Source code for biothings.web.connections

import hashlib
import logging
import os
import pickle
from functools import partial

import boto3
import elasticsearch
import elasticsearch_dsl
import requests
from biothings.utils.common import run_once
from elasticsearch import AIOHttpConnection
from elasticsearch import RequestsHttpConnection as _Conn
from requests_aws4auth import AWS4Auth
from tornado.ioloop import IOLoop

logger = logging.getLogger(__name__)

_should_log = run_once()

def _log_pkg():
    es_ver = elasticsearch.__version__
    es_dsl_ver = elasticsearch_dsl.__version__"Elasticsearch Package Version: %s",
                '.'.join(map(str, es_ver)))"Elasticsearch DSL Package Version: %s",
                '.'.join(map(str, es_dsl_ver)))

def _log_db(client, uri):

def _log_es(client, hosts):
    _log_db(client, hosts)

    # only perform health check with the async client
    # so that it doesn't slow down program start time
    if isinstance(client, elasticsearch.AsyncElasticsearch):
        async def log_cluster(async_client):
            cluster = await
            # not specifying timeout in the function above because
            # there could be a number of es tasks scheduled before
            # this call and would take the cluster a while to respond

            if _should_log():

            cluster_name = cluster['cluster_name']
            version = cluster['version']['number']

  '%s: %s %s', hosts, cluster_name, version)
        IOLoop.current().add_callback(log_cluster, client)

# ------------------------
#   Low Level Functions
# ------------------------

class _AsyncConn(AIOHttpConnection):
    def __init__(self, *args, **kwargs):
        self.aws_auth = None
        if isinstance(kwargs.get('http_auth'), AWS4Auth):
            self.aws_auth = kwargs['http_auth']
            kwargs['http_auth'] = None
        super().__init__(*args, **kwargs)

    async def perform_request(
        self, method, url, params=None, body=None,
        timeout=None, ignore=(), headers=None
        req = requests.PreparedRequest()
        req.prepare(method, + url, headers, None, body, params)
        self.aws_auth(req)  # sign the request
        return await super().perform_request(
            method, url, params, body,
            timeout, ignore, headers


[docs]def get_es_client(hosts=None, async_=False, **settings): """ Enhanced ES client initialization. Additionally support these parameters: async_: use AsyncElasticserach instead of Elasticsearch. aws: setup request signing and provide reasonable ES settings to access AWS OpenSearch, by default assuming it is on HTTPS. sniff: provide resonable default settings to enable client-side LB to an ES cluster. this param itself is not an ES param. """ if settings.pop('aws', False): # find region session = boto3.Session() region = session.region_name if not region: # not in ~/.aws/config region = os.environ.get("AWS_REGION") if not region: # not in environment variable try: # assume same-region service access res = requests.get(AWS_META_URL) region = res.json()["region"] except: # not running in VPC region = "us-west-2" # default # find credentials credentials = session.get_credentials() awsauth = AWS4Auth( refreshable_credentials=credentials, region=region, service='es' ) _cc = _AsyncConn if async_ else _Conn settings.update(http_auth=awsauth, connection_class=_cc) settings.setdefault('use_ssl', True) settings.setdefault('verify_certs', True) # not evaluated when 'aws' flag is set because # AWS OpenSearch is internally load-balanced # and does not support client-side sniffing. elif settings.pop('sniff', False): settings.setdefault('sniff_on_start', True) settings.setdefault('sniff_on_connection_fail', True) settings.setdefault('sniffer_timeout', 60) if async_: from elasticsearch import AsyncElasticsearch client = AsyncElasticsearch else: from elasticsearch import Elasticsearch client = Elasticsearch return client(hosts, **settings)
[docs]def get_sql_client(uri, **settings): from sqlalchemy import create_engine return create_engine(uri, **settings).connect()
[docs]def get_mongo_client(uri, **settings): from pymongo import MongoClient return MongoClient(uri, **settings).get_default_database()
def _not_implemented_client(): raise NotImplementedError() # ------------------------ # High Level Utilities # ------------------------
[docs]class _ClientPool: def __init__(self, client_factory, async_factory, callback=None): self._client_factory = client_factory self._clients = {} self._async_client_factory = async_factory self._async_clients = {} self.callback = callback or _log_db
[docs] @staticmethod def hash(config): _config = pickle.dumps(config) _hash = hashlib.md5(_config) return _hash.hexdigest()
def _get_client(self, repo, factory, uri, settings): hash = self.hash((uri, settings)) if hash in repo: return repo[hash] repo[hash] = factory(uri, **settings) self.callback(repo[hash], uri) return repo[hash]
[docs] def get_client(self, uri, **settings): return self._get_client( self._clients, self._client_factory, uri, settings )
[docs] def get_async_client(self, uri, **settings): return self._get_client( self._async_clients, self._async_client_factory, uri, settings )
es = _ClientPool(get_es_client, partial(get_es_client, async_=True), _log_es) sql = _ClientPool(get_sql_client, _not_implemented_client) mongo = _ClientPool(get_mongo_client, _not_implemented_client)