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Source code for galaxy.webapps.galaxy.api.job_files

""" API for asynchronous job running mechanisms can use to fetch or put files
related to running and queued jobs.

import logging
import os
import re
import shutil

from galaxy import (
from galaxy.managers.context import ProvidesAppContext
from galaxy.model import Job
from galaxy.web import (
from . import BaseGalaxyAPIController

log = logging.getLogger(__name__)

[docs]class JobFilesAPIController(BaseGalaxyAPIController): """This job files controller allows remote job running mechanisms to read and modify the current state of files for queued and running jobs. It is certainly not meant to represent part of Galaxy's stable, user facing API. Furthermore, even if a user key corresponds to the user running the job, it should not be accepted for authorization - this API allows access to low-level unfiltered files and such authorization would break Galaxy's security model for tool execution. """
[docs] @expose_api_raw_anonymous_and_sessionless def index(self, trans: ProvidesAppContext, job_id, **kwargs): """ GET /api/jobs/{job_id}/files Get a file required to staging a job (proper datasets, extra inputs, task-split inputs, working directory files). :type job_id: str :param job_id: encoded id string of the job :type path: str :param path: Path to file. :type job_key: str :param job_key: A key used to authenticate this request as acting on behalf or a job runner for the specified job. ..note: This API method is intended only for consumption by job runners, not end users. :rtype: binary :returns: contents of file """ job = self.__authorize_job_access(trans, job_id, **kwargs) path = kwargs["path"] try: return open(path, "rb") except FileNotFoundError: # We know that the job is not terminal, but users (or admin scripts) can purge input datasets. # Here we discriminate that case from truly unexpected bugs. # Not failing the job here, this is or should be handled by pulsar. match = re.match(r"(galaxy_)?dataset_(.*)\.dat", os.path.basename(path)) if match: # This looks like a galaxy dataset, check if any job input has been deleted. if any(jtid.dataset.dataset.purged for jtid in job.input_datasets): raise exceptions.ItemDeletionException("Input dataset(s) for job have been purged.") else: raise
[docs] @expose_api_anonymous_and_sessionless def create(self, trans, job_id, payload, **kwargs): """ create( self, trans, job_id, payload, **kwargs ) * POST /api/jobs/{job_id}/files Populate an output file (formal dataset, task split part, working directory file (such as those related to metadata)). This should be a multipart post with a 'file' parameter containing the contents of the actual file to create. :type job_id: str :param job_id: encoded id string of the job :type payload: dict :param payload: dictionary structure containing:: 'job_key' = Key authenticating 'path' = Path to file to create. ..note: This API method is intended only for consumption by job runners, not end users. :rtype: dict :returns: an okay message """ job = self.__authorize_job_access(trans, job_id, **payload) path = payload.get("path") if not path: raise exceptions.RequestParameterInvalidException("'path' parameter not provided or empty.") self.__check_job_can_write_to_path(trans, job, path) # Is this writing an unneeded file? Should this just copy in Python? if "__file_path" in payload: file_path = payload.get("__file_path") upload_store = trans.app.config.nginx_upload_job_files_store assert upload_store, ( "Request appears to have been processed by" " nginx_upload_module but Galaxy is not" " configured to recognize it" ) assert file_path.startswith( upload_store ), f"Filename provided by nginx ({file_path}) is not in correct directory ({upload_store})" input_file = open(file_path) elif "session_id" in payload: # code stolen from basic.py session_id = payload["session_id"] upload_store = ( trans.app.config.tus_upload_store_job_files or trans.app.config.tus_upload_store or trans.app.config.new_file_path ) if re.match(r"^[\w-]+$", session_id) is None: raise ValueError("Invalid session id format.") local_filename = os.path.abspath(os.path.join(upload_store, session_id)) input_file = open(local_filename) else: input_file = payload.get("file", payload.get("__file", None)).file target_dir = os.path.dirname(path) util.safe_makedirs(target_dir) try: shutil.move(input_file.name, path) finally: try: input_file.close() except OSError: # Fails to close file if not using nginx upload because the # tempfile has moved and Python wants to delete it. pass return {"message": "ok"}
[docs] @expose_api_anonymous_and_sessionless def tus_patch(self, trans, **kwds): """ Exposed as PATCH /api/job_files/resumable_upload. I think based on the docs, a separate tusd server is needed for job files if also hosting one for use facing uploads. Setting up tusd for job files should just look like (I think): tusd -host localhost -port 1080 -upload-dir=<galaxy_root>/database/tmp See more discussion of checking upload access, but we shouldn't need the API key and session stuff the user upload tusd server should be configured with. Also shouldn't need a hooks endpoint for this reason but if you want to add one the target CLI entry would be -hooks-http=<galaxy_url>/api/job_files/tus_hooks and the action is featured below. I would love to check the job state with __authorize_job_access on the first POST but it seems like TusMiddleware doesn't default to coming in here for that initial POST the way it does for the subsequent PATCHes. Ultimately, the upload is still authorized before the write done with POST /api/jobs/<job_id>/files so I think there is no route here to mess with user data - the worst of the security issues that can be caused is filling up the sever with needless files that aren't acted on. Since this endpoint is not meant for public consumption - all the job files stuff and the TUS server should be blocked to public IPs anyway and restricted to your Pulsar servers and similar targeting could be accomplished with a user account and the user facing upload endpoints. """ return None
[docs] @expose_api_anonymous_and_sessionless def tus_hooks(self, trans, **kwds): """No-op but if hook specified the way we do for user upload it would hit this action. Exposed as PATCH /api/job_files/tus_hooks and documented in the docstring for tus_patch. """ pass
def __authorize_job_access(self, trans, encoded_job_id, **kwargs): for key in ["path", "job_key"]: if key not in kwargs: error_message = f"Job files action requires a valid '{key}'." raise exceptions.ObjectAttributeMissingException(error_message) job_id = trans.security.decode_id(encoded_job_id) job_key = trans.security.encode_id(job_id, kind="jobs_files") if not util.safe_str_cmp(str(kwargs["job_key"]), job_key): raise exceptions.ItemAccessibilityException("Invalid job_key supplied.") # Verify job is active. Don't update the contents of complete jobs. job = trans.sa_session.get(Job, job_id) if job.state not in Job.non_ready_states: error_message = "Attempting to read or modify the files of a job that has already completed." raise exceptions.ItemAccessibilityException(error_message) return job def __check_job_can_write_to_path(self, trans, job, path): """Verify an idealized job runner should actually be able to write to the specified path - it must be a dataset output, a dataset "extra file", or a some place in the working directory of this job. Would like similar checks for reading the unstructured nature of loc files make this very difficult. (See abandoned work here https://gist.github.com/jmchilton/9103619.) """ in_work_dir = self.__in_working_directory(job, path, trans.app) if not in_work_dir and not self.__is_output_dataset_path(job, path): raise exceptions.ItemAccessibilityException("Job is not authorized to write to supplied path.") def __is_output_dataset_path(self, job, path): """Check if is an output path for this job or a file in the an output's extra files path. """ da_lists = [job.output_datasets, job.output_library_datasets] for da_list in da_lists: for job_dataset_association in da_list: dataset = job_dataset_association.dataset if not dataset: continue if os.path.abspath(dataset.get_file_name()) == os.path.abspath(path): return True elif util.in_directory(path, dataset.extra_files_path): return True return False def __in_working_directory(self, job, path, app): working_directory = app.object_store.get_filename( job, base_dir="job_work", dir_only=True, extra_dir=str(job.id) ) return util.in_directory(path, working_directory)