def make_builtin_import(meta, tool_id):
pm = sdk.PluginManager()
inputs = XMLNode('inputs')
# Not a galaxy_ui_var() because this will be taken by name from the
# Cheetah searchList (see `def _inline_code` below)
conditional = XMLNode('conditional', name='import_root')
inputs.append(conditional)
type_ = XMLNode('param',
name='type',
type='select',
label=('Type of data to import:'))
type_.append(
XMLNode('option', 'Select a QIIME 2 type to import.', value='None'))
conditional.append(type_)
when = XMLNode('when', value="None")
conditional.append(when)
default_formats = _get_default_formats(pm)
plugins = set()
known_formats = set()
for record in sorted(pm.get_semantic_types().values(),
key=lambda x: str(x.semantic_type)):
plugins.add(record.plugin)
type_option = XMLNode('option',
str(record.semantic_type),
value=galaxy_esc(str(record.semantic_type)))
type_.append(type_option)
when = XMLNode('when', value=galaxy_esc(str(record.semantic_type)))
fmt_conditional = XMLNode('conditional',
name=galaxy_ui_var(tag='cond',
name='format'))
select = XMLNode('param',
type='select',
name='format',
label="QIIME 2 file format to import from:")
fmt_conditional.append(select)
when.append(fmt_conditional)
default_format = default_formats[record.semantic_type]
for fmt_rec in sorted(pm.get_formats(
filter=GetFormatFilters.IMPORTABLE,
semantic_type=record.semantic_type).values(),
key=lambda x: x.format.__name__):
if issubclass(fmt_rec.format, model.SingleFileDirectoryFormatBase):
# These are really just noise for the galaxy UI
# an implicit transformation from the backing file format
# is simpler and removes the redundancy
continue
plugins.add(fmt_rec.plugin)
known_formats.add(fmt_rec.format)
option = XMLNode(
'option',
pretty_fmt_name(fmt_rec.format),
value=galaxy_esc(fmt_rec.format.__name__),
selected=str(fmt_rec.format == default_format).lower())
select.append(option)
fmt_when = XMLNode('when',
value=galaxy_esc(fmt_rec.format.__name__))
fmt_conditional.append(fmt_when)
_add_format_ui(fmt_when, fmt_rec)
conditional.append(when)
outputs = XMLNode('outputs')
outputs.append(
XMLNode('data',
name='imported_data',
format='qza',
from_work_dir='imported_data.qza'))
tool = XMLNode('tool',
id=tool_id,
name=make_tool_name_from_id(tool_id),
version=make_builtin_version(plugins))
tool.append(inputs)
tool.append(outputs)
tool.append(XMLNode('command', "q2galaxy run tools import '$inputs'"))
tool.append(_make_config())
tool.append(XMLNode('description', 'Import data into a QIIME 2 artifact'))
tool.append(make_citations())
tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
tool.append(_make_help(known_formats))
return tool
outputs.append(output)
tool = XMLNode('tool',
id=make_tool_id(plugin.id, action.id),
name=make_tool_name(plugin.name, action.id),
version=f'{plugin.version}+q2galaxy.{q2galaxy.__version__}')
tool.append(XMLNode('description', action.name))
tool.append(make_command(plugin, action))
tool.append(make_version_command(plugin))
tool.append(make_config())
tool.append(inputs)
tool.append(outputs)
tool.append(make_tests(action))
tool.append(make_help(plugin, action))
tool.append(make_citations(plugin, action))
tool.append(make_requirements(conda_meta, plugin.project_name))
return tool
def make_tests(action):
tests = XMLNode('tests')
for idx, example in enumerate(action.examples.values()):
use = GalaxyTestUsage(example_path=(action, idx))
example(use)
tests.append(use.xml)
return tests
def make_filename(name, spec):
if sdk.util.is_visualization_type(spec.qiime_type):
def make_builtin_export(meta, tool_id):
pm = sdk.PluginManager()
inputs = XMLNode('inputs')
# This also works for qzvs even though the format just says qza so. . .
qza_input = 'input'
inputs.append(XMLNode('param', format="qza", name=qza_input, type='data',
label='input: The path to the artifact you '
'want to export'))
type_peek = XMLNode('param', type='select', name='type_peek',
display='radio',
label="The type of your input qza is:")
type_peek_opts = XMLNode('options')
type_peek_filter = XMLNode('filter', type='data_meta', ref=qza_input,
key='semantic_type')
type_peek_opts.append(type_peek_filter)
type_peek.append(type_peek_opts)
inputs.append(type_peek)
fmt_peek = XMLNode('param', type='select', name='fmt_peek',
display='radio', label="The current QIIME 2 format is:")
fmt_peek_opts = XMLNode('options')
fmt_peek_filter = XMLNode('filter', type='data_meta', ref=qza_input,
key='format')
fmt_peek_opts.append(fmt_peek_filter)
fmt_peek.append(fmt_peek_opts)
inputs.append(fmt_peek)
conditional = XMLNode('conditional', name='fmt_finder')
inputs.append(conditional)
type_ = XMLNode('param', name='type', type='select',
label=('To change the format, select the type indicated'
' above:'))
type_.append(XMLNode('option', 'export as is (no conversion)',
value='None', selected='true'))
conditional.append(type_)
when = XMLNode('when', value="None")
select = XMLNode('param', type='select', name='output_format',
label="QIIME 2 file format to convert to:")
select.append(XMLNode('option', 'export as is (no conversion)',
value='None', selected='true'))
when.append(select)
conditional.append(when)
plugins = set()
known_formats = set()
for record in sorted(pm.get_semantic_types().values(),
key=lambda x: str(x.semantic_type)):
plugins.add(record.plugin)
type_option = XMLNode('option', str(record.semantic_type),
value=galaxy_esc(str(record.semantic_type)))
type_.append(type_option)
when = XMLNode('when', value=galaxy_esc(str(record.semantic_type)))
select = XMLNode('param', type='select', name='output_format',
label="QIIME 2 file format to convert to:")
select.append(XMLNode('option', 'export as is (no conversion)',
value='None', selected='true'))
for fmt_rec in sorted(
pm.get_formats(filter=GetFormatFilters.EXPORTABLE,
semantic_type=record.semantic_type).values(),
key=lambda x: x.format.__name__):
plugins.add(fmt_rec.plugin)
known_formats.add(fmt_rec.format)
if not issubclass(fmt_rec.format,
model.SingleFileDirectoryFormatBase):
option = XMLNode('option', pretty_fmt_name(fmt_rec.format),
value=galaxy_esc(fmt_rec.format.__name__))
select.append(option)
when.append(select)
conditional.append(when)
outputs = XMLNode('outputs')
# default collection:
collection = XMLNode('collection', name='exported', type='list',
label='${tool.name} on ${on_string} as ${fmt_peek}')
_filter_set = repr({galaxy_esc(x.__name__) for x in known_formats})
collection.append(XMLNode('filter', "fmt_finder['output_format'] == 'None'"
f" and fmt_peek not in {_filter_set}"))
collection.append(XMLNode('discover_datasets', visible='false',
pattern='__designation_and_ext__'))
outputs.append(collection)
for fmt in sorted(known_formats, key=lambda x: x.__name__):
esc_fmt = galaxy_esc(fmt.__name__)
filter_exp = (f"fmt_finder['output_format'] == '{esc_fmt}'"
" or (fmt_finder['output_format'] == 'None' and fmt_peek"
f" == '{esc_fmt}')")
label = '${tool.name} on ${on_string} as ' + fmt.__name__
if issubclass(fmt, model.DirectoryFormat):
dyn_data = None
for field in fmt._fields: # file attrs of the dirfmt
file_attr = getattr(fmt, field)
pattern, has_ext = pathspec_to_galaxy_regex(file_attr.pathspec)
extras = {}
if not has_ext:
if issubclass(file_attr.format, model.TextFileFormat):
extras['ext'] = 'txt'
else:
extras['ext'] = 'data'
if isinstance(file_attr, model.FileCollection):
col = XMLNode('collection', type='list',
name='_'.join([esc_fmt, file_attr.name]),
label=label + f' ({file_attr.name})')
col.append(XMLNode('filter', filter_exp))
col.append(XMLNode('discover_datasets', visible='false',
pattern=pattern, **extras))
outputs.append(col)
else:
if dyn_data is None:
# init a root for all of the discoverable datasets
dyn_data = XMLNode('data', name=esc_fmt, label=label)
dyn_data.append(XMLNode('filter', filter_exp))
# only the first one, will take over the history item
extras['assign_primary_output'] = 'true'
dyn_data.append(XMLNode('discover_datasets',
visible='true', pattern=pattern,
**extras))
if dyn_data is not None:
outputs.append(dyn_data)
else:
# as it is not a directory, we don't know much about the original
# filename anymore, so we will let galaxy sort it out
# .gz may be considered the format instead of fastq.gz, but users
# can always re-sniff a history item for the format
collection = XMLNode('data', name=esc_fmt, label=label)
collection.append(XMLNode('filter', filter_exp))
collection.append(XMLNode('discover_datasets', visible='true',
assign_primary_output='true',
pattern='__designation_and_ext__'))
outputs.append(collection)
tool = XMLNode('tool', id=tool_id, name=make_tool_name_from_id(tool_id),
version=make_builtin_version(plugins))
tool.append(XMLNode('description', 'Export data from QIIME 2 artifacts'))
tool.append(XMLNode('command', "q2galaxy run tools export '$inputs'"))
tool.append(make_config())
tool.append(inputs)
tool.append(outputs)
tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
tool.append(XMLNode('help', ''))
return tool