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