Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2022,2023 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #include "CLTool.h"
      23             : #include "core/CLToolRegister.h"
      24             : #include "tools/Tools.h"
      25             : #include "config/Config.h"
      26             : #include "core/ActionRegister.h"
      27             : #include "core/GenericMolInfo.h"
      28             : #include "core/ModuleMap.h"
      29             : #include <cstdio>
      30             : #include <string>
      31             : #include <iostream>
      32             : 
      33             : namespace PLMD {
      34             : namespace cltools {
      35             : 
      36             : //+PLUMEDOC TOOLS gen_json
      37             : /*
      38             : gen_json constructs a json file that includes a dictionary of actions, the keywords for those actions and the components and outputs this to standard output
      39             : 
      40             : \par Examples
      41             : 
      42             : The following command generates the json file
      43             : \verbatim
      44             : plumed gen_json
      45             : \endverbatim
      46             : 
      47             : 
      48             : */
      49             : //+ENDPLUMEDOC
      50             : 
      51             : class GenJson : public CLTool {
      52             : private:
      53             :   std::string version;
      54             :   void printHyperlink(std::string action );
      55             : public:
      56             :   static void registerKeywords( Keywords& keys );
      57             :   explicit GenJson(const CLToolOptions& co );
      58             :   int main(FILE* in, FILE*out,Communicator& pc) override;
      59           4 :   std::string description()const override {
      60           4 :     return "print out a json file that contains the pluemd syntax";
      61             :   }
      62             : };
      63             : 
      64       15953 : PLUMED_REGISTER_CLTOOL(GenJson,"gen_json")
      65             : 
      66        5316 : void GenJson::registerKeywords( Keywords& keys ) {
      67        5316 :   CLTool::registerKeywords( keys );
      68       10632 :   keys.add("compulsory","--actions","a file containing one line descriptions of the various actions");
      69        5316 : }
      70             : 
      71           5 : GenJson::GenJson(const CLToolOptions& co ):
      72             :   CLTool(co),
      73           5 :   version("master")
      74             : {
      75           5 :   inputdata=commandline;
      76          10 :   if( config::getVersionLong().find("dev")==std::string::npos ) version="v"+config::getVersion();
      77           5 : }
      78             : 
      79         482 : void GenJson::printHyperlink( std::string action ) {
      80         964 :   std::cout<<"    \"hyperlink\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/";
      81        6044 :   std::transform(action.begin(), action.end(), action.begin(), [](unsigned char c) { return std::tolower(c); });
      82             :   while(true) {
      83         802 :     std::size_t und=action.find_first_of("_");
      84         802 :     if( und==std::string::npos ) break;
      85         320 :     std::string first=action.substr(0,und);
      86        4192 :     for(auto c : first ) { if( isdigit(c) ) std::cout<<c; else std::cout<<"_"<<c; }
      87         640 :     std::cout<<"_"; action=action.substr(und+1);
      88         320 :   }
      89        7094 :   for(auto c : action ) { if( isdigit(c) ) std::cout<<c; else std::cout<<"_"<<c; }
      90         482 :   std::cout<<".html\","<<std::endl;
      91         482 : }
      92             : 
      93           1 : int GenJson::main(FILE* in, FILE*out,Communicator& pc) {
      94           1 :   std::string line(""), actionfile; parse("--actions",actionfile);
      95           1 :   IFile myfile; myfile.open(actionfile); bool stat;
      96             :   std::map<std::string,std::string> action_map;
      97         464 :   while((stat=myfile.getline(line))) {
      98         463 :     std::size_t col = line.find_first_of(":"); std::string docs = line.substr(col+1);
      99         463 :     if( docs.find("\\")!=std::string::npos ) error("found invalid backslash character in first line of documentation for action " + line.substr(0,col) );
     100         926 :     action_map.insert(std::pair<std::string,std::string>( line.substr(0,col), docs ) );
     101             :   }
     102           1 :   myfile.close();
     103             : 
     104             :   // Cycle over all the action names
     105           1 :   std::cout<<"{"<<std::endl;
     106             :   // Get the vimlink
     107           2 :   std::cout<<"  \"vimlink\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/_vim_syntax.html\","<<std::endl;
     108             :   // And the replicas link
     109           2 :   std::cout<<"  \"replicalink\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/special-replica-syntax.html\","<<std::endl;
     110             :   // Get the names of all the actions
     111           1 :   std::vector<std::string> action_names( actionRegister().getActionNames() ); std::vector<std::string> allmodules;
     112         439 :   for(unsigned i=0; i<action_names.size(); ++i) {
     113        1314 :     std::cout<<"  \""<<action_names[i]<<'"'<<": {"<<std::endl; std::string action=action_names[i];
     114             :     // Handle conversion of action names to links
     115         438 :     printHyperlink( action );
     116         876 :     std::cout<<"    \"description\" : \""<<action_map[action_names[i]]<<"\",\n";
     117         876 :     bool found=false; std::string thismodule = getModuleMap().find(action_names[i])->second;
     118        5780 :     for(unsigned i=0; i<allmodules.size(); ++i) {
     119        5736 :       if( allmodules[i]==thismodule ) { found=true; break; }
     120             :     }
     121         438 :     if( !found ) allmodules.push_back( thismodule );
     122         876 :     std::cout<<"    \"module\" : \""<<thismodule<<"\",\n";
     123             :     // Now output keyword information
     124         438 :     Keywords keys; actionRegister().getKeywords( action_names[i], keys );
     125         876 :     std::cout<<"    \"displayname\" : \""<<keys.getDisplayName()<<"\",\n";
     126         438 :     std::cout<<"    \"syntax\" : {"<<std::endl;
     127        5464 :     for(unsigned j=0; j<keys.size(); ++j) {
     128        5026 :       std::string defa = "", desc = keys.getKeywordDescription( keys.getKeyword(j) );
     129        5026 :       if( desc.find("default=")!=std::string::npos ) {
     130        1637 :         std::size_t defstart = desc.find_first_of("="), brac=desc.find_first_of(")");
     131        4911 :         defa = desc.substr(defstart+1,brac-defstart-2); desc = desc.substr(brac+1);
     132             :       }
     133        5026 :       std::size_t dot=desc.find_first_of("."); std::string mydescrip = desc.substr(0,dot);
     134        5026 :       if( mydescrip.find("\\")!=std::string::npos ) error("found invalid backslash character documentation for keyword " + keys.getKeyword(j) + " in action " + action_names[i] );
     135       10052 :       std::string argtype = keys.getArgumentType( keys.getKeyword(j) );
     136        6116 :       if( argtype.length()>0 ) std::cout<<"       \""<<keys.getKeyword(j)<<"\" : { \"type\": \""<<keys.getStyle(keys.getKeyword(j))<<"\", \"description\": \""<<mydescrip<<"\", \"multiple\": "<<keys.numbered( keys.getKeyword(j) )<<", \"argtype\": \""<<argtype<<"\"}";
     137       12963 :       else if( defa.length()>0 ) std::cout<<"       \""<<keys.getKeyword(j)<<"\" : { \"type\": \""<<keys.getStyle(keys.getKeyword(j))<<"\", \"description\": \""<<mydescrip<<"\", \"multiple\": "<<keys.numbered( keys.getKeyword(j) )<<", \"default\": \""<<defa<<"\"}";
     138       15885 :       else std::cout<<"       \""<<keys.getKeyword(j)<<"\" : { \"type\": \""<<keys.getStyle(keys.getKeyword(j))<<"\", \"description\": \""<<mydescrip<<"\", \"multiple\": "<<keys.numbered( keys.getKeyword(j) )<<"}";
     139        5830 :       if( j==keys.size()-1 && !keys.exists("HAS_VALUES") ) std::cout<<std::endl; else std::cout<<","<<std::endl;
     140             :     }
     141         876 :     if( keys.exists("HAS_VALUES") ) {
     142         366 :       std::cout<<"       \"output\" : {"<<std::endl;
     143         366 :       std::vector<std::string> components( keys.getOutputComponents() );
     144             :       // Check if we have a value
     145             :       bool hasvalue=true;
     146         812 :       for(unsigned k=0; k<components.size(); ++k) {
     147        1600 :         if( keys.getOutputComponentFlag( components[k] )=="default" ) { hasvalue=false; break; }
     148             :       }
     149        1681 :       for(unsigned k=0; k<components.size(); ++k) {
     150        2630 :         std::string compname=components[k]; if( components[k]==".#!value" ) { hasvalue=false; compname="value"; }
     151        2630 :         std::cout<<"         \""<<compname<<"\" : {"<<std::endl;
     152        2630 :         std::cout<<"           \"flag\": \""<<keys.getOutputComponentFlag( components[k] )<<"\","<<std::endl;
     153        3945 :         std::cout<<"           \"type\": \""<<keys.getOutputComponentType( components[k] )<<"\","<<std::endl;
     154        1315 :         std::string desc=keys.getOutputComponentDescription( components[k] );
     155        1315 :         std::size_t dot=desc.find_first_of("."); std::string mydescrip = desc.substr(0,dot);
     156        1315 :         if( mydescrip.find("\\")!=std::string::npos ) error("found invalid backslash character documentation for output component " + compname + " in action " + action_names[i] );
     157        2630 :         std::cout<<"           \"description\": \""<<mydescrip<<"\""<<std::endl;
     158        1315 :         if( k==components.size()-1 ) std::cout<<"         }"<<std::endl; else std::cout<<"         },"<<std::endl;
     159             :       }
     160         366 :       if( hasvalue && components.size()==0 ) printf("WARNING: no components have been registered for action %s \n", action_names[i].c_str() );
     161         366 :       std::cout<<"       }"<<std::endl;
     162             : 
     163         366 :     }
     164         438 :     std::cout<<"    },"<<std::endl;
     165         438 :     if( keys.getNeededKeywords().size()>0 ) {
     166         122 :       std::vector<std::string> neededActions( keys.getNeededKeywords() );
     167         244 :       std::cout<<"    \"needs\" : ["<<"\""<<neededActions[0]<<"\"";
     168        1006 :       for(unsigned j=1; j<neededActions.size(); ++j) std::cout<<", \""<<neededActions[j]<<"\"";
     169         122 :       std::cout<<"],"<<std::endl;
     170         122 :     }
     171             :     // This ensures that \n is replaced by \\n
     172         438 :     std::string unsafen="\n", safen="\\n", helpstr = keys.getHelpString();
     173         438 :     for( std::size_t pos = helpstr.find("\n");
     174       11106 :          pos != std::string::npos;
     175       10668 :          pos = helpstr.find("\n", pos)
     176       10668 :        ) { helpstr.replace(pos, unsafen.size(), safen); pos += safen.size(); }
     177         876 :     std::cout<<"    \"help\" : \""<<helpstr<<"\"\n";
     178         438 :     std::cout<<"  },"<<std::endl;
     179         438 :   }
     180             :   // Get all the special groups
     181           1 :   std::cout<<"  \"groups\" : {"<<std::endl;
     182           1 :   std::cout<<"    \"@allatoms\" : { \n"<<std::endl;
     183           1 :   std::cout<<"        \"description\" : \"refers to all the MD codes atoms and PLUMEDs vatoms\","<<std::endl;
     184           2 :   std::cout<<"        \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/_group.html\""<<std::endl;
     185           1 :   std::cout<<"    },"<<std::endl;
     186           1 :   std::cout<<"    \"@mdatoms\" : { \n"<<std::endl;
     187           1 :   std::cout<<"        \"description\" : \"refers to all the MD codes atoms but not PLUMEDs vatoms\","<<std::endl;
     188           2 :   std::cout<<"        \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/_group.html\""<<std::endl;
     189           1 :   std::cout<<"    },"<<std::endl;
     190           1 :   std::cout<<"    \"@ndx\" : { \n"<<std::endl;
     191           1 :   std::cout<<"        \"description\" : \"load a group from a GROMACS index file\","<<std::endl;
     192           2 :   std::cout<<"        \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/_group.html\""<<std::endl;
     193             :   // Now print all the special keywords in molinfo
     194           1 :   std::map<std::string,std::string> specials( GenericMolInfo::getSpecialKeywords() );
     195          36 :   for(auto const& s : specials ) {
     196          35 :     std::cout<<"    },"<<std::endl;
     197          70 :     std::cout<<"    \""<<s.first<<"\" : { \n"<<std::endl;
     198          70 :     std::cout<<"        \"description\" : \""<<s.second<<"\","<<std::endl;
     199          70 :     std::cout<<"        \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/_m_o_l_i_n_f_o.html\""<<std::endl;
     200             :   }
     201           1 :   std::cout<<"        }"<<std::endl;
     202           1 :   std::cout<<"  },"<<std::endl;
     203           1 :   std::cout<<"  \"modules\" : {"<<std::endl;
     204           2 :   std::cout<<"    \""<<allmodules[0]<<"\" : { "<<std::endl;
     205           1 :   printHyperlink( allmodules[0] );
     206           1 :   std::cout<<"        \"description\" : \"A module that will be used for something\""<<std::endl;
     207          44 :   for(unsigned i=1; i<allmodules.size(); ++i) {
     208          43 :     std::cout<<"    },"<<std::endl;
     209          86 :     std::cout<<"    \""<<allmodules[i]<<"\" : { "<<std::endl;
     210          43 :     printHyperlink( allmodules[i] );
     211          43 :     std::cout<<"        \"description\" : \"A module that will be used for something\""<<std::endl;
     212             :   }
     213           1 :   std::cout<<"        }"<<std::endl;
     214           1 :   std::cout<<"  }"<<std::endl;
     215           1 :   std::cout<<"}"<<std::endl;
     216           1 :   return 0;
     217           2 : }
     218             : 
     219             : } // End of namespace
     220             : }