Added functionality to add DOIs to syntax file and then cite them usi…

…ng plumed.cite command (#1202)

* Added functionality to add DOIs to syntax file and then cite them using plumed.cite command

* Fixed python issue that github points out

---------

Co-authored-by: Gareth Aneurin Tribello <[email protected]>

json/doi_manager.py

@@ -0,0 +1,36 @@
+import subprocess
+import json
+
+def get_dois_from_syntax() :
+  with open("syntax.json") as f :
+    try:
+       plumed_syntax = json.load(f)
+    except ValueError as ve:
+       raise InvalidJSONError(ve)
+
+  doilist = []
+  for key, value in plumed_syntax.items() :
+      if not isinstance(value,dict) or "dois" not in value.keys() : continue
+      for doi in value["dois"] : 
+          if doi not in doilist : doilist.append(doi)
+  return doilist
+
+def get_reference(doi):
+    # initialize strings
+    ref="" 
+    # retrieve citation from doi
+    if(len(doi)>0):
+       # get citation
+       cit = subprocess.check_output('curl -LH "Accept: text/bibliography; style=science" \'http://dx.doi.org/'+doi+'\'', shell=True).decode('utf-8').strip()
+       if("DOI Not Found" in cit) : ref="DOI not found"
+       else: ref=cit[3:cit.find(", doi")]
+    return ref
+
+if __name__ == "__main__" :
+   # Get all the dois that are listed in the syntax file
+   doilist = get_dois_from_syntax()
+   # Now get all the references using Max's magic script and create the map
+   with open("../src/tools/CitationMap.inc","w+") as of :
+       for doi in doilist : 
+           if doi==doilist[-1] : of.write("{\"" + doi + "\",\"" + get_reference(doi) + "\"}") 
+           else : of.write("{\"" + doi + "\",\"" + get_reference(doi) + "\"}")

src/adjmat/AdjacencyMatrixBase.cpp

@@ -43,6 +43,7 @@ void AdjacencyMatrixBase::registerKeywords( Keywords& keys ) {
   keys.addOutputComponent("y","COMPONENTS","matrix","the projection of the bond on the y axis");
   keys.addOutputComponent("z","COMPONENTS","matrix","the projection of the bond on the z axis");
   keys.setValueDescription("matrix","a matrix containing the weights for the bonds between each pair of atoms");
+  keys.addDOI("10.1021/acs.jctc.6b01073");
 }
 
 AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao):
@@ -174,7 +175,7 @@ AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions& ao):
     addComponent( "z", shape );
     componentIsNotPeriodic("z");
   }
-  log<<"  Bibliography "<<plumed.cite("Tribello, Giberti, Sosso, Salvalaglio and Parrinello, J. Chem. Theory Comput. 13, 1317 (2017)")<<"\n";
+  log<<"  Bibliography "<<plumed.cite("10.1021/acs.jctc.6b01073")<<"\n";
 }
 
 unsigned AdjacencyMatrixBase::getNumberOfDerivatives() {

src/cltools/GenJson.cpp

@@ -176,6 +176,15 @@ int GenJson::main(FILE* in, FILE*out,Communicator& pc) {
       }
       std::cout<<"    \"replacement\" : \""<<replacement<<"\",\n";
     }
+    std::cout<<"     \"dois\" : [";
+    unsigned ndoi = keys.getDOIList().size();
+    if( ndoi>0 ) {
+      std::cout<<"\"" + keys.getDOIList()[0] + "\"";
+      for(unsigned j=1; j<ndoi; ++j) {
+        std::cout<<", \"" + keys.getDOIList()[j] + "\"";
+      }
+    }
+    std::cout<<"],\n";
     std::cout<<"    \"syntax\" : {"<<std::endl;
     for(unsigned j=0; j<keys.size(); ++j) {
       std::string defa = "", desc = keys.getKeywordDescription( keys.getKeyword(j) );

src/clusters/ClusteringBase.cpp

@@ -28,6 +28,7 @@ namespace clusters {
 void ClusteringBase::registerKeywords( Keywords& keys ) {
   matrixtools::MatrixOperationBase::registerKeywords( keys );
   keys.setValueDescription("vector","vector with length that is equal to the number of rows in the input matrix.  Elements of this vector are equal to the cluster that each node is a part of");
+  keys.addDOI("10.1021/acs.jctc.6b01073");
 }
 
 ClusteringBase::ClusteringBase(const ActionOptions&ao):
@@ -49,6 +50,7 @@ ClusteringBase::ClusteringBase(const ActionOptions&ao):
   // Resize local variables
   which_cluster.resize( getPntrToArgument(0)->getShape()[0] );
   cluster_sizes.resize( getPntrToArgument(0)->getShape()[0] );
+  log<<"  Bibliography "<<plumed.cite("10.1021/acs.jctc.6b01073")<<"\n";
 }
 
 void ClusteringBase::retrieveAdjacencyLists( std::vector<unsigned>& nneigh, Matrix<unsigned>& adj_list ) {

src/tools/.gitignore

@@ -7,3 +7,4 @@
 !/Makefile
 !/README
 !/module.type
+!/CitationMap.inc

src/tools/CitationMap.inc

@@ -0,0 +1 @@
+{"10.1021/acs.jctc.6b01073","G. A. Tribello, F. Giberti, G. C. Sosso, M. Salvalaglio, M. Parrinello, Analyzing and Driving Cluster Formation in Atomistic Simulations. Journal of Chemical Theory and Computation. 13, 1317–1327 (2017)"}

src/tools/Citations.cpp

@@ -26,14 +26,23 @@
 
 namespace PLMD {
 
+const static Tools::FastStringUnorderedMap<std::string> doi_map = {
+#include "CitationMap.inc"
+};
+
 std::string Citations::cite(const std::string & item) {
+  std::string myref=item;
+  if( doi_map.find(item)!=doi_map.end() ) {
+    myref=doi_map.find(item)->second;
+  }
+
   unsigned i;
   for(i=0; i<items.size(); ++i)
-    if(items[i]==item) {
+    if(items[i]==myref) {
       break;
     }
   if(i==items.size()) {
-    items.push_back(item);
+    items.push_back(myref);
   }
   plumed_assert(i<items.size());
   std::string ret;

src/tools/Keywords.cpp

@@ -1159,6 +1159,14 @@ std::string Keywords::getReplacementAction() const {
   return replaceaction;
 }
 
+void Keywords::addDOI( const std::string& doi ) {
+  doilist.push_back( doi );
+}
+
+const std::vector<std::string>& Keywords::getDOIList() const {
+  return doilist;
+}
+
 void Keywords::linkActionInDocs( const std::string& k, const std::string& action ) {
   plumed_massert( exists(k), "no " + k + " keyword" );
   keywords.at(k).setLinkedAction(action);

src/tools/Keywords.h

@@ -150,6 +150,8 @@ class Keywords {
   std::vector<std::string> neededActions;
 /// List of suffixes that can be used with this action
   std::vector<std::string> actionNameSuffixes;
+/// List of doi's that should appear in the manual
+  std::vector<std::string> doilist;
 /// Print the documentation for the named keyword in html
   void print_html_item( const std::string& ) const;
 public:
@@ -312,6 +314,10 @@ class Keywords {
   std::string getReplacementAction() const ;
 /// Note that this action has been deprecated
   void setDeprecated( const std::string& name );
+/// Add a DOI to the list in the manual page for this action
+  void addDOI( const std::string& doi );
+/// Get the list of DOI
+  const std::vector<std::string>& getDOIList() const ;
 /// Create a link to this action in the documentation for it
   void linkActionInDocs( const std::string& k, const std::string& action );
 /// Get any actions that are linked to this keyword