X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=engine.cpp;h=e4e107168c5723c82b90a7f103ccb8d9ee83cb60;hp=371bda8fb83f2b8ceb4793c49f067ed5987f2094;hb=1a20e24ee786195ab0e1cccd4f5aede7a88f3f4e;hpb=648ec37228eb16075ace911dd5a5773cdfe683da diff --git a/engine.cpp b/engine.cpp index 371bda8..e4e1071 100644 --- a/engine.cpp +++ b/engine.cpp @@ -14,12 +14,30 @@ #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){ - globaldata = GlobalData::getInstance(); - globaldata->argv = path; + + string temppath = path.substr(0, (path.find_last_of("othur")-5)); + + //this will happen if you set the path variable to contain mothur's exe location + if (temppath == "") { path = mout->findProgramPath("mothur"); } + + mout->argv = path; } /***********************************************************************/ @@ -36,89 +54,144 @@ bool InteractEngine::getInput(){ string options = ""; int quitCommandCalled = 0; - while(quitCommandCalled != 1){ - - mothurOutEndLine(); - mothurOut("mothur > "); - - //get input char by char so you can check for use of arrow keys - //if (_kbhit()){ - // _getch(); // edit : if you want to check the arrow-keys you must call getch twice because special-keys have two values - // return _getch(); - //} - //return 0; // if no key is pressed - //setbuf(stdin, NULL); //no buffering -/*if(ch==0) -{ -ch=getch(); -if(ch==72) cout<<"up"; -else if(ch==75) cout<<"left"; -else if(ch==77) cout<<"right"; -else if(ch==80) cout<<"down"; -cout<changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); } + + mout->mothurOutEndLine(); - //save command - //previousInputs.push_back(input); + input = getCommand(); + mout->mothurOutEndLine(); - mothurOutJustToLog(input); - mothurOutEndLine(); + if (mout->control_pressed) { input = "quit()"; } //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } + + + #ifdef USE_MPI + //send commandName + for(int i = 1; i < processors; i++) { + int length = input.length(); + MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD); + + } + }else { + int length; + MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //recieve container + char* tempBuf = new char[length]; + MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); + + input = tempBuf; + if (input.length() > length) { input = input.substr(0, length); } + delete tempBuf; + } + + #endif + CommandOptionParser parser(input); commandName = parser.getCommandString(); - //cout << " command = " << commandName << endl; + options = parser.getOptionString(); if (commandName != "") { - - //executes valid command - 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); + + if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) { + //cout << pid << " is in execute " << commandName << endl; + #endif + //executes valid command + mout->changedSeqNames = false; + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->printedHeaders = false; + mout->commandInputsConvertError = false; + mout->currentBinLabels.clear(); + mout->binLabelsInFile.clear(); + + Command* command = cFactory->getCommand(commandName, options); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } + + //if we aborted command + if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } + + 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); } } /***********************************************************************/ -void Engine::terminateCommand(int dummy) { +string Engine::getCommand() { try { - mothurOut("Stopping command."); mothurOutEndLine(); - cFactory->getCommand(); //terminates command + + #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + #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 = strdup("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) { - errorOut(e, "InteractEngine", "terminateCommand"); + mout->errorOut(e, "Engine", "getCommand"); exit(1); } } @@ -126,14 +199,19 @@ void Engine::terminateCommand(int dummy) { //This function opens the batchfile to be used by BatchEngine::getInput. BatchEngine::BatchEngine(string path, string batchFileName){ try { - globaldata = GlobalData::getInstance(); - openedBatch = openInputFile(batchFileName, inputBatchFile); - globaldata->argv = path; + openedBatch = mout->openInputFile(batchFileName, inputBatchFile); + + string temppath = path.substr(0, (path.find_last_of("othur")-5)); + + //this will happen if you set the path variable to contain mothur's exe location + if (temppath == "") { path = mout->findProgramPath("mothur"); } + + mout->argv = path; } catch(exception& e) { - errorOut(e, "BatchEngine", "BatchEngine"); + mout->errorOut(e, "BatchEngine", "BatchEngine"); exit(1); } } @@ -148,8 +226,8 @@ 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; } @@ -159,18 +237,54 @@ bool BatchEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; - - while(quitCommandCalled == 0){ - - if (inputBatchFile.eof()) { input = "quit()"; } - else { input = getline(inputBatchFile); } + int count = 0; + while(quitCommandCalled != 1){ - if (input[0] != '#') { + #ifdef USE_MPI + int pid, processors; + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); - mothurOutEndLine(); - mothurOut("mothur > " + input); - mothurOutEndLine(); + if (pid == 0) { + #endif + + input = getNextCommand(inputBatchFile); + count++; + + #ifdef USE_MPI + //send commandName + for(int i = 1; i < processors; i++) { + int length = input.length(); + MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD); + + } + }else { + int length; + MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //recieve container + char* tempBuf = new char[length]; + MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); + + input = tempBuf; + if (input.length() > length) { input = input.substr(0, length); } + delete tempBuf; + } + + + #endif + + + + if (input[0] != '#') { + if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); } + 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()"; } @@ -180,44 +294,93 @@ 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 + mout->changedSeqNames = false; + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->printedHeaders = false; + mout->commandInputsConvertError = false; + mout->currentBinLabels.clear(); + mout->binLabelsInFile.clear(); + + Command* command = cFactory->getCommand(commandName, options); - quitCommandCalled = command->execute(); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } + + //if we aborted command + if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } + + mout->control_pressed = 0; + mout->executing = false; + + #ifdef USE_MPI + } + #endif }else { - mothurOut("Invalid."); - mothurOutEndLine(); + mout->mothurOut("Invalid."); + mout->mothurOutEndLine(); } } - gobble(inputBatchFile); + mout->gobble(inputBatchFile); } inputBatchFile.close(); return 1; } catch(exception& e) { - errorOut(e, "BatchEngine", "getInput"); + mout->errorOut(e, "BatchEngine", "getInput"); + exit(1); + } +} +/***********************************************************************/ +string BatchEngine::getNextCommand(ifstream& inputBatchFile) { + try { + + string nextcommand = ""; + + if (inputBatchFile.eof()) { nextcommand = "quit()"; } + else { nextcommand = mout->getline(inputBatchFile); } + + return nextcommand; + } + catch(exception& e) { + mout->errorOut(e, "BatchEngine", "getNextCommand"); exit(1); } } - /***********************************************************************/ /***********************************************************************/ //This function opens the batchfile to be used by BatchEngine::getInput. ScriptEngine::ScriptEngine(string path, string commandString){ try { - globaldata = GlobalData::getInstance(); //remove quotes listOfCommands = commandString.substr(1, (commandString.length()-1)); + + string temppath = path.substr(0, (path.find_last_of("othur")-5)); - globaldata->argv = path; + //this will happen if you set the path variable to contain mothur's exe location + if (temppath == "") { path = mout->findProgramPath("mothur"); } + mout->argv = path; + } catch(exception& e) { - errorOut(e, "ScriptEngine", "ScriptEngine"); + mout->errorOut(e, "ScriptEngine", "ScriptEngine"); exit(1); } } @@ -239,17 +402,57 @@ bool ScriptEngine::getInput(){ //CommandFactory cFactory; int quitCommandCalled = 0; - while(quitCommandCalled == 0){ - + while(quitCommandCalled != 1){ + + #ifdef USE_MPI + int pid, processors; + MPI_Status status; + MPI_Comm_rank(MPI_COMM_WORLD, &pid); + MPI_Comm_size(MPI_COMM_WORLD, &processors); + + if (pid == 0) { + + #endif + input = getNextCommand(listOfCommands); if (input == "") { input = "quit()"; } + + if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); } + if (mout->gui) { + if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {} + else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {} + else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); } + }else{ + mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); + } - mothurOutEndLine(); - mothurOut("mothur > " + input); - mothurOutEndLine(); + #ifdef USE_MPI + //send commandName + for(int i = 1; i < processors; i++) { + int length = input.length(); + MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD); + MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD); + + } + }else { + int length; + MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status); + //recieve container + char* tempBuf = new char[length]; + MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); + + input = tempBuf; + if (input.length() > length) { input = input.substr(0, length); } + delete tempBuf; + } + + #endif + + + if (mout->control_pressed) { input = "quit()"; } //allow user to omit the () on the quit command if (input == "quit") { input = "quit()"; } @@ -259,34 +462,74 @@ bool ScriptEngine::getInput(){ options = parser.getOptionString(); if (commandName != "") { + mout->executing = true; + #ifdef USE_MPI + int pid, numProcesses; + + 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 + mout->changedSeqNames = false; + mout->runParse = true; + mout->clearGroups(); + mout->clearAllGroups(); + mout->Treenames.clear(); + mout->saveNextLabel = ""; + mout->printedHeaders = false; + mout->commandInputsConvertError = false; + mout->currentBinLabels.clear(); + mout->binLabelsInFile.clear(); + + Command* command = cFactory->getCommand(commandName, options); + if (mout->commandInputsConvertError) { quitCommandCalled = 2; } + else { quitCommandCalled = command->execute(); } + + //if we aborted command + if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); } + + 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 - 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 { + string nextcommand = ""; int count = 0; + bool ignoreSemiColons = false; //go through string until you reach ; or end while (count < commandString.length()) { - if (commandString[count] == ';') { break; } + //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++; @@ -304,11 +547,11 @@ 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); } }