Merge pull request #18353 from jdavcs/241_merge3 (9d15f2f1) · Commits · NDIP / Galaxy

lib/galaxy/managers/jobs.py

+15 −4

Original line number	Diff line number	Diff line
		import json
		import logging
		import typing
		from datetime import (
		date,
		datetime,
		)
		from typing import (
		cast,
		Dict,
		List,
		Optional,
		)

		import sqlalchemy
		@@ -38,6 +39,7 @@ from galaxy.job_metrics import (
		Safety,
		)
		from galaxy.managers.collections import DatasetCollectionManager
		from galaxy.managers.context import ProvidesUserContext
		from galaxy.managers.datasets import DatasetManager
		from galaxy.managers.hdas import HDAManager
		from galaxy.managers.lddas import LDDAManager
		@@ -106,7 +108,9 @@ class JobManager:
		self.app = app
		self.dataset_manager = DatasetManager(app)

		def index_query(self, trans, payload: JobIndexQueryPayload) -> sqlalchemy.engine.Result:
		def index_query(
		self, trans: ProvidesUserContext, payload: JobIndexQueryPayload
		) -> Optional[sqlalchemy.engine.ScalarResult]:
		"""The caller is responsible for security checks on the resulting job if
		history_id, invocation_id, or implicit_collection_jobs_id is set.
		Otherwise this will only return the user's jobs or all jobs if the requesting
		@@ -122,6 +126,13 @@ class JobManager:
		search = payload.search
		order_by = payload.order_by

		if trans.user is None:
		# If the user is anonymous we can only return jobs for the current session history
		if trans.galaxy_session and trans.galaxy_session.current_history_id:
		history_id = trans.galaxy_session.current_history_id
		else:
		return None

		def build_and_apply_filters(stmt, objects, filter_func):
		if objects is not None:
		if isinstance(objects, (str, date, datetime)):
		@@ -208,7 +219,7 @@ class JobManager:
		if user_details:
		stmt = stmt.outerjoin(Job.user)
		else:
		if history_id is None and invocation_id is None and implicit_collection_jobs_id is None:
		if history_id is None and invocation_id is None and implicit_collection_jobs_id is None and trans.user:
		stmt = stmt.where(Job.user_id == trans.user.id)
		# caller better check security

		@@ -647,7 +658,7 @@ class JobSearch:
		return stmt


		def view_show_job(trans, job: Job, full: bool) -> typing.Dict:
		def view_show_job(trans, job: Job, full: bool) -> Dict:
		is_admin = trans.user_is_admin
		job_dict = job.to_dict("element", system_details=is_admin)
		if trans.app.config.expose_dataset_path and "command_line" not in job_dict:

lib/galaxy/webapps/galaxy/services/jobs.py

+3 −1

Original line number	Diff line number	Diff line
		@@ -81,7 +81,9 @@ class JobsService(ServiceBase):
		or payload.history_id is not None
		)
		jobs = self.job_manager.index_query(trans, payload)
		out = []
		out: List[Dict[str, Any]] = []
		if jobs is None:
		return out
		for job in jobs.yield_per(model.YIELD_PER_ROWS):
		# TODO: optimize if this crucial
		if check_security_of_jobs and not security_check(trans, job.history, check_accessible=True):

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