def inputs_xml(self):
predicate = self.spec.qiime_type.predicate
if predicate is not None and predicate.name == 'Choices':
param = make_select(self.name, self.spec,
predicate.template.choices)
else:
param = XMLNode('param', name=self.name, type='text')
if self.spec.has_default():
if self.spec.default is None:
self.add_help(param)
self.add_label(param)
param = make_optional(param)
else:
param.set('value', self.spec.default)
else:
param.append(
XMLNode(
# validator type='length' fails on empty input
'validator',
'value is not None and len(value) > 0',
type='expression',
message='Please verify this parameter.'))
self.add_help(param)
self.add_label(param)
return param
def make_select(name, spec, choices, display_func=str):
param = XMLNode('param', name=name, type='select')
default = None
if spec.has_default():
if spec.default is None:
param.append(XMLNode('option', 'None (Use default behavior)',
value=galaxy_esc(None), selected='true'))
else:
default = spec.default
elif len(choices) > 1:
# A validator for this is added a few lines down (after options)
# this is done to force the XML structure to look right
param.append(XMLNode('option', 'Selection required',
value=galaxy_esc(None)))
if len(choices) < 5:
param.set('display', 'radio')
for choice in choices:
option = XMLNode('option', display_func(choice),
value=galaxy_esc(choice))
if choice == default:
option.set('selected', 'true')
param.append(option)
if not spec.has_default() and len(choices) > 1:
param.append(XMLNode(
'validator', f'value != {repr(galaxy_esc(None))}',
type='expression', message='Please verify this parameter.'))
return param
def inputs_xml(self):
predicate = self.spec.qiime_type.predicate
if predicate is not None and predicate.name == 'Choices':
param = make_select(self.name, self.spec,
predicate.template.choices)
else:
param = XMLNode('param', name=self.name, type='text')
# sanitizer prevents default replacement with 'X' for some
# punctuation characters. It appears that this sanitizing requires
# an enumeration of valid characters, so supporting arbitrary
# unicode will likely require a change to Galaxy itself.
sanitizer = XMLNode('sanitizer')
valid = XMLNode('valid', initial='string.printable')
sanitizer.append(valid)
param.append(sanitizer)
if self.spec.has_default():
if self.spec.default is None:
self.add_help(param)
self.add_label(param)
param = make_optional(param)
else:
param.set('value', self.spec.default)
else:
param.append(XMLNode(
# validator type='length' fails on empty input
'validator', 'value is not None and len(value) > 0',
type='expression',
message='Please verify this parameter.'))
self.add_help(param)
self.add_label(param)
return param
def inputs_xml(self):
root = XMLNode('repeat', name=self.name,
title=f'{self.name}: {str(self.spec.qiime_type)}')
self.add_help(root)
if not self.spec.has_default():
root.set('min', '1')
conditional = XMLNode('conditional',
name=galaxy_ui_var(tag='conditional',
name=self.name))
select = XMLNode('param', type='select',
name='type',
label=f'{self.name}: {str(self.spec.qiime_type)}')
select.append(XMLNode('option', 'Metadata from TSV',
value='tsv', selected='true'))
select.append(XMLNode('option', 'Metadata from Artifact',
value='qza'))
conditional.append(select)
when_tsv = XMLNode('when', value='tsv')
tsv = XMLNode('param', type='data', format='tabular,qiime2.tabular',
name='source', label='Metadata Source')
when_tsv.append(tsv)
conditional.append(when_tsv)
when_artifact = XMLNode('when', value='qza')
artifact = XMLNode('param', type='data', format='qza',
name='source', label='Metadata Source')
when_artifact.append(artifact)
conditional.append(when_artifact)
root.append(conditional)
return root
def inputs_xml(self):
root = XMLNode('repeat', name=self.name,
title=f'{self.name}: {str(self.spec.qiime_type)}')
self.add_help(root)
if not self.spec.has_default():
root.set('min', '1')
to_repeat = identify_arg_case('element', self.inner_spec, self.arg)
root.append(to_repeat.inputs_xml())
return root
def inputs_xml(self):
param = XMLNode('param', type='data', format='qza', name=self.name)
self.add_help(param)
self.add_default(param)
self.add_label(param)
if self.multiple:
param.set('multiple', 'true')
options = XMLNode('options',
options_filter_attribute='metadata.semantic_type')
for t in self.qiime_type:
options.append(XMLNode('filter', type='add_value', value=repr(t)))
param.append(options)
if not self.multiple:
param.append(self._make_validator())
return param
def inputs_xml(self):
conditional = XMLNode('conditional', name=self.name)
select = XMLNode('param', type='select',
name='type',
label=f'{self.name}: {str(self.spec.qiime_type)}')
from_tsv = XMLNode('option', 'Metadata from TSV', value='tsv')
if self.spec.has_default():
select.append(XMLNode('option', 'None (default)', value='none',
selected='true'))
conditional.append(XMLNode('when', value='none'))
else:
from_tsv.set('selected', 'true')
select.append(from_tsv)
select.append(XMLNode('option', 'Metadata from Artifact',
value='qza'))
conditional.append(select)
when_tsv = XMLNode('when', value='tsv')
tsv1 = XMLNode('param', type='data', format='tabular,qiime2.tabular',
name='source', label='Metadata Source')
tsv2 = XMLNode('param', type='data_column', use_header_names='true',
data_ref='source', name='column', label='Column Name')
tsv2.append(XMLNode('validator', 'value != "1"', type='expression',
message='The first column cannot be selected ('
'they are IDs).'))
when_tsv.append(tsv1)
when_tsv.append(tsv2)
conditional.append(when_tsv)
when_artifact = XMLNode('when', value='qza')
art1 = XMLNode('param', type='data', format='qza',
name='source', label='Metadata Source')
art2 = XMLNode('param', type='text', name='column',
label='Column Name')
art2.append(XMLNode('validator', type='empty_field'))
when_artifact.append(art1)
when_artifact.append(art2)
conditional.append(when_artifact)
self.add_help(select)
return conditional
def inputs_xml(self):
predicate = self.spec.qiime_type.predicate
if (self.spec.has_default() and type(self.spec.default) is bool
and (predicate is None
or len(predicate.template.choices) == 2)):
param = XMLNode('param', name=self.name, type='boolean',
# Not super necessary, but makes it consistent for
# testing and any dynamic references
truevalue=galaxy_esc(True),
falsevalue=galaxy_esc(False))
if self.spec.default is True:
param.set('checked', 'true')
else:
choices = [True, False]
if predicate is not None:
choices = predicate.template.choices
param = make_select(self.name, self.spec, choices,
lambda x: 'Yes' if x else 'No')
self.add_help(param)
self.add_label(param)
return param
def inputs_xml(self):
param = XMLNode('param', name=self.name)
self.add_type(param)
self.add_help(param)
self.add_default(param)
self.add_label(param)
if not self.spec.has_default():
# trick galaxy
param.set('value', '')
predicate = self.spec.qiime_type.predicate
if predicate is not None:
if predicate.name == 'Range':
if self.spec.qiime_type.name == 'Float':
self.add_range(param, predicate, 0.000001)
else:
self.add_range(param, predicate, 1)
else:
print(self.spec)
raise NotImplementedError
return param
def _add_data_ui(root, file_attr):
name = XMLNode('param', type='text', name='name')
if _guess_regex(file_attr.pathspec):
name.set(
'help', 'Filename to import the data as. Must match'
f' regex: {_regex_xml_escape(file_attr.pathspec)}')
name.append(
XMLNode('validator',
file_attr.pathspec,
type='regex',
message='This filename doesn\'t match the regex.'))
else:
name.set(
'help', 'Filename to import the data as. You shouldn\'t need'
' to change this unless something is wrong.')
name.set('value', file_attr.pathspec)
root.append(name)
root.append(
XMLNode('param',
type='data',
name='data',
help=_format_help_text(file_attr.format)))
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
