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Cleanup to_json caller, slightly improve exception handlers

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This commit is contained in:
guerler
2015-04-08 22:40:08 -04:00
parent d7a7dedce1
commit ba968fde5c
2 changed files with 26 additions and 24 deletions
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lib/galaxy/tools/__init__.py
+21 -19
View File
@@ -2418,33 +2418,35 @@ class Tool( object, Dictifiable ):
current_state = group_state
iterate(tool_dict['cases'][i]['inputs'], input.cases[i].inputs, current_state, other_values)
else:
# create input dictionary, try to pass other_values if to_dict function supports it e.g. dynamic options
# identify name
input_name = tool_dict.get('name')
# create expanded input dictionary incl. repeats and dynamic_parameters
try:
tool_dict = input.to_dict(trans, other_values=other_values)
except Exception:
log.exception('tools::to_json() - Skipping parameter expansion for %s.' % input_name)
pass
# identify name
input_name = tool_dict.get('name')
if input_name:
# backup default value
try:
tool_dict['default_value'] = input.get_initial_value(trans, other_values)
except Exception:
# get initial value failed due to improper late validation
tool_dict['default_value'] = None
pass
# backup default value
try:
tool_dict['default_value'] = input.get_initial_value(trans, other_values)
except Exception:
log.exception('tools::to_json() - Getting initial value failed %s.' % input_name)
# get initial value failed due to improper late validation
tool_dict['default_value'] = None
pass
# update input value from tool state
tool_dict['value'] = state_inputs.get(input_name, None)
# update input value from tool state
tool_dict['value'] = state_inputs.get(input_name, None)
# sanitize values
sanitize(tool_dict, 'value')
sanitize(tool_dict, 'default_value')
# sanitize values
sanitize(tool_dict, 'value')
sanitize(tool_dict, 'default_value')
# use default value
if tool_dict['value'] is None:
tool_dict['value'] = tool_dict['default_value']
# use default value
if tool_dict['value'] is None:
tool_dict['value'] = tool_dict['default_value']
# backup final input dictionary
group_inputs[input_index] = tool_dict
lib/galaxy/tools/parameters/basic.py
+5 -5
View File
@@ -202,7 +202,7 @@ class ToolParameter( object, Dictifiable ):
for validator in self.validators:
validator.validate( value, history )
def to_dict( self, trans, view='collection', value_mapper=None ):
def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
""" to_dict tool parameter. This can be overridden by subclasses. """
tool_dict = super( ToolParameter, self ).to_dict()
#TODO: wrapping html as it causes a lot of errors on subclasses - needs histories, etc.
@@ -277,7 +277,7 @@ class TextToolParameter( ToolParameter ):
def get_initial_value( self, trans, context, history=None ):
return self.value
def to_dict( self, trans, view='collection', value_mapper=None ):
def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
d = super(TextToolParameter, self).to_dict(trans)
d['area'] = self.area
d['size'] = self.size
@@ -482,7 +482,7 @@ class BooleanToolParameter( ToolParameter ):
else:
return self.falsevalue
def to_dict( self, trans, view='collection', value_mapper=None ):
def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
d = super(BooleanToolParameter, self).to_dict(trans)
d['value'] = self.checked
d['truevalue'] = self.truevalue
@@ -692,7 +692,7 @@ class BaseURLToolParameter( ToolParameter ):
# BaseURLToolParameters are ultimately "hidden" parameters
return None
def to_dict( self, trans, view='collection', value_mapper=None ):
def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
d = super( BaseURLToolParameter, self ).to_dict( trans )
d['value'] = self.get_value( trans )
return d
@@ -1079,7 +1079,7 @@ class GenomeBuildParameter( SelectToolParameter ):
def get_legal_values( self, trans, other_values ):
return set( dbkey for dbkey, _ in self._get_dbkey_names( trans=trans ) )
def to_dict( self, trans, view='collection', value_mapper=None ):
def to_dict( self, trans, view='collection', value_mapper=None, other_values={} ):
# skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here
d = ToolParameter.to_dict( self, trans )