#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);
}
}
globaldata = GlobalData::getInstance();
globaldata->argv = path;
+
}
/***********************************************************************/
while(quitCommandCalled != 1){
- mothurOutEndLine();
+
+ 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()"; }
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);
+
+//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
+ }
+ #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 {
+ #ifdef USE_MPI
+ MPI_Barrier(MPI_COMM_WORLD);
+ #endif
+
#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);
}
}
}
catch(exception& e) {
- errorOut(e, "BatchEngine", "BatchEngine");
+ mout->errorOut(e, "BatchEngine", "BatchEngine");
exit(1);
}
}
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;
}
//CommandFactory cFactory;
int quitCommandCalled = 0;
-
+ int count = 0;
while(quitCommandCalled == 0){
- if (inputBatchFile.eof()) { input = "quit()"; }
- else { input = getline(inputBatchFile); }
+ input = getNextCommand(inputBatchFile);
+ count++;
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);
+
+//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();
}
}
return 1;
}
catch(exception& e) {
- errorOut(e, "BatchEngine", "getInput");
+ mout->errorOut(e, "BatchEngine", "getInput");
+ exit(1);
+ }
+}
+/***********************************************************************/
+string BatchEngine::getNextCommand(ifstream& inputBatchFile) {
+ try {
+
+ #ifdef USE_MPI
+ int err = MPI_Barrier(MPI_COMM_WORLD);
+//cout << "barrier = " << err << '\t' << MPI_SUCCESS << endl;
+ #endif
+
+ string nextcommand = "";
+
+ if (inputBatchFile.eof()) { nextcommand = "quit()"; }
+ else { nextcommand = getline(inputBatchFile); }
+
+ return nextcommand;
+ }
+ catch(exception& e) {
+ mout->errorOut(e, "BatchEngine", "getNextCommand");
exit(1);
}
}
-
/***********************************************************************/
/***********************************************************************/
listOfCommands = commandString.substr(1, (commandString.length()-1));
globaldata->argv = path;
-
+
}
catch(exception& e) {
- errorOut(e, "ScriptEngine", "ScriptEngine");
+ mout->errorOut(e, "ScriptEngine", "ScriptEngine");
exit(1);
}
}
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_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 {
+
+ #ifdef USE_MPI
+ MPI_Barrier(MPI_COMM_WORLD);
+ #endif
+
string nextcommand = "";
int count = 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