import os
from planemo.galaxy.profiles import translate_alias
from planemo.galaxy.workflows import GALAXY_WORKFLOWS_PREFIX
from planemo.tools import uri_to_path
from .runnable import (
for_path,
for_uri,
)
[docs]def for_runnable_identifier(ctx, runnable_identifier, kwds, temp_path=None, return_all=False):
"""Convert URI, path, or alias into Runnable."""
# could be a URI, path, or alias
current_profile = kwds.get("profile")
runnable_identifier = translate_alias(ctx, runnable_identifier, current_profile)
if not runnable_identifier.startswith(GALAXY_WORKFLOWS_PREFIX):
runnable_identifier = uri_to_path(ctx, runnable_identifier)
if os.path.exists(runnable_identifier):
runnable = for_path(runnable_identifier, temp_path=temp_path, return_all=return_all)
else: # assume galaxy workflow id
if not runnable_identifier.startswith(GALAXY_WORKFLOWS_PREFIX):
runnable_identifier = f"{GALAXY_WORKFLOWS_PREFIX}{runnable_identifier}"
runnable = for_uri(runnable_identifier)
return runnable
[docs]def for_runnable_identifiers(ctx, runnable_identifiers, kwds, temp_path=None):
"""Convert lists of URIs, paths, and/or aliases into Runnables."""
runnables = []
for r in runnable_identifiers:
runnable = for_runnable_identifier(ctx, r, kwds, temp_path=temp_path, return_all=True)
if isinstance(runnable, list):
runnables.extend(runnable)
else:
runnables.append(runnable)
return runnables