5 * Created by westcott on 4/6/11.
6 * Copyright 2011 Schloss Lab. All rights reserved.
10 #include "getcommandinfocommand.h"
12 //**********************************************************************************************************************
13 vector<string> GetCommandInfoCommand::setParameters(){
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);
19 vector<string> myArray;
20 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
24 m->errorOut(e, "GetCommandInfoCommand", "setParameters");
28 //**********************************************************************************************************************
29 string GetCommandInfoCommand::getHelpString(){
31 string helpString = "";
32 helpString += "This command is used by the gui to get the information about current commands available in mothur.\n";
36 m->errorOut(e, "GetCommandInfoCommand", "getHelpString");
40 //**********************************************************************************************************************
42 GetCommandInfoCommand::GetCommandInfoCommand(string option) {
44 abort = false; calledHelp = false;
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;}
51 vector<string> myArray = setParameters();
53 OptionParser parser(option);
54 map<string, string> parameters = parser.getParameters();
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; }
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; }
68 m->errorOut(e, "GetCommandInfoCommand", "GetCommandInfoCommand");
72 //**********************************************************************************************************************
74 int GetCommandInfoCommand::execute(){
77 if (abort == true) { if (calledHelp) { return 0; } return 2; }
79 commandFactory = CommandFactory::getInstance();
82 m->openOutputFile(output+".temp", out);
86 out << "mothurLocation=" << m->getFullPathName(m->argv) << endl;
87 out << "mothurVersion=" << m->getVersion() << endl;
89 map<string, string> commands = commandFactory->getListCommands();
90 map<string, string>::iterator it;
92 //loop through each command outputting info
93 for (it = commands.begin(); it != commands.end(); it++) {
95 if (m->control_pressed) { m->mothurOut("[ERROR]: did not complete making the file."); m->mothurOutEndLine(); out.close(); m->mothurRemove((output+".temp")); }
97 Command* thisCommand = commandFactory->getCommand(it->first);
99 //don't add hidden commands
100 if (thisCommand->getCommandCategory() != "Hidden") {
104 out << "commandName=" << thisCommand->getCommandName() << endl;
105 //cout << thisCommand->getCommandName() << " current citation = " << thisCommand->getCitation() << endl;
106 out << "commandCategory=" << thisCommand->getCommandCategory() << endl;
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]; }
114 out << "help=" << newHelpString << endl;
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]; }
122 out << "citation=" << newCitationString << endl;
124 out << "description=" << thisCommand->getDescription() << endl;
126 //outputTypes - makes something like outputTypes=fasta-name-qfile
127 map<string, vector<string> > thisOutputTypes = thisCommand->getOutputFiles();
128 map<string, vector<string> >::iterator itTypes;
130 if (thisOutputTypes.size() == 0) { out << "outputTypesNames=0" << endl; }
133 //for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) { types += itTypes->first + "-"; }
135 //types = types.substr(0, types.length()-1);
136 out << "outputTypesNames=" << thisOutputTypes.size() << endl;
138 for (itTypes = thisOutputTypes.begin(); itTypes != thisOutputTypes.end(); itTypes++) {
139 out << itTypes->first << "=" << thisCommand->getOutputPattern(itTypes->first) << endl;
143 vector<string> booleans; vector<string> numbers; vector<string> multiples; vector<string> Strings;
144 vector<string> inputGroupNames; map<string, string> inputTypes;
146 getInfo(thisCommand->getParameters(), booleans, numbers, multiples, Strings, inputGroupNames, inputTypes);
149 out << "Boolean=" << booleans.size() << endl;
150 for (int i = 0; i < booleans.size(); i++) { out << booleans[i] << endl; }
153 out << "Multiple=" << multiples.size() << endl;
154 for (int i = 0; i < multiples.size(); i++) { out << multiples[i] << endl; }
157 out << "Numbers=" << numbers.size() << endl;
158 for (int i = 0; i < numbers.size(); i++) { out << numbers[i] << endl; }
161 out << "String=" << Strings.size() << endl;
162 for (int i = 0; i < Strings.size(); i++) { out << Strings[i] << endl; }
165 out << "inputGroupNames=" << inputGroupNames.size() << endl;
166 for (int i = 0; i < inputGroupNames.size(); i++) { out << inputGroupNames[i] << endl; }
169 if (inputTypes.size() == 0) { out << "inputTypes=" << endl; }
172 for (map<string, string>::iterator it2 = inputTypes.begin(); it2 != inputTypes.end(); it2++) { types += it2->first + "-"; }
174 types = types.substr(0, types.length()-1);
175 out << "inputTypes=" << types << endl;
177 for (map<string, string>::iterator it2 = inputTypes.begin(); it2 != inputTypes.end(); it2++) {
178 out << it2->first << "=" << it2->second << endl;
188 m->openOutputFile(output, out2);
189 out2 << numNonHidden << endl;
192 m->appendFiles(output+".temp", output);
193 m->mothurRemove((output+".temp"));
195 m->mothurOutEndLine();
196 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
197 m->mothurOut(output); m->mothurOutEndLine();
198 m->mothurOutEndLine();
203 catch(exception& e) {
204 m->errorOut(e, "GetCommandInfoCommand", "execute");
208 //**********************************************************************************************************************
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){
213 map<string, set<string> > groups;
214 map<string, set<string> >::iterator itGroups;
216 for (int i = 0; i < para.size(); i++) {
217 if ((para[i].name == "inputdir") || (para[i].name == "outputdir")) {} //ignore
219 string important = "|F";
220 if (para[i].important || para[i].required) { important = "|T"; }
222 string outputType = "|none";
223 if (para[i].outputTypes != "") { outputType = "|" + para[i].outputTypes; }
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;
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);
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);
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);
268 }else { m->mothurOut("[ERROR]: " + para[i].type + " is an unknown parameter type, please correct."); m->mothurOutEndLine(); }
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 + "-";
280 temp = temp.substr(0, temp.length()-1);
281 inputGroupNames.push_back(temp);
288 catch(exception& e) {
289 m->errorOut(e, "GetCommandInfoCommand", "getInfo");
293 //**********************************************************************************************************************/