Added errorString attribute to Network class.

The errorString attribute is used by the readFile() function to store the
error messages that are generated when an invalid MEASURE input file is
loaded. This enables them to remain available after readFile() returns,
so that they can be inspected or displayed in the future.

Note that readFile() now returns the loaded data even when the network
is invalid. Therefore, a proper test for a valid input file is that the
return value from readFile() is not None *and* the errorString of the
returned network is empty.

Author: jwallen

rmgpy/measure/input.py

@@ -517,32 +517,32 @@ def readFile(path):
             errorString0 = ''
             # All isomers must have states data
             if isomer.states is None:
-                errorString0 += '    Required molecular degree of freedom data was not provided.\n'
+                errorString0 += '* Required molecular degree of freedom data was not provided.\n'
             # All isomers must have collision parameters
             if isomer.lennardJones is None:
-                errorString0 += '    Required Lennard-Jones parameters were not provided.\n'
+                errorString0 += '* Required Lennard-Jones parameters were not provided.\n'
             if isomer.molecularWeight == 0:
-                errorString0 += '    Required molecular weight was not provided.\n'
+                errorString0 += '* Required molecular weight was not provided.\n'
             if errorString0 != '':
-                errorString = 'For unimolecular isomer "{0}":\n{1}'.format(isomer, errorString0)
+                errorString = 'For unimolecular isomer "{0}":\n{1}\n'.format(isomer, errorString0)
 
         for rxn in network.pathReactions:
             errorString0 = ''
 
             # If both the reactants and the products are product channels, then the path reaction is invalid
             if rxn.reactants in network.products and rxn.products in network.products:
-                errorString0 += '    Both the reactants and the products are product channels.\n'
+                errorString0 += '* Both the reactants and the products are product channels.\n'
 
             # Reactions of the form A + B -> C + D are not allowed
             elif len(rxn.reactants) > 1 and len(rxn.products) > 1:
-                errorString0 += '    Both the reactants and the products are bimolecular.\n'
+                errorString0 += '* Both the reactants and the products are bimolecular.\n'
 
             # The remaining errors are only meaningful if the path reaction is allowed
             else:
 
                 # All reactions must have either high-pressure-limit kinetics or transition state data
                 if rxn.kinetics is None and rxn.transitionState.states is None:
-                    errorString0 += '    Unable to determine microcanonical rate k(E); you must specify either the high-P kinetics or transition state molecular degrees of freedom.\n'
+                    errorString0 += '* Unable to determine microcanonical rate k(E). you must specify either\n  the high-P kinetics or transition state molecular degrees of freedom.\n'
 
                 # Certain reactions require that both reactants and products have thermo data
                 thermoRequired = False
@@ -557,22 +557,22 @@ def readFile(path):
                 if thermoRequired:
                     for spec in rxn.reactants:
                         if spec.thermo is None:
-                            errorString0 += '    Unable to determine thermo data for reactant "{0}"; you must specify a thermodynamics model.\n'.format(spec)
+                            errorString0 += '* Unable to determine thermodynamics data for reactant "{0}".\n  You must specify molecular degrees of freedom or a thermodynamics model.\n'.format(spec)
                     for spec in rxn.products:
                         if spec.thermo is None:
-                            errorString0 += '    Unable to determine thermo data for product "{0}"; you must specify a thermodynamics model.\n'.format(spec)
+                            errorString0 += '* Unable to determine thermodynamics data for product "{0}".\n  You must specify molecular degrees of freedom or a thermodynamics model.\n'.format(spec)
 
             if errorString0 != '':
-                errorString += 'For path reaction "{0}":\n{1}'.format(rxn, errorString0)
+                errorString += 'For path reaction "{0}":\n{1}\n'.format(rxn, errorString0)
 
         if errorString != '':
             raise InputError(errorString)
 
     except InputError, e:
+        network.errorString = str(e)
         logging.error('The input file "{0}" was invalid:'.format(path))
         logging.info(e)
-        return None
-
+    
     # Print lots of information about the loaded network
     # In particular, we want to give all of the energies on the PES
     # This will help the user decide if the range of energies selected is 
@@ -581,8 +581,9 @@ def readFile(path):
 
     # If there are no isomers, then there's nothing to do
     if len(network.isomers) == 0:
-        logging.info('Could not find any unimolecular isomers based on this network, so there is nothing to do.')
-        return None
+        message = 'Could not find any unimolecular isomers based on this network, so there is nothing to do.'
+        network.errorString = message
+        logging.info(message)
 
     return network, Tlist, Plist, Elist, method, model, Tmin, Tmax, Pmin, Pmax
 

rmgpy/measure/main.py

@@ -131,7 +131,7 @@ def execute(inputFile, outputFile=None, drawFile=None, logFile=None, quiet=False
     params = readFile(os.path.relpath(inputFile))
 
     # Only proceed if the input network is valid
-    if params is not None:
+    if params is not None and params[0].errorString == '':
 
         network, Tlist, Plist, Elist, method, model, Tmin, Tmax, Pmin, Pmax = params
 

rmgpy/measure/network.py

@@ -91,6 +91,7 @@ def __init__(self, index=-1, isomers=None, reactants=None, products=None, pathRe
         self.valid = False
         self.title = title
         self.description = description
+        self.errorString = ''
 
     def __str__(self):
         if self.index != -1: