X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=fbf986dc6965de7d9d269c31f35e99ed85467a9d;hb=11c115c802602be50e106aae56969e15d2c49a62;hp=c6ade387da83e0ebbdcf67addd28f99e7267a500;hpb=a5afca18544555fba2d9c3670ad1f8574916b0a0;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index c6ade38..fbf986d 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -14,23 +14,14 @@
 
 #include "engine.hpp"
 
-/***********************************************************************/
-inline void terminateCommand(int dummy)  {
-	
-		//mothurOut("Stopping command...."); 
-		//CommandFactory* cFactory = CommandFactory::getInstance();
-		//cFactory->getCommand();  //deletes old command and makes new no command.  
-								//this may cause memory leak if old commands execute function allocated memory 
-								//that is freed in the execute function and not the deconstructor 
-		//mothurOut("DONE."); mothurOutEndLine();
-}
 /***********************************************************************/
 Engine::Engine(){
 	try {
 		cFactory = CommandFactory::getInstance();
+		mout = MothurOut::getInstance();
 	}
 	catch(exception& e) {
-		errorOut(e, "Engine", "Engine");
+		mout->errorOut(e, "Engine", "Engine");
 		exit(1);
 	}
 }
@@ -40,6 +31,47 @@ Engine::Engine(){
 InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
+	
+	string temppath = path.substr(0, (path.find_last_of('m')));
+	
+	//this will happen if you set the path variable to contain mothur's exe location
+	if (temppath == "") { 
+	
+		string envPath = getenv("PATH");
+		
+		//delimiting path char
+		char delim;
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			delim = ':';
+		#else
+			delim = ';';
+		#endif
+		
+		//break apart path variable by ':'
+		vector<string> dirs;
+		splitAtChar(envPath, dirs, delim);
+		
+		//get path related to mothur
+		string mothurPath = "";
+		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;  }
+		}
+		
+		//add mothur so it looks like what argv would look like
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+			mothurPath += "/mothur";
+		#else
+			mothurPath += "\\mothur";
+		#endif
+		
+		path = mothurPath;
+	}
+	
 	globaldata->argv = path;
 }
 
@@ -59,64 +91,124 @@ bool InteractEngine::getInput(){
 		
 		while(quitCommandCalled != 1){
 
-			mothurOutEndLine();
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
+			mout->mothurOutEndLine();
 			
-			input = getCommand();			
+			input = getCommand();	
+			mout->mothurOutEndLine();	
+			
+			if (mout->control_pressed) { input = "quit()"; }
 			
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
+
 			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+		
 			CommandOptionParser parser(input);
 			commandName = parser.getCommandString();
 	
 			options = parser.getOptionString();
 			
 			if (commandName != "") {
-			
-				//executes valid command
-				Command* command = cFactory->getCommand(commandName, options);
-				quitCommandCalled = command->execute();
-				
-			}else {
-				mothurOut("Your input contains errors. Please try again."); 
-				mothurOutEndLine();
-			}
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					//cout << pid << " is in execute " << commandName << endl;
+					#endif
+					//executes valid command
+					Command* command = cFactory->getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 		}	
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "InteractEngine", "getInput");
+		mout->errorOut(e, "InteractEngine", "getInput");
 		exit(1);
 	}
 }
 /***********************************************************************/
 string Engine::getCommand()  {
 	try {
+	
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
 				nextCommand = readline("mothur > ");
-				if(nextCommand != NULL) {  add_history(nextCommand);  }		
-				mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
+				if(nextCommand != NULL) {  add_history(nextCommand);  }	
+				else{ //^D causes null string and we want it to quit mothur
+					nextCommand = "quit"; 
+					mout->mothurOut(nextCommand);
+				}	
+				
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 				return nextCommand;
 			#else
 				string nextCommand = "";
-				mothurOut("mothur > ");
+				mout->mothurOut("mothur > ");
 				getline(cin, nextCommand);
+				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+				
 				return nextCommand;
 			#endif
 		#else
-			string nextCommand = "";
-			mothurOut("mothur > ");
-			getline(cin, nextCommand);
-			return nextCommand;
+				string nextCommand = "";
+				
+				mout->mothurOut("mothur > ");
+				getline(cin, nextCommand);
+				mout->mothurOutJustToLog(toString(nextCommand));
+				
+				return nextCommand;
 		#endif
-		
-		mothurOutEndLine();
+	
 						
 	}
 	catch(exception& e) {
-		errorOut(e, "Engine", "getCommand");
+		mout->errorOut(e, "Engine", "getCommand");
 		exit(1);
 	}
 }
@@ -127,11 +219,52 @@ BatchEngine::BatchEngine(string path, string batchFileName){
 		globaldata = GlobalData::getInstance();
 	
 		openedBatch = openInputFile(batchFileName, inputBatchFile);
+		
+		string temppath = path.substr(0, (path.find_last_of('m')));
+	
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { 
+		
+			string envPath = getenv("PATH");
+			
+			//delimiting path char
+			char delim;
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				delim = ':';
+			#else
+				delim = ';';
+			#endif
+			
+			//break apart path variable by ':'
+			vector<string> dirs;
+			splitAtChar(envPath, dirs, delim);
+			
+			//get path related to mothur
+			string mothurPath = "";
+			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;  }
+			}
+			
+			//add mothur so it looks like what argv would look like
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				mothurPath += "/mothur";
+			#else
+				mothurPath += "\\mothur";
+			#endif
+			
+			path = mothurPath;
+		}
+
 		globaldata->argv = path;
 				
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "BatchEngine");
+		mout->errorOut(e, "BatchEngine", "BatchEngine");
 		exit(1);
 	}
 }
@@ -146,8 +279,8 @@ bool BatchEngine::getInput(){
 	try {
 		//check if this is a valid batchfile
 		if (openedBatch == 1) {  
-			mothurOut("unable to open batchfile");  
-			mothurOutEndLine();
+			mout->mothurOut("unable to open batchfile");  
+			mout->mothurOutEndLine();
 			return 1; 
 		}
 	
@@ -157,18 +290,54 @@ bool BatchEngine::getInput(){
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
-	
+	    int count = 0;
 		while(quitCommandCalled == 0){
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
+			input = getNextCommand(inputBatchFile);
+			count++;
+			
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
 	
-			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { input = getline(inputBatchFile); }
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
+
+			
+			#endif
+
+			
 			
 			if (input[0] != '#') {
 				
-				mothurOutEndLine();
-				mothurOut("mothur > " + input);
-				mothurOutEndLine();
-				
+				mout->mothurOutEndLine();
+				mout->mothurOut("mothur > " + input);
+				mout->mothurOutEndLine();
+							
+				if (mout->control_pressed) { input = "quit()"; }
 				
 				//allow user to omit the () on the quit command
 				if (input == "quit") { input = "quit()"; }
@@ -178,13 +347,26 @@ bool BatchEngine::getInput(){
 				options = parser.getOptionString();
 										
 				if (commandName != "") {
-
+					mout->executing = true;
+					#ifdef USE_MPI
+						int pid;
+						MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+						
+//cout << pid << " is here " << commandName << '\t' << count << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+					#endif
 					//executes valid command
 					Command* command = cFactory->getCommand(commandName, options);
 					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+										
+					#ifdef USE_MPI
+						}
+					#endif
 				}else {		
-					mothurOut("Invalid."); 
-					mothurOutEndLine();
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
 				}
 				
 			}
@@ -195,11 +377,26 @@ bool BatchEngine::getInput(){
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "BatchEngine", "getInput");
+		mout->errorOut(e, "BatchEngine", "getInput");
+		exit(1);
+	}
+}
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+	try {
+		
+		string nextcommand = "";
+		
+		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+		else { nextcommand = getline(inputBatchFile); }
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getNextCommand");
 		exit(1);
 	}
 }
-
 
 /***********************************************************************/
 /***********************************************************************/
@@ -210,12 +407,52 @@ ScriptEngine::ScriptEngine(string path, string commandString){
 		
 		//remove quotes
 		listOfCommands = commandString.substr(1, (commandString.length()-1));
+		
+		string temppath = path.substr(0, (path.find_last_of('m')));
+	
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { 
+		
+			string envPath = getenv("PATH");
+			
+			//delimiting path char
+			char delim;
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				delim = ':';
+			#else
+				delim = ';';
+			#endif
+			
+			//break apart path variable by ':'
+			vector<string> dirs;
+			splitAtChar(envPath, dirs, delim);
+			
+			//get path related to mothur
+			string mothurPath = "";
+			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;  }
+			}
+			
+			//add mothur so it looks like what argv would look like
+			#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+				mothurPath += "/mothur";
+			#else
+				mothurPath += "\\mothur";
+			#endif
+			
+			path = mothurPath;
+		}
 
 		globaldata->argv = path;
-		
+				
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "ScriptEngine");
+		mout->errorOut(e, "ScriptEngine", "ScriptEngine");
 		exit(1);
 	}
 }
@@ -238,16 +475,50 @@ bool ScriptEngine::getInput(){
 		int quitCommandCalled = 0;
 	
 		while(quitCommandCalled == 0){
-		
+			
+			#ifdef USE_MPI
+				int pid, processors;
+				MPI_Status status;
+				MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				MPI_Comm_size(MPI_COMM_WORLD, &processors);
+				
+				if (pid == 0) {
+				
+			#endif
+			
 			input = getNextCommand(listOfCommands);	
 			
 			if (input == "") { input = "quit()"; }
 			
+			mout->mothurOutEndLine();
+			mout->mothurOut("mothur > " + input);
+			mout->mothurOutEndLine();
 			
-			mothurOutEndLine();
-			mothurOut("mothur > " + input);
-			mothurOutEndLine();
+			#ifdef USE_MPI
+				//send commandName
+				for(int i = 1; i < processors; i++) { 
+						int length = input.length();
+						MPI_Send(&length, 1, MPI_INT, i, 2001, MPI_COMM_WORLD);
+						MPI_Send(&input[0], length, MPI_CHAR, i, 2001, MPI_COMM_WORLD);
+	
+					}
+				}else {
+					int length;
+					MPI_Recv(&length, 1, MPI_INT, 0, 2001, MPI_COMM_WORLD, &status);
+					//recieve container
+					char* tempBuf = new char[length];
+					MPI_Recv(&tempBuf[0], length, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status);
+					
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
 
+			
+			#endif
+			
+			
+			if (mout->control_pressed) { input = "quit()"; }
 				
 			//allow user to omit the () on the quit command
 			if (input == "quit") { input = "quit()"; }
@@ -257,27 +528,47 @@ bool ScriptEngine::getInput(){
 			options = parser.getOptionString();
 										
 			if (commandName != "") {
+					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); 
+					
+//cout << pid << " is here " << commandName  << endl;
+						if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+							//cout << pid << " is in execute" << endl;	
+					#endif
+					//executes valid command
+					Command* command = cFactory->getCommand(commandName, options);
+					quitCommandCalled = command->execute();
+					mout->control_pressed = 0;
+					mout->executing = false;
+									
+					#ifdef USE_MPI
+					//cout << pid << " is done in execute" << endl;
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 
-				//executes valid command
-				Command* command = cFactory->getCommand(commandName, options);
-				quitCommandCalled = command->execute();
-			}else {		
-				mothurOut("Invalid."); 
-				mothurOutEndLine();
-			}
 			
 		}
 		
 		return 1;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getInput");
+		mout->errorOut(e, "ScriptEngine", "getInput");
 		exit(1);
 	}
 }
 /***********************************************************************/
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
+		
 		string nextcommand = "";
 		int count = 0;
 		
@@ -302,11 +593,11 @@ string ScriptEngine::getNextCommand(string& commandString) {
 				if (commandString.length() == 0) {  break;  }
 			}
 		}
-					
+		
 		return nextcommand;
 	}
 	catch(exception& e) {
-		errorOut(e, "ScriptEngine", "getNextCommand");
+		mout->errorOut(e, "ScriptEngine", "getNextCommand");
 		exit(1);
 	}
 }