hpp"
/***********************************************************************/
//This function opens the batchfile to be used by BatchEngine::getInput.
BatchEngine::BatchEngine(string tpath, string batchFile, map<string, string> ev) : Engine(tpath) {
try {
batchFile = util.removeQuotes(batchFile);
ifstream inBatchTest;
openedBatch = util.openInputFile(batchFile, inBatchTest, "no error");
if (!openedBatch) {
if (util.checkLocations(batchFile, current->getLocations())) { openedBatch = util.openInputFile(batchFile, inBatchTest); }
else { m->mothurOut("[ERROR]: unable to open " + batchFile + " batch file, please correct.\n"); }
}
batchFileName = batchFile;
noBufferNeeded = true;
if (openedBatch) { //check for set.logfile
string nextcommand = "#"; //force grabbing first command
while (!inBatchTest.eof()) {
nextcommand = util.getline(inBatchTest); gobble(inBatchTest);
if (nextcommand[0] != '#') { //skip comments
int pos = nextcommand.find("set.logfile");
if (pos != string::npos) { noBufferNeeded = false; break; }
}
}
inBatchTest.close();
openedBatch = util.openInputFile(batchFileName, inputBatchFile, "no error");
}
if (noBufferNeeded) {
if (m->getLogFileName() == "") {
time_t ltime = time(nullptr); /* calendar time */
string outputPath = current->getOutputDir();
string logFileName = outputPath + "mothur." + toString(ltime) + ".logfile";
m->setLogFileName(logFileName, false);
m->mothurOut("\n");
}
}
setEnvironmentVariables(ev); //inherit environmental variables from nested batch files
bstart = time(nullptr);
numBatches = 0;
}
catch(exception& e) {
m->errorOut(e, "BatchEngine", "BatchEngine");
exit(1);
}
}
/***********************************************************************/
BatchEngine::~BatchEngine(){
string batchesOutput = "";
if (numBatches != 0) {
batchesOutput = " and " + toString(numBatches) + " batch file";
if (numBatches > 1) { batchesOutput += "s"; }
}
time_t end = time(nullptr);
m->mothurOut("\n\nIt took " + toString(end-bstart) + " seconds to run " + toString(numCommandsRun) + " commands" + batchesOutput + " from " + batchFileName + " batch file.\n\n");
}
/***********************************************************************/
//This Function allows the user to run a batchfile containing several commands on Dotur
bool BatchEngine::getInput(){
try {
//check if this is a valid batchfile
if (!openedBatch) { return true; }
int quitCommandCalled = 0;
while(quitCommandCalled != 1){
string input = getNextCommand(inputBatchFile);
CommandOptionParser parser(input);
string commandName = parser.getCommandString();
string options = parser.getOptionString();
m->mothurOut("\nmothur > " + input + "\n");
if (m->getControl_pressed()) { input = "quit()"; }
if (commandName != "") {
numCommandsRun++;
m->setExecuting(true); m->resetCommandErrors(); m->setChangedSeqNames(true); m->setChangedGroupNames(true);
Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
delete command;
//if we aborted command
if (quitCommandCalled == 2) { m->mothurOut("[ERROR]: did not complete " + commandName + ".\n"); }
if (m->getControl_pressed()) { break; }
m->setControl_pressed(false); m->setExecuting(false);
}else { m->mothurOut("[ERROR]: Invalid command.\n"); }
}
inputBatchFile.close();
return true;
}
catch(exception& e) {
m->errorOut(e, "BatchEngine", "getInput");
exit(1);
}
}
/***********************************************************************/
string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
try {
string nextcommand = "#"; //force grabbing first command
while (nextcommand[0] == '#') { //skip comments
if (!inputBatchFile.eof()) {
nextcommand = util.getline(inputBatchFile);
gobble(inputBatchFile);
}else { nextcommand = "quit()"; break; } //end of file, quit
}
//allow user to omit the () on the help and quit commands
if (nextcommand == "quit") { nextcommand = "quit()"; }
if (nextcommand == "help") { nextcommand = "help()"; }
string type = findType(nextcommand);
if (type == "batch") {
m->mothurOut("/*****************************************************************************/\n");
BatchEngine newBatchEngine(path, nextcommand, environmentalVariables);
if (newBatchEngine.getOpenedBatch()) {
bool bail = false;
while(!bail) { bail = newBatchEngine.getInput(); }
numBatches++;
}
m->mothurOut("/*****************************************************************************/\n");
nextcommand = getNextCommand(inputBatchFile);
}else if (type == "environment") {
//set environmental variables
string key, value; value = nextcommand;
util.splitAtEquals(key, value);
map<string, string>::iterator it = environmentalVariables.find(key);
if (it == environmentalVariables.end()) { environmentalVariables[key] = value; }
else { it->second = value; }
m->mothurOut("Setting environment variable " + key + " to " + value + "\n");
nextcommand = getNextCommand(inputBatchFile);
}else { //assume command, look for environmental variables to replace
int evPos = nextcommand.find_first_of('$');
if (evPos == string::npos) { //no '$' , check for mothurhome
evPos = nextcommand.find("mothurhome");
if (evPos != string::npos) { replaceVariables(nextcommand); }
}else { replaceVariables(nextcommand); }
}
if (m->getDebug()) {
double ramUsed, total;
ramUsed = util.getRAMUsed(); total = util.getTotalRAM();
m->mothurOut("RAM used: " + toString(ramUsed/(double)GIG) + " Gigabytes. Total Ram: " + toString(total/(double)GIG) + " Gigabytes.\n\n");
}
return nextcommand;
}
catch(exception& e) {
m->errorOut(e, "BatchEngine", "getNextCommand");
exit(1);
}
}
/***********************************************************************/
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