Source code for biothings.web.handlers.query

Elasticsearch Handlers


    Supports: (all features above and)
    - access to biothing_type attribute
    - access to ES query pipeline stages
    - pretty print elasticsearch exceptions
    - common control option out_format

    - biothings.web.handlers.MetadataSourceHandler
    - biothings.web.handlers.MetadataFieldHandler
    - myvariant.web.beacon.BeaconHandler


    Supports: (all features above and)
    - common control options (raw, rawquery)
    - common transform options (dotfield, always_list...)
    - query pipeline customization hooks
    - single query through GET
    - multiple quers through POST

    - biothings.web.handlers.BiothingHandler
    - biothings.web.handlers.QueryHandler


import logging
from collections import UserDict
from types import CoroutineType

import elasticsearch
from import GAEvent
from biothings.web.query.builder import RawQueryInterrupt
from biothings.web.query.engine import EndScrollInterrupt, RawResultInterrupt
from biothings.web.query.pipeline import QueryPipelineException
from tornado.web import Finish, HTTPError

from .api import BaseAPIHandler
from .exceptions import BadRequest, EndRequest

__all__ = [

[docs]class BaseESRequestHandler(BaseAPIHandler): kwargs = { '*': { 'out_format': { 'type': str, 'default': 'json', 'enum': ('json', 'yaml', 'html', 'msgpack'), 'alias': ['format'] } } } def initialize(self, biothing_type=None): super(BaseESRequestHandler, self).initialize() self.biothing_type = biothing_type self.pipeline = self.biothings.pipeline self.metadata = self.biothings.metadata
[docs] def prepare(self): super().prepare() # provide convenient access to next stages self.args.biothing_type = self.biothing_type # supported across es requests self.format = self.args.out_format or 'json' self.event = GAEvent({ 'category': '{}_api'.format(self.biothings.config.API_VERSION), # eg.'v1_api' 'action': '_'.join((, self.request.method.lower())), # eg.'query_get' # 'label': 'fetch_all', etc. # 'value': 100, # number of queries })
[docs] def parse_exception(self, exception): message = super().parse_exception(exception) # TODO merge this into ESQueryPipelineHandler # or not? consider implications when we support # additional discovery-like applications and # eventually other than tornado web frameworks if '_es_error' in message: _es_error = message.pop('_es_error') message['error'] = _es_error.error try: root_cause ='error', root_cause = root_cause['root_cause'][0]['reason'] root_cause = root_cause.replace('\"', '\'').split('\n') for index, cause in enumerate(root_cause): message['root_cuase_line_'+f'{index:02}'] = cause except IndexError: pass # no root cause except Exception: self.logger.exception('Error parsing es exception.') return message
[docs]class MetadataSourceHandler(BaseESRequestHandler): """ GET /metadata """ name = 'metadata' kwargs = dict(BaseESRequestHandler.kwargs) kwargs['GET'] = { 'dev': {'type': bool, 'default': False}, 'raw': {'type': bool, 'default': False} } async def get(self): info = await self.metadata.refresh(self.biothing_type) meta = self.metadata.get_metadata(self.biothing_type) if self.args.raw: raise Finish(info) elif meta['software'] = self.biothings.devinfo.get() else: # remove debug info for field in list(meta): if field.startswith('_'): meta.pop(field, None) meta = self.extras(meta) # override here self.finish(dict(sorted(meta.items())))
[docs] def extras(self, _meta): """ Override to add app specific metadata """ return _meta
[docs]class MetadataFieldHandler(BaseESRequestHandler): """ GET /metadata/fields """ name = 'fields' kwargs = dict(BaseESRequestHandler.kwargs) kwargs['GET'] = { 'raw': {'type': bool, 'default': False}, 'search': {'type': str, 'default': None}, 'prefix': {'type': str, 'default': None} } async def get(self): await self.metadata.refresh(self.biothing_type) mapping = self.metadata.get_mappings(self.biothing_type) if self.args.raw: raise Finish(mapping) result = self.pipeline.formatter.transform_mapping( mapping, self.args.prefix, self.finish(result)
class InterruptResult(UserDict): pass def ESQueryPipelineHandler(handler_class): def handle_exceptions(method): async def _method(*args, **kwargs): try: return await method(*args, **kwargs) except ( RawQueryInterrupt, # correspond to 'rawquery' option RawResultInterrupt, # correspond to 'raw' option EndScrollInterrupt ) as exc: _exc = EndRequest() _exc.kwargs = InterruptResult( \ if isinstance(, dict) else # use a non-dict wrapper so that the data # is not merged with the error template. raise _exc except AssertionError as exc: # in our application, AssertionError should be internal # the individual components raising the error should instead # rasie exceptions like ValueError and TypeError for bad input logging.error("FIXME: Unexpected Assertion Error.") raise HTTPError(reason=str(exc)) except (ValueError, TypeError) as exc: raise BadRequest(reason=type(exc).__name__, details=str(exc)) except QueryPipelineException as exc: raise HTTPError(exc.code, except elasticsearch.ConnectionError: # like timeouts.. raise HTTPError(503) except elasticsearch.RequestError as exc: # 400s raise BadRequest(_es_error=exc) except elasticsearch.TransportError as exc: # >400 if exc.error == 'search_phase_execution_exception': reason ="caused_by", {}).get("reason", "") if "rejected execution" in reason: raise EndRequest(503, reason="server busy") 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 return _method handler_class.get = handle_exceptions(handler_class.get) = handle_exceptions( return handler_class async def ensure_awaitable(obj): if isinstance(obj, CoroutineType): return await obj return obj
[docs]@ESQueryPipelineHandler class BiothingHandler(BaseESRequestHandler): """ Biothings Annotation Endpoint URL pattern examples: /{pre}/{ver}/{typ}/? /{pre}/{ver}/{typ}/([^\/]+)/? queries a term against a pre-determined field that represents the id of a document, like _id and dbsnp.rsid GET -> {...} or [{...}, ...] POST -> [{...}, ...] """ name = 'annotation' async def post(self, *args, **kwargs): self.event['value'] = len(self.args['id']) result = await ensure_awaitable( self.pipeline.fetch(**self.args)) self.finish(result) async def get(self, *args, **kwargs): self.event['value'] = 1 result = await ensure_awaitable( self.pipeline.fetch(**self.args)) self.finish(result)
[docs]@ESQueryPipelineHandler class QueryHandler(BaseESRequestHandler): ''' Biothings Query Endpoint URL pattern examples: /{pre}/{ver}/{typ}/query/? /{pre}/{ver}//query/? GET -> {...} POST -> [{...}, ...] ''' name = 'query' async def post(self, *args, **kwargs): self.event['value'] = len(self.args['q']) result = await ensure_awaitable(**self.args)) self.finish(result) async def get(self, *args, **kwargs): self.event['value'] = 1 if self.args.get('fetch_all'): self.event['label'] = 'fetch_all' if self.args.get('fetch_all') or \ self.args.get('scroll_id') or \ self.args.get('q') == '__any__': self.clear_header('Cache-Control') response = await ensure_awaitable(**self.args)) self.finish(response)