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//
// scriptengine.cpp
// Mothur
//
// Created by Sarah Westcott on 10/21/19.
// Copyright © 2019 Schloss Lab. All rights reserved.
//
#include "scriptengine.hpp"
/***********************************************************************/
ScriptEngine::ScriptEngine(string tpath, string commandString, map<string, string> ev) : Engine(tpath){
try {
//remove quotes
listOfCommands = commandString.substr(1, (commandString.length()-1));
noBufferNeeded = true;
int pos = listOfCommands.find("set.logfile");
if (pos != string::npos) { noBufferNeeded = false; }
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);
}
catch(exception& e) {
m->errorOut(e, "ScriptEngine", "ScriptEngine");
exit(1);
}
}
/***********************************************************************/
ScriptEngine::~ScriptEngine(){
time_t end = time(nullptr);
m->mothurOut("\n\nIt took " + toString(end-start) + " seconds to run " + toString(numCommandsRun) + " commands from your script.\n\n");
}
/***********************************************************************/
//This Function allows the user to run a batchfile containing several commands on mothur
bool ScriptEngine::getInput(){
try {
string input = "";
string commandName = "";
string options = "";
int quitCommandCalled = 0;
while(quitCommandCalled != 1){
input = getNextCommand(listOfCommands);
if (input == "") { input = "quit()"; }
CommandOptionParser parser(input);
commandName = parser.getCommandString();
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);
//executes valid command
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.\n"); }
}
return true;
}
catch(exception& e) {
m->errorOut(e, "ScriptEngine", "getInput");
exit(1);
}
}
/***********************************************************************/
string ScriptEngine::getNextCommand(string& commandString) {
try {
string nextcommand = "";
int count = 0;
bool ignoreSemiColons = false;
//go through string until you reach ; or end
while (count < commandString.length()) {
//you want to ignore any ; until you reach the next '
if ((commandString[count] == '\'') && (!ignoreSemiColons)) { ignoreSemiColons = true; }
else if ((commandString[count] == '\'') && (ignoreSemiColons)) { ignoreSemiColons = false; }
if ((commandString[count] == ';') && (!ignoreSemiColons)) { break; }
else { nextcommand += commandString[count]; }
count++;
}
//if you are not at the end
if (count != commandString.length()) { commandString = commandString.substr(count+1, commandString.length()); }
else { commandString = ""; }
//get rid of spaces in between commands if any
if (commandString.length() > 0) {
while (commandString[0] == ' ') {
commandString = commandString.substr(1,commandString.length());
if (commandString.length() == 0) { break; }
}
}
//allow user to omit the () on the quit command
if (nextcommand == "quit") { nextcommand = "quit()"; }
if (nextcommand == "help") { nextcommand = "help()"; }
string type = findType(nextcommand);
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(commandString);
}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, "ScriptEngine", "getNextCommand");
exit(1);
}
}
/***********************************************************************/
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