X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=systemcommand.cpp;h=b5b4945b92b6d664e6d81aa2dc6911a2d30414c3;hp=f341d0a03e3d35177895ab49696f7fb4f1f7ad20;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=348a7bac1d3c5d17ae0e4a93b78f69f4e200a190

diff --git a/systemcommand.cpp b/systemcommand.cpp
index f341d0a..b5b4945 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -10,36 +10,76 @@
 #include "systemcommand.h"
 
 //**********************************************************************************************************************
-
-SystemCommand::SystemCommand(string option){
+vector<string> SystemCommand::setParameters(){	
+	try {
+		CommandParameter pcommand("command", "String", "", "", "", "", "","",false,false); parameters.push_back(pcommand);
+				
+		vector<string> myArray;
+		for (int i = 0; i < parameters.size(); i++) {	myArray.push_back(parameters[i].name);		}
+		return myArray;
+	}
+	catch(exception& e) {
+		m->errorOut(e, "SystemCommand", "setParameters");
+		exit(1);
+	}
+}
+//**********************************************************************************************************************
+SystemCommand::SystemCommand(string option)  {
 	try {
-		abort = false;
+		abort = false; calledHelp = false;   
 		
 		//allow user to run help
-		if(option == "help") { help(); abort = true; }
+		if(option == "help") { help(); abort = true; calledHelp = true; }
+		else if(option == "citation") { citation(); abort = true; calledHelp = true;}
 		
 		else {
-			if (option == "") { mothurOut("You must enter a command to run."); mothurOutEndLine(); abort = true; }
-			else { command = option; }
+			vector<string> myArray = setParameters();
+			
+			OptionParser parser(option);
+			map<string, string> parameters = parser.getParameters();
+			map<string, string>::iterator it;
+			
+			ValidParameters validParameter;
+			
+			//check for optional parameter and set defaults
+			// ...at some point should added some additional type checking...
+			string commandOption = validParameter.validFile(parameters, "command", false);			
+			if (commandOption == "not found") { commandOption = ""; }
+			else { command = commandOption; }
+			
+			if ((option == "") && (commandOption == "")) { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
+			else if (commandOption == "") { 
+				//check for outputdir and inputdir parameters
+				int commaPos = option.find_first_of(',');
+				
+				//if there is a comma then grab string up to that pos
+				if (commaPos != option.npos) {
+					option = option.substr(0, commaPos);
+				}
+			
+				command = option;
+			}
 		}	
 
 	}
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "SystemCommand");
+		m->errorOut(e, "SystemCommand", "SystemCommand");
 		exit(1);
 	}
 }
 //**********************************************************************************************************************
 
-void SystemCommand::help(){
+string SystemCommand::getHelpString(){
 	try {
-		mothurOut("The system command allows you to execute a system command from within mothur.\n");
-		mothurOut("The system has no parameters.\n");
-		mothurOut("The system command should be in the following format: system(yourCommand).\n");
-		mothurOut("Example system(clear).\n");
+		string helpString = "";
+		helpString += "The system command allows you to execute a system command from within mothur.\n";
+		helpString += "The system has no parameters.\n";
+		helpString += "The system command should be in the following format: system(yourCommand).\n";
+		helpString += "Example system(clear).\n";
+		return helpString;
 	}
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "help");
+		m->errorOut(e, "SystemCommand", "help");
 		exit(1);
 	}
 }
@@ -49,15 +89,38 @@ void SystemCommand::help(){
 int SystemCommand::execute(){
 	try {
 		
-		if (abort == true) { return 0; }
+		if (abort == true) { if (calledHelp) { return 0; }  return 2;	}
+		
+		//if command contains a redirect don't add the redirect
+		bool usedRedirect = false;
+		if ((command.find('>')) == string::npos) {
+			command += " > ./commandScreen.output 2>&1";
+			usedRedirect = true;
+		}
 		
 		system(command.c_str());
 		
+		if (usedRedirect) {
+			ifstream in;
+			string filename = "./commandScreen.output";
+			m->openInputFile(filename, in, "no error");
+			
+			string output = "";
+			while(char c = in.get()){
+				if(in.eof())		{	break;			}
+				else				{	output += c;	}
+			}
+			in.close();
+			
+			m->mothurOut(output); m->mothurOutEndLine();
+			m->mothurRemove(filename);
+		}
+		
 		return 0;		
 	}
 
 	catch(exception& e) {
-		errorOut(e, "SystemCommand", "execute");
+		m->errorOut(e, "SystemCommand", "execute");
 		exit(1);
 	}
 }