X-Git-Url: https://git.donarmstrong.com/?p=mothur.git;a=blobdiff_plain;f=systemcommand.cpp;h=b5b4945b92b6d664e6d81aa2dc6911a2d30414c3;hp=fb250d7fe96cb4ed38df8c0ce33d1c7e17911945;hb=a8e2df1b96a57f5f29576b08361b86a96a8eff4f;hpb=8bc3e5b38c2317a1715f53be22fa96455868c281

diff --git a/systemcommand.cpp b/systemcommand.cpp
index fb250d7..b5b4945 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -10,50 +10,45 @@
 #include "systemcommand.h"
 
 //**********************************************************************************************************************
-vector<string> SystemCommand::getValidParameters(){	
-	try {
-		vector<string> myArray;
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SystemCommand", "getValidParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-vector<string> SystemCommand::getRequiredParameters(){	
-	try {
-		vector<string> myArray;
-		return myArray;
-	}
-	catch(exception& e) {
-		m->errorOut(e, "SystemCommand", "getRequiredParameters");
-		exit(1);
-	}
-}
-//**********************************************************************************************************************
-vector<string> SystemCommand::getRequiredFiles(){	
+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", "getRequiredFiles");
+		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 == "") { m->mothurOut("You must enter a command to run."); m->mothurOutEndLine(); abort = true; }
-			else { 
+			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(',');
 				
@@ -74,12 +69,14 @@ SystemCommand::SystemCommand(string option)  {
 }
 //**********************************************************************************************************************
 
-void SystemCommand::help(){
+string SystemCommand::getHelpString(){
 	try {
-		m->mothurOut("The system command allows you to execute a system command from within mothur.\n");
-		m->mothurOut("The system has no parameters.\n");
-		m->mothurOut("The system command should be in the following format: system(yourCommand).\n");
-		m->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) {
 		m->errorOut(e, "SystemCommand", "help");
@@ -92,10 +89,33 @@ 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;		
 	}