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task_runs.py
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task_runs.py
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"""Class implementing TES API-server-side controller methods."""
from copy import deepcopy
from datetime import datetime
import logging
from typing import Optional, Sequence
from bson.objectid import ObjectId # type: ignore
from celery import uuid
from dateutil.parser import parse as parse_time
from flask import current_app, request
from foca.models.config import Config # type: ignore
from foca.utils.misc import generate_id # type: ignore
from pymongo.collection import Collection # type: ignore
from pymongo.errors import DuplicateKeyError, PyMongoError # type: ignore
import requests
import tes # type: ignore
from tes.models import Task # type: ignore
from pro_tes.exceptions import (
BadRequest,
NoTesInstancesAvailable,
TaskNotFound,
)
from pro_tes.ga4gh.tes.models import (
BasicAuth,
DbDocument,
TesEndpoint,
TesState,
TesTask,
TesTaskLog,
TesNextTes,
)
from pro_tes.ga4gh.tes.states import States
from pro_tes.middleware.middleware_handler import MiddlewareHandler
from pro_tes.tasks.track_task_progress import task__track_task_progress
from pro_tes.utils.db import DbDocumentConnector
from pro_tes.utils.misc import strip_auth
from pro_tes.utils.models import TaskModelConverter
# pragma pylint: disable=invalid-name,redefined-builtin,unused-argument
# pragma pylint: disable=too-many-locals
# pylint: disable=unsubscriptable-object
logger = logging.getLogger(__name__)
class TaskRuns:
"""Class for TES API server-side controller methods.
Attributes:
foca_config: FOCA configuration.
db_client: Database collection storing task objects.
document: Document to be inserted into the collection. Note that it is
built up iteratively.
"""
def __init__(self) -> None:
"""Construct object instance."""
self.foca_config: Config = current_app.config.foca
self.db_client: Collection = (
self.foca_config.db.dbs["taskStore"].collections["tasks"].client
)
self.store_logs = self.foca_config.storeLogs["execution_trace"]
def create_task( # pylint: disable=too-many-statements,too-many-branches
self, **kwargs
) -> dict:
"""Start task.
Args:
**kwargs: Additional keyword arguments passed along with request.
Returns:
Task identifier.
"""
# create task document
start_time = datetime.now().strftime("%m-%d-%Y %H:%M:%S")
db_document: DbDocument = DbDocument()
db_document.basic_auth = self.parse_basic_auth(request.authorization)
assert request.json is not None
payload_original: dict = deepcopy(request.json)
db_document.task_original = TesTask(**payload_original)
# apply middlewares
mw_handler = MiddlewareHandler()
mw_handler.set_middlewares(paths=current_app.config.foca.middlewares)
logger.debug(f"Middlewares registered: {mw_handler.middlewares}")
request_modified = mw_handler.apply_middlewares(request=request)
# update task document
assert request_modified.json is not None
payload: dict = request_modified.json
tes_urls = deepcopy(payload["tes_urls"])
del payload["tes_urls"]
db_document.task = TesTask(**payload)
# create database document
db_document = self._update_task(
payload=payload,
db_document=db_document,
start_time=start_time,
**kwargs,
)
db_connector = DbDocumentConnector(
collection=self.db_client,
worker_id=db_document.worker_id,
)
logger.info(
"Created task record with task identifier"
f" '{db_document.task.id}' and worker job identifier"
f" '{db_document.worker_id}'"
)
# validate request
payload = self._sanitize_request(payload=payload)
try:
payload_marshalled = tes.Task(**payload)
except TypeError as exc:
db_connector.update_task_state(state=TesState.SYSTEM_ERROR.value)
raise BadRequest(
f"Task '{db_document.task.id}' could not be "
f"validated. Original error message: '{type(exc).__name__}: "
f"{exc}'"
) from exc
# relay request
logger.info(
"Attempting to forward the task request to any of the known TES"
f" instances, in the following order: {tes_urls}"
)
for tes_url in tes_urls:
db_document.tes_endpoint = TesEndpoint(host=tes_url)
url: str = (
f"{db_document.tes_endpoint.host.rstrip('/')}/"
f"{db_document.tes_endpoint.base_path.lstrip('/')}"
)
try:
cli = tes.HTTPClient(
url,
timeout=5,
user=db_document.basic_auth.username,
password=db_document.basic_auth.password,
)
except ValueError as exc:
logger.warning(
f"Task '{db_document.task.id}' could not "
f"be sent to TES endpoint hosted at: {url}. Invalid TES"
" endpoint URL. Original error message: "
f"'{type(exc).__name__}: {exc}'"
)
continue
# fix for FTP URLs with credentials on non-Funnel services
def strip_none_items(_seq: Sequence) -> list:
"""Remove empty items from Sequence.
Args:
_seq: Sequence of items.
Returns:
List of none empty items.
"""
return [item for item in _seq if item is not None]
def remove_auth(_list: list) -> list:
"""Forward the list to 'remove_auth_from_url'.
Args:
_list: List
Returns:
List of items without basic authentication information.
"""
return [
strip_auth(item.url)
for item in _list
if getattr(item, "url", None) is not None
]
is_funnel = False
try:
response = cli.get_service_info()
if response.name == "Funnel":
is_funnel = True
except requests.exceptions.HTTPError:
pass
if not is_funnel:
if payload_marshalled.inputs is not None:
inputs = strip_none_items(payload_marshalled.inputs)
payload_marshalled.inputs = remove_auth(inputs)
if payload_marshalled.outputs is not None:
outputs = strip_none_items(payload_marshalled.outputs)
payload_marshalled.outputs = remove_auth(outputs)
try:
remote_task_id = cli.create_task(payload_marshalled)
except requests.HTTPError as exc:
logger.warning(
f"Task '{db_document.task.id}' could not be sent to TES"
f" endpoint hosted at: {url}. Original error message:"
f" '{type(exc).__name__}: {exc}'"
)
continue
logger.info(
f"Task '{db_document.task.id}' successfully forwarded to TES"
f" endpoint hosted at: {url}. Remote tak identifier:"
f" {remote_task_id}"
)
try:
task: Task = cli.get_task(remote_task_id)
task_model_converter = TaskModelConverter(task=task)
task_converted: TesTask = task_model_converter.convert_task()
db_document.task.state = task_converted.state
except requests.HTTPError as exc:
logger.error(
f"Task '{db_document.task.id}' info could "
"not be retrieved from TES endpoint hosted at: "
f"{url}. Original error message: "
f"'{type(exc).__name__}: {exc}'"
)
except PyMongoError as exc:
logger.error(
"Database could not be updated with task info "
f"retrieved for task '{db_document.task.id}'"
f"sent to TES endpoint hosted at: {url}. "
f"Original error message:'{type(exc).__name__}: {exc}'"
)
# update task_logs, tes_endpoint and task in db
db_document = self._update_doc_in_db(
db_connector=db_connector,
tes_url=tes_url,
remote_task_id=remote_task_id,
)
task__track_task_progress.apply_async(
None,
{
"worker_id": db_document.worker_id,
"remote_host": db_document.tes_endpoint.host,
"remote_base_path": db_document.tes_endpoint.base_path,
"remote_task_id": remote_task_id,
"user": db_document.basic_auth.username,
"password": db_document.basic_auth.password,
},
)
return {"id": db_document.task.id}
db_connector.update_task_state(state=TesState.SYSTEM_ERROR.value)
raise NoTesInstancesAvailable(
"Could not forward the task request to any TES instance. Task"
" state set to 'SYSTEM_ERROR'."
)
def list_tasks(self, **kwargs) -> dict:
"""Return list of tasks.
Args:
**kwargs: Keyword arguments passed along with request.
Returns:
Response object according to TES API schema . Cf.
https://github.com/ga4gh/task-execution-schemas/blob/9e9c5aa2648d683d5574f9dbd63a025b4aea285d/openapi/task_execution_service.openapi.yaml
"""
page_size = kwargs.get(
"page_size",
self.foca_config.controllers["list_tasks"]["default_page_size"],
)
page_token = kwargs.get("page_token")
filter_dict = {}
filter_dict["user_id"] = kwargs.get("user_id")
if page_token is not None:
filter_dict["_id"] = {"$lt": ObjectId(page_token)}
view = kwargs.get("view", "BASIC")
projection = self._set_projection(view=view)
name_prefix: str = kwargs.get("name_prefix")
if name_prefix is not None:
filter_dict["task_original.name"] = {"$regex": f"^{name_prefix}"}
cursor = (
self.db_client.find(filter=filter_dict, projection=projection)
.sort("_id", -1)
.limit(page_size)
)
tasks_list = list(cursor)
logger.debug(f"Tasks list: {tasks_list}")
if tasks_list:
next_page_token = str(tasks_list[-1]["_id"])
else:
next_page_token = ""
tasks_lists = []
for task in tasks_list:
del task["_id"]
if view == "MINIMAL":
task["id"] = task["task"]["id"]
task["state"] = task["task"]["state"]
tasks_lists.append({"id": task["id"], "state": task["state"]})
if view == "BASIC":
tasks_lists.append(task["task"])
if view == "FULL":
tasks_lists.append(task["task"])
return {"next_page_token": next_page_token, "tasks": tasks_lists}
def get_task(self, id=str, **kwargs) -> dict:
"""Return detailed information about a task.
Args:
task_id: Task identifier.
**kwargs: Additional keyword arguments passed along with request.
Returns:
Response object according to TES API schema . Cf.
https://github.com/ga4gh/task-execution-schemas/blob/9e9c5aa2648d683d5574f9dbd63a025b4aea285d/openapi/task_execution_service.openapi.yaml
Raises:
pro_tes.exceptions.TaskNotFound: The requested task is not
available.
"""
projection = self._set_projection(view=kwargs.get("view", "BASIC"))
document = self.db_client.find_one(
filter={"task.id": id}, projection=projection
)
if document is None:
logger.error(f"Task '{id}' not found.")
raise TaskNotFound
return document["task"]
def cancel_task(self, id: str, **kwargs) -> dict:
"""Cancel task.
Args:
id: Task identifier.
**kwargs: Additional keyword arguments passed along with request.
Returns:
Task identifier.
Raises:
pro_tes.exceptions.Forbidden: The requester is not allowed
to access the resource.
pro_tes.exceptions.TaskNotFound: The requested task is not
available.
"""
document = self.db_client.find_one(
filter={"task.id": id},
projection={"_id": False},
)
if document is None:
logger.error(f"task '{id}' not found.")
raise TaskNotFound
db_document = DbDocument(**document)
if db_document.task.state in States.CANCELABLE:
db_connector = DbDocumentConnector(
collection=self.db_client,
worker_id=db_document.worker_id,
)
url: str = (
f"{db_document.tes_endpoint.host.rstrip('/')}/"
f"{db_document.tes_endpoint.base_path.strip('/')}"
)
if self.store_logs:
task_id = db_document.task.logs[0].metadata.forwarded_to.id
else:
task_id = db_document.task.logs[0].metadata["remote_task_id"]
logger.info(
"Trying to cancel task with task identifier"
f" '{task_id}' and worker job"
f" identifier '{db_document.worker_id}' running at TES"
f" endpoint hosted at: {url}"
)
cli = tes.HTTPClient(
url,
timeout=5,
user=db_document.basic_auth.username,
password=db_document.basic_auth.password,
)
cli.cancel_task(task_id=task_id)
db_connector.update_task_state(
state="CANCELED",
)
logger.info(
f"Task '{id}' with worker ID '{db_document.worker_id}'"
" canceled."
)
return {}
def _write_doc_to_db(
self,
document: DbDocument,
) -> tuple[str, str]:
"""Create database entry for task.
Args:
document: Document to be written to database.
Returns:
Tuple of task id and worker id.
"""
controller_config = self.foca_config.controllers["post_task"]
charset = controller_config["task_id"]["charset"]
length = controller_config["task_id"]["length"]
# try inserting until unused task id found
for _ in range(controller_config["db"]["insert_attempts"]):
document.task.id = generate_id(
charset=charset,
length=length,
)
document.worker_id = uuid()
try:
self.db_client.insert(document.dict(exclude_none=True))
except DuplicateKeyError:
continue
assert document is not None
return document.task.id, document.worker_id
raise DuplicateKeyError("Could not insert document into database.")
def _sanitize_request(self, payload: dict) -> dict:
"""Sanitize request for use with py-tes.
Args:
payload: Request payload.
Returns:
Sanitized request payload.
"""
time_now = datetime.now().strftime("%m-%d-%Y %H:%M:%S")
if "creation_time" not in payload:
payload["creation_time"] = parse_time(time_now)
if "inputs" in payload:
payload["inputs"] = [
tes.models.Input(**input) for input in payload["inputs"]
]
if "outputs" in payload:
payload["outputs"] = [
tes.models.Output(**output) for output in payload["outputs"]
]
if "resources" in payload:
payload["resources"] = tes.models.Resources(**payload["resources"])
if "executors" in payload:
payload["executors"] = [
tes.models.Executor(**executor)
for executor in payload["executors"]
]
if "logs" in payload:
payload["logs"] = [
tes.models.TaskLog(**log) for log in payload["logs"]
]
return payload
def _set_projection(self, view: str) -> dict:
"""Set database projection for selected view.
Args:
view: View path parameter.
Returns:
Database projection for selected view.
Raises:
pro_tes.exceptions.BadRequest: Invalid view parameter.
"""
if view == "MINIMAL":
projection = {
"task.id": True,
"task.state": True,
}
elif view == "BASIC":
projection = {
"task.inputs.content": False,
"task.system_logs": False,
"task.logs.stdout": False,
"task.logs.stderr": False,
"tes_endpoint": False,
}
elif view == "FULL":
projection = {
"worker_id": False,
"tes_endpoint": False,
}
else:
raise BadRequest
return projection
def _update_task(
self, payload: dict, db_document: DbDocument, start_time: str, **kwargs
) -> DbDocument:
"""Update the task object.
Args:
payload: A dictionary containing the payload for the update.
db_document: The document in the database to be updated.
start_time: The starting time of the incoming TES request.
**kwargs: Additional keyword arguments passed along with request.
Returns:
DbDocument: The updated database document.
"""
logs = self._set_logs(
payloads=deepcopy(payload), start_time=start_time
)
db_document.task.logs = [TesTaskLog(**logs) for logs in logs]
db_document.task.state = TesState.UNKNOWN
db_document.user_id = kwargs.get("user_id", None)
(task_id, worker_id) = self._write_doc_to_db(document=db_document)
db_document.task.id = task_id
db_document.worker_id = worker_id
return db_document
def _set_logs(self, payloads: dict, start_time: str) -> dict:
"""Create or update `TesTask.logs` and set start time.
Args:
payload: A dictionary containing the payload for the update.
start_time: The starting time of the incoming TES request.
Returns:
Task logs with start time set.
"""
if "logs" not in payloads.keys():
logs = [
{
"logs": [],
"metadata": {},
"start_time": start_time,
"end_time": None,
"outputs": [],
"system_logs": [],
}
]
payloads["logs"] = logs
else:
for log in payloads["logs"]:
log["start_time"] = start_time
return payloads["logs"]
def _update_doc_in_db(
self,
db_connector,
tes_url: str,
remote_task_id: str,
) -> DbDocument:
"""Set end time, task metadata in `TesTask.logs`, and update document.
Args:
db_connector: The database connector.
tes_url: The TES URL where the task if forwarded.
remote_task_id: Task identifier at the remote TES instance.
Returns:
The updated database document.
"""
time_now = datetime.now().strftime("%m-%d-%Y %H:%M:%S")
tes_endpoint_dict = {"host": tes_url, "base_path": ""}
db_document = db_connector.upsert_fields_in_root_object(
root="tes_endpoint",
**tes_endpoint_dict,
)
# updating the end time in TesTask logs
for logs in db_document.task.logs:
logs.end_time = time_now
# updating the metadata in TesTask logs
if self.store_logs:
db_document = self._update_task_metadata(
db_document=db_document,
tes_url=tes_url,
remote_task_id=remote_task_id,
)
else:
for logs in db_document.task.logs:
logs.metadata = {"remote_task_id": remote_task_id}
db_document = db_connector.upsert_fields_in_root_object(
root="task",
**db_document.dict()["task"],
)
logger.debug(f"Task '{db_document.task}' inserted to database ")
return db_document
def _update_task_metadata(
self, db_document: DbDocument, tes_url: str, remote_task_id: str
) -> DbDocument:
"""Update the task metadata.
Set TES endpoint and remote task identifier in `TesTask.logs.metadata`.
Args:
db_document: The document in the database to be updated.
tes_url: The TES URL where the task if forwarded.
remote_task_id: Task identifier at the remote TES instance.
Returns:
The updated database document.
"""
for logs in db_document.task.logs:
tesNextTes_obj = TesNextTes(id=remote_task_id, url=tes_url)
if logs.metadata.forwarded_to is None:
logs.metadata.forwarded_to = tesNextTes_obj
return db_document
@staticmethod
def parse_basic_auth(auth: Optional[dict[str, str]]) -> BasicAuth:
"""Parse basic auth header.
Args:
auth: Request authorization information.
Returns:
Basic authorization model instance with username and password;
missing values are set to `None`.
"""
if auth is None:
return BasicAuth()
return BasicAuth(
username=auth.get("username"),
password=auth.get("password"),
)