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                                         mout->runParse = true;
 183                                         mout->clearGroups();
 184                                         mout->clearAllGroups();
 185                                         mout->Treenames.clear();
 186                                         mout->names.clear();
 187                                         mout->saveNextLabel = "";
 188                                         mout->printedHeaders = false;
 189                                         mout->currentBinLabels.clear();
 190                                         mout->binLabelsInFile.clear();
 191
 192                                         Command* command = cFactory->getCommand(commandName, options);
 193                                         quitCommandCalled = command->execute();
 194
 195                                         //if we aborted command
 196                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 197
 198                                         mout->control_pressed = 0;
 199                                         mout->executing = false;
 200
 201                                         #ifdef USE_MPI
 202                                                 }
 203                                         #endif
 204                                 }else {
 205                                         mout->mothurOut("Invalid.");
 206                                         mout->mothurOutEndLine();
 207                                 }
 208                 }
 209                 return 1;
 210         }
 211         catch(exception& e) {
 212                 mout->errorOut(e, "InteractEngine", "getInput");
 213                 exit(1);
 214         }
 215 }
 216 /***********************************************************************/
 217 string Engine::getCommand()  {
 218         try {
 219
 220                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 221                         #ifdef USE_READLINE
 222                                 char* nextCommand = NULL;
 223                                 nextCommand = readline("mothur > ");
 224
 225                                 if(nextCommand != NULL) {  add_history(nextCommand);  }
 226                                 else{ //^D causes null string and we want it to quit mothur
 227                                         nextCommand = strdup("quit");
 228                                         mout->mothurOut(nextCommand);
 229                                 }
 230
 231                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 232                                 return nextCommand;
 233                         #else
 234                                 string nextCommand = "";
 235                                 mout->mothurOut("mothur > ");
 236                                 getline(cin, nextCommand);
 237                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 238
 239                                 return nextCommand;
 240                         #endif
 241                 #else
 242                                 string nextCommand = "";
 243
 244                                 mout->mothurOut("mothur > ");
 245                                 getline(cin, nextCommand);
 246                                 mout->mothurOutJustToLog(toString(nextCommand));
 247
 248                                 return nextCommand;
 249                 #endif
 250
 251
 252         }
 253         catch(exception& e) {
 254                 mout->errorOut(e, "Engine", "getCommand");
 255                 exit(1);
 256         }
 257 }
 258 /***********************************************************************/
 259 //This function opens the batchfile to be used by BatchEngine::getInput.
 260 BatchEngine::BatchEngine(string path, string batchFileName){
 261         try {
 262
 263                 openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
 264
 265                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 266
 267                 //this will happen if you set the path variable to contain mothur's exe location
 268                 if (temppath == "") { path = findMothursPath(); }
 269
 270                 mout->argv = path;
 271
 272         }
 273         catch(exception& e) {
 274                 mout->errorOut(e, "BatchEngine", "BatchEngine");
 275                 exit(1);
 276         }
 277 }
 278
 279 /***********************************************************************/
 280
 281 BatchEngine::~BatchEngine(){    }
 282
 283 /***********************************************************************/
 284 //This Function allows the user to run a batchfile containing several commands on Dotur
 285 bool BatchEngine::getInput(){
 286         try {
 287                 //check if this is a valid batchfile
 288                 if (openedBatch == 1) {
 289                         mout->mothurOut("unable to open batchfile");
 290                         mout->mothurOutEndLine();
 291                         return 1;
 292                 }
 293
 294                 string input = "";
 295                 string commandName = "";
 296                 string options = "";
 297
 298                 //CommandFactory cFactory;
 299                 int quitCommandCalled = 0;
 300             int count = 0;
 301                 while(quitCommandCalled != 1){
 302
 303                         #ifdef USE_MPI
 304                                 int pid, processors;
 305                                 MPI_Status status;
 306                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 307                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 308
 309                                 if (pid == 0) {
 310
 311                         #endif
 312
 313                         input = getNextCommand(inputBatchFile);
 314                         count++;
 315
 316                         #ifdef USE_MPI
 317                                 //send commandName
 318                                 for(int i = 1; i < processors; i++) {
 319                                                 int length = input.length();
 320                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 321                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 322
 323                                         }
 324                                 }else {
 325                                         int length;
 326                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 327                                         //recieve container
 328                                         char* tempBuf = new char[length];
 329                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 330
 331                                         input = tempBuf;
 332                                         if (input.length() > length) { input = input.substr(0, length);  }
 333                                         delete tempBuf;
 334                                 }
 335
 336
 337                         #endif
 338
 339
 340
 341                         if (input[0] != '#') {
 342
 343                                 mout->mothurOutEndLine();
 344                                 mout->mothurOut("mothur > " + input);
 345                                 mout->mothurOutEndLine();
 346
 347                                 if (mout->control_pressed) { input = "quit()"; }
 348
 349                                 //allow user to omit the () on the quit command
 350                                 if (input == "quit") { input = "quit()"; }
 351
 352                                 CommandOptionParser parser(input);
 353                                 commandName = parser.getCommandString();
 354                                 options = parser.getOptionString();
 355
 356                                 if (commandName != "") {
 357                                         mout->executing = true;
 358                                         #ifdef USE_MPI
 359                                                 int pid;
 360                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 361
 362 //cout << pid << " is here " << commandName << '\t' << count << endl;
 363                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 364                                         #endif
 365                                         //executes valid command
 366                                         mout->runParse = true;
 367                                         mout->clearGroups();
 368                                         mout->clearAllGroups();
 369                                         mout->Treenames.clear();
 370                                         mout->names.clear();
 371                                         mout->saveNextLabel = "";
 372                                         mout->printedHeaders = false;
 373                                         mout->currentBinLabels.clear();
 374                                         mout->binLabelsInFile.clear();
 375
 376
 377                                         Command* command = cFactory->getCommand(commandName, options);
 378                                         quitCommandCalled = command->execute();
 379
 380                                         //if we aborted command
 381                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 382
 383                                         mout->control_pressed = 0;
 384                                         mout->executing = false;
 385
 386                                         #ifdef USE_MPI
 387                                                 }
 388                                         #endif
 389                                 }else {
 390                                         mout->mothurOut("Invalid.");
 391                                         mout->mothurOutEndLine();
 392                                 }
 393
 394                         }
 395                         mout->gobble(inputBatchFile);
 396                 }
 397
 398                 inputBatchFile.close();
 399                 return 1;
 400         }
 401         catch(exception& e) {
 402                 mout->errorOut(e, "BatchEngine", "getInput");
 403                 exit(1);
 404         }
 405 }
 406 /***********************************************************************/
 407 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 408         try {
 409
 410                 string nextcommand = "";
 411
 412                 if (inputBatchFile.eof()) { nextcommand = "quit()"; }
 413                 else { nextcommand = mout->getline(inputBatchFile); }
 414
 415                 return nextcommand;
 416         }
 417         catch(exception& e) {
 418                 mout->errorOut(e, "BatchEngine", "getNextCommand");
 419                 exit(1);
 420         }
 421 }
 422
 423 /***********************************************************************/
 424 /***********************************************************************/
 425 //This function opens the batchfile to be used by BatchEngine::getInput.
 426 ScriptEngine::ScriptEngine(string path, string commandString){
 427         try {
 428
 429                 //remove quotes
 430                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 431
 432                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 433
 434                 //this will happen if you set the path variable to contain mothur's exe location
 435                 if (temppath == "") { path = findMothursPath(); }
 436
 437                 mout->argv = path;
 438
 439         }
 440         catch(exception& e) {
 441                 mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 442                 exit(1);
 443         }
 444 }
 445
 446 /***********************************************************************/
 447
 448 ScriptEngine::~ScriptEngine(){  }
 449
 450 /***********************************************************************/
 451 //This Function allows the user to run a batchfile containing several commands on mothur
 452 bool ScriptEngine::getInput(){
 453         try {
 454
 455                 string input = "";
 456                 string commandName = "";
 457                 string options = "";
 458
 459
 460                 //CommandFactory cFactory;
 461                 int quitCommandCalled = 0;
 462
 463                 while(quitCommandCalled != 1){
 464
 465                         #ifdef USE_MPI
 466                                 int pid, processors;
 467                                 MPI_Status status;
 468                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 469                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 470
 471                                 if (pid == 0) {
 472
 473                         #endif
 474
 475                         input = getNextCommand(listOfCommands);
 476
 477                         if (input == "") { input = "quit()"; }
 478
 479                         if (mout->gui) {
 480                                 if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
 481                                 else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {}
 482                                 else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); }
 483                         }else{
 484                                 mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine();
 485                         }
 486
 487                         #ifdef USE_MPI
 488                                 //send commandName
 489                                 for(int i = 1; i < processors; i++) {
 490                                                 int length = input.length();
 491                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 492                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 493
 494                                         }
 495                                 }else {
 496                                         int length;
 497                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 498                                         //recieve container
 499                                         char* tempBuf = new char[length];
 500                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 501
 502                                         input = tempBuf;
 503                                         if (input.length() > length) { input = input.substr(0, length);  }
 504                                         delete tempBuf;
 505                                 }
 506
 507
 508                         #endif
 509
 510
 511                         if (mout->control_pressed) { input = "quit()"; }
 512
 513                         //allow user to omit the () on the quit command
 514                         if (input == "quit") { input = "quit()"; }
 515
 516                         CommandOptionParser parser(input);
 517                         commandName = parser.getCommandString();
 518                         options = parser.getOptionString();
 519
 520                         if (commandName != "") {
 521                                         mout->executing = true;
 522                                         #ifdef USE_MPI
 523                                                 int pid, numProcesses;
 524
 525                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 526                                                 MPI_Comm_size(MPI_COMM_WORLD, &numProcesses);
 527
 528 //cout << pid << " is here " << commandName  << endl;
 529                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 530                                                         //cout << pid << " is in execute" << endl;
 531                                         #endif
 532                                         //executes valid command
 533                                         mout->runParse = true;
 534                                         mout->clearGroups();
 535                                         mout->clearAllGroups();
 536                                         mout->Treenames.clear();
 537                                         mout->names.clear();
 538                                         mout->saveNextLabel = "";
 539                                         mout->printedHeaders = false;
 540                                         mout->currentBinLabels.clear();
 541                                         mout->binLabelsInFile.clear();
 542
 543
 544                                         Command* command = cFactory->getCommand(commandName, options);
 545                                         quitCommandCalled = command->execute();
 546
 547                                         //if we aborted command
 548                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 549
 550                                         mout->control_pressed = 0;
 551                                         mout->executing = false;
 552
 553                                         #ifdef USE_MPI
 554                                         //cout << pid << " is done in execute" << endl;
 555                                                 }
 556                                         #endif
 557                                 }else {
 558                                         mout->mothurOut("Invalid.");
 559                                         mout->mothurOutEndLine();
 560                                 }
 561
 562
 563                 }
 564
 565                 return 1;
 566         }
 567         catch(exception& e) {
 568                 mout->errorOut(e, "ScriptEngine", "getInput");
 569                 exit(1);
 570         }
 571 }
 572 /***********************************************************************/
 573 string ScriptEngine::getNextCommand(string& commandString) {
 574         try {
 575
 576                 string nextcommand = "";
 577                 int count = 0;
 578                 bool ignoreSemiColons = false;
 579
 580                 //go through string until you reach ; or end
 581                 while (count < commandString.length()) {
 582
 583                          //you want to ignore any ; until you reach the next '
 584                         if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  }
 585                         else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  }
 586
 587                         if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
 588                         else {          nextcommand += commandString[count];    }
 589
 590                         count++;
 591                 }
 592
 593                 //if you are not at the end
 594                 if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
 595                 else { commandString = ""; }
 596
 597
 598                 //get rid of spaces in between commands if any
 599                 if (commandString.length() > 0) {
 600                         while (commandString[0] == ' ') {
 601                                 commandString = commandString.substr(1,commandString.length());
 602                                 if (commandString.length() == 0) {  break;  }
 603                         }
 604                 }
 605
 606                 return nextcommand;
 607         }
 608         catch(exception& e) {
 609                 mout->errorOut(e, "ScriptEngine", "getNextCommand");
 610                 exit(1);
 611         }
 612 }
 613 /***********************************************************************/