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