def __init__(self,
email=default_email,
cache_path=default_cache_path,
default_args=default_default_args,
request_interval=time_dep_request_interval,
tool=default_tool,
):
"""
:param str email: email of user (for abuse reports)
:param str cache_path: full path to sqlite file (created if necessary)
:param dict default_args: dictionary of query args that should accompany all requests
:param request_interval: seconds between requests
:type request_interval: int or a callable returning an int
:param str tool: name of client
:rtype: None
:raises OSError: if sqlite file can't be opened
"""
self.default_args = default_args
self.email = email
self.request_interval = request_interval
self.tool = tool
self._last_request_clock = 0
self._cache = SQLiteCache(cache_path) if cache_path else None
self._ident_args = {'tool': tool, 'email': email}
self._request_count = 0
def __init__(self,
email=default_email,
cache=False,
default_args=default_default_args,
request_interval=None,
tool=default_tool,
api_key=None):
"""
:param str email: email of user (for abuse reports)
:param str cache: if True, cache at ~/.cache/eutils-db.sqlite; if string, cache there; if False, don't cache
:param dict default_args: dictionary of query args that should accompany all requests
:param request_interval: seconds between requests; default: auto-select based on API key
:type request_interval: int or a callable returning an int
:param str api_key: api key assigned by NCBI
:param str tool: name of client
:rtype: None
:raises OSError: if sqlite file can't be opened
"""
self.default_args = default_args
self.email = email
self.tool = tool
self.api_key = api_key
if request_interval is not None:
_logger.warning(
"eutils QueryService: request_interval no longer supported; ignoring passed parameter"
)
if self.api_key is None:
requests_per_second = 3
_logger.warning(
"No NCBI API key provided; throttling to {} requests/second; see "
"https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/"
.format(requests_per_second))
else:
requests_per_second = 10
_logger.info(
"Using NCBI API key; throttling to {} requests/second".format(
requests_per_second))
self.request_interval = 1.0 / requests_per_second
self._last_request_clock = 0
self._ident_args = {'tool': tool, 'email': email}
self._request_count = 0
if cache is True:
cache_path = default_cache_path
elif cache:
cache_path = cache # better act like a path string
else:
cache_path = False
self._cache = SQLiteCache(cache_path) if cache_path else None
def __init__(
self,
cache_path=default_cache_path,
default_args=default_default_args,
email=default_email,
request_interval=time_dep_request_interval,
tool=default_tool,
):
self.default_args = default_args
self.email = email
self.request_interval = request_interval
self.tool = tool
self._logger = logging.getLogger(__name__)
self._last_request_clock = 0
self._cache = SQLiteCache(cache_path) if cache_path else None
self._ident_args = {'tool': tool, 'email': email}
self._request_count = 0
self.session = requests.Session()
def __init__(
self,
email=default_email,
cache=False,
default_args=default_default_args,
request_interval=time_dep_request_interval,
tool=default_tool,
):
"""
:param str email: email of user (for abuse reports)
:param str cache: if True, cache at ~/.cache/eutils-db.sqlite; if string, cache there; if False, don't cache
:param dict default_args: dictionary of query args that should accompany all requests
:param request_interval: seconds between requests
:type request_interval: int or a callable returning an int
:param str tool: name of client
:rtype: None
:raises OSError: if sqlite file can't be opened
"""
self.default_args = default_args
self.email = email
self.request_interval = request_interval
self.tool = tool
self._last_request_clock = 0
self._ident_args = {'tool': tool, 'email': email}
self._request_count = 0
if cache is True:
cache_path = default_cache_path
elif cache:
cache_path = cache # better act like a path string
else:
cache_path = False
self._cache = SQLiteCache(cache_path) if cache_path else None
def setUp(self):
_, self._fn = tempfile.mkstemp(suffix='.db')
atexit.register(lambda: os.remove(self._fn))
self.cache = SQLiteCache(self._fn)