X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=systemcommand.cpp;h=b5b4945b92b6d664e6d81aa2dc6911a2d30414c3;hb=a0f1fca79d2ddfa7ad36b4485039c68b5704fe8d;hp=6b0a6d06474809f16fae1a0c17338ef1f7458dc7;hpb=ca9ac1d80c62f57270b0dcd49410ebe08a8aecd6;p=mothur.git

diff --git a/systemcommand.cpp b/systemcommand.cpp
index 6b0a6d0..b5b4945 100644
--- a/systemcommand.cpp
+++ b/systemcommand.cpp
@@ -9,7 +9,20 @@
 
 #include "systemcommand.h"
 
-
+//**********************************************************************************************************************
+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 {
@@ -17,10 +30,25 @@ SystemCommand::SystemCommand(string option)  {
 		
 		//allow user to run help
 		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(',');
 				
@@ -63,8 +91,31 @@ int SystemCommand::execute(){
 		
 		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;		
 	}