def action(self, action, inputs, outputs):
variables = super().action(action, inputs, outputs)
vars_dict = variables._asdict()
plugin_name = util.to_cli_name(action.plugin_id)
action_name = util.to_cli_name(action.action_id)
self.recorder.append('qiime %s %s \\' % (plugin_name, action_name))
action_f = action.get_action()
action_state = get_action_state(action_f)
ins = inputs.map_variables(lambda v: v.to_interface_name())
outs = {k: v.to_interface_name() for k, v in vars_dict.items()}
signature = {s['name']: s for s in action_state['signature']}
for param_name, value in ins.items():
self._append_action_line(signature, param_name, value)
max_collection_size = self.action_collection_size
if max_collection_size is not None and len(outs) > max_collection_size:
dir_name = self._build_output_dir_name(plugin_name, action_name)
self.recorder.append(self.INDENT + '--output-dir %s \\' %
(dir_name))
self._rename_outputs(vars_dict, dir_name)
else:
for param_name, value in outs.items():
self._append_action_line(signature, param_name, value)
self.recorder[-1] = self.recorder[-1][:-2] # remove trailing \
return variables
def action(self, action, inputs, outputs):
variables = super().action(action, inputs, outputs)
vars_dict = variables._asdict()
plugin_name = util.to_cli_name(action.plugin_id)
action_name = util.to_cli_name(action.action_id)
self.recorder.append("qiime %s %s \\" % (plugin_name, action_name))
action_f = action.get_action()
action_state = get_action_state(action_f)
ins = inputs.map_variables(lambda v: v.to_interface_name())
outs = {k: v.to_interface_name() for k, v in vars_dict.items()}
signature = {s['name']: s for s in action_state['signature']}
for param_name, value in {**ins, **outs}.items():
param_state = signature[param_name]
if value is not None:
for opt, val in self._make_param(value, param_state):
line = self.INDENT + opt
if val is not None:
line += ' ' + val
line += ' \\'
self.recorder.append(line)
self.recorder[-1] = self.recorder[-1][:-2] # remove trailing \
return variables
def to_interface_name(self):
if hasattr(self, '_q2cli_ref'):
return self._q2cli_ref
ext = {
'artifact': 'qza',
'visualization': 'qzv',
'metadata': 'tsv',
}[self.var_type]
cli_name = util.to_cli_name(self.name)
fn = '%s.%s' % (cli_name, ext)
return shlex.quote(fn)
def write_example_data(action, output_dir):
for example_name, example in action.examples.items():
cli_name = util.to_cli_name(example_name)
example_path = os.path.join(output_dir, cli_name)
use = CLIUsage()
example(use)
for fn, val in use.get_example_data():
os.makedirs(example_path, exist_ok=True)
path = os.path.join(example_path, fn)
val.save(path)
try:
hint = repr(val.type)
except AttributeError:
hint = 'Metadata'
yield hint, path
def to_cli_name(val):
return util.to_cli_name(val)
def write_plugin_example_data(plugin, output_dir):
for name, action in plugin.actions.items():
path = os.path.join(output_dir, util.to_cli_name(name))
yield from write_example_data(action, path)
