1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/commits/530fb4f8204f/ changeset: 530fb4f8204f user: dan date: 2013-01-08 16:41:32 summary: Fix for grouping parameters value_from_basic when ignore_errors is True. Fixes issue seen in workflows and rerun where an invalid stored value (e.g. due to changing parameter types) is provided. affected #: 1 file

diff -r 94bfcccdaf0625448e623d1d88ba9a1b7785ee78 -r 530fb4f8204f2106e11f419c381fd53d2319ce24 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -68,21 +68,25 @@ return rval def value_from_basic( self, value, app, ignore_errors=False ): rval = [] - for i, d in enumerate( value ): - rval_dict = {} - # If the special __index__ key is not set, create it (for backward - # compatibility) - rval_dict['__index__'] = d.get( '__index__', i ) - # Restore child inputs - for input in self.inputs.itervalues(): - if ignore_errors and input.name not in d: - # If we do not have a value, and are ignoring errors, we simply - # do nothing. There will be no value for the parameter in the - # conditional's values dictionary. - pass - else: - rval_dict[ input.name ] = input.value_from_basic( d[input.name], app, ignore_errors ) - rval.append( rval_dict ) + try: + for i, d in enumerate( value ): + rval_dict = {} + # If the special __index__ key is not set, create it (for backward + # compatibility) + rval_dict['__index__'] = d.get( '__index__', i ) + # Restore child inputs + for input in self.inputs.itervalues(): + if ignore_errors and input.name not in d: + # If we do not have a value, and are ignoring errors, we simply + # do nothing. There will be no value for the parameter in the + # conditional's values dictionary. + pass + else: + rval_dict[ input.name ] = input.value_from_basic( d[input.name], app, ignore_errors ) + rval.append( rval_dict ) + except Exception, e: + if not ignore_errors: + raise e return rval def visit_inputs( self, prefix, value, callback ): for i, d in enumerate( value ): @@ -441,24 +445,28 @@ return rval def value_from_basic( self, value, app, ignore_errors=False ): rval = dict() - current_case = rval['__current_case__'] = value['__current_case__'] - # Test param - if ignore_errors and self.test_param.name not in value: - # If ignoring errors, do nothing. However this is potentially very - # problematic since if we are missing the value of test param, - # the entire conditional is wrong. - pass - else: - rval[ self.test_param.name ] = self.test_param.value_from_basic( value[ self.test_param.name ], app, ignore_errors ) - # Inputs associated with current case - for input in self.cases[current_case].inputs.itervalues(): - if ignore_errors and input.name not in value: - # If we do not have a value, and are ignoring errors, we simply - # do nothing. There will be no value for the parameter in the - # conditional's values dictionary. + try: + current_case = rval['__current_case__'] = value['__current_case__'] + # Test param + if ignore_errors and self.test_param.name not in value: + # If ignoring errors, do nothing. However this is potentially very + # problematic since if we are missing the value of test param, + # the entire conditional is wrong. pass else: - rval[ input.name ] = input.value_from_basic( value[ input.name ], app, ignore_errors ) + rval[ self.test_param.name ] = self.test_param.value_from_basic( value[ self.test_param.name ], app, ignore_errors ) + # Inputs associated with current case + for input in self.cases[current_case].inputs.itervalues(): + if ignore_errors and input.name not in value: + # If we do not have a value, and are ignoring errors, we simply + # do nothing. There will be no value for the parameter in the + # conditional's values dictionary. + pass + else: + rval[ input.name ] = input.value_from_basic( value[ input.name ], app, ignore_errors ) + except Exception, e: + if not ignore_errors: + raise e return rval def visit_inputs( self, prefix, value, callback ): current_case = value['__current_case__']

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