X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=54524ba9e6a8aa3fe8b678abf060db68529b7177;hb=c6e5f84783b39a558119835963dec3c4facb0154;hp=b68bf61e4703fbd77133f8ba72c8488a78519d29;hpb=813f0516e9c7533859f57ebe6d7b8854896bf009;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index b68bf61..54524ba 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -31,8 +31,48 @@ Engine::Engine(){
 InteractEngine::InteractEngine(string path){
 
 	globaldata = GlobalData::getInstance();
-	globaldata->argv = path;
 	
+	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;
+		mout->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;
 }
 
 /***********************************************************************/
@@ -51,6 +91,16 @@ bool InteractEngine::getInput(){
 		
 		while(quitCommandCalled != 1){
 
+			#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();	
@@ -60,34 +110,58 @@ bool InteractEngine::getInput(){
 			
 			//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 != "") {
-				mout->executing = true;
-				
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					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 {
-				mout->mothurOut("Your input contains errors. Please try again."); 
-				mout->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;
 	}
@@ -99,15 +173,7 @@ bool InteractEngine::getInput(){
 /***********************************************************************/
 string Engine::getCommand()  {
 	try {
-	#ifdef USE_MPI //mpirun doesn't work with readline
-				string nextCommand = "";
-				
-				mout->mothurOut("mothur > ");
-				getline(cin, nextCommand);
-				mout->mothurOutJustToLog(toString(nextCommand));
-				
-				return nextCommand;
-	#else
+	
 		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
@@ -138,7 +204,7 @@ string Engine::getCommand()  {
 				
 				return nextCommand;
 		#endif
-	#endif
+	
 						
 	}
 	catch(exception& e) {
@@ -152,7 +218,48 @@ 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('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;
+			mout->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;
 				
 	}
@@ -183,11 +290,46 @@ 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] != '#') {
 				
@@ -209,7 +351,8 @@ bool BatchEngine::getInput(){
 					#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
@@ -217,7 +360,7 @@ bool BatchEngine::getInput(){
 					quitCommandCalled = command->execute();
 					mout->control_pressed = 0;
 					mout->executing = false;
-				
+										
 					#ifdef USE_MPI
 						}
 					#endif
@@ -227,7 +370,7 @@ bool BatchEngine::getInput(){
 				}
 				
 			}
-			gobble(inputBatchFile);
+			mout->gobble(inputBatchFile);
 		}
 		
 		inputBatchFile.close();
@@ -238,7 +381,22 @@ bool BatchEngine::getInput(){
 		exit(1);
 	}
 }
-
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+	try {
+		
+		string nextcommand = "";
+		
+		if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+		else { nextcommand = mout->getline(inputBatchFile); }
+		
+		return nextcommand;
+	}
+	catch(exception& e) {
+		mout->errorOut(e, "BatchEngine", "getNextCommand");
+		exit(1);
+	}
+}
 
 /***********************************************************************/
 /***********************************************************************/
@@ -249,6 +407,46 @@ 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;
+			mout->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;
 				
@@ -277,7 +475,17 @@ 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()"; }
@@ -286,6 +494,30 @@ bool ScriptEngine::getInput(){
 			mout->mothurOut("mothur > " + input);
 			mout->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
@@ -296,26 +528,33 @@ bool ScriptEngine::getInput(){
 			options = parser.getOptionString();
 										
 			if (commandName != "") {
-				mout->executing = true;
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+					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); 
 					
-					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 {		
-				mout->mothurOut("Invalid."); 
-				mout->mothurOutEndLine();
-			}
+//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();
+				}
+
 			
 		}
 		
@@ -329,6 +568,7 @@ bool ScriptEngine::getInput(){
 /***********************************************************************/
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
+		
 		string nextcommand = "";
 		int count = 0;
 		
@@ -353,7 +593,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
 				if (commandString.length() == 0) {  break;  }
 			}
 		}
-					
+		
 		return nextcommand;
 	}
 	catch(exception& e) {