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
 134         }
 135         catch(exception& e) {
 136                 mout->errorOut(e, "Engine", "getCommand");
 137                 exit(1);
 138         }
 139 }
 140 /***********************************************************************/
 141 //This function opens the batchfile to be used by BatchEngine::getInput.
 142 BatchEngine::BatchEngine(string path, string batchFileName){
 143         try {
 144                 globaldata = GlobalData::getInstance();
 145
 146                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 147                 globaldata->argv = path;
 148
 149         }
 150         catch(exception& e) {
 151                 mout->errorOut(e, "BatchEngine", "BatchEngine");
 152                 exit(1);
 153         }
 154 }
 155
 156 /***********************************************************************/
 157
 158 BatchEngine::~BatchEngine(){    }
 159
 160 /***********************************************************************/
 161 //This Function allows the user to run a batchfile containing several commands on Dotur
 162 bool BatchEngine::getInput(){
 163         try {
 164                 //check if this is a valid batchfile
 165                 if (openedBatch == 1) {
 166                         mout->mothurOut("unable to open batchfile");
 167                         mout->mothurOutEndLine();
 168                         return 1;
 169                 }
 170
 171                 string input = "";
 172                 string commandName = "";
 173                 string options = "";
 174
 175                 //CommandFactory cFactory;
 176                 int quitCommandCalled = 0;
 177
 178                 while(quitCommandCalled == 0){
 179
 180                         if (inputBatchFile.eof()) { input = "quit()"; }
 181                         else { input = getline(inputBatchFile); }
 182
 183                         if (input[0] != '#') {
 184
 185                                 mout->mothurOutEndLine();
 186                                 mout->mothurOut("mothur > " + input);
 187                                 mout->mothurOutEndLine();
 188
 189                                 if (mout->control_pressed) { input = "quit()"; }
 190
 191                                 //allow user to omit the () on the quit command
 192                                 if (input == "quit") { input = "quit()"; }
 193
 194                                 CommandOptionParser parser(input);
 195                                 commandName = parser.getCommandString();
 196                                 options = parser.getOptionString();
 197
 198                                 if (commandName != "") {
 199                                         mout->executing = true;
 200                                         #ifdef USE_MPI
 201                                                 int pid;
 202                                                 MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 203
 204                                                 if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 205                                         #endif
 206                                         //executes valid command
 207                                         Command* command = cFactory->getCommand(commandName, options);
 208                                         quitCommandCalled = command->execute();
 209                                         mout->control_pressed = 0;
 210                                         mout->executing = false;
 211
 212                                         #ifdef USE_MPI
 213                                                 }
 214                                         #endif
 215                                 }else {
 216                                         mout->mothurOut("Invalid.");
 217                                         mout->mothurOutEndLine();
 218                                 }
 219
 220                         }
 221                         gobble(inputBatchFile);
 222                 }
 223
 224                 inputBatchFile.close();
 225                 return 1;
 226         }
 227         catch(exception& e) {
 228                 mout->errorOut(e, "BatchEngine", "getInput");
 229                 exit(1);
 230         }
 231 }
 232
 233
 234 /***********************************************************************/
 235 /***********************************************************************/
 236 //This function opens the batchfile to be used by BatchEngine::getInput.
 237 ScriptEngine::ScriptEngine(string path, string commandString){
 238         try {
 239                 globaldata = GlobalData::getInstance();
 240
 241                 //remove quotes
 242                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 243
 244                 globaldata->argv = path;
 245
 246         }
 247         catch(exception& e) {
 248                 mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 249                 exit(1);
 250         }
 251 }
 252
 253 /***********************************************************************/
 254
 255 ScriptEngine::~ScriptEngine(){  }
 256
 257 /***********************************************************************/
 258 //This Function allows the user to run a batchfile containing several commands on mothur
 259 bool ScriptEngine::getInput(){
 260         try {
 261
 262                 string input = "";
 263                 string commandName = "";
 264                 string options = "";
 265
 266
 267                 //CommandFactory cFactory;
 268                 int quitCommandCalled = 0;
 269
 270                 while(quitCommandCalled == 0){
 271
 272                         input = getNextCommand(listOfCommands);
 273
 274                         if (input == "") { input = "quit()"; }
 275
 276                         mout->mothurOutEndLine();
 277                         mout->mothurOut("mothur > " + input);
 278                         mout->mothurOutEndLine();
 279
 280                         if (mout->control_pressed) { input = "quit()"; }
 281
 282                         //allow user to omit the () on the quit command
 283                         if (input == "quit") { input = "quit()"; }
 284
 285                         CommandOptionParser parser(input);
 286                         commandName = parser.getCommandString();
 287                         options = parser.getOptionString();
 288
 289                         if (commandName != "") {
 290                                 mout->executing = true;
 291                                 #ifdef USE_MPI
 292                                         int pid;
 293                                         MPI_Comm_rank(MPI_COMM_WORLD, &pid);
 294
 295                                         if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
 296                                 #endif
 297                                 //executes valid command
 298                                 Command* command = cFactory->getCommand(commandName, options);
 299                                 quitCommandCalled = command->execute();
 300                                 mout->control_pressed = 0;
 301                                 mout->executing = false;
 302
 303                                 #ifdef USE_MPI
 304                                         }
 305                                 #endif
 306                         }else {
 307                                 mout->mothurOut("Invalid.");
 308                                 mout->mothurOutEndLine();
 309                         }
 310
 311                 }
 312
 313                 return 1;
 314         }
 315         catch(exception& e) {
 316                 mout->errorOut(e, "ScriptEngine", "getInput");
 317                 exit(1);
 318         }
 319 }
 320 /***********************************************************************/
 321 string ScriptEngine::getNextCommand(string& commandString) {
 322         try {
 323                 string nextcommand = "";
 324                 int count = 0;
 325
 326                 //go through string until you reach ; or end
 327                 while (count < commandString.length()) {
 328
 329                         if (commandString[count] == ';') {  break;   }
 330                         else {          nextcommand += commandString[count];    }
 331
 332                         count++;
 333                 }
 334
 335                 //if you are not at the end
 336                 if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
 337                 else { commandString = ""; }
 338
 339
 340                 //get rid of spaces in between commands if any
 341                 if (commandString.length() > 0) {
 342                         while (commandString[0] == ' ') {
 343                                 commandString = commandString.substr(1,commandString.length());
 344                                 if (commandString.length() == 0) {  break;  }
 345                         }
 346                 }
 347
 348                 return nextcommand;
 349         }
 350         catch(exception& e) {
 351                 mout->errorOut(e, "ScriptEngine", "getNextCommand");
 352                 exit(1);
 353         }
 354 }
 355 /***********************************************************************/