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Source code for galaxy.jobs.runners.godocker
import json
import logging
import time
from datetime import datetime
import requests
from galaxy import model
from galaxy.jobs.runners import (
AsynchronousJobRunner,
AsynchronousJobState
)
log = logging.getLogger(__name__)
__all__ = ('GodockerJobRunner', )
class Godocker(object):
"""
API parameters
"""
def __init__(self, server, login, apikey, noCert):
self.token = None
self.server = server
self.login = login
self.apikey = apikey
self.noCert = noCert
def setToken(self, token):
self.token = token
def http_post_request(self, query, data, header):
""" post request with query """
verify_ssl = not self.noCert
try:
url = self.server + query
res = requests.post(url, data, headers=header, verify=verify_ssl)
except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
log.error('A transport error occurred in the GoDocker job runner:', e)
return False
return self.test_status_code(res)
def http_get_request(self, query, header):
""" get request with query, server and header required """
# remove warnings if using --no-certificate
requests.packages.urllib3.disable_warnings()
verify_ssl = not self.noCert
try:
url = self.server + query
res = requests.get(url, headers=header, verify=verify_ssl)
except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
log.error('A communication error occurred in the GoDocker job runner:', e)
return False
return self.test_status_code(res)
def http_delete_request(self, query, header):
""" delete request with query, server and header required """
# remove warnings if using --no-certificate
requests.packages.urllib3.disable_warnings()
verify_ssl = not self.noCert
try:
url = self.server + query
res = requests.delete(url, headers=header, verify=verify_ssl)
except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
log.error('A communication error occurred in the GoDocker job runner:', e)
return False
return self.test_status_code(res)
def http_put_request(self, query, data, header):
""" put request with query """
# remove warnings if using --no-certificate
requests.packages.urllib3.disable_warnings()
verify_ssl = not self.noCert
try:
url = self.server + query
res = requests.put(url, data, headers=header, verify=verify_ssl)
except (requests.exceptions.ConnectionError, requests.exceptions.HTTPError) as e:
log.error('A communication error occurred in the GoDocker job runner:', e)
return False
return self.test_status_code(res)
def test_status_code(self, httpresult):
""" exit if status code is 401 or 403 or 404 or 200"""
if httpresult.status_code == 401:
log.debug('Unauthorized : this server could not verify that you are authorized to access the document you requested.')
elif httpresult.status_code == 403:
log.debug('Forbidden : Access was denied to this resource. Not authorized to access this resource.')
elif httpresult.status_code == 404:
log.debug('Not Found : The resource could not be found.')
elif httpresult.status_code == 200:
return httpresult
return False
[docs]class GodockerJobRunner(AsynchronousJobRunner):
"""
Job runner backed by a finite pool of worker threads. FIFO scheduling
"""
runner_name = "GodockerJobRunner"
[docs] def __init__(self, app, nworkers, **kwargs):
""" 1: Get runner_param_specs from job_conf.xml
2: Initialise job runner parent object
3: Login to godocker and store the token
4: Start the worker and monitor threads
"""
runner_param_specs = dict(godocker_master=dict(map=str), user=dict(map=str), key=dict(map=str), godocker_project=dict(map=str))
if 'runner_param_specs' not in kwargs:
kwargs['runner_param_specs'] = dict()
kwargs['runner_param_specs'].update(runner_param_specs)
# Start the job runner parent object
super(GodockerJobRunner, self).__init__(app, nworkers, **kwargs)
# godocker API login call
self.auth = self.login(self.runner_params["key"], self.runner_params["user"], self.runner_params["godocker_master"])
if not self.auth:
log.error("Authentication failure, GoDocker runner cannot be started")
else:
""" Following methods starts threads.
These methods invoke threading.Thread(name,target)
which in turn invokes methods monitor() and run_next().
"""
self._init_monitor_thread()
self._init_worker_threads()
[docs] def queue_job(self, job_wrapper):
""" Create job script and submit it to godocker """
if not self.prepare_job(job_wrapper, include_metadata=False, include_work_dir_outputs=True, modify_command_for_container=False):
return
job_destination = job_wrapper.job_destination
""" Submit job to godocker """
job_id = self.post_task(job_wrapper)
if not job_id:
log.error("Job creation failure. No Response from GoDocker")
job_wrapper.fail("Not submitted")
else:
log.debug("Starting queue_job for job " + job_id)
# Create an object of AsynchronousJobState and add it to the monitor queue.
ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper, job_id=job_id, job_destination=job_destination)
self.monitor_queue.put(ajs)
return None
[docs] def check_watched_item(self, job_state):
""" Get the job current status from GoDocker
using job_id and update the status in galaxy.
If the job execution is successful, call
mark_as_finished() and return 'None' to galaxy.
else if the job failed, call mark_as_failed()
and return 'None' to galaxy.
else if the job is running or in pending state, simply
return the 'AsynchronousJobState object' (job_state).
"""
''' This function is called by check_watched_items() where
param job_state is an object of AsynchronousJobState.
Expected return type of this function is None or
AsynchronousJobState object with updated running status.
'''
""" Get task from GoDocker """
job_status_god = self.get_task(job_state.job_id)
log.debug("Job ID: " + str(job_state.job_id) + " Job Status: " + str(job_status_god['status']['primary']))
if job_status_god['status']['primary'] == "over":
job_state.running = False
job_state.job_wrapper.change_state(model.Job.states.OK)
if self.create_log_file(job_state, job_status_god):
self.mark_as_finished(job_state)
else:
self.mark_as_failed(job_state)
'''The function mark_as_finished() executes:
self.work_queue.put((self.finish_job, job_state))
*self.finish_job ->
job_state.job_wrapper.finish( stdout, stderr, exit_code )
job_state.job_wrapper.reclaim_ownership()
job_state.cleanup()
*self.work_queue.put( method , arg ) ->
The run_next() method starts execution on starting worker threads.
This run_next() method executes method(arg)
by using self.work_queue.get()
*Possible outcomes of finish_job(job_state) ->
job_state.job_wrapper.finish( stdout, stderr, exit_code )
job_state.job_wrapper.fail( "Unable to finish job", exception=True)
*Similar workflow is done for mark_as_failed() method.
'''
return None
elif job_status_god['status']['primary'] == "running":
job_state.running = True
job_state.job_wrapper.change_state(model.Job.states.RUNNING)
return job_state
elif job_status_god['status']['primary'] == "pending":
return job_state
elif job_status_god['status']['exitcode'] not in [None, 0]:
job_state.running = False
job_state.job_wrapper.change_state(model.Job.states.ERROR)
self.create_log_file(job_state, job_status_god)
self.mark_as_failed(job_state)
return None
else:
job_state.running = False
self.create_log_file(job_state, job_status_god)
self.mark_as_failed(job_state)
return None
[docs] def stop_job(self, job):
""" Attempts to delete a dispatched executing Job in GoDocker """
'''This function is called by fail_job()
where param job = self.sa_session.query( self.app.model.Job ).get( job_state.job_wrapper.job_id )
No Return data expected
'''
log.debug("STOP JOB EXECUTION OF JOB ID: " + str(job.id))
# Get task status from GoDocker.
job_status_god = self.get_task_status(job.id)
if job_status_god['status']['primary'] != "over":
# Initiate a delete call,if the job is running in GoDocker.
self.delete_task(job.id)
return None
[docs] def recover(self, job, job_wrapper):
""" Recovers jobs stuck in the queued/running state when Galaxy started """
""" This method is called by galaxy at the time of startup.
Jobs in Running & Queued status in galaxy are put in the monitor_queue by creating an AsynchronousJobState object
"""
job_id = job_wrapper.job_id
ajs = AsynchronousJobState(files_dir=job_wrapper.working_directory, job_wrapper=job_wrapper)
ajs.job_id = str(job_id)
ajs.job_destination = job_wrapper.job_destination
job_wrapper.command_line = job.command_line
ajs.job_wrapper = job_wrapper
if job.state == model.Job.states.RUNNING:
log.debug("(%s/%s) is still in running state, adding to the god queue" % (job.id, job.get_job_runner_external_id()))
ajs.old_state = 'R'
ajs.running = True
self.monitor_queue.put(ajs)
elif job.state == model.Job.states.QUEUED:
log.debug("(%s/%s) is still in god queued state, adding to the god queue" % (job.id, job.get_job_runner_external_id()))
ajs.old_state = 'Q'
ajs.running = False
self.monitor_queue.put(ajs)
# Helper functions
[docs] def create_log_file(self, job_state, job_status_god):
""" Create log files in galaxy, namely error_file, output_file, exit_code_file
Return true, if all the file creations are successful
"""
path = None
for vol in job_status_god['container']['volumes']:
if vol['name'] == "go-docker":
path = str(vol['path'])
if path:
god_output_file = path + "/god.log"
god_error_file = path + "/god.err"
try:
# Read from GoDocker output_file and write it into galaxy output_file.
f = open(god_output_file, "r")
out_log = f.read()
log_file = open(job_state.output_file, "w")
log_file.write(out_log)
log_file.close()
f.close()
# Read from GoDocker error_file and write it into galaxy error_file.
f = open(god_error_file, "r")
out_log = f.read()
log_file = open(job_state.error_file, "w")
log_file.write(out_log)
log_file.close()
f.close()
# Read from GoDocker exit_code and write it into galaxy exit_code_file.
out_log = str(job_status_god['status']['exitcode'])
log_file = open(job_state.exit_code_file, "w")
log_file.write(out_log)
log_file.close()
f.close()
log.debug("CREATE OUTPUT FILE: " + str(job_state.output_file))
log.debug("CREATE ERROR FILE: " + str(job_state.error_file))
log.debug("CREATE EXIT CODE FILE: " + str(job_state.exit_code_file))
except IOError as e:
log.error('Could not access task log file %s' % str(e))
log.debug("IO Error occurred when accessing the files.")
return False
return True
# GoDocker API helper functions
[docs] def login(self, apikey, login, server, noCert=False):
""" Login to GoDocker and return the token
Create Login model schema of GoDocker and call the http_post_request method.
"""
log.debug("LOGIN TASK TO BE EXECUTED \n")
log.debug("GODOCKER LOGIN: " + str(login))
data = json.dumps({'user': login, 'apikey': apikey})
# Create object of Godocker class
g_auth = Godocker(server, login, apikey, noCert)
auth = g_auth.http_post_request("/api/1.0/authenticate", data, {'Content-type': 'application/json', 'Accept': 'application/json'})
if not auth:
log.error("GoDocker authentication Error.")
else:
log.debug("GoDocker authentication successful.")
token = auth.json()['token']
g_auth.setToken(token)
# Return the object of Godocker class
return g_auth
[docs] def post_task(self, job_wrapper):
""" Sumbit job to GoDocker and return jobid
Create Job model schema of GoDocker and call the http_post_request method.
"""
# Get the params from <destination> tag in job_conf by using job_destination.params[param]
if self.auth.token:
job_destination = job_wrapper.job_destination
try:
docker_cpu = int(job_destination.params["docker_cpu"])
except Exception:
docker_cpu = 1
try:
docker_ram = int(job_destination.params["docker_memory"])
except Exception:
docker_ram = 1
try:
docker_image = self._find_container(job_wrapper).container_id
log.debug("GoDocker runner using container %s.", docker_image)
except Exception:
log.error("Unable to find docker_image for job %s, failing." % job_wrapper.job_id)
return False
volumes = []
labels = []
tags_tab = ['galaxy', job_wrapper.tool.id]
tasks_depends = []
name = job_wrapper.tool.name
description = "galaxy job"
array = None
project = None
try:
project = str(self.runner_params["godocker_project"])
except KeyError:
log.debug("godocker_project not defined, using default.")
try:
volume = job_destination.params["godocker_volumes"]
volume = volume.split(",")
for i in volume:
temp = dict({"name": i})
volumes.append(temp)
except Exception:
log.debug("godocker_volume not set, using default.")
dt = datetime.now()
# Enable galaxy venv in the docker containers
try:
if(job_destination.params["virtualenv"] == "true"):
GALAXY_VENV_TEMPLATE = """GALAXY_VIRTUAL_ENV="%s"; if [ "$GALAXY_VIRTUAL_ENV" != "None" -a -z "$VIRTUAL_ENV" -a -f "$GALAXY_VIRTUAL_ENV/bin/activate" ]; then . "$GALAXY_VIRTUAL_ENV/bin/activate"; fi;"""
venv = GALAXY_VENV_TEMPLATE % job_wrapper.galaxy_virtual_env
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + venv + "\n" + job_wrapper.runner_command_line
else:
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line
except Exception:
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line
# GoDocker Job model schema
job = {
'date': time.mktime(dt.timetuple()),
'meta': {
'name': name,
'description': description,
'tags': tags_tab
},
'requirements': {
'cpu': docker_cpu,
'ram': docker_ram,
'array': {'values': array},
'label': labels,
'tasks': tasks_depends,
'tmpstorage': None
},
'container': {
'image': str(docker_image),
'volumes': volumes,
'network': True,
'id': None,
'meta': None,
'stats': None,
'ports': [],
'root': False
},
'command': {
'interactive': False,
'cmd': command,
},
'status': {
'primary': None,
'secondary': None
}
}
if project is not None:
job['user'] = {"project": project}
result = self.auth.http_post_request(
"/api/1.0/task", json.dumps(job),
{'Authorization': 'Bearer ' + self.auth.token, 'Content-type': 'application/json', 'Accept': 'application/json'}
)
# Return job_id
return str(result.json()['id'])
[docs] def get_task(self, job_id):
""" Get job details from GoDocker and return the job.
Pass job_id to the http_get_request method.
"""
job = False
if self.auth.token:
result = self.auth.http_get_request("/api/1.0/task/" + str(job_id), {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return the job
return job
[docs] def task_suspend(self, job_id):
""" Suspend actively running job in galaxy.
Pass job_id to the http_get_request method.
"""
job = False
if self.auth.token:
result = self.auth.http_get_request("/api/1.0/task/" + str(job_id) + "/suspend", {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return the job
return job
[docs] def get_task_status(self, job_id):
""" Get job status from GoDocker and return the status of job.
Pass job_id to http_get_request method.
"""
job = False
if self.auth.token:
result = self.auth.http_get_request("/api/1.0/task/" + str(job_id) + "/status", {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return task status
return job
[docs] def delete_task(self, job_id):
""" Delete a suspended task in GoDocker.
Pass job_id to http_delete_request method.
"""
job = False
if self.auth.token:
result = self.auth.http_delete_request("/api/1.0/task/" + str(job_id), {'Authorization': 'Bearer ' + self.auth.token})
job = result.json()
# Return the job
return job