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) || (__linux__) || (__unix__) || (__unix)
  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) || (__linux__) || (__unix__) || (__unix)
  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) || (__linux__) || (__unix__) || (__unix)
  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->saveNextLabel = "";
 187                                         mout->printedHeaders = false;
 188                                         mout->commandInputsConvertError = false;
 189                                         mout->currentBinLabels.clear();
 190                                         mout->binLabelsInFile.clear();
 191
 192                                         Command* command = cFactory->getCommand(commandName, options);
 193                                         if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
 194                                         else { quitCommandCalled = command->execute(); }
 195
 196                                         //if we aborted command
 197                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 198
 199                                         mout->control_pressed = 0;
 200                                         mout->executing = false;
 201
 202                                         #ifdef USE_MPI
 203                                                 }
 204                                         #endif
 205                                 }else {
 206                                         mout->mothurOut("Invalid.");
 207                                         mout->mothurOutEndLine();
 208                                 }
 209                 }
 210                 return 1;
 211         }
 212         catch(exception& e) {
 213                 mout->errorOut(e, "InteractEngine", "getInput");
 214                 exit(1);
 215         }
 216 }
 217 /***********************************************************************/
 218 string Engine::getCommand()  {
 219         try {
 220
 221                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 222                         #ifdef USE_READLINE
 223                                 char* nextCommand = NULL;
 224                                 nextCommand = readline("mothur > ");
 225
 226                                 if(nextCommand != NULL) {  add_history(nextCommand);  }
 227                                 else{ //^D causes null string and we want it to quit mothur
 228                                         nextCommand = strdup("quit");
 229                                         mout->mothurOut(nextCommand);
 230                                 }
 231
 232                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 233                                 return nextCommand;
 234                         #else
 235                                 string nextCommand = "";
 236                                 mout->mothurOut("mothur > ");
 237                                 getline(cin, nextCommand);
 238                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 239
 240                                 return nextCommand;
 241                         #endif
 242                 #else
 243                                 string nextCommand = "";
 244
 245                                 mout->mothurOut("mothur > ");
 246                                 getline(cin, nextCommand);
 247                                 mout->mothurOutJustToLog(toString(nextCommand));
 248
 249                                 return nextCommand;
 250                 #endif
 251
 252
 253         }
 254         catch(exception& e) {
 255                 mout->errorOut(e, "Engine", "getCommand");
 256                 exit(1);
 257         }
 258 }
 259 /***********************************************************************/
 260 //This function opens the batchfile to be used by BatchEngine::getInput.
 261 BatchEngine::BatchEngine(string path, string batchFileName){
 262         try {
 263
 264                 openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
 265
 266                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 267
 268                 //this will happen if you set the path variable to contain mothur's exe location
 269                 if (temppath == "") { path = findMothursPath(); }
 270
 271                 mout->argv = path;
 272
 273         }
 274         catch(exception& e) {
 275                 mout->errorOut(e, "BatchEngine", "BatchEngine");
 276                 exit(1);
 277         }
 278 }
 279
 280 /***********************************************************************/
 281
 282 BatchEngine::~BatchEngine(){    }
 283
 284 /***********************************************************************/
 285 //This Function allows the user to run a batchfile containing several commands on Dotur
 286 bool BatchEngine::getInput(){
 287         try {
 288                 //check if this is a valid batchfile
 289                 if (openedBatch == 1) {
 290                         mout->mothurOut("unable to open batchfile");
 291                         mout->mothurOutEndLine();
 292                         return 1;
 293                 }
 294
 295                 string input = "";
 296                 string commandName = "";
 297                 string options = "";
 298
 299                 //CommandFactory cFactory;
 300                 int quitCommandCalled = 0;
 301             int count = 0;
 302                 while(quitCommandCalled != 1){
 303
 304                         #ifdef USE_MPI
 305                                 int pid, processors;
 306                                 MPI_Status status;
 307                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 308                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 309
 310                                 if (pid == 0) {
 311
 312                         #endif
 313
 314                         input = getNextCommand(inputBatchFile);
 315                         count++;
 316
 317                         #ifdef USE_MPI
 318                                 //send commandName
 319                                 for(int i = 1; i < processors; i++) {
 320                                                 int length = input.length();
 321                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 322                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 323
 324                                         }
 325                                 }else {
 326                                         int length;
 327                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 328                                         //recieve container
 329                                         char* tempBuf = new char[length];
 330                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 331
 332                                         input = tempBuf;
 333                                         if (input.length() > length) { input = input.substr(0, length);  }
 334                                         delete tempBuf;
 335                                 }
 336
 337
 338                         #endif
 339
 340
 341
 342                         if (input[0] != '#') {
 343
 344                                 mout->mothurOutEndLine();
 345                                 mout->mothurOut("mothur > " + input);
 346                                 mout->mothurOutEndLine();
 347
 348                                 if (mout->control_pressed) { input = "quit()"; }
 349
 350                                 //allow user to omit the () on the quit command
 351                                 if (input == "quit") { input = "quit()"; }
 352
 353                                 CommandOptionParser parser(input);
 354                                 commandName = parser.getCommandString();
 355                                 options = parser.getOptionString();
 356
 357                                 if (commandName != "") {
 358                                         mout->executing = true;
 359                                         #ifdef USE_MPI
 360                                                 int pid;
 361                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 362
 363 //cout << pid << " is here " << commandName << '\t' << count << endl;
 364                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 365                                         #endif
 366                                         //executes valid command
 367                                         mout->runParse = true;
 368                                         mout->clearGroups();
 369                                         mout->clearAllGroups();
 370                                         mout->Treenames.clear();
 371                                         mout->saveNextLabel = "";
 372                                         mout->printedHeaders = false;
 373                                         mout->commandInputsConvertError = false;
 374                                         mout->currentBinLabels.clear();
 375                                         mout->binLabelsInFile.clear();
 376
 377
 378                                         Command* command = cFactory->getCommand(commandName, options);
 379                                         if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
 380                                         else { quitCommandCalled = command->execute(); }
 381
 382                                         //if we aborted command
 383                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 384
 385                                         mout->control_pressed = 0;
 386                                         mout->executing = false;
 387
 388                                         #ifdef USE_MPI
 389                                                 }
 390                                         #endif
 391                                 }else {
 392                                         mout->mothurOut("Invalid.");
 393                                         mout->mothurOutEndLine();
 394                                 }
 395
 396                         }
 397                         mout->gobble(inputBatchFile);
 398                 }
 399
 400                 inputBatchFile.close();
 401                 return 1;
 402         }
 403         catch(exception& e) {
 404                 mout->errorOut(e, "BatchEngine", "getInput");
 405                 exit(1);
 406         }
 407 }
 408 /***********************************************************************/
 409 string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
 410         try {
 411
 412                 string nextcommand = "";
 413
 414                 if (inputBatchFile.eof()) { nextcommand = "quit()"; }
 415                 else { nextcommand = mout->getline(inputBatchFile); }
 416
 417                 return nextcommand;
 418         }
 419         catch(exception& e) {
 420                 mout->errorOut(e, "BatchEngine", "getNextCommand");
 421                 exit(1);
 422         }
 423 }
 424
 425 /***********************************************************************/
 426 /***********************************************************************/
 427 //This function opens the batchfile to be used by BatchEngine::getInput.
 428 ScriptEngine::ScriptEngine(string path, string commandString){
 429         try {
 430
 431                 //remove quotes
 432                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 433
 434                 string temppath = path.substr(0, (path.find_last_of("othur")-5));
 435
 436                 //this will happen if you set the path variable to contain mothur's exe location
 437                 if (temppath == "") { path = findMothursPath(); }
 438
 439                 mout->argv = path;
 440
 441         }
 442         catch(exception& e) {
 443                 mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 444                 exit(1);
 445         }
 446 }
 447
 448 /***********************************************************************/
 449
 450 ScriptEngine::~ScriptEngine(){  }
 451
 452 /***********************************************************************/
 453 //This Function allows the user to run a batchfile containing several commands on mothur
 454 bool ScriptEngine::getInput(){
 455         try {
 456
 457                 string input = "";
 458                 string commandName = "";
 459                 string options = "";
 460
 461
 462                 //CommandFactory cFactory;
 463                 int quitCommandCalled = 0;
 464
 465                 while(quitCommandCalled != 1){
 466
 467                         #ifdef USE_MPI
 468                                 int pid, processors;
 469                                 MPI_Status status;
 470                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 471                                 MPI_Comm_size(MPI_COMM_WORLD, &processors);
 472
 473                                 if (pid == 0) {
 474
 475                         #endif
 476
 477                         input = getNextCommand(listOfCommands);
 478
 479                         if (input == "") { input = "quit()"; }
 480
 481                         if (mout->gui) {
 482                                 if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
 483                                 else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {}
 484                                 else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); }
 485                         }else{
 486                                 mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine();
 487                         }
 488
 489                         #ifdef USE_MPI
 490                                 //send commandName
 491                                 for(int i = 1; i < processors; i++) {
 492                                                 int length = input.length();
 493                                                 MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
 494                                                 MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 495
 496                                         }
 497                                 }else {
 498                                         int length;
 499                                         MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
 500                                         //recieve container
 501                                         char* tempBuf = new char[length];
 502                                         MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
 503
 504                                         input = tempBuf;
 505                                         if (input.length() > length) { input = input.substr(0, length);  }
 506                                         delete tempBuf;
 507                                 }
 508
 509
 510                         #endif
 511
 512
 513                         if (mout->control_pressed) { input = "quit()"; }
 514
 515                         //allow user to omit the () on the quit command
 516                         if (input == "quit") { input = "quit()"; }
 517
 518                         CommandOptionParser parser(input);
 519                         commandName = parser.getCommandString();
 520                         options = parser.getOptionString();
 521
 522                         if (commandName != "") {
 523                                         mout->executing = true;
 524                                         #ifdef USE_MPI
 525                                                 int pid, numProcesses;
 526
 527                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 528                                                 MPI_Comm_size(MPI_COMM_WORLD, &numProcesses);
 529
 530 //cout << pid << " is here " << commandName  << endl;
 531                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 532                                                         //cout << pid << " is in execute" << endl;
 533                                         #endif
 534                                         //executes valid command
 535                                         mout->runParse = true;
 536                                         mout->clearGroups();
 537                                         mout->clearAllGroups();
 538                                         mout->Treenames.clear();
 539                                         mout->saveNextLabel = "";
 540                                         mout->printedHeaders = false;
 541                                         mout->commandInputsConvertError = false;
 542                                         mout->currentBinLabels.clear();
 543                                         mout->binLabelsInFile.clear();
 544
 545                                         Command* command = cFactory->getCommand(commandName, options);
 546                                         if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
 547                                         else { quitCommandCalled = command->execute(); }
 548
 549                                         //if we aborted command
 550                                         if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
 551
 552                                         mout->control_pressed = 0;
 553                                         mout->executing = false;
 554
 555                                         #ifdef USE_MPI
 556                                         //cout << pid << " is done in execute" << endl;
 557                                                 }
 558                                         #endif
 559                                 }else {
 560                                         mout->mothurOut("Invalid.");
 561                                         mout->mothurOutEndLine();
 562                                 }
 563
 564
 565                 }
 566
 567                 return 1;
 568         }
 569         catch(exception& e) {
 570                 mout->errorOut(e, "ScriptEngine", "getInput");
 571                 exit(1);
 572         }
 573 }
 574 /***********************************************************************/
 575 string ScriptEngine::getNextCommand(string& commandString) {
 576         try {
 577
 578                 string nextcommand = "";
 579                 int count = 0;
 580                 bool ignoreSemiColons = false;
 581
 582                 //go through string until you reach ; or end
 583                 while (count < commandString.length()) {
 584
 585                          //you want to ignore any ; until you reach the next '
 586                         if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  }
 587                         else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  }
 588
 589                         if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
 590                         else {          nextcommand += commandString[count];    }
 591
 592                         count++;
 593                 }
 594
 595                 //if you are not at the end
 596                 if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
 597                 else { commandString = ""; }
 598
 599
 600                 //get rid of spaces in between commands if any
 601                 if (commandString.length() > 0) {
 602                         while (commandString[0] == ' ') {
 603                                 commandString = commandString.substr(1,commandString.length());
 604                                 if (commandString.length() == 0) {  break;  }
 605                         }
 606                 }
 607
 608                 return nextcommand;
 609         }
 610         catch(exception& e) {
 611                 mout->errorOut(e, "ScriptEngine", "getNextCommand");
 612                 exit(1);
 613         }
 614 }
 615 /***********************************************************************/