added modify names parameter to set.dir

[mothur.git] / systemcommand.cpp

diff --git a/systemcommand.cpp b/systemcommand.cpp
index fb250d7fe96cb4ed38df8c0ce33d1c7e17911945..b5b4945b92b6d664e6d81aa2dc6911a2d30414c3 100644 (file)
--- 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;               
        }