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