From 131c668d51011adea68832310a0c15f875399fdf Mon Sep 17 00:00:00 2001
From: Gareth Aneurin Tribello <garethtribello@Gareths-MacBook-Pro.local>
Date: Sat, 26 Oct 2024 16:21:37 +0100
Subject: [PATCH] Further work on modals that contain extracts from auxilliary
 input files

---
 PlumedToHTML/PlumedFormatter.py      | 16 +++++++++-------
 PlumedToHTML/PlumedToHTML.py         | 14 +++++++++++---
 PlumedToHTML/tests/test_formatter.py |  2 +-
 setup.py                             |  2 +-
 4 files changed, 22 insertions(+), 12 deletions(-)

diff --git a/PlumedToHTML/PlumedFormatter.py b/PlumedToHTML/PlumedFormatter.py
index 504a359..7d5035a 100644
--- a/PlumedToHTML/PlumedFormatter.py
+++ b/PlumedToHTML/PlumedFormatter.py
@@ -18,6 +18,7 @@ def __init__(self, **options) :
         self.hasload=options["hasload"]
         self.broken=options["broken"]
         self.auxinputs=options["auxinputs"]
+        self.auxinputlines=options["auxinputlines"]
         self.valuedict=options["valuedict"]
         self.actions=options["actions"]
         self.valcolors = { 
@@ -140,13 +141,13 @@ def format(self, tokensource, outfile):
                         iff = open( inp, 'r' )
                         fcontent = iff.read()
                         iff.close()
-                        if len(fcontent.splitlines())>5 : 
-                           n, shortversion = 0, ""
-                           for l in fcontent.splitlines() :
-                               shortversion += l + "\n"
-                               n = n + 1
-                               if n==5 : break
-                           shortversion += "...\n" + fcontent.splitlines()[-1]
+                        if len(self.auxinputlines)>0 : 
+                           shortversion, allines = "", fcontent.splitlines()
+                           for n, l in enumerate(self.auxinputlines) : 
+                               bounds = l.split("-")
+                               start, end = int( bounds[0] ), int( bounds[1] )
+                               if n>0 : shortversion += "...\n"
+                               for kk in range(start,end+1) : shortversion += allines[kk-1] + "\n"
                            fcontent = shortversion
                         outfile.write('<div class="tooltip">' + inp + '<div class="right"> Click <a onclick=\'openModal("' + self.egname + inp + '")\'>here</a> to see an extract from this file.<i></i></div></div>')
                         outfile.write('<div id="' + self.egname + inp + '" class="modal">')
@@ -223,6 +224,7 @@ def format(self, tokensource, outfile):
                         else : raise Exception("keyword " + value.strip().upper() + " is not in syntax for action " + action )
                   if desc=="" and self.broken : outfile.write( value )
                   else :
+                     if action not in self.keyword_dict : raise Exception("action " + action + " not present in keyword dictionary")
                      if "actionlink" in self.keyword_dict[action]["syntax"][mykey].keys() and self.keyword_dict[action]["syntax"][mykey]["actionlink"]!="none" : 
                         linkaction = self.keyword_dict[action]["syntax"][mykey]["actionlink"]
                         desc = desc + ". Options for this keyword are explained in the documentation for <a href=\"" + self.keyword_dict[linkaction]["hyperlink"] + "\">" + linkaction + "</a>.";  
diff --git a/PlumedToHTML/PlumedToHTML.py b/PlumedToHTML/PlumedToHTML.py
index 29436bf..ac33254 100644
--- a/PlumedToHTML/PlumedToHTML.py
+++ b/PlumedToHTML/PlumedToHTML.py
@@ -186,14 +186,22 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxch
     inpt, incomplete = manage_incomplete_inputs( inpt )
 
     # Create a list of all the auxiliary input files that are needed by the plumed input 
-    inputfiles = []
+    inputfiles, inputfilelines = [], []
     for line in inpt.splitlines() :
         if "#SETTINGS" in line :
            for word in line.split() :
                if "MOLFILE=" in word : 
-                   inputfiles.append( word.replace("MOLFILE=","") )
+                   molfile = word.replace("MOLFILE=","")
+                   iff = open( molfile, 'r' )
+                   content = iff.read()
+                   iff.close()
+                   inputfiles.append(molfile)
+                   inputfilelines.append("1-5")
+                   inputfilelines.append( str(len(content.splitlines())-4) + "-" + str(len(content.splitlines())) ) 
                elif "INPUTFILES=" in word : 
                    for n in word.replace("INPUTFILES=","").split(",") : inputfiles.append( n )
+               elif "INPUTFILELINES=" in word : 
+                   inputfilelines = word.replace("INPUTFILELINES=","").split(",")
 
     # Check for include files
     foundincludedfiles, srcdir = True, str(pathlib.PurePosixPath(name).parent)
@@ -235,7 +243,7 @@ def get_html( inpt, name, outloc, tested, broken, plumedexe, usejson=None, maxch
     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), auxinputs=inputfiles, valuedict=valuedict, actions=actions )
+    plumed_formatter = load_formatter_from_file(formatfile, "PlumedFormatter", keyword_file=keyfile, input_name=name, hasload=found_load, broken=any(broken), auxinputs=inputfiles, auxinputlines=inputfilelines, valuedict=valuedict, actions=actions )
 
     # Now generate html of input
     html = '<div style="width: 100%; float:left">\n'
diff --git a/PlumedToHTML/tests/test_formatter.py b/PlumedToHTML/tests/test_formatter.py
index e8c91ef..dd3895b 100644
--- a/PlumedToHTML/tests/test_formatter.py
+++ b/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({}), valuedict=dict({}), auxinputs=[] )
+       f = PlumedFormatter( keyword_file=keyfile, input_name="testout", hasload=False, broken=False, actions=set({}), valuedict=dict({}), auxinputs=[], auxinputlines=[] )
 
        # Now run over all the inputs in the json
        for item in tests["regtests"] :
diff --git a/setup.py b/setup.py
index cd82fc3..52b9e56 100644
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 setuptools.setup(
      name='PlumedToHTML',  
-     version='0.87',
+     version='0.89',
      author="Gareth Tribello",
      author_email="gareth.tribello@gmail.com",
      description="A package for creating pretified HTML for PLUMED files",