Source code for biothings.web.pipeline.execute

    Elasticsearch Query Execution
import asyncio

from biothings.web.handlers.exceptions import BadRequest, EndRequest
from elasticsearch import (ConnectionError, ConnectionTimeout, NotFoundError,
                           RequestError, TransportError)
from elasticsearch_dsl import MultiSearch
from tornado.web import HTTPError

semaphore = asyncio.Semaphore()

[docs]class ESQueryBackend(object): ''' Execute an Elasticsearch query ''' def __init__(self, web_settings): self.client = web_settings.connections.async_client # es indices self.indices = web_settings.ES_INDICES self.default_index = web_settings.ES_INDEX self.default_type = web_settings.ES_DOC_TYPE # for scroll queries self.scroll_time = web_settings.ES_SCROLL_TIME self.scroll_size = web_settings.ES_SCROLL_SIZE
[docs] async def execute(self, query, options): ''' Execute the corresponding query. Must return an awaitable. May override to add more. Handle uncaught exceptions. Options: Required: either an es-dsl query object or scroll_id Optional: fetch_all: also return a scroll_id for this query (default: false) biothing_type: which type's corresponding indices to query (default in ''' if options.scroll_id: try: res = await self.client.scroll( scroll_id=options.scroll_id, scroll=self.scroll_time) except ConnectionError: raise HTTPError(503) except (NotFoundError, RequestError, TransportError): raise BadRequest(reason="Invalid or stale scroll_id.") else: if not res['hits']['hits']: raise EndRequest(reason="No more results to return.") return res if query: if isinstance(query, MultiSearch): await semaphore.acquire() biothing_type = options.get('biothing_type', None) or self.default_type query = query.index(self.indices.get(biothing_type, self.default_index)) if options.get('fetch_all', False): query = query.params(scroll=self.scroll_time) query = query.extra(size=self.scroll_size) try: res = await query.using(self.client).execute() except (ConnectionError, ConnectionTimeout): raise HTTPError(503) except RequestError as exc: raise BadRequest(_es_error=exc) except TransportError as exc: if exc.error == 'search_phase_execution_exception': reason ="caused_by", {}).get("reason", "") if "rejected execution" in reason: raise EndRequest(503, reason="server overload") else: # unexpected, provide additional information raise EndRequest(500, _es_error=exc, ** elif exc.error == 'index_not_found_exception': raise HTTPError(500, reason=exc.error) elif exc.status_code == 'N/A': raise HTTPError(503) else: # unexpected raise else: # format to {} or [{}...] if isinstance(res, list): return [res_.to_dict() for res_ in res] return res.to_dict() finally: if isinstance(query, MultiSearch): semaphore.release() return asyncio.sleep(0, {})