#include "engine.hpp"
+/***********************************************************************/
+Engine::Engine(){
+ try {
+ cFactory = CommandFactory::getInstance();
+ mout = MothurOut::getInstance();
+ }
+ catch(exception& e) {
+ mout->errorOut(e, "Engine", "Engine");
+ exit(1);
+ }
+}
+
/***********************************************************************/
InteractEngine::InteractEngine(string path){
globaldata = GlobalData::getInstance();
globaldata->argv = path;
- string logFileName = "mothur.logFile";
- remove(logFileName.c_str());
- system("clear");
}
/***********************************************************************/
-InteractEngine::~InteractEngine(){
- }
+InteractEngine::~InteractEngine(){}
/***********************************************************************/
//This function allows the user to input commands one line at a time until they quit.
string options = "";
int quitCommandCalled = 0;
- mothurOut("mothur v.1.4.1");
- mothurOutEndLine();
- mothurOut("Last updated: 6/23/2009");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("by");
- mothurOutEndLine();
- mothurOut("Patrick D. Schloss");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Department of Microbiology");
- mothurOutEndLine();
- mothurOut("pschloss@micro.umass.edu");
- mothurOutEndLine();
- mothurOut("http://schloss.micro.umass.edu/mothur");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Distributed under the GNU General Public License");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Type 'help()' for information on the commands that are available");
- mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("Type 'quit()' to exit program");
- mothurOutEndLine();
-
while(quitCommandCalled != 1){
+
+ mout->mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("mothur > ");
- getline(cin, input);
- if (cin.eof()) { input = "quit()"; }
+ input = getCommand();
+ mout->mothurOutEndLine();
- mothurOutJustToLog(input);
- mothurOutEndLine();
+ if (mout->control_pressed) { input = "quit()"; }
//allow user to omit the () on the quit command
if (input == "quit") { input = "quit()"; }
CommandOptionParser parser(input);
commandName = parser.getCommandString();
+
options = parser.getOptionString();
if (commandName != "") {
-
- //executes valid command
- CommandFactory cFactory;
- 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 ((pid != 0) && !(cFactory->MPIEnabled(commandName))) {
+cout << pid << " is waiting " << commandName << endl;
+ char buf[4];
+ MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+ }
+
+cout << pid << " is here " << commandName << 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
+ if (!(cFactory->MPIEnabled(commandName))) {
+ char buf[4];
+ strcpy(buf, "done");
+
+ MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+ cout << pid << " is broadcasting " << endl;
+ }
+ }
+ #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); }
+ 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 = "";
+ mout->mothurOut("mothur > ");
+ getline(cin, nextCommand);
+ mout->mothurOutJustToLog("mothur > " + toString(nextCommand));
+
+ return nextCommand;
+ #endif
+ #else
+ string nextCommand = "";
+
+ mout->mothurOut("mothur > ");
+ getline(cin, nextCommand);
+ mout->mothurOutJustToLog(toString(nextCommand));
+
+ return nextCommand;
+ #endif
+
+
+ }
+ catch(exception& e) {
+ mout->errorOut(e, "Engine", "getCommand");
exit(1);
}
}
-
/***********************************************************************/
//This function opens the batchfile to be used by BatchEngine::getInput.
BatchEngine::BatchEngine(string path, string batchFileName){
openedBatch = openInputFile(batchFileName, inputBatchFile);
globaldata->argv = path;
- string logFileName = "mothur.logFile";
- remove(logFileName.c_str());
-
- system("clear");
-
- // char buffer = ' ';
- // ifstream header("introtext.txt");
- // while(!header.eof()){
- // cout << buffer;
- // buffer = header.get();
- // }
+
}
catch(exception& e) {
- errorOut(e, "BatchEngine", "BatchEngine");
+ mout->errorOut(e, "BatchEngine", "BatchEngine");
exit(1);
}
}
/***********************************************************************/
-BatchEngine::~BatchEngine(){
- }
+BatchEngine::~BatchEngine(){ }
/***********************************************************************/
//This Function allows the user to run a batchfile containing several commands on Dotur
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;
}
while(quitCommandCalled == 0){
if (inputBatchFile.eof()) { input = "quit()"; }
- else { getline(inputBatchFile, input); }
-
-
+ else { input = getline(inputBatchFile); }
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()"; }
options = parser.getOptionString();
if (commandName != "") {
-
+ mout->executing = true;
+ #ifdef USE_MPI
+ int pid;
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+
+ if ((pid != 0) && !(cFactory->MPIEnabled(commandName))) {
+cout << pid << " is waiting " << commandName << endl;
+ char buf[4];
+ MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+ }
+
+cout << pid << " is here " << commandName << endl;
+ if ((cFactory->MPIEnabled(commandName)) || (pid == 0)) {
+ #endif
//executes valid command
- CommandFactory cFactory;
- Command* command = cFactory.getCommand(commandName, options);
+ Command* command = cFactory->getCommand(commandName, options);
quitCommandCalled = command->execute();
+ mout->control_pressed = 0;
+ mout->executing = false;
+
+ #ifdef USE_MPI
+ if (!(cFactory->MPIEnabled(commandName))) {
+ char buf[4];
+ strcpy(buf, "done");
+
+ MPI_Bcast(buf, 4, MPI_CHAR, 0, MPI_COMM_WORLD); //make everyone wait - just in case
+ cout << pid << " is broadcasting " << endl;
+ }
+ }
+ #endif
}else {
- mothurOut("Invalid.");
- mothurOutEndLine();
+ mout->mothurOut("Invalid.");
+ mout->mothurOutEndLine();
}
}
return 1;
}
catch(exception& e) {
- errorOut(e, "BatchEngine", "getInput");
+ mout->errorOut(e, "BatchEngine", "getInput");
exit(1);
}
}
listOfCommands = commandString.substr(1, (commandString.length()-1));
globaldata->argv = path;
- string logFileName = "mothur.logFile";
- remove(logFileName.c_str());
-
- system("clear");
-
+
}
catch(exception& e) {
- errorOut(e, "ScriptEngine", "ScriptEngine");
+ mout->errorOut(e, "ScriptEngine", "ScriptEngine");
exit(1);
}
}
/***********************************************************************/
-ScriptEngine::~ScriptEngine(){
- }
+ScriptEngine::~ScriptEngine(){ }
/***********************************************************************/
//This Function allows the user to run a batchfile containing several commands on mothur
if (input == "") { input = "quit()"; }
+ mout->mothurOutEndLine();
+ mout->mothurOut("mothur > " + input);
+ mout->mothurOutEndLine();
- mothurOutEndLine();
- mothurOut("mothur > " + input);
- mothurOutEndLine();
-
+ if (mout->control_pressed) { input = "quit()"; }
//allow user to omit the () on the quit command
if (input == "quit") { input = "quit()"; }
options = parser.getOptionString();
if (commandName != "") {
+ mout->executing = true;
+ #ifdef USE_MPI
+ int pid, numProcesses;
+ MPI_Status status;
+ //MPI_Request request;
+
+ MPI_Comm_rank(MPI_COMM_WORLD, &pid);
+ MPI_Comm_size(MPI_COMM_WORLD, &numProcesses);
+
+ if ((pid != 0) && (!(cFactory->MPIEnabled(commandName)))) {
+cout << pid << " is waiting " << commandName << endl;
+ char buf[12];
+
+ MPI_Recv(buf, 12, MPI_CHAR, 0, 2001, MPI_COMM_WORLD, &status); //make everyone wait - just in case
+ //MPI_Wait(&request, &status);
+ cout << pid << " received " << buf << endl;
+ }
+
+
+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;
+ if ((pid == 0) && (!(cFactory->MPIEnabled(commandName)))) {
+ char buf[12];
+ strcpy(buf, "command done");
+
+ for(int i = 1; i < numProcesses; i++) {
+ MPI_Send(buf, 12, MPI_CHAR, i, 2001, MPI_COMM_WORLD); //make everyone wait - just in case
+ //MPI_Wait(&request, &status);
+ cout << pid << " sent " << buf << endl;
+ }
+ cout << pid << " is sending " << endl;
+ }
+ }
+ #endif
+ }else {
+ mout->mothurOut("Invalid.");
+ mout->mothurOutEndLine();
+ }
- //executes valid command
- CommandFactory cFactory;
- 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 {
+
+ #ifdef USE_MPI
+ int ierr = MPI_Barrier(MPI_COMM_WORLD);
+cout << "barrier = " << ierr << endl;
+ #endif
+
string nextcommand = "";
+ int count = 0;
- nextcommand = commandString.substr(0,commandString.find_first_of(';'));
-
+ //go through string until you reach ; or end
+ while (count < commandString.length()) {
+
+ if (commandString[count] == ';') { break; }
+ else { nextcommand += commandString[count]; }
+
+ count++;
+ }
+
+ //if you are not at the end
+ if (count != commandString.length()) { commandString = commandString.substr(count+1, commandString.length()); }
+ else { commandString = ""; }
- if ((commandString.find_first_of(';')+1) <= commandString.length()) {
- commandString = commandString.substr(commandString.find_first_of(';')+1, commandString.length());
- }else { commandString = ""; } //you have reached the last command.
//get rid of spaces in between commands if any
if (commandString.length() > 0) {
if (commandString.length() == 0) { break; }
}
}
-
+
return nextcommand;
}
catch(exception& e) {
- errorOut(e, "ScriptEngine", "getNextCommand");
+ mout->errorOut(e, "ScriptEngine", "getNextCommand");
exit(1);
}
}
projects / mothur.git / blobdiff