fixed catchall PATH variable bug added trimera to chimera.slayer

[mothur.git] / engine.cpp

diff --git a/engine.cpp b/engine.cpp
index 7bacec5c0e757c7b77d3c8801970c17bd3cc5a4a..54197174e1fa3da14861614734b1dc58314a466a 100644 (file)
--- a/engine.cpp
+++ b/engine.cpp
@@ -25,14 +25,84 @@ Engine::Engine(){
                exit(1);
        }
 }
-
+/***********************************************************************/
+string Engine::findMothursPath(){
+       try { 
+               
+               string envPath = getenv("PATH");
+               string mothurPath = "";
+               
+               //delimiting path char
+               char delim;
+               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                       delim = ':';
+               #else
+                       delim = ';';
+               #endif
+               
+               //break apart path variable by ':'
+               vector<string> dirs;
+               mout->splitAtChar(envPath, dirs, delim);
+               
+               //get path related to mothur
+               for (int i = 0; i < dirs.size(); i++) {
+                       //to lower so we can find it
+                       string tempLower = "";
+                       for (int j = 0; j < dirs[i].length(); j++) {  tempLower += tolower(dirs[i][j]);  }
+                       
+                       //is this mothurs path?
+                       if (tempLower.find("mothur") != -1) {  mothurPath = dirs[i]; break;  }
+               }
+               
+               if (mothurPath != "") {
+                       //add mothur so it looks like what argv would look like
+                       #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                               mothurPath += "/mothur";
+                       #else
+                               mothurPath += "\\mothur";
+                       #endif
+               }else {
+                       //okay mothur is not in the path, so the folder mothur is in must be in the path
+                       //lets find out which one
+                       
+                       //get path related to mothur
+                       for (int i = 0; i < dirs.size(); i++) {
+                                                               
+                               //is this mothurs path?
+                               ifstream in;
+                               string tempIn = dirs[i];
+                               #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+                                       tempIn += "/mothur";
+                               #else
+                                       tempIn += "\\mothur";
+                               #endif
+                               mout->openInputFile(tempIn, in, "");
+                               
+                               //if this file exists
+                               if (in) { in.close(); mothurPath = tempIn;  break;  }
+                       }
+               }
+               
+               return mothurPath;
+               
+       }
+       catch(exception& e) {
+               mout->errorOut(e, "Engine", "findMothursPath");
+               exit(1);
+       }
+}
 /***********************************************************************/
 
 InteractEngine::InteractEngine(string path){
 
        globaldata = GlobalData::getInstance();
-       globaldata->argv = path;
        
+       string temppath = path.substr(0, (path.find_last_of("othur")-5));
+       
+       //this will happen if you set the path variable to contain mothur's exe location
+       if (temppath == "") { path = findMothursPath(); }
+       
+       globaldata->argv = path;
 }
 
 /***********************************************************************/
@@ -112,6 +182,10 @@ bool InteractEngine::getInput(){
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
+                                                       
+                                       //if we aborted command
+                                       if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                                
@@ -141,7 +215,7 @@ string Engine::getCommand()  {
                                
                                if(nextCommand != NULL) {  add_history(nextCommand);  } 
                                else{ //^D causes null string and we want it to quit mothur
-                                       nextCommand = "quit"; 
+                                       strcpy(nextCommand, "quit"); 
                                        mout->mothurOut(nextCommand);
                                }       
                                
@@ -178,7 +252,13 @@ BatchEngine::BatchEngine(string path, string batchFileName){
        try {
                globaldata = GlobalData::getInstance();
        
-               openedBatch = openInputFile(batchFileName, inputBatchFile);
+               openedBatch = mout->openInputFile(batchFileName, inputBatchFile);
+               
+               string temppath = path.substr(0, (path.find_last_of("othur")-5));
+       
+               //this will happen if you set the path variable to contain mothur's exe location
+               if (temppath == "") { path = findMothursPath(); }
+               
                globaldata->argv = path;
                                
        }
@@ -210,7 +290,7 @@ bool BatchEngine::getInput(){
                //CommandFactory cFactory;
                int quitCommandCalled = 0;
            int count = 0;
-               while(quitCommandCalled == 0){
+               while(quitCommandCalled != 1){
                        
                        #ifdef USE_MPI
                                int pid, processors;
@@ -277,6 +357,10 @@ bool BatchEngine::getInput(){
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
+                                                       
+                                       //if we aborted command
+                                       if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                                
@@ -289,7 +373,7 @@ bool BatchEngine::getInput(){
                                }
                                
                        }
-                       gobble(inputBatchFile);
+                       mout->gobble(inputBatchFile);
                }
                
                inputBatchFile.close();
@@ -307,7 +391,7 @@ string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
                string nextcommand = "";
                
                if (inputBatchFile.eof()) { nextcommand = "quit()"; }
-               else { nextcommand = getline(inputBatchFile); }
+               else { nextcommand = mout->getline(inputBatchFile); }
                
                return nextcommand;
        }
@@ -326,7 +410,12 @@ ScriptEngine::ScriptEngine(string path, string commandString){
                
                //remove quotes
                listOfCommands = commandString.substr(1, (commandString.length()-1));
+               
+               string temppath = path.substr(0, (path.find_last_of("othur")-5));
 
+               //this will happen if you set the path variable to contain mothur's exe location
+               if (temppath == "") { path = findMothursPath(); }
+               
                globaldata->argv = path;
                                
        }
@@ -353,7 +442,7 @@ bool ScriptEngine::getInput(){
                //CommandFactory cFactory;
                int quitCommandCalled = 0;
        
-               while(quitCommandCalled == 0){
+               while(quitCommandCalled != 1){
                        
                        #ifdef USE_MPI
                                int pid, processors;
@@ -410,7 +499,6 @@ bool ScriptEngine::getInput(){
                                        mout->executing = true;
                                        #ifdef USE_MPI
                                                int pid, numProcesses;
-                                               MPI_Status status; 
                                                
                                                MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
                                                MPI_Comm_size(MPI_COMM_WORLD, &numProcesses); 
@@ -422,6 +510,10 @@ bool ScriptEngine::getInput(){
                                        //executes valid command
                                        Command* command = cFactory->getCommand(commandName, options);
                                        quitCommandCalled = command->execute();
+                                       
+                                       //if we aborted command
+                                       if (quitCommandCalled == 2) {  mout->mothurOut("[ERROR]: did not complete " + commandName + "."); mout->mothurOutEndLine(); }
+                                                       
                                        mout->control_pressed = 0;
                                        mout->executing = false;
                                                                        
@@ -450,11 +542,16 @@ string ScriptEngine::getNextCommand(string& commandString) {
                
                string nextcommand = "";
                int count = 0;
+               bool ignoreSemiColons = false;
                
                //go through string until you reach ; or end
                while (count < commandString.length()) { 
                        
-                       if (commandString[count] == ';') {  break;   }
+                        //you want to ignore any ; until you reach the next '
+                       if ((commandString[count] == '\'') && (!ignoreSemiColons)) {  ignoreSemiColons = true;  } 
+                       else if ((commandString[count] == '\'') && (ignoreSemiColons)) {  ignoreSemiColons = false;  } 
+                               
+                       if ((commandString[count] == ';') && (!ignoreSemiColons)) {  break;   }
                        else {          nextcommand += commandString[count];    }
                        
                        count++;