Added code to deal with value types that we can get from plumed

PlumedToHTML/PlumedFormatter.py

@@ -16,7 +16,16 @@ def __init__(self, **options) :
         self.egname=options["input_name"]
         self.hasload=options["hasload"]
         self.broken=options["broken"]
+        self.valuedict=options["valuedict"]
         self.actions=options["actions"]
+        self.valcolors = { 
+           "scalar": "black", 
+           "atoms": "violet", 
+           "vector": "blue", 
+           "matrix": "red", 
+           "grid": "green", 
+           "mix": "brown" 
+        }
 
     def format(self, tokensource, outfile):
         action, label, all_labels, keywords, shortcut_state, shortcut_depth, default_state, notooltips, expansion_label = "", "", set(), [], 0, 0, 0, False, ""
@@ -31,7 +40,8 @@ def format(self, tokensource, outfile):
                   # This outputs information on the values computed in the previous action for the header
                   if label not in all_labels : 
                      all_labels.add(label)
-                     if action in self.keyword_dict and "output" in self.keyword_dict[action]["syntax"] : self.writeValuesData( outfile, action, label, keywords, self.keyword_dict[action]["syntax"]["output"] )
+                     if label in self.valuedict.keys() : self.writeValueInfo( outfile, action, label, self.valuedict[label] )
+                     elif action in self.keyword_dict and "output" in self.keyword_dict[action]["syntax"] : self.writeValuesData( outfile, action, label, keywords, self.keyword_dict[action]["syntax"]["output"] )
                      else : 
                         outfile.write('<span style="display:none;" id="' + self.egname + label + r'">')
                         outfile.write('The ' + action + ' action with label <b>' + label + '</b> calculates something') 
@@ -137,7 +147,13 @@ def format(self, tokensource, outfile):
                # Labels of actions
                if not self.broken and action!="" and label!="" and label!=value.strip() : raise Exception("label for " + action + " is not what is expected.  Is " + label + " should be " + value.strip() )
                elif label=="" : label = value.strip() 
-               outfile.write('<b name="' + self.egname + label + '" onclick=\'showPath("' + self.divname + '","' + self.egname + label + '")\'>' + value + '</b>')
+               valtype = "mix"
+               if label in self.valuedict.keys() :
+                  valtype = "unset"
+                  for key, ddd in self.valuedict[label].items() :
+                      if valtype=="unset" : valtype = ddd["type"]
+                      elif valtype!=ddd["type"] : valtype = "mix" 
+               outfile.write('<b name="' + self.egname + label + '" onclick=\'showPath("' + self.divname + '","' + self.egname + label + '","' + self.valcolors[valtype] + '")\'>' + value + '</b>')
             elif ttype==Comment :
                # Comments
                outfile.write('<span style="color:blue" class="comment">' + value + '</span>' )
@@ -194,7 +210,8 @@ def format(self, tokensource, outfile):
         # Check if there is stuff to output for the last action in the file
         if len(label)>0 and label not in all_labels :
            all_labels.add( label )
-           if action in self.keyword_dict and "output" in self.keyword_dict[action]["syntax"] : self.writeValuesData( outfile, action, label, keywords, self.keyword_dict[action]["syntax"]["output"] )
+           if label in self.valuedict.keys() : self.writeValueInfo( outfile, action, label, self.valuedict[label] )
+           elif action in self.keyword_dict and "output" in self.keyword_dict[action]["syntax"] : self.writeValuesData( outfile, action, label, keywords, self.keyword_dict[action]["syntax"]["output"] )
            else : 
               outfile.write('<span style="display:none;" id="' + self.egname + label + r'">')
               outfile.write('The ' + action + ' action with label <b>' + label + '</b> calculates something')
@@ -224,6 +241,17 @@ def writeValuesData( self, outfile, action, label, keywords, outdict ) :
                     if flag==value["flag"] : present=True
                 if present or value["flag"]=="default" : outfile.write('<tr><td width="5%">' + label + "." + key + '</td><td>' + value["description"] + '</td></tr>')
             outfile.write('</table>')
+        outfile.write('</span>')
 
+    def writeValueInfo( self, outfile, action, label, valinfo ) :
+        # Some header stuff 
+        outfile.write('<span style="display:none;" id="' + self.egname + label + r'">')
+        outfile.write('The ' + action + ' action with label <b>' + label + '</b>')
+        outfile.write(' calculates the following quantities:')
+        outfile.write('<table  align="center" frame="void" width="95%" cellpadding="5%">')
+        outfile.write('<tr><td width="5%"><b> Quantity </b>  </td><td width="5%"><b> Type </b>  </td><td><b> Description </b> </td></tr>')
+        for key, value in valinfo.items() :
+            outfile.write('<tr><td width="5%">' + key + '</td><td width="5%"><font color="' + self.valcolors[value["type"]] +'">' + value["type"] + '</font></td><td>' + value["description"] + '</td></tr>')
+        outfile.write('</table>') 
         outfile.write('</span>')
 

PlumedToHTML/PlumedToHTML.py

@@ -52,15 +52,15 @@ def test_and_get_html( inpt, name, actions=set({}) ) :
     iff.write(test_inpt + "\n")
     iff.close()
     # Now do the test
-    broken = test_plumed( "plumed", filename, header="", shortcutfile=name + '.json' )
+    broken = test_plumed( "plumed", filename, header="", shortcutfile=name + '.json' ) #, valuefile='values_' + name + '.json' )
     # Retrieve the html that is output by plumed
     html = get_html( inpt, name, name, ("master",), (broken,), ("plumed",), actions )
     # Remove the tempory files that we created
     if not keepfile : os.remove(filename)
 
     return html
 
-def test_plumed( executible, filename, header=[], shortcutfile=[] ) :
+def test_plumed( executible, filename, header=[], shortcutfile=[], valuefile=[] ) :
     """
         Test if plumed can parse this input file
 
@@ -71,6 +71,7 @@ def test_plumed( executible, filename, header=[], shortcutfile=[] ) :
         filename     -- A string that contains the name of the plumed input file to parse
         header       -- A string to put at the top of the error page that is output
         shortcutfile -- The file on which to output the json file containing the expansed shortcuts.  If not present this is not output 
+        valuefile -- The file on which to output the dictionary explaining what each value represents.  If not present this is not output
     """
     # Get the information for running the code
     run_folder = str(pathlib.PurePosixPath(filename).parent)
@@ -88,6 +89,8 @@ def test_plumed( executible, filename, header=[], shortcutfile=[] ) :
     if int(nreplicas)>1 : cmd = ['mpirun', '-np', str(nreplicas)] + cmd + ['--multi', str(nreplicas)]
     # Add the shortcutfile output if the user has asked for it
     if len(shortcutfile)>0 : cmd = cmd + ['--shortcut-ofile', shortcutfile]
+    # Add the value dictionary if the user has asked for it
+    if len(valuefile)>0 : cmd = cmd + ['--valuedict-ofile', valuefile] 
     # raw std output - to be zipped
     outfile=filename + "." + executible + ".stdout.txt"
     # raw std error - to be zipped
@@ -189,6 +192,15 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
        os.remove( name + ".json") 
     else : final_inpt = inpt   
 
+    # Check for value dictionary to use to create labels
+    if os.path.exists( 'values_' + name + '.json') :
+       with open('values_' + name + '.json') as f :
+           try:
+              valuedict = json.load(f)
+           except ValueError as ve:
+              raise InvalidJSONError(ve)
+    else : valuedict = {}
+
     # Create the lexer that will generate the pretty plumed input
     lexerfile = os.path.join(os.path.dirname(__file__),"PlumedLexer.py")
     plumed_lexer = load_lexer_from_file(lexerfile, "PlumedLexer" )
@@ -197,7 +209,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
     plumed_info = subprocess.run(cmd, capture_output=True, text=True ) 
     keyfile = plumed_info.stdout.strip() + "/json/syntax.json"
     formatfile = os.path.join(os.path.dirname(__file__),"PlumedFormatter.py")
-    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_file=keyfile, input_name=name, hasload=found_load, broken=any(broken), actions=actions )
+    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_file=keyfile, input_name=name, hasload=found_load, broken=any(broken), valuedict=valuedict, actions=actions )
 
     # Now generate html of input
     html = '<div style="width: 100%; float:left">\n'
@@ -239,8 +251,8 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, actions=set({}) ) :
     for val in soup.find_all("b") :
         if "onclick" in val.attrs.keys() :
            vallabels = val.attrs["onclick"].split("\"")
-           if not soup.find("span", {"id": vallabels[3]}) : raise Exception("Generated html is invalid as label hidden box for label " + vallabel + " is missing")
-           if not soup.find("div", {"id": "value_details_" + vallabels[1]}) : raise Exception("Generated html is invalid as there is no place to show data for " + vallabel)
+           if not soup.find("span", {"id": vallabels[3]}) : raise Exception("Generated html is invalid as label hidden box for label " + vallabels[3] + " is missing")
+           if not soup.find("div", {"id": "value_details_" + vallabels[1]}) : raise Exception("Generated html is invalid as there is no place to show data for " + vallabell[1])
 
     # Now check the togglers
     for val in soup.find_all(attrs={'class': 'toggler'}) :

PlumedToHTML/assets/header.html

@@ -62,11 +62,11 @@
 </style>
 <script>
 var redpath="";
-function showPath(eg,name) {
+function showPath(eg,name,color) {
   var i; var y = document.getElementsByName(redpath);
-  for (i=0; i < y.length; i++ ) { y[i].style.color="black"; }
+  for (i=0; i < y.length; i++ ) { y[i].style.color=""; }
   var x = document.getElementsByName(name); redpath=name;
-  for (i = 0; i < x.length; i++) { x[i].style.color="red"; }
+  for (i = 0; i < x.length; i++) { x[i].style.color=color; }
   var valid="value_details_".concat(eg);
   var valueField = document.getElementById(valid);
   var dataField = document.getElementById(name);

PlumedToHTML/tests/test_formatter.py

@@ -22,7 +22,7 @@ def testSimple(self) :
        keyfile = plumed_info.stdout.strip() + "/json/syntax.json"
 
        # Setup a plumed formatter
-       f = PlumedFormatter( keyword_file=keyfile, input_name="testout", hasload=False, broken=False, actions=set({}) )
+       f = PlumedFormatter( keyword_file=keyfile, input_name="testout", hasload=False, broken=False, actions=set({}), valuedict=dict({}) )
 
        # Now run over all the inputs in the json
        for item in tests["regtests"] :