def __init__(self, name, spec, arg=None):
super().__init__(name, spec, arg)
self.branches = {}
def _sanitize(t):
return galaxy_ui_var(value=galaxy_esc(str(t).replace('%', 'X')))
for type_ in spec.qiime_type:
if type_.predicate is not None and is_union(type_.predicate):
for pred in type_.predicate.unpack_union():
new_type = type_.duplicate(predicate=pred)
self.branches[_sanitize(new_type)] = new_type
elif (type_.predicate is not None
and type_.predicate.name == 'Choices'):
for choice in type_.predicate.template.choices:
new_type = type_.duplicate(predicate=Choices(choice))
self.branches[galaxy_esc(choice)] = new_type
elif type_.name == 'Bool':
for choice in [True, False]:
new_type = type_.duplicate(predicate=Choices(choice))
self.branches[galaxy_esc(choice)] = new_type
else:
self.branches[_sanitize(type_)] = type_
if self.spec.default is None:
self.branches[galaxy_esc(None)] = {None}
def inputs_xml(self):
base_types = []
for t in self.spec.qiime_type:
if t.predicate is not None and is_union(t.predicate):
for pred in t.predicate.unpack_union():
base_types.append(t.duplicate(predicate=pred))
else:
base_types.append(t)
to_add = []
for t in base_types:
if ((t.name == "Str" and t.predicate is None) or t.name == 'Float'
or t.name == 'Int'):
to_add.append(t)
root = None
if to_add:
root = XMLNode('conditional',
name=galaxy_ui_var(tag='conditional',
name=self.name))
select = XMLNode('param',
type='select',
name=galaxy_ui_var(tag='select'))
root.append(select)
else:
select = XMLNode('param', type='select', name=self.name)
choices = []
for t in base_types:
if t.predicate is not None and t.predicate.name == 'Choices':
choices.extend(t.predicate.template.choices)
elif t.name == 'Bool':
choices.extend([True, False])
display = None
if not self.spec.has_default():
display = 'Selection required'
elif self.spec.default is None:
display = 'None (Use default behavior)'
if display is not None:
value = galaxy_esc(None)
select.append(
XMLNode('option', display, value=value, selected='true'))
if root is not None:
when = XMLNode('when', value=value)
hidden = XMLNode('param',
type='hidden',
name=self.name,
value=value)
when.append(hidden)
root.append(when)
for choice in choices:
value = galaxy_esc(choice)
option = XMLNode('option', self._display_func(choice), value=value)
if self.spec.has_default() and self.spec.default == choice:
option.set('selected', 'true')
select.append(option)
if root is not None:
when = XMLNode('when', value=value)
hidden = XMLNode('param',
type='hidden',
name=self.name,
value=value)
when.append(hidden)
root.append(when)
default = self.spec.default # NOVALUE is fine
for addition in to_add:
value = galaxy_ui_var(value=galaxy_esc(
# Galaxy will convert % to X internally and then complain
# about a lack of matching cases, so we'll just do it now
str(addition).replace('%', 'X')))
option = XMLNode('option',
f'Provide a value ({addition})',
value=value)
select.append(option)
when = XMLNode('when', value=value)
dispatch = {
'Float': NumericCase,
'Int': NumericCase,
'Str': StrCase
}
try:
ParamCase = dispatch[addition.name]
except KeyError:
raise NotImplementedError
if default in addition:
spec_default = default
option.set('selected', 'true')
else:
spec_default = self.spec.NOVALUE
new_spec = self.spec.duplicate(qiime_type=addition,
default=spec_default)
sub_ui = ParamCase(self.name, new_spec).inputs_xml()
when.append(sub_ui)
root.append(when)
self.add_help(select)
self.add_label(select)
if not self.spec.has_default():
select.append(
XMLNode('validator',
f'value != {repr(galaxy_esc(None))}',
type='expression',
message='Please verify this parameter.'))
if root is None:
return select
else:
return root
def is_union_anywhere(qiime_type):
return is_union(qiime_type) or (qiime_type.predicate is not None
and is_union(qiime_type.predicate))