X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=engine.cpp;h=24adcb53b59f39f049269d74b4da953a5f387262;hb=a6cf29fa4dac0909c7582cb1094151d34093ee76;hp=2d5fd75959d479826f5239b364879ff316f4eaca;hpb=17a6a53298a907c005fa93fb82af9e533adcda09;p=mothur.git

diff --git a/engine.cpp b/engine.cpp
index 2d5fd75..24adcb5 100644
--- a/engine.cpp
+++ b/engine.cpp
@@ -25,14 +25,83 @@ 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) || (__linux__) || (__unix__) || (__unix)
+			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) || (__linux__) || (__unix__) || (__unix)
+				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) || (__linux__) || (__unix__) || (__unix)
+					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(); }
+	
+	mout->argv = path;
 }
 
 /***********************************************************************/
@@ -51,53 +120,92 @@ 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();	
-			#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					if (pid == 0) {
-			#endif
 			mout->mothurOutEndLine();	
 			
-			#ifdef USE_MPI
-				}
-			#endif
-			
 			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 != "") {
-				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
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+							
+					Command* command = cFactory->getCommand(commandName, options);
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { 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;
+										
+					#ifdef USE_MPI
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
 		}	
 		return 1;
 	}
@@ -109,97 +217,38 @@ bool InteractEngine::getInput(){
 /***********************************************************************/
 string Engine::getCommand()  {
 	try {
-		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+	
+		#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 			#ifdef USE_READLINE
 				char* nextCommand = NULL;
 				nextCommand = readline("mothur > ");
 				
 				if(nextCommand != NULL) {  add_history(nextCommand);  }	
 				else{ //^D causes null string and we want it to quit mothur
-					nextCommand = "quit"; 
-					cout << nextCommand << endl;
+					nextCommand = strdup("quit");
+					mout->mothurOut(nextCommand);
 				}	
 				
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					if (pid == 0) { //only one process should output to screen
-				#endif
-
 				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
-				
-				#ifdef USE_MPI
-					}
-				#endif
-				
 				return nextCommand;
 			#else
 				string nextCommand = "";
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					if (pid == 0) { //only one process should output to screen
-				#endif
-
 				mout->mothurOut("mothur > ");
-				
-				#ifdef USE_MPI
-					}
-				#endif
-				
 				getline(cin, nextCommand);
-				
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					if (pid == 0) { //only one process should output to screen
-				#endif
-				
 				mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
 				
-				#ifdef USE_MPI
-					}
-				#endif
-
 				return nextCommand;
 			#endif
 		#else
-			string nextCommand = "";
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					if (pid == 0) { //only one process should output to screen
-				#endif
-
-				mout->mothurOut("mothur > ");
-				
-				#ifdef USE_MPI
-					}
-				#endif
+				string nextCommand = "";
 				
+				mout->mothurOut("mothur > ");
 				getline(cin, nextCommand);
-				
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
-					
-					if (pid == 0) { //only one process should output to screen
-				#endif
-				
 				mout->mothurOutJustToLog(toString(nextCommand));
 				
-				#ifdef USE_MPI
-					}
-				#endif
-
 				return nextCommand;
 		#endif
-		
-		mout->mothurOutEndLine();
+	
 						
 	}
 	catch(exception& e) {
@@ -211,10 +260,15 @@ string Engine::getCommand()  {
 //This function opens the batchfile to be used by BatchEngine::getInput.
 BatchEngine::BatchEngine(string path, string batchFileName){
 	try {
-		globaldata = GlobalData::getInstance();
 	
-		openedBatch = openInputFile(batchFileName, inputBatchFile);
-		globaldata->argv = path;
+		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(); }
+		
+		mout->argv = path;
 				
 	}
 	catch(exception& e) {
@@ -244,29 +298,53 @@ bool BatchEngine::getInput(){
 		
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
-	
-		while(quitCommandCalled == 0){
-	
-			if (inputBatchFile.eof()) { input = "quit()"; }
-			else { input = getline(inputBatchFile); }
+	    int count = 0;
+		while(quitCommandCalled != 1){
 			
-			if (input[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) {
 				
-				#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+			#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);
+	
+					}
+				}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);
 					
-					if (pid == 0) { //only one process should output to screen
-				#endif
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
 
+			
+			#endif
+
+			
+			
+			if (input[0] != '#') {
+				
 				mout->mothurOutEndLine();
 				mout->mothurOut("mothur > " + input);
 				mout->mothurOutEndLine();
-				
-				#ifdef USE_MPI
-					}
-				#endif
-				
+							
 				if (mout->control_pressed) { input = "quit()"; }
 				
 				//allow user to omit the () on the quit command
@@ -281,15 +359,32 @@ 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
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
+							
 					Command* command = cFactory->getCommand(commandName, options);
-					quitCommandCalled = command->execute();
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { 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;
-				
+										
 					#ifdef USE_MPI
 						}
 					#endif
@@ -299,7 +394,7 @@ bool BatchEngine::getInput(){
 				}
 				
 			}
-			gobble(inputBatchFile);
+			mout->gobble(inputBatchFile);
 		}
 		
 		inputBatchFile.close();
@@ -310,19 +405,38 @@ 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);
+	}
+}
 
 /***********************************************************************/
 /***********************************************************************/
 //This function opens the batchfile to be used by BatchEngine::getInput.
 ScriptEngine::ScriptEngine(string path, string commandString){
 	try {
-		globaldata = GlobalData::getInstance();
 		
 		//remove quotes
 		listOfCommands = commandString.substr(1, (commandString.length()-1));
+		
+		string temppath = path.substr(0, (path.find_last_of("othur")-5));
 
-		globaldata->argv = path;
+		//this will happen if you set the path variable to contain mothur's exe location
+		if (temppath == "") { path = findMothursPath(); }
+		
+		mout->argv = path;
 				
 	}
 	catch(exception& e) {
@@ -348,27 +462,54 @@ bool ScriptEngine::getInput(){
 		//CommandFactory cFactory;
 		int quitCommandCalled = 0;
 	
-		while(quitCommandCalled == 0){
-		
+		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
+			
 			input = getNextCommand(listOfCommands);	
 			
 			if (input == "") { input = "quit()"; }
 			
+			if (mout->gui) {
+				if ((input.find("quit") != string::npos) || (input.find("set.logfile") != string::npos)) {}
+				else if ((input.find("get.current") != string::npos) && (!mout->hasCurrentFiles())) {}
+				else { mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine(); }
+			}else{
+				mout->mothurOutEndLine(); mout->mothurOut("mothur > " + input); mout->mothurOutEndLine();
+			}
+			
 			#ifdef USE_MPI
-					int pid;
-					MPI_Comm_rank(MPI_COMM_WORLD, &pid); 
+				//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);
 					
-					if (pid == 0) {
-			#endif
+					input = tempBuf;
+					if (input.length() > length) { input = input.substr(0, length);  }
+					delete tempBuf;	
+				}
 
-			mout->mothurOutEndLine();
-			mout->mothurOut("mothur > " + input);
-			mout->mothurOutEndLine();
 			
-			#ifdef USE_MPI
-					}
 			#endif
 			
+			
 			if (mout->control_pressed) { input = "quit()"; }
 				
 			//allow user to omit the () on the quit command
@@ -379,26 +520,47 @@ 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_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
+					mout->runParse = true;
+					mout->clearGroups();
+					mout->clearAllGroups();
+					mout->Treenames.clear();
+					mout->saveNextLabel = "";
+					mout->printedHeaders = false;
+					mout->commandInputsConvertError = false;
+					mout->currentBinLabels.clear();
+					mout->binLabelsInFile.clear();
+
+					Command* command = cFactory->getCommand(commandName, options);
+					if (mout->commandInputsConvertError) { quitCommandCalled = 2; }
+					else { 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;
+									
+					#ifdef USE_MPI
+					//cout << pid << " is done in execute" << endl;
+						}
+					#endif
+				}else {		
+					mout->mothurOut("Invalid."); 
+					mout->mothurOutEndLine();
+				}
+
 			
 		}
 		
@@ -412,13 +574,19 @@ bool ScriptEngine::getInput(){
 /***********************************************************************/
 string ScriptEngine::getNextCommand(string& commandString) {
 	try {
+		
 		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++;
@@ -436,7 +604,7 @@ string ScriptEngine::getNextCommand(string& commandString) {
 				if (commandString.length() == 0) {  break;  }
 			}
 		}
-					
+		
 		return nextcommand;
 	}
 	catch(exception& e) {