engine.cpp

   1 /*
   2  *  engine.cpp
   3  *
   4  *
   5  *  Created by Pat Schloss on 8/15/08.
   6  *  Copyright 2008 Patrick D. Schloss. All rights reserved.
   7  *
   8  *  There's a TON of duplicated code between InteractEngine and BatchEngine
   9  *  I couldn't figure out how to transition between ifstream (batch) and cin (interact)
  10  *  Fix later, don't have time now.
  11  *
  12  */
  13
  14
  15 #include "engine.hpp"
  16
  17 /***********************************************************************/
  18 Engine::Engine(){
  19         try {
  20                 cFactory = CommandFactory::getInstance();
  21                 mout = MothurOut::getInstance();
  22         }
  23         catch(exception& e) {
  24                 mout->errorOut(e, "Engine", "Engine");
  25                 exit(1);
  26         }
  27 }
  28 /***********************************************************************/
  29 string Engine::findMothursPath(){
  30         try {
  31
  32                 string envPath = getenv("PATH");
  33                 string mothurPath = "";
  34
  35                 //delimiting path char
  36                 char delim;
  37                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  38                         delim = ':';
  39                 #else
  40                         delim = ';';
  41                 #endif
  42
  43                 //break apart path variable by ':'
  44                 vector<string> dirs;
  45                 mout->splitAtChar(envPath, dirs, delim);
  46
  47                 //get path related to mothur
  48                 for (int i = 0; i < dirs.size(); i++) {
  49                         //to lower so we can find it
  50                         string tempLower = "";
  51                         for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
  52
  53                         //is this mothurs path?
  54                         if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
  55                 }
  56
  57                 if (mothurPath != "") {
  58                         //add mothur so it looks like what argv would look like
  59                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  60                                 mothurPath += "/mothur";
  61                         #else
  62                                 mothurPath += "\\mothur";
  63                         #endif
  64                 }else {
  65                         //okay mothur is not in the path, so the folder mothur is in must be in the path
  66                         //lets find out which one
  67
  68                         //get path related to mothur
  69                         for (int i = 0; i < dirs.size(); i++) {
  70
  71                                 //is this mothurs path?
  72                                 ifstream in;
  73                                 string tempIn = dirs[i];
  74                                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  75                                         tempIn += "/mothur";
  76                                 #else
  77                                         tempIn += "\\mothur";
  78                                 #endif
  79                                 mout->openInputFile(tempIn, in, "");
  80
  81                                 //if this file exists
  82                                 if (in) { in.close(); mothurPath = tempIn;  break;  }
  83                         }
  84                 }
  85
  86                 return mothurPath;
  87
  88         }
  89         catch(exception& e) {
  90                 mout->errorOut(e, "Engine", "findMothursPath");
  91                 exit(1);
  92         }
  93 }
  94 /***********************************************************************/
  95
  96 InteractEngine::InteractEngine(string path){
  97
  98
  99         string temppath = path.substr(0, (path.find_last_of("othur")-5));
 100
 101         //this will happen if you set the path variable to contain mothur's exe location
 102         if (temppath == "") { path = findMothursPath(); }
 103
 104         mout->argv = path;
 105 }
 106
 107 /***********************************************************************/
 108
 109 InteractEngine::~InteractEngine(){}
 110
 111 /***********************************************************************/
 112 //This function allows the user to input commands one line at a time until they quit.
 113 //If the command is garbage it does nothing.
 114 bool InteractEngine::getInput(){
 115         try {
 116                 string input = "";
 117                 string commandName = "";
 118                 string options = "";
 119                 int quitCommandCalled = 0;
 120
 121                 while(quitCommandCalled != 1){
 122
 123                         #ifdef USE_MPI
 124                                 int pid, processors;
 125                                 MPI_Status status;
 126                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 127                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 128
 129                                 if (pid == 0) {
 130
 131                         #endif
 132
 133                         mout->mothurOutEndLine();
 134
 135                         input = getCommand();
 136                         mout->mothurOutEndLine();
 137
 138                         if (mout->control_pressed) { input = "quit()"; }
 139
 140                         //allow user to omit the () on the quit command
 141                         if (input == "quit") { input = "quit()"; }
 142
 143
 144                         #ifdef USE_MPI
 145                                 //send commandName
 146                                 for(int i = 1; i < processors; i++) {
 147                                                 int length = input.length();
 148                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 149                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 150
 151                                         }
 152                                 }else {
 153                                         int length;
 154                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 155                                         //recieve container
 156                                         char* tempBuf = new char[length];
 157                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 158
 159                                         input = tempBuf;
 160                                         if (input.length() > length) { input = input.substr(0, length);  }
 161                                         delete tempBuf;
 162                                 }
 163
 164
 165                         #endif
 166
 167                         CommandOptionParser parser(input);
 168                         commandName = parser.getCommandString();
 169
 170                         options = parser.getOptionString();
 171
 172                         if (commandName != "") {
 173                                         mout->executing = true;
 174                                         #ifdef USE_MPI
 175                                                 int pid;
 176                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 177
 178                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 179                                         //cout << pid << " is in execute " << commandName << endl;
 180                                         #endif
 181                                         //executes valid command
 182                                         Command* command = cFactory->getCommand(commandName, options);
 183                                         quitCommandCalled = command->execute();
 184
 185                                         //if we aborted command
 186                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 187
 188                                         mout->control_pressed = 0;
 189                                         mout->executing = false;
 190
 191                                         #ifdef USE_MPI
 192                                                 }
 193                                         #endif
 194                                 }else {
 195                                         mout->mothurOut("Invalid.");
 196                                         mout->mothurOutEndLine();
 197                                 }
 198                 }
 199                 return 1;
 200         }
 201         catch(exception& e) {
 202                 mout->errorOut(e, "InteractEngine", "getInput");
 203                 exit(1);
 204         }
 205 }
 206 /***********************************************************************/
 207 string Engine::getCommand()  {
 208         try {
 209
 210                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 211                         #ifdef USE_READLINE
 212                                 char* nextCommand = NULL;
 213                                 nextCommand = readline("mothur > ");
 214
 215                                 if(nextCommand != NULL) {  add_history(nextCommand);  }
 216                                 else{ //^D causes null string and we want it to quit mothur
 217                                         strcpy(nextCommand, "quit");
 218                                         mout->mothurOut(nextCommand);
 219                                 }
 220
 221                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 222                                 return nextCommand;
 223                         #else
 224                                 string nextCommand = "";
 225                                 mout->mothurOut("mothur > ");
 226                                 getline(cin, nextCommand);
 227                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 228
 229                                 return nextCommand;
 230                         #endif
 231                 #else
 232                                 string nextCommand = "";
 233
 234                                 mout->mothurOut("mothur > ");
 235                                 getline(cin, nextCommand);
 236                                 mout->mothurOutJustToLog(toString(nextCommand));
 237
 238                                 return nextCommand;
 239                 #endif
 240
 241
 242         }
 243         catch(exception& e) {
 244                 mout->errorOut(e, "Engine", "getCommand");
 245                 exit(1);
 246         }
 247 }
 248 /***********************************************************************/
 249 //This function opens the batchfile to be used by BatchEngine::getInput.
 250 BatchEngine::BatchEngine(string path, string batchFileName){
 251         try {
 252
 253                 openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
 254
 255                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 256
 257                 //this will happen if you set the path variable to contain mothur's exe location
 258                 if (temppath == "") { path = findMothursPath(); }
 259
 260                 mout->argv = path;
 261
 262         }
 263         catch(exception& e) {
 264                 mout->errorOut(e, "BatchEngine", "BatchEngine");
 265                 exit(1);
 266         }
 267 }
 268
 269 /***********************************************************************/
 270
 271 BatchEngine::~BatchEngine(){    }
 272
 273 /***********************************************************************/
 274 //This Function allows the user to run a batchfile containing several commands on Dotur
 275 bool BatchEngine::getInput(){
 276         try {
 277                 //check if this is a valid batchfile
 278                 if (openedBatch == 1) {
 279                         mout->mothurOut("unable to open batchfile");
 280                         mout->mothurOutEndLine();
 281                         return 1;
 282                 }
 283
 284                 string input = "";
 285                 string commandName = "";
 286                 string options = "";
 287
 288                 //CommandFactory cFactory;
 289                 int quitCommandCalled = 0;
 290             int count = 0;
 291                 while(quitCommandCalled != 1){
 292
 293                         #ifdef USE_MPI
 294                                 int pid, processors;
 295                                 MPI_Status status;
 296                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 297                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 298
 299                                 if (pid == 0) {
 300
 301                         #endif
 302
 303                         input = getNextCommand(inputBatchFile);
 304                         count++;
 305
 306                         #ifdef USE_MPI
 307                                 //send commandName
 308                                 for(int i = 1; i < processors; i++) {
 309                                                 int length = input.length();
 310                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 311                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 312
 313                                         }
 314                                 }else {
 315                                         int length;
 316                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 317                                         //recieve container
 318                                         char* tempBuf = new char[length];
 319                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 320
 321                                         input = tempBuf;
 322                                         if (input.length() > length) { input = input.substr(0, length);  }
 323                                         delete tempBuf;
 324                                 }
 325
 326
 327                         #endif
 328
 329
 330
 331                         if (input[0] != '#') {
 332
 333                                 mout->mothurOutEndLine();
 334                                 mout->mothurOut("mothur > " + input);
 335                                 mout->mothurOutEndLine();
 336
 337                                 if (mout->control_pressed) { input = "quit()"; }
 338
 339                                 //allow user to omit the () on the quit command
 340                                 if (input == "quit") { input = "quit()"; }
 341
 342                                 CommandOptionParser parser(input);
 343                                 commandName = parser.getCommandString();
 344                                 options = parser.getOptionString();
 345
 346                                 if (commandName != "") {
 347                                         mout->executing = true;
 348                                         #ifdef USE_MPI
 349                                                 int pid;
 350                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 351
 352 //cout << pid << " is here " << commandName << '\t' << count << endl;
 353                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 354                                         #endif
 355                                         //executes valid command
 356                                         Command* command = cFactory->getCommand(commandName, options);
 357                                         quitCommandCalled = command->execute();
 358
 359                                         //if we aborted command
 360                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 361
 362                                         mout->control_pressed = 0;
 363                                         mout->executing = false;
 364
 365                                         #ifdef USE_MPI
 366                                                 }
 367                                         #endif
 368                                 }else {
 369                                         mout->mothurOut("Invalid.");
 370                                         mout->mothurOutEndLine();
 371                                 }
 372
 373                         }
 374                         mout->gobble(inputBatchFile);
 375                 }
 376
 377                 inputBatchFile.close();
 378                 return 1;
 379         }
 380         catch(exception& e) {
 381                 mout->errorOut(e, "BatchEngine", "getInput");
 382                 exit(1);
 383         }
 384 }
 385 /***********************************************************************/
 386 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 387         try {
 388
 389                 string nextcommand = "";
 390
 391                 if (inputBatchFile.eof()) { nextcommand = "quit()"; }
 392                 else { nextcommand = mout->getline(inputBatchFile); }
 393
 394                 return nextcommand;
 395         }
 396         catch(exception& e) {
 397                 mout->errorOut(e, "BatchEngine", "getNextCommand");
 398                 exit(1);
 399         }
 400 }
 401
 402 /***********************************************************************/
 403 /***********************************************************************/
 404 //This function opens the batchfile to be used by BatchEngine::getInput.
 405 ScriptEngine::ScriptEngine(string path, string commandString){
 406         try {
 407
 408                 //remove quotes
 409                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 410
 411                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 412
 413                 //this will happen if you set the path variable to contain mothur's exe location
 414                 if (temppath == "") { path = findMothursPath(); }
 415
 416                 mout->argv = path;
 417
 418         }
 419         catch(exception& e) {
 420                 mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 421                 exit(1);
 422         }
 423 }
 424
 425 /***********************************************************************/
 426
 427 ScriptEngine::~ScriptEngine(){  }
 428
 429 /***********************************************************************/
 430 //This Function allows the user to run a batchfile containing several commands on mothur
 431 bool ScriptEngine::getInput(){
 432         try {
 433
 434                 string input = "";
 435                 string commandName = "";
 436                 string options = "";
 437
 438
 439                 //CommandFactory cFactory;
 440                 int quitCommandCalled = 0;
 441
 442                 while(quitCommandCalled != 1){
 443
 444                         #ifdef USE_MPI
 445                                 int pid, processors;
 446                                 MPI_Status status;
 447                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 448                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 449
 450                                 if (pid == 0) {
 451
 452                         #endif
 453
 454                         input = getNextCommand(listOfCommands);
 455
 456                         if (input == "") { input = "quit()"; }
 457
 458                         mout->mothurOutEndLine();
 459                         mout->mothurOut("mothur > " + input);
 460                         mout->mothurOutEndLine();
 461
 462                         #ifdef USE_MPI
 463                                 //send commandName
 464                                 for(int i = 1; i < processors; i++) {
 465                                                 int length = input.length();
 466                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 467                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 468
 469                                         }
 470                                 }else {
 471                                         int length;
 472                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 473                                         //recieve container
 474                                         char* tempBuf = new char[length];
 475                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 476
 477                                         input = tempBuf;
 478                                         if (input.length() > length) { input = input.substr(0, length);  }
 479                                         delete tempBuf;
 480                                 }
 481
 482
 483                         #endif
 484
 485
 486                         if (mout->control_pressed) { input = "quit()"; }
 487
 488                         //allow user to omit the () on the quit command
 489                         if (input == "quit") { input = "quit()"; }
 490
 491                         CommandOptionParser parser(input);
 492                         commandName = parser.getCommandString();
 493                         options = parser.getOptionString();
 494
 495                         if (commandName != "") {
 496                                         mout->executing = true;
 497                                         #ifdef USE_MPI
 498                                                 int pid, numProcesses;
 499
 500                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 501                                                 MPI_Comm_size(MPI_COMM_WORLD, &numProcesses);
 502
 503 //cout << pid << " is here " << commandName  << endl;
 504                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 505                                                         //cout << pid << " is in execute" << endl;
 506                                         #endif
 507                                         //executes valid command
 508                                         Command* command = cFactory->getCommand(commandName, options);
 509                                         quitCommandCalled = command->execute();
 510
 511                                         //if we aborted command
 512                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 513
 514                                         mout->control_pressed = 0;
 515                                         mout->executing = false;
 516
 517                                         #ifdef USE_MPI
 518                                         //cout << pid << " is done in execute" << endl;
 519                                                 }
 520                                         #endif
 521                                 }else {
 522                                         mout->mothurOut("Invalid.");
 523                                         mout->mothurOutEndLine();
 524                                 }
 525
 526
 527                 }
 528
 529                 return 1;
 530         }
 531         catch(exception& e) {
 532                 mout->errorOut(e, "ScriptEngine", "getInput");
 533                 exit(1);
 534         }
 535 }
 536 /***********************************************************************/
 537 string ScriptEngine::getNextCommand(string& commandString) {
 538         try {
 539
 540                 string nextcommand = "";
 541                 int count = 0;
 542                 bool ignoreSemiColons = false;
 543
 544                 //go through string until you reach ; or end
 545                 while (count < commandString.length()) {
 546
 547                          //you want to ignore any ; until you reach the next '
 548                         if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  }
 549                         else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  }
 550
 551                         if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
 552                         else {          nextcommand += commandString[count];    }
 553
 554                         count++;
 555                 }
 556
 557                 //if you are not at the end
 558                 if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
 559                 else { commandString = ""; }
 560
 561
 562                 //get rid of spaces in between commands if any
 563                 if (commandString.length() > 0) {
 564                         while (commandString[0] == ' ') {
 565                                 commandString = commandString.substr(1,commandString.length());
 566                                 if (commandString.length() == 0) {  break;  }
 567                         }
 568                 }
 569
 570                 return nextcommand;
 571         }
 572         catch(exception& e) {
 573                 mout->errorOut(e, "ScriptEngine", "getNextCommand");
 574                 exit(1);
 575         }
 576 }
 577 /***********************************************************************/