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 = mout->findProgramPath("mothur"); }
+
+ mout->argv = path;
}
/***********************************************************************/
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
+
+ if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+
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->changedSeqNames = false;
+ 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;
}
/***********************************************************************/
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) {
//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 = mout->findProgramPath("mothur"); }
+
+ mout->argv = path;
}
catch(exception& e) {
//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] != '#') {
+ if (mout->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); }
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
#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->changedSeqNames = false;
+ 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
}
}
- gobble(inputBatchFile);
+ mout->gobble(inputBatchFile);
}
inputBatchFile.close();
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 = mout->findProgramPath("mothur"); }
+
+ mout->argv = path;
}
catch(exception& e) {
//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->changedSeqNames) { mout->mothurOut("[WARNING]: your sequence names contained ':'. I changed them to '_' to avoid problems in your downstream analysis.\n"); }
+
+ 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
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->changedSeqNames = false;
+ 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();
+ }
+
}
/***********************************************************************/
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++;
if (commandString.length() == 0) { break; }
}
}
-
+
return nextcommand;
}
catch(exception& e) {
projects / mothur.git / blobdiff