Source code for planemo.galaxy.api

"""A high-level interface to local Galaxy instances using bioblend."""

from io import StringIO
from typing import Optional

from bioblend.galaxy import GalaxyInstance


def get_dict_from_workflow(gi: GalaxyInstance, workflow_id: str, instance: bool = False):
    return gi.workflows._get(f"{workflow_id}/download", params={"instance": instance})

[docs] def gi(port: Optional[int] = None, url: Optional[str] = None, key: Optional[str] = None) -> GalaxyInstance: """Return a bioblend ``GalaxyInstance`` for Galaxy on this port.""" if key is None: key = DEFAULT_ADMIN_API_KEY if port is not None and url is not None: raise ValueError("Either port or url parameter needs to be None") if port is None: url = url else: url = f"http://localhost:{int(port)}" g = GalaxyInstance(url=url, key=key) g.max_get_attempts = 10 return g
def test_credentials_valid(port=None, url=None, key=None, is_admin=False): """Test if provided API credentials are valid""" test_gi = gi(port, url, key) try: current_user = test_gi.users.get_current_user() if is_admin: return current_user["is_admin"] else: return True except Exception: return False
[docs] def user_api_key(admin_gi): """Use an admin authenticated account to generate a user API key.""" # TODO: thread-safe users = admin_gi.users all_users = users.get_users() user_id = None for user in all_users: if user["email"] == "": user_id = user["id"] if user_id is None: # TODO: Allow override with --user_api_key. galaxy_config = admin_gi.config.get_config() use_remote_user = bool(galaxy_config["use_remote_user"]) if not use_remote_user: user_response = users.create_local_user( "planemo", "", "planemo", ) user_id = user_response["id"] else: user_response = users.create_remote_user( "", ) user_id = user_response["id"] return users.create_user_apikey(user_id)
def summarize_history(ctx, gi, history_id): """Summarize a history with print() based on similar code in Galaxy for populators.""" if not ctx.verbose: return if history_id is None: raise ValueError("summarize_history passed empty history_id") try: history_contents = gi.histories.show_history(history_id, contents=True) except Exception: print("Failed to fetch history contents in summarize_history.") return for history_content in history_contents: history_content_id = history_content.get("id", None) print("| %d - %s (HID - NAME) " % (int(history_content["hid"]), history_content["name"])) if history_content["history_content_type"] == "dataset_collection": history_contents_json = gi.histories.show_dataset_collection(history_id, history_content["id"]) print("| Dataset Collection: %s" % history_contents_json) continue try: dataset_info = gi.histories.show_dataset(history_id, history_content_id) print("| Dataset State:") print(_format_for_summary(dataset_info.get("state"), "Dataset state is unknown.")) print("| Dataset Blurb:") print(_format_for_summary(dataset_info.get("misc_blurb", ""), "Dataset blurb was empty.")) print("| Dataset Info:") print(_format_for_summary(dataset_info.get("misc_info", ""), "Dataset info is empty.")) print("| Peek:") print(_format_for_summary(dataset_info.get("peek", ""), "Peek unavailable.")) except Exception: print("| *PLANEMO ERROR FETCHING DATASET DETAILS*") try: provenance_info = _dataset_provenance(gi, history_id, history_content_id) print("| Dataset Job Standard Output:") print(_format_for_summary(provenance_info.get("stdout", ""), "Standard output was empty.")) print("| Dataset Job Standard Error:") print(_format_for_summary(provenance_info.get("stderr", ""), "Standard error was empty.")) except Exception: print("| *PLANEMO ERROR FETCHING JOB DETAILS*") print("|") def get_invocations(url, key, workflow_id): inv_gi = gi(None, url, key) invocations = inv_gi.workflows.get_invocations(workflow_id) return { invocation["id"]: { "states": inv_gi.invocations.get_invocation_summary(invocation["id"])["states"], "history_id": invocation["history_id"], } for invocation in invocations } def _format_for_summary(blob, empty_message, prefix="| "): contents = "\n".join([f"{prefix}{line.strip()}" for line in StringIO(blob).readlines() if line.rstrip("\n\r")]) return contents or f"{prefix}*{empty_message}*" def _dataset_provenance(gi, history_id, id): provenance = gi.histories.show_dataset_provenance(history_id, id) return provenance __all__ = ( "DEFAULT_ADMIN_API_KEY", "gi", "user_api_key", )