Add LibSBML conversion option

.gitignore

@@ -17,3 +17,4 @@ README.html
 ABOUT.html
 NEWS.html
 *.~is
+*.bak

moccasin/converter/cleaner.py

@@ -21,6 +21,7 @@
 # ------------------------------------------------------------------------- -->
 
 import sys
+import os
 
 try:
     thisdir = os.path.dirname(os.path.abspath(__file__))

moccasin/converter/converter.py

@@ -898,7 +898,7 @@ def valid_id(text, search=re.compile(r'\A[a-zA-Z_][a-zA-Z0-9_]*\Z').search):
 # -----------------------------------------------------------------------------
 
 def create_raterule_model(parse_results, use_species=True, output_format="sbml",
-                          name_vars_after_param=False, add_comments=True):
+                          name_vars_after_param=False, add_comments=True, convert_to_reactions=False):
 
     # First, gather some initial information.
     working_context = first_function_context(parse_results)
@@ -1022,6 +1022,13 @@ def create_raterule_model(parse_results, use_species=True, output_format="sbml",
             # (in poss-processing) a definition to the SBML produced by Biocham.
             document.post_add.append(('t', 'time'))
 
+    # convert to reactions
+    if convert_to_reactions:
+        prop = ConversionProperties()
+        prop.addOption("inferReactions", True,
+                 "Infer reactions from rateRules in the model");
+        check(document.convert(prop), 'infering reactions failed')
+
     # Finally, return the model, with extra info about things that may need
     # to be added back in post-processing if we are hand this to BIOCHAM.
     output = generate_output(document, add_comments)

moccasin/converter/evaluate_formula.py

@@ -119,6 +119,9 @@ def __init__(self):
             "/": operator.truediv,
             "^": operator.pow
         }
+        self.int_fn = {            
+            "factorial": math.factorial,
+        }
         self.fn = {
             "abs": abs,
             "acos": math.acos,
@@ -131,7 +134,6 @@ def __init__(self):
             "cos": math.cos,
             "cosh": math.cosh,
             "exp": math.exp,  # not working
-            "factorial": math.factorial,
             "floor": math.floor,
             "fix": self.fix,
             "ln": math.log,
@@ -174,6 +176,8 @@ def evaluate_stack(self, s):
             return Decimal(math.e)   # 2.718281828
         elif op in self.fn:
             return Decimal(self.fn[op](self.evaluate_stack(s)))
+        elif op in self.int_fn:
+            return Decimal(self.int_fn[op](int(self.evaluate_stack(s))))
         elif op in self.bin_fn:
             op2 = Decimal(self.evaluate_stack(s))
             op1 = Decimal(self.evaluate_stack(s))

moccasin/converter/expr_tester.py

@@ -22,6 +22,7 @@
 
 import sys
 from collections import defaultdict
+import os
 
 try:
     thisdir = os.path.dirname(os.path.abspath(__file__))

moccasin/converter/finder.py

@@ -21,6 +21,7 @@
 # ------------------------------------------------------------------------- -->
 
 import sys
+import os
 
 try:
     thisdir = os.path.dirname(os.path.abspath(__file__))

moccasin/converter/recognizer.py

@@ -22,6 +22,7 @@
 
 import sys
 from collections import defaultdict
+import os
 
 try:
     thisdir = os.path.dirname(os.path.abspath(__file__))

moccasin/converter/rewriter.py

@@ -22,6 +22,7 @@
 
 import sys
 from decimal import *
+import os
 
 try:
     thisdir = os.path.dirname(os.path.abspath(__file__))

moccasin/interfaces/controller.py

@@ -89,6 +89,14 @@ def build_model(self, use_species, output_format, name_after_param, add_comments
                                                add_comments)
         return output
 
+    def build_reaction_model_libsbml(self, use_species, name_after_param, add_comments):
+        '''Converts a parsed file into reaction-based SBML.'''
+
+        (output, _, _) = create_raterule_model(self.parse_results, use_species,
+                                               'sbml', name_after_param,
+                                               add_comments, convert_to_reactions=True)
+        return output
+
 
     def build_reaction_model(self, use_species, name_after_param, add_comments):
         '''Converts a parsed file into reaction-based SBML.'''

moccasin/interfaces/moccasin_CLI.py

@@ -61,11 +61,12 @@
     debug_parser  = ('print debug information about the parsed MATLAB',        'flag', 'D'),
     version       = ('print MOCCASIN version info and exit',                   'flag', 'V'),
     no_comments   = ('do not insert version comments into SBML output',        'flag', 'X'),
+    use_libsbml   = ('use libsbml converter for reaction-based SBML (default=False)',   'flag', 'l'),
     paths         = 'paths to MATLAB input files to convert'
 )
 
 def cli_main(gui, use_equations, use_params, quiet, relaxed, xpp_output,
-             no_color, debug_parser, version, no_comments, *paths):
+             no_color, debug_parser, version, no_comments, use_libsbml=False, *paths):
     '''Interface for controlling MOCCASIN, the MATLAB ODE converter for SBML.
 MOCCASIN can take certain forms of ODE (ordinary differential equation) models
 written in MATLAB and Octave and export them as SBML files.  MOCCASIN does not
@@ -128,6 +129,9 @@ def cli_main(gui, use_equations, use_params, quiet, relaxed, xpp_output,
   -e  (/e on Windows) makes the translator create equation-based SBML output,
       instead of converting the model to reaction-based form (the default)
 
+  -l  (/l on Windows) makes the translator use libsbml for the reaction-based
+        SBML output, instead of biocham
+
   -p  (/p on windows) makes the translator encode variables as SBML
       parameters, instead of the default, which is to use SBML species
 
@@ -153,7 +157,7 @@ def cli_main(gui, use_equations, use_params, quiet, relaxed, xpp_output,
     add_comments = not no_comments
 
     if gui or not any([paths, use_equations, use_params, xpp_output,
-                       version, debug_parser, quiet, no_comments]):
+                       version, debug_parser, quiet, no_comments, use_libsbml]):
         moccasin_GUI.gui_main()
         sys.exit()
     if version:
@@ -166,7 +170,7 @@ def cli_main(gui, use_equations, use_params, quiet, relaxed, xpp_output,
         sys.exit()
     if not paths:
         raise SystemExit(color('Must provide a path to a file.', 'error', colorize))
-    if not xpp_output and not use_equations and not have_network():
+    if not xpp_output and not use_equations and not use_libsbml and not have_network():
         raise SystemExit(color('No network connection.', 'error', colorize))
     if not quiet:
         from halo import Halo
@@ -204,10 +208,16 @@ def convert(path):
                                             name_after_param = False,
                                             add_comments = add_comments)
         else:
-            text = 'Reaction-based SBML output'
-            output = controller.build_reaction_model(use_species = (not use_params),
-                                                     name_after_param = False,
-                                                     add_comments = add_comments)
+            if use_libsbml:
+                text = 'Reaction-based SBML output (libsbml)'
+                output = controller.build_reaction_model_libsbml(use_species = (not use_params),
+                                                        name_after_param = False,
+                                                        add_comments = add_comments)
+            else:
+                text = 'Reaction-based SBML output (biocham)'
+                output = controller.build_reaction_model(use_species = (not use_params),
+                                                        name_after_param = False,
+                                                        add_comments = add_comments)
         if debug_parser:
             print_header(text, 'info', quiet, colorize)
             msg(output)
@@ -222,6 +232,9 @@ def convert(path):
                         'warning', colorize)
                     msg('Renaming to "{}".'.format(backup_path),
                         'warning', colorize)
+                # remove backup if it exists (otherwise rename will fail)
+                if os.path.exists(backup_path):
+                    os.remove(backup_path)
                 os.rename(output_path, backup_path)
             with open(output_path, 'w') as output_file:
                 output_file.write(output)

moccasin/interfaces/moccasin_GUI.py

@@ -303,7 +303,7 @@ def __init__(self, parent):
         sbSizer9.Add(gSizer7, 0, wx.EXPAND, 5)
 
         optionInset = wx.StaticBoxSizer(wx.StaticBox(self, wx.ID_ANY, "Conversion options"), wx.VERTICAL)
-        optionGrid = wx.GridSizer(1, 2, 10, 10)
+        optionGrid = wx.GridSizer(1, 3, 10, 10)
 
         self.assumeTranslatable = wx.CheckBox(self, id = wx.ID_ANY,
                                               label = 'Assume array operations are not used')
@@ -318,6 +318,15 @@ def __init__(self, parent):
         self.addMoccasinComments.Value = True
         self.addMoccasinComments.SetToolTip("Write a comment into the output file with the MOCCASIN version, time stamp, and other information.")
         optionGrid.Add(self.addMoccasinComments, flag = wx.ALL, border = 6)
+
+        self.useLibSBML = wx.CheckBox(self, id = wx.ID_ANY,
+                                      label = 'Use LibSBML Conveter')
+        self.useLibSBML.SetToolTip("Use LibSBML to convert from raterules to reactions (if false, it will use BIOCHAM)")
+        self.useLibSBML.SetFont(labelFont)
+        self.useLibSBML.Value = True
+        self.useLibSBML.SetToolTip("Use LibSBML to convert from raterules to reactions (if false, it will use BIOCHAM)")
+        optionGrid.Add(self.useLibSBML, flag = wx.ALL, border = 6)
+
         optionInset.Add(optionGrid, 0, wx.EXPAND, 0)
 
         self.convertButton = wx.Button(self, wx.ID_ANY, "Convert",
@@ -339,29 +348,32 @@ def __init__(self, parent):
         panelTextFont = wx.Font(wx.NORMAL_FONT.GetPointSize() -1, 70, 90,
                                 wx.FONTWEIGHT_NORMAL, False, wx.EmptyString)
 
-        midPanelSizer = wx.StaticBoxSizer(wx.StaticBox(self, wx.ID_ANY, "MATLAB File"),
-                                          wx.VERTICAL)
-        self.matlabWebView = wx.html2.WebView.New(self, wx.ALIGN_BOTTOM|wx.ALL|wx.EXPAND )
+        #midPanelSizer = wx.StaticBoxSizer(wx.StaticBox(self, wx.ID_ANY, "MATLAB File"),
+        #                                  wx.VERTICAL)
+        midPanelSizer = wx.BoxSizer(wx.VERTICAL)
+        self.matlabWebView = wx.html2.WebView.New(self, wx.ALL|wx.EXPAND )
         self.matlabWebView.SetForegroundColour(wx.SystemSettings.GetColour(wx.SYS_COLOUR_WINDOWTEXT))
         wxSetToolTip(self.matlabWebView, "Input file for conversion")
         self.matlabWebView.SetFont(panelTextFont)
         self.matlabWebView.SetPage(_EMPTY_PAGE, "")
-        midPanelSizer.Add(self.matlabWebView, 1, wx.ALIGN_BOTTOM|wx.ALL|wx.EXPAND, 5)
+        midPanelSizer.Add(self.matlabWebView, 1, wx.ALL|wx.EXPAND, 5)
         mainSizer.Add(midPanelSizer, 2, wx.ALL|wx.EXPAND, 5)
         mainSizer.Add(buttonVSizer, 0, wx.ALL|wx.EXPAND, 0)
 
         # Bottom sizer
-        bottomPanelSizer = wx.StaticBoxSizer(
-            wx.StaticBox(self, wx.ID_ANY, "Converted File"), wx.VERTICAL)
+        #bottomPanelSizer = wx.StaticBoxSizer(
+        #    wx.StaticBox(self, wx.ID_ANY, "Converted File"), wx.VERTICAL)
+        bottomPanelSizer = wx.BoxSizer(wx.VERTICAL)
         self.convertedWebView = wx.html2.WebView.New(
-            self, wx.ALIGN_BOTTOM|wx.ALL|wx.EXPAND)
+            self, wx.ALL|wx.EXPAND)
         self.convertedWebView.SetForegroundColour(
             wx.SystemSettings.GetColour(wx.SYS_COLOUR_WINDOWTEXT))
         self.convertedWebView.SetFont(panelTextFont)
+        self.convertedWebView.SetZoomType(wx.html2.WEBVIEW_ZOOM_TYPE_LAYOUT)
         wxSetToolTip(self.convertedWebView, "Output file after conversion")
         self.convertedWebView.SetPage(_EMPTY_PAGE, "")
         bottomPanelSizer.Add(
-            self.convertedWebView, 1, wx.ALIGN_BOTTOM|wx.ALL|wx.EXPAND, 5)
+            self.convertedWebView, 1, wx.ALL|wx.EXPAND, 5)
         mainSizer.Add(bottomPanelSizer, 2, wx.ALL|wx.EXPAND, 5)
 
         # Set frame sizer
@@ -384,8 +396,7 @@ def __init__(self, parent):
         self.Bind(wx.EVT_MENU, self.OnPageSetup, id= self.pageSetup.GetId())
         self.Bind(wx.EVT_MENU, self.OnPrint, id=self.printOption.GetId())
         self.Bind(wx.EVT_MENU_RANGE, self.onFileHistory, id=wx.ID_FILE1, id2=wx.ID_FILE9)
-        self.Bind(wx.EVT_CLOSE, self.onClose)
-
+        self.Bind(wx.EVT_CLOSE, self.onClose)        
 
     def __del__(self):
         pass
@@ -494,20 +505,31 @@ def onConvert(self, event):
                 self.statusBar.SetStatusText("SBML format - equations", 2)
             # Output reaction-based SBML
             else:
-                if not have_network():
-                    msg = "A network connection is needed for this feature, but the network appears to be unavailable."
-                    dlg = wx.MessageDialog(self, msg, "Warning", wx.OK | wx.ICON_WARNING)
-                    dlg.ShowModal()
-                    dlg.Destroy()
-                else:
-                    sbml = self.controller.build_reaction_model(
-                        use_species = self.varsAsSpecies.GetValue(),
-                        name_after_param = False,
-                        add_comments = self.addMoccasinComments.Value)
+                use_libSBML = self.useLibSBML.GetValue()
+                if use_libSBML:
+                    sbml = self.controller.build_reaction_model_libsbml(
+                            use_species = self.varsAsSpecies.GetValue(),
+                            name_after_param = False,
+                            add_comments = self.addMoccasinComments.Value)
 
                     self.convertedWebView.SetPage(tokenize(sbml, "xml", "borland"), "")
-                    self.statusBar.SetStatusText("SBML format - reactions",  2)
+                    self.statusBar.SetStatusText("SBML format - reactions (libsbml)",  2)
                     self._output_saved = False
+                else:
+                    if not have_network():
+                        msg = "A network connection is needed for this feature, but the network appears to be unavailable."
+                        dlg = wx.MessageDialog(self, msg, "Warning", wx.OK | wx.ICON_WARNING)
+                        dlg.ShowModal()
+                        dlg.Destroy()
+                    else:
+                        sbml = self.controller.build_reaction_model(
+                            use_species = self.varsAsSpecies.GetValue(),
+                            name_after_param = False,
+                            add_comments = self.addMoccasinComments.Value)
+
+                        self.convertedWebView.SetPage(tokenize(sbml, "xml", "borland"), "")
+                        self.statusBar.SetStatusText("SBML format - reactions (BIOCHAM)",  2)
+                        self._output_saved = False
 
         except IOError as err:
             wx.EndBusyCursor()

moccasin/matlab_parser/context.py

@@ -22,6 +22,7 @@
 
 from __future__ import print_function
 import collections
+from collections.abc import MutableMapping
 from pyparsing import ParseResults
 
 
@@ -34,7 +35,7 @@
 #
 # This next class def is based on http://stackoverflow.com/a/7760938/743730
 
-class ContextDict(collections.MutableMapping, dict):
+class ContextDict(MutableMapping, dict):
     """Class used to implement MatlabContext properties that are dictionaries."""
 
     def __getitem__(self, key):

moccasin/matlab_parser/matlab.py

@@ -229,7 +229,7 @@ def row_to_string(row):
             body = MatlabNode.as_string(thing.body)
             return '@(' + arg_list + ')' + body
         elif isinstance(thing, Comment) or isinstance(thing, FunDef) \
-             or isinstance(thing, Command):
+             or isinstance(thing, ShellCommand):
             # No reason for as_string called for these things, but must catch
             # random mayhem before falling through to the final case.
             return None
@@ -853,10 +853,11 @@ def visit(self, node):
 
     def default_visit(self, node):
         """Default visitor.  Users can redefine this if desired."""
-        for a in type(node)._visitable_attr:
-            value = getattr(node, a, None)
-            if value:
-                setattr(node, a, self.visit(value))
+        if isinstance(node, MatlabNode):
+            for a in type(node)._visitable_attr:
+                value = getattr(node, a, None)
+                if value:
+                    setattr(node, a, self.visit(value))
         return node