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 InteractEngine::InteractEngine(string path){
  32
  33         globaldata = GlobalData::getInstance();
  34         globaldata->argv = path;
  35
  36 }
  37
  38 /***********************************************************************/
  39
  40 InteractEngine::~InteractEngine(){}
  41
  42 /***********************************************************************/
  43 //This function allows the user to input commands one line at a time until they quit.
  44 //If the command is garbage it does nothing.
  45 bool InteractEngine::getInput(){
  46         try {
  47                 string input = "";
  48                 string commandName = "";
  49                 string options = "";
  50                 int quitCommandCalled = 0;
  51
  52                 while(quitCommandCalled != 1){
  53
  54                         mout->mothurOutEndLine();
  55
  56                         input = getCommand();
  57                         mout->mothurOutEndLine();
  58
  59                         if (mout->control_pressed) { input = "quit()"; }
  60
  61                         //allow user to omit the () on the quit command
  62                         if (input == "quit") { input = "quit()"; }
  63
  64                         CommandOptionParser parser(input);
  65                         commandName = parser.getCommandString();
  66
  67                         options = parser.getOptionString();
  68
  69                         if (commandName != "") {
  70                                 mout->executing = true;
  71
  72                                 #ifdef USE_MPI
  73                                         int pid;
  74                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
  75
  76                                         if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
  77                                 #endif
  78                                 //executes valid command
  79                                 Command* command = cFactory->getCommand(commandName, options);
  80                                 quitCommandCalled = command->execute();
  81                                 mout->control_pressed = 0;
  82                                 mout->executing = false;
  83
  84                                 #ifdef USE_MPI
  85                                         }
  86                                 #endif
  87                         }else {
  88                                 mout->mothurOut("Your input contains errors. Please try again.");
  89                                 mout->mothurOutEndLine();
  90                         }
  91                 }
  92                 return 1;
  93         }
  94         catch(exception& e) {
  95                 mout->errorOut(e, "InteractEngine", "getInput");
  96                 exit(1);
  97         }
  98 }
  99 /***********************************************************************/
 100 string Engine::getCommand()  {
 101         try {
 102                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 103                         #ifdef USE_READLINE
 104                                 char* nextCommand = NULL;
 105                                 nextCommand = readline("mothur > ");
 106
 107                                 if(nextCommand != NULL) {  add_history(nextCommand);  }
 108                                 else{ //^D causes null string and we want it to quit mothur
 109                                         nextCommand = "quit";
 110                                         mout->mothurOut(nextCommand);
 111                                 }
 112
 113                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 114                                 return nextCommand;
 115                         #else
 116                                 string nextCommand = "";
 117                                 mout->mothurOut("mothur > ");
 118                                 getline(cin, nextCommand);
 119                                 mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 120
 121                                 return nextCommand;
 122                         #endif
 123                 #else
 124                                 string nextCommand = "";
 125
 126                                 mout->mothurOut("mothur > ");
 127                                 getline(cin, nextCommand);
 128                                 mout->mothurOutJustToLog(toString(nextCommand));
 129
 130                                 return nextCommand;
 131                 #endif
 132
 133                 mout->mothurOutEndLine();
 134
 135         }
 136         catch(exception& e) {
 137                 mout->errorOut(e, "Engine", "getCommand");
 138                 exit(1);
 139         }
 140 }
 141 /***********************************************************************/
 142 //This function opens the batchfile to be used by BatchEngine::getInput.
 143 BatchEngine::BatchEngine(string path, string batchFileName){
 144         try {
 145                 globaldata = GlobalData::getInstance();
 146
 147                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 148                 globaldata->argv = path;
 149
 150         }
 151         catch(exception& e) {
 152                 mout->errorOut(e, "BatchEngine", "BatchEngine");
 153                 exit(1);
 154         }
 155 }
 156
 157 /***********************************************************************/
 158
 159 BatchEngine::~BatchEngine(){    }
 160
 161 /***********************************************************************/
 162 //This Function allows the user to run a batchfile containing several commands on Dotur
 163 bool BatchEngine::getInput(){
 164         try {
 165                 //check if this is a valid batchfile
 166                 if (openedBatch == 1) {
 167                         mout->mothurOut("unable to open batchfile");
 168                         mout->mothurOutEndLine();
 169                         return 1;
 170                 }
 171
 172                 string input = "";
 173                 string commandName = "";
 174                 string options = "";
 175
 176                 //CommandFactory cFactory;
 177                 int quitCommandCalled = 0;
 178
 179                 while(quitCommandCalled == 0){
 180
 181                         if (inputBatchFile.eof()) { input = "quit()"; }
 182                         else { input = getline(inputBatchFile); }
 183
 184                         if (input[0] != '#') {
 185
 186                                 mout->mothurOutEndLine();
 187                                 mout->mothurOut("mothur > " + input);
 188                                 mout->mothurOutEndLine();
 189
 190                                 if (mout->control_pressed) { input = "quit()"; }
 191
 192                                 //allow user to omit the () on the quit command
 193                                 if (input == "quit") { input = "quit()"; }
 194
 195                                 CommandOptionParser parser(input);
 196                                 commandName = parser.getCommandString();
 197                                 options = parser.getOptionString();
 198
 199                                 if (commandName != "") {
 200                                         mout->executing = true;
 201                                         #ifdef USE_MPI
 202                                                 int pid;
 203                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 204
 205                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 206                                         #endif
 207                                         //executes valid command
 208                                         Command* command = cFactory->getCommand(commandName, options);
 209                                         quitCommandCalled = command->execute();
 210                                         mout->control_pressed = 0;
 211                                         mout->executing = false;
 212
 213                                         #ifdef USE_MPI
 214                                                 }
 215                                         #endif
 216                                 }else {
 217                                         mout->mothurOut("Invalid.");
 218                                         mout->mothurOutEndLine();
 219                                 }
 220
 221                         }
 222                         gobble(inputBatchFile);
 223                 }
 224
 225                 inputBatchFile.close();
 226                 return 1;
 227         }
 228         catch(exception& e) {
 229                 mout->errorOut(e, "BatchEngine", "getInput");
 230                 exit(1);
 231         }
 232 }
 233
 234
 235 /***********************************************************************/
 236 /***********************************************************************/
 237 //This function opens the batchfile to be used by BatchEngine::getInput.
 238 ScriptEngine::ScriptEngine(string path, string commandString){
 239         try {
 240                 globaldata = GlobalData::getInstance();
 241
 242                 //remove quotes
 243                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 244
 245                 globaldata->argv = path;
 246
 247         }
 248         catch(exception& e) {
 249                 mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 250                 exit(1);
 251         }
 252 }
 253
 254 /***********************************************************************/
 255
 256 ScriptEngine::~ScriptEngine(){  }
 257
 258 /***********************************************************************/
 259 //This Function allows the user to run a batchfile containing several commands on mothur
 260 bool ScriptEngine::getInput(){
 261         try {
 262
 263                 string input = "";
 264                 string commandName = "";
 265                 string options = "";
 266
 267
 268                 //CommandFactory cFactory;
 269                 int quitCommandCalled = 0;
 270
 271                 while(quitCommandCalled == 0){
 272
 273                         input = getNextCommand(listOfCommands);
 274
 275                         if (input == "") { input = "quit()"; }
 276
 277                         mout->mothurOutEndLine();
 278                         mout->mothurOut("mothur > " + input);
 279                         mout->mothurOutEndLine();
 280
 281                         if (mout->control_pressed) { input = "quit()"; }
 282
 283                         //allow user to omit the () on the quit command
 284                         if (input == "quit") { input = "quit()"; }
 285
 286                         CommandOptionParser parser(input);
 287                         commandName = parser.getCommandString();
 288                         options = parser.getOptionString();
 289
 290                         if (commandName != "") {
 291                                 mout->executing = true;
 292                                 #ifdef USE_MPI
 293                                         int pid;
 294                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 295
 296                                         if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 297                                 #endif
 298                                 //executes valid command
 299                                 Command* command = cFactory->getCommand(commandName, options);
 300                                 quitCommandCalled = command->execute();
 301                                 mout->control_pressed = 0;
 302                                 mout->executing = false;
 303
 304                                 #ifdef USE_MPI
 305                                         }
 306                                 #endif
 307                         }else {
 308                                 mout->mothurOut("Invalid.");
 309                                 mout->mothurOutEndLine();
 310                         }
 311
 312                 }
 313
 314                 return 1;
 315         }
 316         catch(exception& e) {
 317                 mout->errorOut(e, "ScriptEngine", "getInput");
 318                 exit(1);
 319         }
 320 }
 321 /***********************************************************************/
 322 string ScriptEngine::getNextCommand(string& commandString) {
 323         try {
 324                 string nextcommand = "";
 325                 int count = 0;
 326
 327                 //go through string until you reach ; or end
 328                 while (count < commandString.length()) {
 329
 330                         if (commandString[count] == ';') {  break;   }
 331                         else {          nextcommand += commandString[count];    }
 332
 333                         count++;
 334                 }
 335
 336                 //if you are not at the end
 337                 if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
 338                 else { commandString = ""; }
 339
 340
 341                 //get rid of spaces in between commands if any
 342                 if (commandString.length() > 0) {
 343                         while (commandString[0] == ' ') {
 344                                 commandString = commandString.substr(1,commandString.length());
 345                                 if (commandString.length() == 0) {  break;  }
 346                         }
 347                 }
 348
 349                 return nextcommand;
 350         }
 351         catch(exception& e) {
 352                 mout->errorOut(e, "ScriptEngine", "getNextCommand");
 353                 exit(1);
 354         }
 355 }
 356 /***********************************************************************/