getcommandinfocommand.cpp

   1 /*
   2  *  getcommandinfo.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 4/6/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getcommandinfocommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetCommandInfoCommand::setParameters(){
  14         try {
  15                 CommandParameter poutput("output", "String", "", "", "", "", "","",false,false); parameters.push_back(poutput);
  16                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  17                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  18
  19                 vector<string> myArray;
  20                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  21                 return myArray;
  22         }
  23         catch(exception& e) {
  24                 m->errorOut(e, "GetCommandInfoCommand", "setParameters");
  25                 exit(1);
  26         }
  27 }
  28 //**********************************************************************************************************************
  29 string GetCommandInfoCommand::getHelpString(){
  30         try {
  31                 string helpString = "";
  32                 helpString += "This command is used by the gui to get the information about current commands available in mothur.\n";
  33                 return helpString;
  34         }
  35         catch(exception& e) {
  36                 m->errorOut(e, "GetCommandInfoCommand", "getHelpString");
  37                 exit(1);
  38         }
  39 }
  40 //**********************************************************************************************************************
  41
  42 GetCommandInfoCommand::GetCommandInfoCommand(string option)  {
  43         try {
  44                 abort = false; calledHelp = false;
  45
  46                 //allow user to run help
  47                 if(option == "help") { help(); abort = true; calledHelp = true; }
  48                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  49
  50                 else {
  51                         vector<string> myArray = setParameters();
  52
  53                         OptionParser parser(option);
  54                         map<string, string> parameters = parser.getParameters();
  55
  56                         ValidParameters validParameter;
  57                         //check to make sure all parameters are valid for command
  58                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  59                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  60                         }
  61
  62                         output = validParameter.validFile(parameters, "output", false);
  63                         if (output == "not found") {  output = ""; m->mothurOut("You must provide an output filename."); m->mothurOutEndLine(); abort=true; }
  64
  65                 }
  66         }
  67         catch(exception& e) {
  68                 m->errorOut(e, "GetCommandInfoCommand", "GetCommandInfoCommand");
  69                 exit(1);
  70         }
  71 }
  72 //**********************************************************************************************************************
  73
  74 int GetCommandInfoCommand::execute(){
  75         try {
  76
  77                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  78
  79                 commandFactory = CommandFactory::getInstance();
  80
  81                 ofstream out;
  82                 m->openOutputFile(output+".temp", out);
  83
  84                 int numNonHidden = 0;
  85
  86                 out << "mothurLocation=" << m->getFullPathName(m->argv) << endl;
  87                 out << "mothurVersion=" << m->getVersion() << endl;
  88
  89                 map<string, string> commands = commandFactory->getListCommands();
  90                 map<string, string>::iterator it;
  91
  92                 //loop through each command outputting info
  93                 for (it = commands.begin(); it != commands.end(); it++) {
  94
  95                         if (m->control_pressed) { m->mothurOut("[ERROR]: did not complete making the file."); m->mothurOutEndLine(); out.close(); m->mothurRemove((output+".temp")); }
  96
  97                         Command* thisCommand = commandFactory->getCommand(it->first);
  98
  99                         //don't add hidden commands
 100                         if (thisCommand->getCommandCategory() != "Hidden") {
 101                                 numNonHidden++;
 102
 103                                 //general info
 104                                 out << "commandName=" << thisCommand->getCommandName() << endl;
 105                                 //cout << thisCommand->getCommandName() << " current citation = " << thisCommand->getCitation() << endl;
 106                                 out << "commandCategory=" << thisCommand->getCommandCategory() << endl;
 107
 108                                 //remove /n from help string since gui reads line by line
 109                                 string myhelpString = thisCommand->getHelpString();
 110                                 string newHelpString = "";
 111                                 for (int i = 0; i < myhelpString.length(); i++) {
 112                                         if (myhelpString[i] != '\n') { newHelpString += myhelpString[i]; }
 113                                 }
 114                                 out << "help=" << newHelpString << endl;
 115
 116                                 //remove /n from citation string since gui reads line by line
 117                                 string mycitationString = thisCommand->getCitation();
 118                                 string newCitationString = "";
 119                                 for (int i = 0; i < mycitationString.length(); i++) {
 120                                         if (mycitationString[i] != '\n') { newCitationString += mycitationString[i]; }
 121                                 }
 122                                 out << "citation=" << newCitationString << endl;
 123
 124                                 out << "description=" << thisCommand->getDescription() << endl;
 125
 126                                 //outputTypes - makes something like outputTypes=fasta-name-qfile
 127                                 map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
 128                                 map<string, vector<string> >::iterator itTypes;
 129
 130                                 if (thisOutputTypes.size() == 0) { out << "outputTypesNames=0" << endl; }
 131                                 else {
 132                                         //string types = "";
 133                                         //for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {        types += itTypes->first + "-";  }
 134                                         //rip off last -
 135                                         //types = types.substr(0, types.length()-1);
 136                                         out << "outputTypesNames=" << thisOutputTypes.size() << endl;
 137
 138                     for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {
 139                         out << itTypes->first << "=" << thisCommand->getOutputPattern(itTypes->first) << endl;
 140                     }
 141                                 }
 142
 143                                 vector<string> booleans; vector<string> numbers; vector<string> multiples; vector<string> Strings;
 144                                 vector<string> inputGroupNames; map<string, string> inputTypes;
 145
 146                                 getInfo(thisCommand->getParameters(), booleans, numbers, multiples, Strings, inputGroupNames, inputTypes);
 147
 148                                 //output booleans
 149                                 out << "Boolean=" << booleans.size() << endl;
 150                                 for (int i = 0; i < booleans.size(); i++) { out << booleans[i] << endl; }
 151
 152                                 //output mulitples
 153                                 out << "Multiple=" << multiples.size() << endl;
 154                                 for (int i = 0; i < multiples.size(); i++) { out << multiples[i] << endl; }
 155
 156                                 //output numbers
 157                                 out << "Numbers=" << numbers.size() << endl;
 158                                 for (int i = 0; i < numbers.size(); i++) { out << numbers[i] << endl; }
 159
 160                                 //output strings
 161                                 out << "String=" << Strings.size() << endl;
 162                                 for (int i = 0; i < Strings.size(); i++) { out << Strings[i] << endl; }
 163
 164                                 //output groups
 165                                 out << "inputGroupNames=" << inputGroupNames.size() << endl;
 166                                 for (int i = 0; i < inputGroupNames.size(); i++) { out << inputGroupNames[i] << endl; }
 167
 168                                 //output input types
 169                                 if (inputTypes.size() == 0) { out << "inputTypes=" << endl; }
 170                                 else {
 171                                         string types = "";
 172                                         for (map<string, string>::iterator it2 = inputTypes.begin(); it2 != inputTypes.end(); it2++) {  types += it2->first + "-";      }
 173                                         //rip off last -
 174                                         types = types.substr(0, types.length()-1);
 175                                         out << "inputTypes=" << types << endl;
 176
 177                                         for (map<string, string>::iterator it2 = inputTypes.begin(); it2 != inputTypes.end(); it2++) {
 178                                                 out << it2->first << "=" << it2->second << endl;
 179                                         }
 180                                 }
 181
 182                         }
 183                 }
 184
 185                 out.close();
 186
 187                 ofstream out2;
 188                 m->openOutputFile(output, out2);
 189                 out2 << numNonHidden << endl;
 190                 out2.close();
 191
 192                 m->appendFiles(output+".temp", output);
 193                 m->mothurRemove((output+".temp"));
 194
 195                 m->mothurOutEndLine();
 196                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 197                 m->mothurOut(output); m->mothurOutEndLine();
 198                 m->mothurOutEndLine();
 199
 200
 201                 return 0;
 202         }
 203         catch(exception& e) {
 204                 m->errorOut(e, "GetCommandInfoCommand", "execute");
 205                 exit(1);
 206         }
 207 }
 208 //**********************************************************************************************************************
 209
 210 int GetCommandInfoCommand::getInfo(vector<CommandParameter> para, vector<string>& booleans, vector<string>& numbers, vector<string>& multiples, vector<string>& strings, vector<string>& inputGroupNames, map<string, string>& inputTypes){
 211         try {
 212
 213                 map<string, set<string> > groups;
 214                 map<string,  set<string> >::iterator itGroups;
 215
 216                 for (int i = 0; i < para.size(); i++) {
 217                         if ((para[i].name == "inputdir") || (para[i].name == "outputdir")) {} //ignore
 218                         else {
 219                 string important = "|F";
 220                 if (para[i].important || para[i].required) { important = "|T"; }
 221
 222                 string outputType = "|none";
 223                 if (para[i].outputTypes != "") { outputType = "|" + para[i].outputTypes; }
 224
 225                                 if (para[i].type == "Boolean") {
 226                                         string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
 227                                         booleans.push_back(temp);
 228                                 }else if (para[i].type == "Multiple") {
 229                                         string multAllowed = "F";
 230                                         if (para[i].multipleSelectionAllowed) { multAllowed = "T"; }
 231                                         string temp = para[i].name + "=" + para[i].options + "|" + para[i].optionsDefault + "|" + multAllowed + important + outputType;
 232                                         multiples.push_back(temp);
 233                                 }else if (para[i].type == "Number") {
 234                                         string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
 235                                         numbers.push_back(temp);
 236                                 }else if (para[i].type == "String") {
 237                                         string temp = para[i].name + "=" + para[i].optionsDefault + important + outputType;
 238                                         strings.push_back(temp);
 239                                 }else if (para[i].type == "InputTypes") {
 240                                         string required = "F";
 241                                         if (para[i].required) { required = "T"; }
 242                                         string temp = required + important + "|" + para[i].chooseOnlyOneGroup + "|" + para[i].chooseAtLeastOneGroup + "|" + para[i].linkedGroup + outputType;
 243                                         inputTypes[para[i].name] = temp;
 244
 245                                         //add choose only one groups
 246                     vector<string> tempGroups;
 247                     m->splitAtDash(para[i].chooseOnlyOneGroup, tempGroups);
 248                     for (int l = 0; l < tempGroups.size(); l++) {
 249                         groups[tempGroups[l]].insert(para[i].name);
 250                     }
 251                                         tempGroups.clear();
 252
 253                                         //add at least one group names
 254                     m->splitAtDash(para[i].chooseAtLeastOneGroup, tempGroups);
 255                     for (int l = 0; l < tempGroups.size(); l++) {
 256                         groups[tempGroups[l]].insert(para[i].name);
 257                     }
 258                                         tempGroups.clear();
 259
 260
 261                                         //add at linked group names
 262                     m->splitAtDash(para[i].linkedGroup, tempGroups);
 263                     for (int l = 0; l < tempGroups.size(); l++) {
 264                         groups[tempGroups[l]].insert(para[i].name);
 265                     }
 266                                         tempGroups.clear();
 267
 268                                 }else { m->mothurOut("[ERROR]: " + para[i].type + " is an unknown parameter type, please correct."); m->mothurOutEndLine(); }
 269                         }
 270                 }
 271
 272                 for (itGroups = groups.begin(); itGroups != groups.end(); itGroups++) {
 273                         if (itGroups->first != "none") {
 274                                 set<string> tempNames = itGroups->second;
 275                                 string temp = itGroups->first + "=";
 276                                 for (set<string>::iterator itNames = tempNames.begin(); itNames != tempNames.end(); itNames++) {
 277                                         temp += *itNames + "-";
 278                                 }
 279                                 //rip off last -
 280                                 temp = temp.substr(0, temp.length()-1);
 281                                 inputGroupNames.push_back(temp);
 282                         }
 283                 }
 284
 285                 return 0;
 286
 287         }
 288         catch(exception& e) {
 289                 m->errorOut(e, "GetCommandInfoCommand", "getInfo");
 290                 exit(1);
 291         }
 292 }
 293 //**********************************************************************************************************************/