Source code for planemo.runnable_resolve

import os

import requests

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,
    GALAXY_TOOLS_PREFIX,
)


[docs]def for_runnable_identifier(ctx, runnable_identifier, kwds): """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) else: # assume galaxy workflow or tool id if "/repos/" in runnable_identifier: runnable_identifier = f"{GALAXY_TOOLS_PREFIX}{runnable_identifier}" elif 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): """Convert lists of URIs, paths, and/or aliases into Runnables.""" runnables = [] for r in runnable_identifiers: runnable = for_runnable_identifier(ctx, r, kwds) if isinstance(runnable, list): runnables.extend(runnable) else: runnables.append(runnable) return runnables
[docs]def install_args_list_to_runnables(ctx, install_args_list, kwds): runnables = [] for repo in install_args_list: url = f'{repo["tool_shed_url"]}api/repositories/get_repository_revision_install_info' response = requests.get( url, params={"name": repo["name"], "owner": repo["owner"], "changeset_revision": repo["changeset_revision"]} ) response.raise_for_status() install_info = response.json() repository_metadata = install_info[1] assert repository_metadata and repository_metadata["model_class"] == "RepositoryMetadata", repository_metadata for tool in repository_metadata.get("valid_tools", []): runnable = for_runnable_identifier(ctx, tool["guid"], kwds) runnables.append(runnable) return runnables