+++ /dev/null
-/*
- * engine.cpp
- *
- *
- * Created by Pat Schloss on 8/15/08.
- * Copyright 2008 Patrick D. Schloss. All rights reserved.
- *
- * There's a TON of duplicated code between InteractEngine and BatchEngine
- * I couldn't figure out how to transition between ifstream (batch) and cin (interact)
- * Fix later, don't have time now.
- *
- */
-
-
-#include "engine.hpp"
-
-/***********************************************************************/
-Engine::Engine(){
- try {
- cFactory = CommandFactory::getInstance();
- mout = MothurOut::getInstance();
- }
- catch(exception& e) {
- mout->errorOut(e, "Engine", "Engine");
- exit(1);
- }
-}
-/***********************************************************************/
-string Engine::findMothursPath(){
- try {
-
- string envPath = getenv("PATH");
- string mothurPath = "";
-
- //delimiting path char
- char delim;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- delim = ':';
- #else
- delim = ';';
- #endif
-
- //break apart path variable by ':'
- vector<string> dirs;
- mout->splitAtChar(envPath, dirs, delim);
-
- //get path related to mothur
- for (int i = 0; i < dirs.size(); i++) {
- //to lower so we can find it
- string tempLower = "";
- for (int j = 0; j < dirs[i].length(); j++) { tempLower += tolower(dirs[i][j]); }
-
- //is this mothurs path?
- if (tempLower.find("mothur") != -1) { mothurPath = dirs[i]; break; }
- }
-
- if (mothurPath != "") {
- //add mothur so it looks like what argv would look like
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- mothurPath += "/mothur";
- #else
- mothurPath += "\\mothur";
- #endif
- }else {
- //okay mothur is not in the path, so the folder mothur is in must be in the path
- //lets find out which one
-
- //get path related to mothur
- for (int i = 0; i < dirs.size(); i++) {
-
- //is this mothurs path?
- ifstream in;
- string tempIn = dirs[i];
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- tempIn += "/mothur";
- #else
- tempIn += "\\mothur";
- #endif
- mout->openInputFile(tempIn, in, "");
-
- //if this file exists
- if (in) { in.close(); mothurPath = tempIn; break; }
- }
- }
-
- return mothurPath;
-
- }
- catch(exception& e) {
- mout->errorOut(e, "Engine", "findMothursPath");
- exit(1);
- }
-}
-/***********************************************************************/
-
-InteractEngine::InteractEngine(string 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 = findMothursPath(); }
-
- mout->argv = path;
-}
-
-/***********************************************************************/
-
-InteractEngine::~InteractEngine(){}
-
-/***********************************************************************/
-//This function allows the user to input commands one line at a time until they quit.
-//If the command is garbage it does nothing.
-bool InteractEngine::getInput(){
- try {
- string input = "";
- string commandName = "";
- string options = "";
- int 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
-
- mout->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()"; }
-
-
- #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();
-
- options = parser.getOptionString();
-
- if (commandName != "") {
- 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->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) {
- mout->errorOut(e, "InteractEngine", "getInput");
- exit(1);
- }
-}
-/***********************************************************************/
-string Engine::getCommand() {
- try {
-
- #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) {
- mout->errorOut(e, "Engine", "getCommand");
- exit(1);
- }
-}
-/***********************************************************************/
-//This function opens the batchfile to be used by BatchEngine::getInput.
-BatchEngine::BatchEngine(string path, string batchFileName){
- try {
-
- 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 = findMothursPath(); }
-
- mout->argv = path;
-
- }
- catch(exception& e) {
- mout->errorOut(e, "BatchEngine", "BatchEngine");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-BatchEngine::~BatchEngine(){ }
-
-/***********************************************************************/
-//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 == 1) {
- mout->mothurOut("unable to open batchfile");
- mout->mothurOutEndLine();
- return 1;
- }
-
- string input = "";
- string commandName = "";
- string options = "";
-
- //CommandFactory cFactory;
- int quitCommandCalled = 0;
- int count = 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(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] != '#') {
-
- 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()"; }
-
- CommandOptionParser parser(input);
- commandName = parser.getCommandString();
- 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->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();
- }
-
- }
- mout->gobble(inputBatchFile);
- }
-
- inputBatchFile.close();
- return 1;
- }
- catch(exception& e) {
- 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 {
-
- //remove quotes
- listOfCommands = commandString.substr(1, (commandString.length()-1));
-
- 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 = findMothursPath(); }
-
- mout->argv = path;
-
- }
- catch(exception& e) {
- mout->errorOut(e, "ScriptEngine", "ScriptEngine");
- exit(1);
- }
-}
-
-/***********************************************************************/
-
-ScriptEngine::~ScriptEngine(){ }
-
-/***********************************************************************/
-//This Function allows the user to run a batchfile containing several commands on mothur
-bool ScriptEngine::getInput(){
- try {
-
- string input = "";
- string commandName = "";
- string options = "";
-
-
- //CommandFactory cFactory;
- int 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->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();
- }
-
- #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()"; }
-
- CommandOptionParser parser(input);
- commandName = parser.getCommandString();
- 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->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();
- }
-
-
- }
-
- return 1;
- }
- catch(exception& e) {
- 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()) {
-
- //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; }
- }
- }
-
- return nextcommand;
- }
- catch(exception& e) {
- mout->errorOut(e, "ScriptEngine", "getNextCommand");
- exit(1);
- }
-}
-/***********************************************************************/
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