Source code for biothings.web.services.namespace

import inspect
import logging
from pydoc import locate
from types import SimpleNamespace

from biothings.utils.info import DevInfo, FieldNote
from biothings.web import connections
from biothings.web.analytics.notifiers import Notifier
from biothings.web.options import OptionsManager as OptionSets
from biothings.web.query.builder import ESUserQuery, MongoQueryBuilder, SQLQueryBuilder
from biothings.web.query.engine import MongoQueryBackend, SQLQueryBackend
from biothings.web.query.formatter import MongoResultFormatter, SQLResultFormatter
from biothings.web.query.pipeline import MongoQueryPipeline, SQLQueryPipeline
from biothings.web.services.health import ESHealth, MongoHealth, SQLHealth
from biothings.web.services.metadata import BiothingsESMetadata, BiothingsMongoMetadata, BiothingsSQLMetadata

logger = logging.getLogger(__name__)




def load_class(kls):
    if inspect.isclass(kls):
        return kls
    if isinstance(kls, str):
        _kls = locate(kls)
        if _kls:  # could be None
            return _kls
    raise ValueError(kls)



def _requires(config_key):
    def requires(f):
        def _(self):
            if not getattr(self.config, config_key, None):
                return  # skip this database context
            return f(self)

        return _

    return requires




class BiothingsDBProxy:
    """
    Provide database-agnostic access to
    common biothings service components,
    for single database application.
    """

    def __init__(self):
        self.pipeline = None
        self.metadata = None
        self.health = None



    def configure(self, db):
        self.pipeline = db.pipeline
        self.metadata = db.metadata
        self.health = db.health






class BiothingsNamespace:
    # toolbox to use when writing handlers
    # contains common biothings services

    def __init__(self, config):
        self.config = config

        self.fieldnote = FieldNote(config.AVAILABLE_FIELDS_NOTES_PATH)
        self.devinfo = DevInfo()

        # web application
        self.notifier = Notifier(config)
        self.optionsets = OptionSets()
        self.handlers = {}

        # database access
        self.db = BiothingsDBProxy()
        self._configure_elasticsearch()
        self._configure_mongodb()
        self._configure_sql()

        # db uitility shortcuts
        self.pipeline = self.db.pipeline
        self.metadata = self.db.metadata
        self.health = self.db.health

    @_requires("ES_HOST")
    def _configure_elasticsearch(self):
        self.elasticsearch = SimpleNamespace()

        self.elasticsearch.client = connections.es.get_client(self.config.ES_HOST, **self.config.ES_ARGS)
        self.elasticsearch.async_client = connections.es.get_async_client(self.config.ES_HOST, **self.config.ES_ARGS)

        self.elasticsearch.userquery = ESUserQuery(self.config.USERQUERY_DIR)
        self.elasticsearch.metadata = BiothingsESMetadata(
            self.config.ES_INDICES,
            self.elasticsearch.async_client,
        )
        self.elasticsearch.pipeline = load_class(self.config.ES_QUERY_PIPELINE)(
            load_class(self.config.ES_QUERY_BUILDER)(
                self.elasticsearch.userquery,
                self.config.ANNOTATION_ID_REGEX_LIST,
                self.config.ANNOTATION_DEFAULT_SCOPES,
                self.config.ALLOW_RANDOM_QUERY,
                self.config.ALLOW_NESTED_AGGS,
                self.elasticsearch.metadata.biothing_metadata,
            ),
            load_class(self.config.ES_QUERY_BACKEND)(
                self.elasticsearch.async_client,
                self.config.ES_INDICES,
                self.config.ES_SCROLL_TIME,
                self.config.ES_SCROLL_SIZE,
            ),
            load_class(self.config.ES_RESULT_TRANSFORM)(
                self.elasticsearch.metadata.biothing_licenses,
                self.config.LICENSE_TRANSFORM,
                self.fieldnote.get_field_notes(),
                self.config.AVAILABLE_FIELDS_EXCLUDED,
            ),
            fetch_max_match=self.config.ANNOTATION_MAX_MATCH,
        )
        self.elasticsearch.health = ESHealth(self.elasticsearch.async_client, self.config.STATUS_CHECK)
        self.db.configure(self.elasticsearch)

    @_requires("MONGO_URI")
    def _configure_mongodb(self):
        self.mongo = SimpleNamespace()

        self.mongo.client = connections.mongo.get_client(self.config.MONGO_URI, **self.config.MONGO_ARGS)
        self.mongo.metadata = BiothingsMongoMetadata(
            self.config.MONGO_COLS,
            self.mongo.client,
        )
        self.mongo.pipeline = MongoQueryPipeline(
            MongoQueryBuilder(),
            MongoQueryBackend(self.mongo.client, self.config.MONGO_COLS),
            MongoResultFormatter(),
        )
        self.mongo.health = MongoHealth(self.mongo.client)
        self.db.configure(self.mongo)

    @_requires("SQL_URI")
    def _configure_sql(self):
        self.sql = SimpleNamespace()

        self.sql.client = connections.sql.get_client(self.config.SQL_URI, **self.config.SQL_ARGS)
        self.sql.metadata = BiothingsSQLMetadata(self.config.SQL_TBLS, self.sql.client)
        self.sql.pipeline = SQLQueryPipeline(
            SQLQueryBuilder(self.config.SQL_TBLS),
            SQLQueryBackend(self.sql.client),
            SQLResultFormatter(),
        )
        self.sql.health = SQLHealth(self.sql.client)
        self.db.configure(self.sql)