def submit_tesk_action(job_id, task_name):
response = None
http_status = None
if request.method == 'GET':
pass
elif request.method == 'POST':
'''
Handler for using the TESK service.
'''
if task_name.lower() in ['apbs', 'pdb2pqr']:
if task_name == 'apbs':
if 'infile' in request.args.to_dict() and request.args['infile'].lower() == 'true':
infile_name = request.json['filename']
runner = apbs_runner.Runner(STORAGE_HOST, job_id=job_id, infile_name=infile_name)
redirectURL = runner.start(STORAGE_HOST, TESK_HOST)
else:
form = request.json
for key in form.keys():
# unravels output parameters from form
if key == 'output_scalar':
for option in form[key]:
form[option] = option
form.pop('output_scalar')
elif not isinstance(form[key], str):
form[key] = str(form[key])
runner = apbs_runner.Runner(STORAGE_HOST, job_id=job_id, form=form)
redirectURL = runner.start(STORAGE_HOST, TESK_HOST)
elif task_name == 'pdb2pqr':
pass
form = request.json
runner = pdb2pqr_runner.Runner(form, request.files, STORAGE_HOST, job_id=job_id)
redirectURL = runner.start(STORAGE_HOST, TESK_HOST)
response = {
'message': "Task type '%s' accepted. Beginning execution" % (task_name),
'jobURL': redirectURL
}
http_status = 202
else:
response = {
'error': "task type '%s' does not exist or is not implemented" % (task_name)
}
http_status = 404
# import pprint as pp
# pp.pprint(response)
sys.stdout.flush()
return response, http_status
def execute_task(job_id, task_name):
response = None
http_status = None
if task_name.lower() in ['apbs', 'pdb2pqr']:
if task_name.lower() == 'apbs':
print("initiating APBS runner")
if 'infile' in request.args and request.args['infile'].lower() == 'true':
print('found infile in args')
if request.data.has_key('filename'):
infile_name = request.data['filename']
# print(infile_name)
runner = apbs_runner.Runner(STORAGE_HOST, job_id=job_id, infile_name=infile_name)
else:
'''CONSTRUCT SOME TYPE OF ERROR RESPONSE HERE'''
pass
else:
form = request.data
for key in form.keys():
if key == 'output_scalar':
for option in form[key]:
form[option] = option
form.pop('output_scalar')
elif not isinstance(form[key], str):
form[key] = str(form[key])
runner = apbs_runner.Runner(STORAGE_HOST, job_id=job_id, form=form)
print("launching APBS runner")
redirectURL = runner.start(STORAGE_HOST)
elif task_name.lower() == 'pdb2pqr':
import pprint as pp
# form_dict = json.loads(request.data)
# print(type(form_dict))
form = request.data
pp.pprint(form)
# runner = pdb2pqr_runner.Runner(request.form, request.files, STORAGE_HOST)
runner = pdb2pqr_runner.Runner(form, request.files, STORAGE_HOST, job_id=job_id)
redirectURL = runner.start(STORAGE_HOST)
'''=== DEBUG LINE FOR DEV: REMOVE IN FINAL ==='''
if 'http://localhost:5000' in redirectURL:
print(redirectURL)
redirectURL = redirectURL.replace('http://localhost:5000', 'http://localhost:3000')
print(redirectURL)
'''==========================================='''
# return redirect(redirectURL)
response = {
'message': "Task type '%s' accepted. Beginning execution" % (task_name),
'jobURL': redirectURL
}
http_status = 202
else:
response = {
'error': "task type '%s' does not exist or is not implemented" % (task_name)
}
http_status = 404
return response, http_status
def submit_tesk_action(job_id, task_name):
response = None
http_status = None
if request.method == 'GET':
#TODO: Get task status from scheduling service (Volcano.sh)
response = {}
http_status = None
volcano_namespace = os.environ.get('VOLCANO_NAMESPACE')
try:
vcjob_info = get_volcano_job(job_id, task_name, volcano_namespace)
if 'status' in vcjob_info and vcjob_info['status'] == 404:
# If job not found, return 404
http_status = 404
response['error'] = vcjob_info['reason']
response[
'message'] = "Could not find instance of task '%s' for jobid '%s'" % (
task_name, job_id)
logging.info("Task '%s->%s' could not be found. Status: %s",
job_id, task_name,
json.dumps(vcjob_info['status'], indent=2))
else:
response = parse_volcano_job_info(vcjob_info, STORAGE_HOST)
http_status = 200
except Exception as err:
response = {}
response['message'] = None
response['error'] = (
'Internal error while processing request. '
'If error persists, please report through usual channels (email, issues, etc.)'
)
http_status = 500
logging.error(traceback.format_exc())
# raise
elif request.method == 'POST':
'''
Handler for using the TESK service.
'''
if task_name.lower() in ['apbs', 'pdb2pqr']:
response = {
'message':
"Task type '%s' accepted. Beginning execution" % (task_name),
}
if task_name == 'apbs':
# TODO: wrap in try/except; set response/http_code when initializing apbs_runner.Runner()
try:
if 'infile' in request.args.to_dict(
) and request.args['infile'].lower() == 'true':
infile_name = request.json['filename']
if infile_name is None:
raise apbs_runner.MissingFilesError(
'No APBS input file specified.')
runner = apbs_runner.Runner(STORAGE_HOST,
job_id=job_id,
infile_name=infile_name)
redirectURL = runner.start(STORAGE_HOST, TESK_HOST,
IMAGE_PULL_POLICY,
GA_TRACKING_ID)
# Update response with URL to monitor on a browser
response['jobURL'] = redirectURL
else:
form = request.json
for key in form.keys():
# unravels output parameters from form
if key == 'output_scalar':
for option in form[key]:
form[option] = option
form.pop('output_scalar')
elif not isinstance(form[key], str):
form[key] = str(form[key])
runner = apbs_runner.Runner(STORAGE_HOST,
job_id=job_id,
form=form)
redirectURL = runner.start(STORAGE_HOST, TESK_HOST,
IMAGE_PULL_POLICY,
GA_TRACKING_ID)
# Update response with URL to monitor on a browser
response['jobURL'] = redirectURL
http_status = 202
# except FileNotFoundError as err:
except apbs_runner.MissingFilesError as err:
logging.error('%s: %s',
type(err).__name__,
err) # # Print error to log
response['message'] = None
response['error'] = str(err)
response['missing_files'] = err.missing_files
http_status = 400
# print traceback for debugging
logging.error(
traceback.format_exc()) # # Print error to log
except Exception as err:
logging.error('%s: %s',
type(err).__name__,
err) # Print error to log
response['message'] = None
response['error'] = (
'Internal error while processing request. '
'If error persists, please report through usual channels (email, issues, etc.)'
)
http_status = 500
# print traceback for debugging
logging.error(traceback.format_exc()) # Print error to log
elif task_name == 'pdb2pqr':
try:
form = request.json
runner = pdb2pqr_runner.Runner(form,
request.files,
STORAGE_HOST,
job_id=job_id)
redirectURL = runner.start(STORAGE_HOST, TESK_HOST,
IMAGE_PULL_POLICY,
GA_TRACKING_ID)
# Update response with URL to monitor on a browser
response['jobURL'] = redirectURL
http_status = 202
except WebOptionsError as err:
logging.error('JOB_ID--%s TASK_NAME--%s: %s', job_id,
task_name, str(err))
response.pop('message')
response['error'] = str(err)
if err.bad_weboption is not None:
response['name'] = err.bad_weboption
http_status = 400
except Exception as err:
logging.error('%s: %s',
type(err).__name__,
err) # Print error to log
response['message'] = None
response['error'] = (
'Internal error while processing request. '
'If error persists, please report through usual channels (email, issues, etc.)'
)
http_status = 500
# print traceback for debugging
logging.error(traceback.format_exc()) # Print error to log
# response = {
# 'message': "Task type '%s' accepted. Beginning execution" % (task_name),
# 'jobURL': redirectURL
# }
# http_status = 202
else:
response = {
'error':
"task type '%s' does not exist or is not implemented" %
(task_name)
}
http_status = 404
# import pprint as pp
# pp.pprint(response)
sys.stdout.flush()
return response, http_status