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Merge pull request #73 from bcgsc/release/v1.8.0_constants_usablity
Release/v1.8.0 constants usablity
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,206 +1,2 @@ | ||
| import hashlib | ||
| import json | ||
| from datetime import datetime | ||
| from typing import Any, Dict, List, cast, Optional | ||
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| import requests | ||
| from requests.adapters import HTTPAdapter | ||
| from requests.packages.urllib3.util.retry import Retry | ||
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| from .types import ParsedVariant, Record | ||
| from .util import logger | ||
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| DEFAULT_URL = 'https://graphkb-api.bcgsc.ca/api' | ||
| DEFAULT_LIMIT = 1000 | ||
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| QUERY_CACHE: Dict[Any, Any] = {} | ||
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| def join_url(base_url: str, *parts) -> str: | ||
| """ | ||
| Join parts of a URL into a full URL | ||
| """ | ||
| if not parts: | ||
| return base_url | ||
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| if base_url.endswith('/'): | ||
| base_url = base_url[:-1] | ||
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| url = [base_url] | ||
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| for part in parts: | ||
| if not part.startswith('/'): | ||
| url.append('/') | ||
| url.append(part) | ||
| return ''.join(url) | ||
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| def millis_interval(start: datetime, end: datetime) -> int: | ||
| """start and end are datetime instances""" | ||
| diff = end - start | ||
| millis = diff.days * 24 * 60 * 60 * 1000 | ||
| millis += diff.seconds * 1000 | ||
| millis += diff.microseconds // 1000 | ||
| return millis | ||
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| def cache_key(request_body): | ||
| """ | ||
| create a cache key for a query request to GraphKB | ||
| """ | ||
| body = json.dumps(request_body, sort_keys=True) | ||
| hash_code = hashlib.md5(f'/query{body}'.encode('utf-8')).hexdigest() | ||
| return hash_code | ||
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| class GraphKBConnection: | ||
| def __init__(self, url: str = DEFAULT_URL, use_global_cache: bool = True): | ||
| self.http = requests.Session() | ||
| retries = Retry(total=3, backoff_factor=1, status_forcelist=[429, 500, 502, 503, 504]) | ||
| self.http.mount("https://", HTTPAdapter(max_retries=retries)) | ||
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| self.token = '' | ||
| self.url = url | ||
| self.username = '' | ||
| self.password = '' | ||
| self.headers = {'Accept': 'application/json', 'Content-Type': 'application/json'} | ||
| self.cache: Dict[Any, Any] = {} if not use_global_cache else QUERY_CACHE | ||
| self.request_count = 0 | ||
| self.first_request: Optional[datetime] = None | ||
| self.last_request: Optional[datetime] = None | ||
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| @property | ||
| def load(self) -> Optional[float]: | ||
| if self.first_request and self.last_request: | ||
| return ( | ||
| self.request_count * 1000 / millis_interval(self.first_request, self.last_request) | ||
| ) | ||
| return None | ||
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| def request(self, endpoint: str, method: str = 'GET', **kwargs) -> Dict: | ||
| """Request wrapper to handle adding common headers and logging | ||
| Args: | ||
| endpoint (string): api endpoint, excluding the base uri | ||
| method (str, optional): the http method. Defaults to 'GET'. | ||
| Returns: | ||
| dict: the json response as a python dict | ||
| """ | ||
| url = join_url(self.url, endpoint) | ||
| self.request_count += 1 | ||
| start_time = datetime.now() | ||
| if not self.first_request: | ||
| self.first_request = start_time | ||
| self.last_request = start_time | ||
| resp = requests.request(method, url, headers=self.headers, **kwargs) | ||
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| if resp.status_code == 401 or resp.status_code == 403: | ||
| # try to re-login if the token expired | ||
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| self.refresh_login() | ||
| self.request_count += 1 | ||
| resp = requests.request(method, url, headers=self.headers, **kwargs) | ||
| timing = millis_interval(start_time, datetime.now()) | ||
| logger.verbose(f'/{endpoint} - {resp.status_code} - {timing} ms') # type: ignore | ||
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| try: | ||
| resp.raise_for_status() | ||
| except requests.exceptions.HTTPError as err: | ||
| # try to get more error details | ||
| message = str(err) | ||
| try: | ||
| message += ' ' + resp.json()['message'] | ||
| except Exception: | ||
| pass | ||
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| raise requests.exceptions.HTTPError(message) | ||
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| return resp.json() | ||
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| def post(self, uri: str, data: Dict = {}, **kwargs) -> Dict: | ||
| """Convenience method for making post requests""" | ||
| return self.request(uri, method='POST', data=json.dumps(data), **kwargs) | ||
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| def login(self, username: str, password: str) -> None: | ||
| self.username = username | ||
| self.password = password | ||
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| # use requests package directly to avoid recursion loop on login failure | ||
| self.request_count += 1 | ||
| resp = requests.request( | ||
| url=f'{self.url}/token', | ||
| method='POST', | ||
| headers=self.headers, | ||
| data=json.dumps({'username': username, 'password': password}), | ||
| ) | ||
| resp.raise_for_status() | ||
| content = resp.json() | ||
| self.token = content['kbToken'] | ||
| self.headers['Authorization'] = self.token | ||
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| def refresh_login(self) -> None: | ||
| self.login(self.username, self.password) | ||
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| def set_cache_data(self, request_body: Dict, result: List[Record]) -> None: | ||
| """ | ||
| Explicitly add a query to the cache | ||
| """ | ||
| hash_code = cache_key(request_body) | ||
| self.cache[hash_code] = result | ||
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| def query( | ||
| self, | ||
| request_body: Dict = {}, | ||
| paginate: bool = True, | ||
| ignore_cache: bool = False, | ||
| force_refresh: bool = False, | ||
| limit: int = DEFAULT_LIMIT, | ||
| ) -> List[Record]: | ||
| """ | ||
| Query GraphKB | ||
| """ | ||
| result: List[Record] = [] | ||
| hash_code = "" | ||
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| if not ignore_cache and paginate: | ||
| hash_code = cache_key(request_body) | ||
| if hash_code in self.cache and not force_refresh: | ||
| return self.cache[hash_code] | ||
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| while True: | ||
| content = self.post('query', data={**request_body, 'limit': limit, 'skip': len(result)}) | ||
| records = content['result'] | ||
| result.extend(records) | ||
| if len(records) < limit or not paginate: | ||
| break | ||
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| if not ignore_cache and paginate: | ||
| self.cache[hash_code] = result | ||
| return result | ||
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| def parse(self, hgvs_string: str, requireFeatures: bool = False) -> ParsedVariant: | ||
| content = self.post( | ||
| 'parse', data={'content': hgvs_string, 'requireFeatures': requireFeatures} | ||
| ) | ||
| return cast(ParsedVariant, content['result']) | ||
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| def get_records_by_id(self, record_ids: List[str]) -> List[Record]: | ||
| if not record_ids: | ||
| return [] | ||
| result = self.query({'target': record_ids}) | ||
| if len(record_ids) != len(result): | ||
| raise AssertionError( | ||
| f'The number of Ids given ({len(record_ids)}) does not match the number of records fetched ({len(result)})' | ||
| ) | ||
| return result | ||
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| def get_record_by_id(self, record_id: str) -> Record: | ||
| result = self.get_records_by_id([record_id]) | ||
| return result[0] | ||
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| def get_source(self, name: str) -> Record: | ||
| source = self.query({'target': 'Source', 'filters': {'name': name}}) | ||
| if len(source) != 1: | ||
| raise AssertionError(f'Unable to unqiuely identify source with name {name}') | ||
| return source[0] | ||
| from .constants import DEFAULT_URL | ||
| from .util import GraphKBConnection, logger |
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