<commit_before>import logging
from collections import defaultdict
from datetime import datetime
from functools import reduce
from operator import add

import elasticsearch
from dateutil.parser import parse as dtparse

logger = logging.getLogger(__name__)

# TODO
# auto refresh upon start
# not sure if it happens in this module
# but this affects some query pipeline behaviors

class BiothingsMetadata:

    def __init__(self):

        # cached, generated from mappings
        self.biothing_metadata = defaultdict(dict)
        # {
        #     "variant": {
        #         "biothing_type": "variant",
        #         "build_date": "2020-05-08T17:33:59.756164",
        #         "build_version": "20200508",
        #         "src": {"cosmic": { ... }, ... },
        #         "stats": {"total": 928585791 } }
        #     "gene": { ... }
        # }
        self.biothing_mappings = defaultdict(dict)
        # {
        #     "variant": {
        #         'aeolus': {'properties': {'drug_code': {...}, ...}},
        #         'cadd': {'properties': {'1000g': {...}, 'alt': {...}, ...}},
        #         'cgi': {'properties': {'association': {...}, ...}},
        #         'chebi': {'properties': {'brand_names': {...}, ...}}, ... }
        #     "gene": { ... }
        # }
        self.biothing_licenses = defaultdict(dict)
        # {
        #     "variant": {
        #         'aeolus': 'http://bit.ly/2DIxWwF',
        #         'cadd': 'http://bit.ly/2TIuab9',
        #         'cgi': 'http://bit.ly/2FqS871',
        #         'chebi': 'http://bit.ly/2KAUCAm', ... }
        #     "gene": { ... }
        # }

    def get_metadata(self, biothing_type):  # hub
        return self.biothing_metadata[biothing_type]

    def get_mappings(self, biothing_type):
        return self.biothing_mappings[biothing_type]

    def get_licenses(self, biothing_type):
        return self.biothing_licenses[biothing_type]

    async def refresh(self, biothing_type):
        pass

class BiothingsESMetadata(BiothingsMetadata):

    def __init__(self, indices, client):
        super().__init__()

        if not indices:
            # all indices on the host
            indices = {None: "_all"}
        if None not in indices:
            # default index pattern when no type specified
            indices[None] = next(iter(indices.values()))

        self.indices = indices
        self.client = client

    @property
    def types(self):  # biothing_type(s)
        return tuple(filter(None, self.indices.keys()))

    def update(self, biothing_type, info, count):
        """
        Read ES index mappings for the corresponding biothing_type,
        Populate datasource info and field properties from mappings.
        """
        _type = biothing_type

        # try to resolve default to an equivalent
        # and concrete biothing_type to display
        if _type is None:
            for type_, pattern in self.indices.items():
                if self.indices[None] == pattern:
                    _type = type_<commit_msg>auto load metadata upon start<commit_after>import asyncio
import logging
from collections import defaultdict
from datetime import datetime
from functools import reduce
from operator import add

import elasticsearch
from dateutil.parser import parse as dtparse

logger = logging.getLogger(__name__)

class BiothingsMetadata:

    def __init__(self):

        # cached, generated from mappings
        self.biothing_metadata = defaultdict(dict)
        # {
        #     "variant": {
        #         "biothing_type": "variant",
        #         "build_date": "2020-05-08T17:33:59.756164",
        #         "build_version": "20200508",
        #         "src": {"cosmic": { ... }, ... },
        #         "stats": {"total": 928585791 } }
        #     "gene": { ... }
        # }
        self.biothing_mappings = defaultdict(dict)
        # {
        #     "variant": {
        #         'aeolus': {'properties': {'drug_code': {...}, ...}},
        #         'cadd': {'properties': {'1000g': {...}, 'alt': {...}, ...}},
        #         'cgi': {'properties': {'association': {...}, ...}},
        #         'chebi': {'properties': {'brand_names': {...}, ...}}, ... }
        #     "gene": { ... }
        # }
        self.biothing_licenses = defaultdict(dict)
        # {
        #     "variant": {
        #         'aeolus': 'http://bit.ly/2DIxWwF',
        #         'cadd': 'http://bit.ly/2TIuab9',
        #         'cgi': 'http://bit.ly/2FqS871',
        #         'chebi': 'http://bit.ly/2KAUCAm', ... }
        #     "gene": { ... }
        # }

    def get_metadata(self, biothing_type):  # hub
        return self.biothing_metadata[biothing_type]

    def get_mappings(self, biothing_type):
        return self.biothing_mappings[biothing_type]

    def get_licenses(self, biothing_type):
        return self.biothing_licenses[biothing_type]

    async def refresh(self, biothing_type):
        pass

class BiothingsESMetadata(BiothingsMetadata):

    def __init__(self, indices, client):
        super().__init__()

        if not indices:
            # all indices on the host
            indices = {None: "_all"}
        if None not in indices:
            # default index pattern when no type specified
            indices[None] = next(iter(indices.values()))

        self.indices = indices
        self.client = client

        # initial refresh
        loop = asyncio.get_event_loop()
        for btype in self.indices:
            obj = self.refresh(btype)
            if asyncio.iscoroutine(obj):
                task = loop.create_task(obj, name=btype)
                task.add_done_callback(logger.debug)

    @property
    def types(self):  # biothing_type(s)
        return tuple(filter(None, self.indices.keys()))

    def update(self, biothing_type, info, count):
        """
        Read ES index mappings for the corresponding biothing_type,
        Populate datasource info and field properties from mappings.
        """
        _type = biothing_type

        # try to resolve default to an equivalent
        # and concrete biothing_type to display
        if _type is None:
            for type_, pattern in self.indices.items():
                if self.indices[None] == pattern:
                    _type = type_
{'fraction_non_alphanumeric': 0.1336405529953917, 'fraction_numerical': 0.01557285873192436, 'mean_word_length': 1.9031365313653137, 'pattern_counts': {'":': 26, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '4132208', 'n_tokens_mistral': 1893, 'n_tokens_neox': 1786, 'n_words': 427}