X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=7bcb4e41185bfa2104b3ef29432db0af7cbe58a2;hb=b4f80c1d2be78a8743a408a2b6d462b07f9f71ff;hp=55617bc3f80a97e1832ff61c3e09678de8eca1ca;hpb=29c0d3ec01be5372807eb86261100d77de253787;p=mothur.git diff --git a/engine.cpp b/engine.cpp index 55617bc..7bcb4e4 100644 --- a/engine.cpp +++ b/engine.cpp @@ -14,6 +14,18 @@ #include "engine.hpp" +/***********************************************************************/ +Engine::Engine(){ + try { + cFactory = CommandFactory::getInstance(); + mout = MothurOut::getInstance(); + } + catch(exception& e) { + mout->errorOut(e, "Engine", "Engine"); + exit(1); + } +} + /***********************************************************************/ InteractEngine::InteractEngine(string path){ @@ -21,13 +33,11 @@ InteractEngine::InteractEngine(string path){ globaldata = GlobalData::getInstance(); globaldata->argv = path; - system("clear"); } /***********************************************************************/ -InteractEngine::~InteractEngine(){ - } +InteractEngine::~InteractEngine(){} /***********************************************************************/ //This function allows the user to input commands one line at a time until they quit. @@ -39,44 +49,99 @@ bool InteractEngine::getInput(){ string options = ""; int quitCommandCalled = 0; - while(quitCommandCalled != 1){ + + + mout->mothurOutEndLine(); - mothurOutEndLine(); - mothurOut("mothur > "); - getline(cin, input); - if (cin.eof()) { input = "quit()"; } - - mothurOutJustToLog(input); - mothurOutEndLine(); + input = getCommand(); + mout->mothurOutEndLine(); + + if (mout->control_pressed) { input = "quit()"; } //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } CommandOptionParser parser(input); commandName = parser.getCommandString(); + options = parser.getOptionString(); if (commandName != "") { - - //executes valid command - CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName, options); - quitCommandCalled = command->execute(); - - }else { - mothurOut("Your input contains errors. Please try again."); - mothurOutEndLine(); - } + mout->executing = true; + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + +//cout << pid << " is here " << commandName << endl; + if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { + #endif + //executes valid command + Command* command = cFactory->getCommand(commandName, options); + quitCommandCalled = command->execute(); + mout->control_pressed = 0; + mout->executing = false; + + #ifdef USE_MPI + } + #endif + }else { + mout->mothurOut("Invalid."); + mout->mothurOutEndLine(); + } } return 1; } catch(exception& e) { - errorOut(e, "InteractEngine", "getInput"); + mout->errorOut(e, "InteractEngine", "getInput"); + exit(1); + } +} +/***********************************************************************/ +string Engine::getCommand() { + try { + #ifdef USE_MPI + MPI_Barrier(MPI_COMM_WORLD); + #endif + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) + #ifdef USE_READLINE + char* nextCommand = NULL; + nextCommand = readline("mothur > "); + + if(nextCommand != NULL) { add_history(nextCommand); } + else{ //^D causes null string and we want it to quit mothur + nextCommand = "quit"; + mout->mothurOut(nextCommand); + } + + mout->mothurOutJustToLog("mothur > " + toString(nextCommand)); + return nextCommand; + #else + string nextCommand = ""; + mout->mothurOut("mothur > "); + getline(cin, nextCommand); + mout->mothurOutJustToLog("mothur > " + toString(nextCommand)); + + return nextCommand; + #endif + #else + string nextCommand = ""; + + mout->mothurOut("mothur > "); + getline(cin, nextCommand); + mout->mothurOutJustToLog(toString(nextCommand)); + + return nextCommand; + #endif + + + } + catch(exception& e) { + mout->errorOut(e, "Engine", "getCommand"); exit(1); } } - /***********************************************************************/ //This function opens the batchfile to be used by BatchEngine::getInput. BatchEngine::BatchEngine(string path, string batchFileName){ @@ -86,25 +151,16 @@ BatchEngine::BatchEngine(string path, string batchFileName){ openedBatch = openInputFile(batchFileName, inputBatchFile); globaldata->argv = path; - system("clear"); - - // char buffer = ' '; - // ifstream header("introtext.txt"); - // while(!header.eof()){ - // cout << buffer; - // buffer = header.get(); - // } } catch(exception& e) { - errorOut(e, "BatchEngine", "BatchEngine"); + mout->errorOut(e, "BatchEngine", "BatchEngine"); exit(1); } } /***********************************************************************/ -BatchEngine::~BatchEngine(){ - } +BatchEngine::~BatchEngine(){ } /***********************************************************************/ //This Function allows the user to run a batchfile containing several commands on Dotur @@ -112,8 +168,8 @@ bool BatchEngine::getInput(){ try { //check if this is a valid batchfile if (openedBatch == 1) { - mothurOut("unable to open batchfile"); - mothurOutEndLine(); + mout->mothurOut("unable to open batchfile"); + mout->mothurOutEndLine(); return 1; } @@ -123,20 +179,19 @@ bool BatchEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; - + int count = 0; while(quitCommandCalled == 0){ - if (inputBatchFile.eof()) { input = "quit()"; } - else { getline(inputBatchFile, input); } - - + input = getNextCommand(inputBatchFile); + count++; if (input[0] != '#') { - mothurOutEndLine(); - mothurOut("mothur > " + input); - mothurOutEndLine(); - + mout->mothurOutEndLine(); + mout->mothurOut("mothur > " + input); + mout->mothurOutEndLine(); + + if (mout->control_pressed) { input = "quit()"; } //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } @@ -146,14 +201,26 @@ bool BatchEngine::getInput(){ options = parser.getOptionString(); if (commandName != "") { - + mout->executing = true; + #ifdef USE_MPI + int pid; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + +//cout << pid << " is here " << commandName << '\t' << count << endl; + if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { + #endif //executes valid command - CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName, options); + Command* command = cFactory->getCommand(commandName, options); quitCommandCalled = command->execute(); + mout->control_pressed = 0; + mout->executing = false; + + #ifdef USE_MPI + } + #endif }else { - mothurOut("Invalid."); - mothurOutEndLine(); + mout->mothurOut("Invalid."); + mout->mothurOutEndLine(); } } @@ -164,11 +231,31 @@ bool BatchEngine::getInput(){ return 1; } catch(exception& e) { - errorOut(e, "BatchEngine", "getInput"); + mout->errorOut(e, "BatchEngine", "getInput"); + exit(1); + } +} +/***********************************************************************/ +string BatchEngine::getNextCommand(ifstream& inputBatchFile) { + try { + + #ifdef USE_MPI + int err = MPI_Barrier(MPI_COMM_WORLD); +//cout << "barrier = " << err << '\t' << MPI_SUCCESS << endl; + #endif + + string nextcommand = ""; + + if (inputBatchFile.eof()) { nextcommand = "quit()"; } + else { nextcommand = getline(inputBatchFile); } + + return nextcommand; + } + catch(exception& e) { + mout->errorOut(e, "BatchEngine", "getNextCommand"); exit(1); } } - /***********************************************************************/ /***********************************************************************/ @@ -181,20 +268,17 @@ ScriptEngine::ScriptEngine(string path, string commandString){ listOfCommands = commandString.substr(1, (commandString.length()-1)); globaldata->argv = path; - - system("clear"); - + } catch(exception& e) { - errorOut(e, "ScriptEngine", "ScriptEngine"); + mout->errorOut(e, "ScriptEngine", "ScriptEngine"); exit(1); } } /***********************************************************************/ -ScriptEngine::~ScriptEngine(){ - } +ScriptEngine::~ScriptEngine(){ } /***********************************************************************/ //This Function allows the user to run a batchfile containing several commands on mothur @@ -215,11 +299,11 @@ bool ScriptEngine::getInput(){ if (input == "") { input = "quit()"; } + mout->mothurOutEndLine(); + mout->mothurOut("mothur > " + input); + mout->mothurOutEndLine(); - mothurOutEndLine(); - mothurOut("mothur > " + input); - mothurOutEndLine(); - + if (mout->control_pressed) { input = "quit()"; } //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } @@ -229,36 +313,67 @@ bool ScriptEngine::getInput(){ options = parser.getOptionString(); if (commandName != "") { + mout->executing = true; + #ifdef USE_MPI + int pid, numProcesses; + MPI_Status status; + + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); + +//cout << pid << " is here " << commandName << endl; + if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { + //cout << pid << " is in execute" << endl; + #endif + //executes valid command + Command* command = cFactory->getCommand(commandName, options); + quitCommandCalled = command->execute(); + mout->control_pressed = 0; + mout->executing = false; + + #ifdef USE_MPI + //cout << pid << " is done in execute" << endl; + } + #endif + }else { + mout->mothurOut("Invalid."); + mout->mothurOutEndLine(); + } - //executes valid command - CommandFactory cFactory; - Command* command = cFactory.getCommand(commandName, options); - quitCommandCalled = command->execute(); - }else { - mothurOut("Invalid."); - mothurOutEndLine(); - } } return 1; } catch(exception& e) { - errorOut(e, "ScriptEngine", "getInput"); + mout->errorOut(e, "ScriptEngine", "getInput"); exit(1); } } /***********************************************************************/ string ScriptEngine::getNextCommand(string& commandString) { try { + + #ifdef USE_MPI + MPI_Barrier(MPI_COMM_WORLD); + #endif + string nextcommand = ""; + int count = 0; - nextcommand = commandString.substr(0,commandString.find_first_of(';')); - + //go through string until you reach ; or end + while (count < commandString.length()) { + + if (commandString[count] == ';') { 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 = ""; } - if ((commandString.find_first_of(';')+1) <= commandString.length()) { - commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length()); - }else { commandString = ""; } //you have reached the last command. //get rid of spaces in between commands if any if (commandString.length() > 0) { @@ -267,11 +382,11 @@ string ScriptEngine::getNextCommand(string& commandString) { if (commandString.length() == 0) { break; } } } - + return nextcommand; } catch(exception& e) { - errorOut(e, "ScriptEngine", "getNextCommand"); + mout->errorOut(e, "ScriptEngine", "getNextCommand"); exit(1); } }