def abort(code):
if code == 400: return web.HTTPBadRequest()
elif code == 401: return web.HTTPUnauthorized()
elif code == 402: return web.HTTPPaymentRequired()
elif code == 403: return web.HTTPForbidden()
elif code == 404: return web.HTTPNotFound()
elif code == 405: return web.HTTPMethodNotAllowed()
elif code == 406: return web.HTTPNotAcceptable()
elif code == 407: return web.HTTPProxyAuthenticationRequired()
elif code == 408: return web.HTTPRequestTimeout()
elif code == 409: return web.HTTPConflict()
elif code == 410: return web.HTTPGone()
elif code == 411: return web.HTTPLengthRequired()
elif code == 412: return web.HTTPPreconditionFailed()
elif code == 413: return web.HTTPRequestEntityTooLarge()
elif code == 414: return web.HTTPRequestURITooLong()
elif code == 415: return web.HTTPUnsupportedMediaType()
elif code == 416: return web.HTTPRequestRangeNotSatisfiable()
elif code == 417: return web.HTTPExpectationFailed()
elif code == 421: return web.HTTPMisdirectedRequest()
elif code == 422: return web.HTTPUnprocessableEntity()
elif code == 424: return web.HTTPFailedDependency()
elif code == 426: return web.HTTPUpgradeRequired()
elif code == 428: return web.HTTPPreconditionRequired()
elif code == 429: return web.HTTPTooManyRequests()
elif code == 431: return web.HTTPRequestHeaderFieldsTooLarge()
elif code == 451: return web.HTTPUnavailableForLegalReasons()
else: return web.HTTPBadRequest()
async def handle_kkdcp(request):
length = request.content_length
if length is None:
raise web.HTTPLengthRequired(text="Length is required.")
if length > MAX_LENGTH:
raise web.HTTPRequestEntityTooLarge(text="Request is too large.")
try:
data = await request.read()
proxy_request = codec.decode(data)
except codec.ParserError as e:
raise web.HTTPBadRequest(text=str(e))
loop = asyncio.get_event_loop()
# TODO: Change this to look up the KDC to talk to
try:
krb5_response = await asyncio.wait_for(forward_kerberos(proxy_request.message, loop=loop), timeout=15, loop=loop)
except asyncio.TimeoutError:
raise web.HTTPServiceUnavailable(text="Timeout waiting for Kerberos server")
return web.Response(body=codec.encode(krb5_response), content_type="application/kerberos")
async def submit(request):
global filerouter
global servermode
sysconf = au.get_system_conf()
size_cutoff = sysconf['gui_input_size_limit']
if request.content_length is None:
return web.HTTPLengthRequired(
text=json.dumps({
'status': 'fail',
'msg': 'Content-Length header required'
}))
if request.content_length > size_cutoff * 1024 * 1024:
return web.HTTPRequestEntityTooLarge(text=json.dumps(
{
'status': 'fail',
'msg': f'Input is too big. Limit is {size_cutoff}MB.'
}))
if servermode and server_ready:
r = await cravat_multiuser.is_loggedin(request)
if r == False:
return web.json_response({'status': 'notloggedin'})
jobs_dirs = await filerouter.get_jobs_dirs(request)
jobs_dir = jobs_dirs[0]
job_id = get_next_job_id()
job_dir = os.path.join(jobs_dir, job_id)
os.makedirs(job_dir, exist_ok=True)
reader = await request.multipart()
job_options = {}
input_files = []
while True:
part = await reader.next()
if not part:
break
if part.name.startswith('file_'):
input_files.append(part)
# Have to write to disk here
wfname = part.filename
wpath = os.path.join(job_dir, wfname)
with open(wpath, 'wb') as wf:
wf.write(await part.read())
elif part.name == 'options':
job_options = await part.json()
input_fnames = [fp.filename for fp in input_files]
run_name = input_fnames[0]
if len(input_fnames) > 1:
run_name += '_and_' + str(len(input_fnames) - 1) + '_files'
info_fname = '{}.status.json'.format(run_name)
job_info_fpath = os.path.join(job_dir, info_fname)
job = WebJob(job_dir, job_info_fpath)
job.save_job_options(job_options)
job.set_info_values(orig_input_fname=input_fnames,
run_name=run_name,
submission_time=datetime.datetime.now().isoformat(),
viewable=False)
# Subprocess arguments
input_fpaths = [os.path.join(job_dir, fn) for fn in input_fnames]
run_args = ['oc', 'run']
for fn in input_fnames:
run_args.append(os.path.join(job_dir, fn))
# Annotators
if 'annotators' in job_options and len(
job_options['annotators']
) > 0 and job_options['annotators'][0] != '':
annotators = job_options['annotators']
annotators.sort()
run_args.append('-a')
run_args.extend(annotators)
else:
annotators = ''
run_args.append('-e')
run_args.append('*')
# Liftover assembly
run_args.append('-l')
if 'assembly' in job_options:
assembly = job_options['assembly']
else:
assembly = constants.default_assembly
run_args.append(assembly)
if servermode and server_ready:
await cravat_multiuser.update_user_settings(request,
{'lastAssembly': assembly})
else:
au.set_cravat_conf_prop('last_assembly', assembly)
# Reports
if 'reports' in job_options and len(job_options['reports']) > 0:
run_args.append('-t')
run_args.extend(job_options['reports'])
else:
run_args.extend(['--skip', 'reporter'])
# Note
if 'note' in job_options:
note = job_options['note']
if note != '':
run_args.append('--note')
run_args.append(note)
# Forced input format
if 'forcedinputformat' in job_options and job_options['forcedinputformat']:
run_args.append('--input-format')
run_args.append(job_options['forcedinputformat'])
if servermode:
run_args.append('--writeadmindb')
run_args.extend(['--jobid', job_id])
run_args.append('--temp-files')
global job_queue
global run_jobs_info
job_ids = run_jobs_info['job_ids']
job_ids.append(job_id)
run_jobs_info['job_ids'] = job_ids
qitem = {'cmd': 'submit', 'job_id': job_id, 'run_args': run_args}
job_queue.put(qitem)
status = {'status': 'Submitted'}
job.set_info_values(status=status)
if servermode and server_ready:
await cravat_multiuser.add_job_info(request, job)
# makes temporary status.json
status_json = {}
status_json['job_dir'] = job_dir
status_json['id'] = job_id
status_json['run_name'] = run_name
status_json['assembly'] = assembly
status_json['db_path'] = ''
status_json['orig_input_fname'] = input_fnames
status_json['orig_input_path'] = input_fpaths
status_json['submission_time'] = datetime.datetime.now().isoformat()
status_json['viewable'] = False
status_json['note'] = note
status_json['status'] = 'Submitted'
status_json['reports'] = []
pkg_ver = au.get_current_package_version()
status_json['open_cravat_version'] = pkg_ver
status_json['annotators'] = annotators
with open(os.path.join(job_dir, run_name + '.status.json'), 'w') as wf:
json.dump(status_json, wf, indent=2, sort_keys=True)
return web.json_response(job.get_info_dict())