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         }
  22         catch(exception& e) {
  23                 errorOut(e, "Engine", "Engine");
  24                 exit(1);
  25         }
  26 }
  27
  28 /***********************************************************************/
  29
  30 InteractEngine::InteractEngine(string path){
  31
  32         globaldata = GlobalData::getInstance();
  33         globaldata->argv = path;
  34 }
  35
  36 /***********************************************************************/
  37
  38 InteractEngine::~InteractEngine(){}
  39
  40 /***********************************************************************/
  41 //This function allows the user to input commands one line at a time until they quit.
  42 //If the command is garbage it does nothing.
  43 bool InteractEngine::getInput(){
  44         try {
  45                 string input = "";
  46                 string commandName = "";
  47                 string options = "";
  48                 int quitCommandCalled = 0;
  49
  50                 while(quitCommandCalled != 1){
  51
  52                         mothurOutEndLine();
  53
  54                         input = getCommand();
  55
  56                         //allow user to omit the () on the quit command
  57                         if (input == "quit") { input = "quit()"; }
  58
  59                         CommandOptionParser parser(input);
  60                         commandName = parser.getCommandString();
  61
  62                         options = parser.getOptionString();
  63
  64                         if (commandName != "") {
  65
  66                                 //executes valid command
  67                                 Command* command = cFactory->getCommand(commandName, options);
  68                                 quitCommandCalled = command->execute();
  69
  70                         }else {
  71                                 mothurOut("Your input contains errors. Please try again.");
  72                                 mothurOutEndLine();
  73                         }
  74                 }
  75                 return 1;
  76         }
  77         catch(exception& e) {
  78                 errorOut(e, "InteractEngine", "getInput");
  79                 exit(1);
  80         }
  81 }
  82 /***********************************************************************/
  83 string Engine::getCommand()  {
  84         try {
  85                 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
  86                         #ifdef USE_READLINE
  87                                 char* nextCommand = NULL;
  88                                 nextCommand = readline("mothur > ");
  89                                 if(nextCommand != NULL) {  add_history(nextCommand);  }
  90                                 mothurOutJustToLog("mothur > " + toString(nextCommand));
  91                                 return nextCommand;
  92                         #else
  93                                 string nextCommand = "";
  94                                 mothurOut("mothur > ");
  95                                 getline(cin, nextCommand);
  96                                 return nextCommand;
  97                         #endif
  98                 #else
  99                         string nextCommand = "";
 100                         mothurOut("mothur > ");
 101                         getline(cin, nextCommand);
 102                         return nextCommand;
 103                 #endif
 104
 105                 mothurOutEndLine();
 106
 107         }
 108         catch(exception& e) {
 109                 errorOut(e, "Engine", "getCommand");
 110                 exit(1);
 111         }
 112 }
 113 /***********************************************************************/
 114 //This function opens the batchfile to be used by BatchEngine::getInput.
 115 BatchEngine::BatchEngine(string path, string batchFileName){
 116         try {
 117                 globaldata = GlobalData::getInstance();
 118
 119                 openedBatch = openInputFile(batchFileName, inputBatchFile);
 120                 globaldata->argv = path;
 121
 122         }
 123         catch(exception& e) {
 124                 errorOut(e, "BatchEngine", "BatchEngine");
 125                 exit(1);
 126         }
 127 }
 128
 129 /***********************************************************************/
 130
 131 BatchEngine::~BatchEngine(){    }
 132
 133 /***********************************************************************/
 134 //This Function allows the user to run a batchfile containing several commands on Dotur
 135 bool BatchEngine::getInput(){
 136         try {
 137                 //check if this is a valid batchfile
 138                 if (openedBatch == 1) {
 139                         mothurOut("unable to open batchfile");
 140                         mothurOutEndLine();
 141                         return 1;
 142                 }
 143
 144                 string input = "";
 145                 string commandName = "";
 146                 string options = "";
 147
 148                 //CommandFactory cFactory;
 149                 int quitCommandCalled = 0;
 150
 151                 while(quitCommandCalled == 0){
 152
 153                         if (inputBatchFile.eof()) { input = "quit()"; }
 154                         else { input = getline(inputBatchFile); }
 155
 156                         if (input[0] != '#') {
 157
 158                                 mothurOutEndLine();
 159                                 mothurOut("mothur > " + input);
 160                                 mothurOutEndLine();
 161
 162
 163                                 //allow user to omit the () on the quit command
 164                                 if (input == "quit") { input = "quit()"; }
 165
 166                                 CommandOptionParser parser(input);
 167                                 commandName = parser.getCommandString();
 168                                 options = parser.getOptionString();
 169
 170                                 if (commandName != "") {
 171
 172                                         //executes valid command
 173                                         Command* command = cFactory->getCommand(commandName, options);
 174                                         quitCommandCalled = command->execute();
 175                                 }else {
 176                                         mothurOut("Invalid.");
 177                                         mothurOutEndLine();
 178                                 }
 179
 180                         }
 181                         gobble(inputBatchFile);
 182                 }
 183
 184                 inputBatchFile.close();
 185                 return 1;
 186         }
 187         catch(exception& e) {
 188                 errorOut(e, "BatchEngine", "getInput");
 189                 exit(1);
 190         }
 191 }
 192
 193
 194 /***********************************************************************/
 195 /***********************************************************************/
 196 //This function opens the batchfile to be used by BatchEngine::getInput.
 197 ScriptEngine::ScriptEngine(string path, string commandString){
 198         try {
 199                 globaldata = GlobalData::getInstance();
 200
 201                 //remove quotes
 202                 listOfCommands = commandString.substr(1, (commandString.length()-1));
 203
 204                 globaldata->argv = path;
 205
 206         }
 207         catch(exception& e) {
 208                 errorOut(e, "ScriptEngine", "ScriptEngine");
 209                 exit(1);
 210         }
 211 }
 212
 213 /***********************************************************************/
 214
 215 ScriptEngine::~ScriptEngine(){  }
 216
 217 /***********************************************************************/
 218 //This Function allows the user to run a batchfile containing several commands on mothur
 219 bool ScriptEngine::getInput(){
 220         try {
 221
 222                 string input = "";
 223                 string commandName = "";
 224                 string options = "";
 225
 226
 227                 //CommandFactory cFactory;
 228                 int quitCommandCalled = 0;
 229
 230                 while(quitCommandCalled == 0){
 231
 232                         input = getNextCommand(listOfCommands);
 233
 234                         if (input == "") { input = "quit()"; }
 235
 236
 237                         mothurOutEndLine();
 238                         mothurOut("mothur > " + input);
 239                         mothurOutEndLine();
 240
 241
 242                         //allow user to omit the () on the quit command
 243                         if (input == "quit") { input = "quit()"; }
 244
 245                         CommandOptionParser parser(input);
 246                         commandName = parser.getCommandString();
 247                         options = parser.getOptionString();
 248
 249                         if (commandName != "") {
 250
 251                                 //executes valid command
 252                                 Command* command = cFactory->getCommand(commandName, options);
 253                                 quitCommandCalled = command->execute();
 254                         }else {
 255                                 mothurOut("Invalid.");
 256                                 mothurOutEndLine();
 257                         }
 258
 259                 }
 260
 261                 return 1;
 262         }
 263         catch(exception& e) {
 264                 errorOut(e, "ScriptEngine", "getInput");
 265                 exit(1);
 266         }
 267 }
 268 /***********************************************************************/
 269 string ScriptEngine::getNextCommand(string& commandString) {
 270         try {
 271                 string nextcommand = "";
 272                 int count = 0;
 273
 274                 //go through string until you reach ; or end
 275                 while (count < commandString.length()) {
 276
 277                         if (commandString[count] == ';') {  break;   }
 278                         else {          nextcommand += commandString[count];    }
 279
 280                         count++;
 281                 }
 282
 283                 //if you are not at the end
 284                 if (count != commandString.length())  {   commandString = commandString.substr(count+1, commandString.length());  }
 285                 else { commandString = ""; }
 286
 287
 288                 //get rid of spaces in between commands if any
 289                 if (commandString.length() > 0) {
 290                         while (commandString[0] == ' ') {
 291                                 commandString = commandString.substr(1,commandString.length());
 292                                 if (commandString.length() == 0) {  break;  }
 293                         }
 294                 }
 295
 296                 return nextcommand;
 297         }
 298         catch(exception& e) {
 299                 errorOut(e, "ScriptEngine", "getNextCommand");
 300                 exit(1);
 301         }
 302 }
 303 /***********************************************************************/