def get_domain_ranges(self, sequence):
if self.url is None:
raise InitError("interpro url is not set")
job_id = self._interpro_submit(sequence)
t0 = time()
while (time() - t0) < self.job_timout:
status = self._interpro_status(job_id)
if status in ['RUNNING', 'PENDING', 'STARTED']:
sleep(self.poll_interval)
elif status == 'NOT_FOUND':
job_id = self._interpro_submit(sequence)
else:
break
if status == 'RUNNING':
raise ServiceError("inteproscan job timed out")
elif status in ['FAILURE', 'ERROR']:
raise ServiceError(self._interpro_error(job_id))
elif status != 'FINISHED':
raise ServiceError("inteproscan job status = " + status)
xml_str = self._interpro_result(job_id)
return self._parse_interpro_ranges(xml_str)
def _get_redis(self):
if self.redis_hostname is None:
raise ServiceError("redis hostname is not set")
if self.redis_port is None:
raise ServiceError("redis port is not set")
if self.redis_db is None:
raise ServiceError("redis db is not set")
return redis.StrictRedis(host=self.redis_hostname,
port=self.redis_port,
db=self.redis_db)
def _interpro_error(self, job_id):
result_url = '/'.join([self.url, 'result', job_id, 'xml'])
try:
r = requests.get(result_url, timeout=self.http_timeout)
except requests.exceptions.ConnectTimeout:
raise ServiceError("timeout connecting with interpro")
r.raise_for_status()
return r.text
def _interpro_submit(self, sequence):
params = {'email': "*****@*****.**",
'sequence': sequence,
'goterms': True,
'pathways': False}
submit_url = '/'.join([self.url, 'run'])
try:
r = requests.post(submit_url, data=params, timeout=self.http_timeout)
except requests.exceptions.ConnectTimeout:
raise ServiceError("timeout connecting with interpro")
r.raise_for_status()
return r.text