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/CLToolRegister.h"
28 : #include "core/GenericMolInfo.h"
29 : #include "core/ModuleMap.h"
30 : #include <cstdio>
31 : #include <string>
32 : #include <iostream>
33 :
34 : namespace PLMD {
35 : namespace cltools {
36 :
37 : //+PLUMEDOC TOOLS gen_json
38 : /*
39 : 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
40 :
41 : This command is used during the build process of plumed. It constructs a json file that contains documentation information on all actions and cltools. This json
42 : file is then used by the python package [PlumedToHTML](https://github.com/plumed/PlumedToHTML). This package is used to construct the example input files that
43 : appear in [the plumed nest](www.plumed-nest.org), [plumed tutorials](www.plumed-tutorials.org) and this manual.
44 :
45 : You will likely not ever need to run this command. When it runs during the build proess we use the following command:
46 :
47 : ```plumed
48 : plumed --no-mpi gen_json --actions action_list > syntax.json
49 : ```
50 :
51 : You can find the syntax json file that is generated by this comamnd as `plumed2/json/syntax.json`.
52 :
53 : */
54 : //+ENDPLUMEDOC
55 :
56 : class GenJson : public CLTool {
57 : private:
58 : std::string version;
59 : void printHyperlink( const std::string& action );
60 : void printKeywordDocs( const std::string& k, const std::string& action, const Keywords& keys );
61 : public:
62 : static void registerKeywords( Keywords& keys );
63 : explicit GenJson(const CLToolOptions& co );
64 : int main(FILE* in, FILE*out,Communicator& pc) override;
65 5 : std::string description()const override {
66 5 : return "print out a json file that contains the pluemd syntax";
67 : }
68 : };
69 :
70 16260 : PLUMED_REGISTER_CLTOOL(GenJson,"gen_json")
71 :
72 5418 : void GenJson::registerKeywords( Keywords& keys ) {
73 5418 : CLTool::registerKeywords( keys );
74 5418 : keys.add("compulsory","--actions","a file containing one line descriptions of the various actions");
75 5418 : }
76 :
77 6 : GenJson::GenJson(const CLToolOptions& co ):
78 : CLTool(co),
79 6 : version("master") {
80 6 : inputdata=commandline;
81 12 : if( config::getVersionLong().find("dev")==std::string::npos ) {
82 0 : version="v"+config::getVersion();
83 : }
84 6 : }
85 :
86 504 : void GenJson::printHyperlink( const std::string& action ) {
87 1512 : std::cout<<" \"hyperlink\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/"<<action<<"\","<<std::endl;
88 504 : }
89 :
90 5307 : void GenJson::printKeywordDocs( const std::string& k, const std::string& action, const Keywords& keys ) {
91 5307 : std::string defa = "", desc = keys.getKeywordDescription( k );
92 5307 : if( desc.find("default=")!=std::string::npos ) {
93 1779 : std::size_t defstart = desc.find_first_of("="), brac=desc.find_first_of(")");
94 1779 : defa = desc.substr(defstart+1,brac-defstart-2);
95 3558 : desc = desc.substr(brac+1);
96 : }
97 5307 : std::size_t dot=desc.find_first_of(".");
98 5307 : std::string mydescrip = desc.substr(0,dot);
99 5307 : if( mydescrip.find("\\")!=std::string::npos ) {
100 0 : error("found invalid backslash character documentation for keyword " + k + " in action " + action );
101 : }
102 31842 : std::cout<<" \""<<k<<"\" : { \"type\": \""<<keys.getStyle(k)<<"\", \"description\": \""<<mydescrip<<"\", \"multiple\": "<<keys.numbered(k)<<", \"actionlink\": \""<<keys.getLinkedActions(k)<<"\"";
103 5307 : std::string argtype = keys.getArgumentType( k );
104 5307 : if( argtype.length()>0 ) {
105 444 : std::cout<<", \"argtype\": \""<<argtype<<"\"}";
106 5085 : } else if( defa.length()>0 ) {
107 3546 : std::cout<<", \"default\": \""<<defa<<"\"}";
108 : } else {
109 3312 : std::cout<<"}";
110 : }
111 5307 : }
112 :
113 1 : int GenJson::main(FILE* in, FILE*out,Communicator& pc) {
114 1 : std::string line(""), actionfile;
115 1 : parse("--actions",actionfile);
116 1 : IFile myfile;
117 1 : myfile.open(actionfile);
118 : bool stat;
119 : std::map<std::string,std::string> action_map;
120 458 : while((stat=myfile.getline(line))) {
121 457 : std::size_t col = line.find_first_of(":");
122 457 : std::string docs = line.substr(col+1);
123 457 : if( docs.find("\\")!=std::string::npos ) {
124 0 : error("found invalid backslash character in first line of documentation for action " + line.substr(0,col) );
125 : }
126 914 : action_map.insert(std::pair<std::string,std::string>( line.substr(0,col), docs ) );
127 : }
128 1 : myfile.close();
129 :
130 : // Cycle over all the action names
131 1 : std::cout<<"{"<<std::endl;
132 : // Get the vimlink
133 2 : std::cout<<" \"vimlink\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/vim\","<<std::endl;
134 : // And the replicas link
135 2 : std::cout<<" \"replicalink\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/parsing.html\","<<std::endl;
136 : // Get the names of all the actions
137 1 : std::vector<std::string> action_names( actionRegister().getActionNames() );
138 : std::vector<std::string> allmodules;
139 442 : for(unsigned i=0; i<action_names.size(); ++i) {
140 882 : std::cout<<" \""<<action_names[i]<<'"'<<": {"<<std::endl;
141 441 : std::string action=action_names[i];
142 : // Handle conversion of action names to links
143 441 : printHyperlink( action );
144 882 : std::cout<<" \"description\" : \""<<action_map[action_names[i]]<<"\",\n";
145 : bool found=false;
146 882 : plumed_massert( getModuleMap().find(action)!=getModuleMap().end(), "could not find action named " + action + " in module map");
147 882 : std::string thismodule = getModuleMap().find(action_names[i])->second;
148 5816 : for(unsigned i=0; i<allmodules.size(); ++i) {
149 5772 : if( allmodules[i]==thismodule ) {
150 : found=true;
151 : break;
152 : }
153 : }
154 441 : if( !found ) {
155 44 : allmodules.push_back( thismodule );
156 : }
157 882 : std::cout<<" \"module\" : \""<<thismodule<<"\",\n";
158 : // Now output keyword information
159 441 : Keywords keys;
160 441 : actionRegister().getKeywords( action_names[i], keys );
161 882 : std::cout<<" \"displayname\" : \""<<keys.getDisplayName()<<"\",\n";
162 : // This is used for noting actions that have been deprecated
163 441 : std::string replacement = keys.getReplacementAction();
164 441 : if( replacement!="none" ) {
165 : bool found_replacement=false;
166 1202 : for(unsigned j=0; j<action_names.size(); ++j) {
167 1202 : if( action_names[j]==replacement ) {
168 : found_replacement=true;
169 : break;
170 : }
171 : }
172 5 : if( !found_replacement ) {
173 0 : error("could not find action named " + replacement + " that is supposed to be used to replace " + action_names[i] );
174 : }
175 10 : std::cout<<" \"replacement\" : \""<<replacement<<"\",\n";
176 : }
177 441 : std::cout<<" \"dois\" : [";
178 441 : unsigned ndoi = keys.getDOIList().size();
179 441 : if( ndoi>0 ) {
180 156 : std::cout<<"\"" + keys.getDOIList()[0] + "\"";
181 120 : for(unsigned j=1; j<ndoi; ++j) {
182 84 : std::cout<<", \"" + keys.getDOIList()[j] + "\"";
183 : }
184 : }
185 441 : std::cout<<"],\n";
186 441 : std::cout<<" \"syntax\" : {"<<std::endl;
187 5512 : for(unsigned j=0; j<keys.size(); ++j) {
188 5071 : printKeywordDocs( keys.getKeyword(j), action, keys );
189 5071 : if( j==keys.size()-1 && !keys.exists("HAS_VALUES") ) {
190 : std::cout<<std::endl;
191 : } else {
192 4999 : std::cout<<","<<std::endl;
193 : }
194 : }
195 441 : if( keys.exists("HAS_VALUES") ) {
196 369 : std::cout<<" \"output\" : {"<<std::endl;
197 369 : std::vector<std::string> components( keys.getOutputComponents() );
198 : // Check if we have a value
199 : bool hasvalue=true;
200 815 : for(unsigned k=0; k<components.size(); ++k) {
201 1606 : if( keys.getOutputComponentFlag( components[k] )=="default" ) {
202 : hasvalue=false;
203 : break;
204 : }
205 : }
206 1687 : for(unsigned k=0; k<components.size(); ++k) {
207 1318 : std::string compname=components[k];
208 1318 : if( components[k]==".#!value" ) {
209 : hasvalue=false;
210 : compname="value";
211 : }
212 2636 : std::cout<<" \""<<compname<<"\" : {"<<std::endl;
213 2636 : std::cout<<" \"flag\": \""<<keys.getOutputComponentFlag( components[k] )<<"\","<<std::endl;
214 3954 : std::cout<<" \"type\": \""<<keys.getOutputComponentType( components[k] )<<"\","<<std::endl;
215 1318 : std::string desc=keys.getOutputComponentDescription( components[k] );
216 1318 : std::size_t dot=desc.find_first_of(".");
217 1318 : std::string mydescrip = desc.substr(0,dot);
218 1318 : if( mydescrip.find("\\")!=std::string::npos ) {
219 0 : error("found invalid backslash character documentation for output component " + compname + " in action " + action_names[i] );
220 : }
221 2636 : std::cout<<" \"description\": \""<<mydescrip<<"\""<<std::endl;
222 1318 : if( k==components.size()-1 ) {
223 369 : std::cout<<" }"<<std::endl;
224 : } else {
225 949 : std::cout<<" },"<<std::endl;
226 : }
227 : }
228 369 : if( hasvalue && components.size()==0 ) {
229 : printf("WARNING: no components have been registered for action %s \n", action_names[i].c_str() );
230 : }
231 369 : std::cout<<" }"<<std::endl;
232 :
233 369 : }
234 441 : std::cout<<" },"<<std::endl;
235 441 : if( keys.getNeededKeywords().size()>0 ) {
236 123 : std::vector<std::string> neededActions( keys.getNeededKeywords() );
237 246 : std::cout<<" \"needs\" : ["<<"\""<<neededActions[0]<<"\"";
238 1008 : for(unsigned j=1; j<neededActions.size(); ++j) {
239 1770 : std::cout<<", \""<<neededActions[j]<<"\"";
240 : }
241 123 : std::cout<<"],"<<std::endl;
242 123 : }
243 : // This ensures that \n is replaced by \\n
244 441 : std::string unsafen="\n", safen="\\n", helpstr = keys.getHelpString();
245 441 : for( std::size_t pos = helpstr.find("\n");
246 11110 : pos != std::string::npos;
247 10669 : pos = helpstr.find("\n", pos)
248 : ) {
249 : helpstr.replace(pos, unsafen.size(), safen);
250 10669 : pos += safen.size();
251 : }
252 882 : std::cout<<" \"help\" : \""<<helpstr<<"\"\n";
253 441 : std::cout<<" },"<<std::endl;
254 441 : }
255 : // Get all the special groups
256 1 : std::cout<<" \"groups\" : {"<<std::endl;
257 1 : std::cout<<" \"@allatoms\" : { \n"<<std::endl;
258 1 : std::cout<<" \"description\" : \"refers to all the MD codes atoms and PLUMEDs vatoms\","<<std::endl;
259 2 : std::cout<<" \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/specifying_atoms\""<<std::endl;
260 1 : std::cout<<" },"<<std::endl;
261 1 : std::cout<<" \"@mdatoms\" : { \n"<<std::endl;
262 1 : std::cout<<" \"description\" : \"refers to all the MD codes atoms but not PLUMEDs vatoms\","<<std::endl;
263 2 : std::cout<<" \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/specifying_atoms\""<<std::endl;
264 1 : std::cout<<" },"<<std::endl;
265 1 : std::cout<<" \"@ndx:\" : { \n"<<std::endl;
266 1 : std::cout<<" \"description\" : \"load a group from a GROMACS index file\","<<std::endl;
267 2 : std::cout<<" \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/specifying_atoms.html\""<<std::endl;
268 : // Now print all the special keywords in molinfo
269 1 : std::map<std::string,std::string> specials( GenericMolInfo::getSpecialKeywords() );
270 36 : for(auto const& s : specials ) {
271 35 : std::cout<<" },"<<std::endl;
272 70 : std::cout<<" \""<<s.first<<"\" : { \n"<<std::endl;
273 70 : std::cout<<" \"description\" : \""<<s.second<<"\","<<std::endl;
274 70 : std::cout<<" \"link\" : \"https://www.plumed.org/doc-"<<version<<"/user-doc/html/MOLINFO\""<<std::endl;
275 : }
276 1 : std::cout<<" }"<<std::endl;
277 1 : std::cout<<" },"<<std::endl;
278 1 : std::cout<<" \"modules\" : {"<<std::endl;
279 2 : std::cout<<" \""<<allmodules[0]<<"\" : { "<<std::endl;
280 1 : printHyperlink( allmodules[0] );
281 1 : std::cout<<" \"description\" : \"A module that will be used for something\""<<std::endl;
282 44 : for(unsigned i=1; i<allmodules.size(); ++i) {
283 43 : std::cout<<" },"<<std::endl;
284 86 : std::cout<<" \""<<allmodules[i]<<"\" : { "<<std::endl;
285 43 : printHyperlink( allmodules[i] );
286 43 : std::cout<<" \"description\" : \"A module that will be used for something\""<<std::endl;
287 : }
288 1 : std::cout<<" }"<<std::endl;
289 1 : std::cout<<" },"<<std::endl;
290 1 : std::cout<<" \"cltools\" : {"<<std::endl;
291 1 : std::vector<std::string> cltool_names( cltoolRegister().list() );
292 20 : for(unsigned i=0; i<cltool_names.size(); ++i) {
293 38 : std::cout<<" \""<<cltool_names[i]<<'"'<<": {"<<std::endl;
294 19 : std::string cltool=cltool_names[i];
295 : // Handle converstion to link
296 19 : printHyperlink( cltool );
297 38 : plumed_massert( getModuleMap().find(cltool)!=getModuleMap().end(), "could not find cltool named " + cltool + " in module map" );
298 38 : std::string thismodule = getModuleMap().find(cltool_names[i])->second;
299 38 : std::cout<<" \"module\" : \""<<thismodule<<"\",\n";
300 19 : auto mytool = cltoolRegister().create( CLToolOptions(cltool) );
301 57 : std::cout<<" \"description\" : \""<<mytool->description()<<"\",\n";
302 19 : if( mytool->inputdata==commandline ) {
303 16 : std::cout<<" \"inputtype\" : \"command line args\",\n";
304 3 : } else if( mytool->inputdata==ifile ) {
305 3 : std::cout<<" \"inputtype\" : \"file\",\n";
306 : } else {
307 0 : error("input type for cltool was not specified");
308 : }
309 19 : std::cout<<" \"syntax\" : {"<<std::endl;
310 255 : for(unsigned j=0; j<cltoolRegister().get(cltool).keys.size(); ++j) {
311 236 : std::string k = cltoolRegister().get(cltool).keys.getKeyword(j);
312 236 : printKeywordDocs( k, cltool, cltoolRegister().get(cltool).keys );
313 236 : if( j==cltoolRegister().get(cltool).keys.size()-1 ) {
314 : std::cout<<std::endl;
315 : } else {
316 217 : std::cout<<","<<std::endl;
317 : }
318 : }
319 19 : std::cout<<" }"<<std::endl;
320 19 : std::cout<<" }";
321 19 : if( i==cltool_names.size()-1 ) {
322 : std::cout<<std::endl;
323 : } else {
324 18 : std::cout<<","<<std::endl;
325 : }
326 19 : }
327 1 : std::cout<<" }"<<std::endl;
328 1 : std::cout<<"}"<<std::endl;
329 1 : return 0;
330 3 : }
331 :
332 : } // End of namespace
333 : }
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