_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f092984b5e0>
_stacktrace = <traceback object at 0x7f0928b07900>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09298492d0>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError
During handling of the above exception, another exception occurred:
@app.route("/get-organ-curies/")
def get_available_uberonids():
species = request.args.getlist('species')
requestBody = create_request_body_for_curies(species)
result = {}
try:
> response = requests.post(
f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
json=requestBody)
app/main.py:1952:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f092984ace0>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
raise SSLError(e, request=request)
> raise ConnectionError(e, request=request)
E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09298492d0>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_getting_curies(client):
# Test if we get a shorter list of uberons with species specified
> r = client.get('/get-organ-curies/')
tests/test_scicrunch.py:467:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:1957: in get_available_uberonids
logging.error("Failed getting Uberon IDs", ex)
/usr/lib/python3.10/logging/__init__.py:2105: in error
root.error(msg, *args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1506: in error
self._log(ERROR, msg, args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1624: in _log
self.handle(record)
/usr/lib/python3.10/logging/__init__.py:1634: in handle
self.callHandlers(record)
/usr/lib/python3.10/logging/__init__.py:1696: in callHandlers
hdlr.handle(record)
/usr/lib/python3.10/logging/__init__.py:968: in handle
self.emit(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:386: in emit
super().emit(record)
/usr/lib/python3.10/logging/__init__.py:1108: in emit
self.handleError(record)
/usr/lib/python3.10/logging/__init__.py:1100: in emit
msg = self.format(record)
/usr/lib/python3.10/logging/__init__.py:943: in format
return fmt.format(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:139: in format
return super().format(record)
/usr/lib/python3.10/logging/__init__.py:678: in format
record.message = record.getMessage()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API/app/main.py, 1957, "Failed getting Uberon IDs">
def getMessage(self):
"""
Return the message for this LogRecord.
Return the message for this LogRecord after merging any user-supplied
arguments with the message.
"""
msg = str(self.msg)
if self.args:
> msg = msg % self.args
E TypeError: not all arguments converted during string formatting
/usr/lib/python3.10/logging/__init__.py:368: TypeError
____________________________ test_get_related_terms ____________________________
self = <urllib3.connection.HTTPSConnection object at 0x7f0928a2ec20>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
> conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection
raise err
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
address = ('scicrunch.org', 443), timeout = None, source_address = None
socket_options = [(6, 1, 1)]
def create_connection(
address,
timeout=socket._GLOBAL_DEFAULT_TIMEOUT,
source_address=None,
socket_options=None,
):
"""Connect to *address* and return the socket object.
Convenience function. Connect to *address* (a 2-tuple ``(host,
port)``) and return the socket object. Passing the optional
*timeout* parameter will set the timeout on the socket instance
before attempting to connect. If no *timeout* is supplied, the
global default timeout setting returned by :func:`socket.getdefaulttimeout`
is used. If *source_address* is set it must be a tuple of (host, port)
for the socket to bind as a source address before making the connection.
An host of '' or port 0 tells the OS to use the default.
"""
host, port = address
if host.startswith("["):
host = host.strip("[]")
err = None
# Using the value from allowed_gai_family() in the context of getaddrinfo lets
# us select whether to work with IPv4 DNS records, IPv6 records, or both.
# The original create_connection function always returns all records.
family = allowed_gai_family()
try:
host.encode("idna")
except UnicodeError:
return six.raise_from(
LocationParseError(u"'%s', label empty or too long" % host), None
)
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
af, socktype, proto, canonname, sa = res
sock = None
try:
sock = socket.socket(af, socktype, proto)
# If provided, set socket level options before connecting.
_set_socket_options(sock, socket_options)
if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT:
sock.settimeout(timeout)
if source_address:
sock.bind(source_address)
> sock.connect(sa)
E OSError: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f0928a2f0d0>
method = 'GET'
url = '/api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = None
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/sparc-scigraph/graph/neighbors/UBERON:0002084', query='direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request
self._validate_conn(conn)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn
conn.connect()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect
conn = self._new_conn()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f0928a2ec20>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
except SocketTimeout:
raise ConnectTimeoutError(
self,
"Connection to %s timed out. (connect timeout=%s)"
% (self.host, self.timeout),
)
except SocketError as e:
> raise NewConnectionError(
self, "Failed to establish a new connection: %s" % e
)
E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f0928a2ec20>: Failed to establish a new connection: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f0928a2f250>
request = <PreparedRequest [GET]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen
retries = retries.increment(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'GET'
url = '/api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928a2ec20>: Failed to establish a new connection: [Errno 113] No route to host')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f0928a2f0d0>
_stacktrace = <traceback object at 0x7f0928a28240>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928a2ec20>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError
During handling of the above exception, another exception occurred:
query = 'UBERON:0002084'
@app.route("/get-related-terms/<query>")
def get_related_terms(query):
payload = {
'direction': request.args.get('direction', default='OUTGOING'),
'relationshipType': request.args.get('relationshipType', default='BFO:0000050'),
'entail': request.args.get('entail', default='true'),
'api_key': Config.KNOWLEDGEBASE_KEY
}
result = {}
try:
> response = requests.get(
f'{Config.SCI_CRUNCH_SCIGRAPH_HOST}/graph/neighbors/{query}',
params=payload)
app/main.py:1979:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:73: in get
return request("get", url, params=params, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f0928a2f250>
request = <PreparedRequest [GET]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
raise SSLError(e, request=request)
> raise ConnectionError(e, request=request)
E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/sparc-scigraph/graph/neighbors/UBERON:0002084?direction=OUTGOING&relationshipType=BFO%3A0000050&entail=true&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928a2ec20>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_get_related_terms(client):
# Test if we can get the uberon term of heart using the uberon term
# of left ventricle
> r = client.get('/get-related-terms/UBERON:0002084')
tests/test_scicrunch.py:484:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:1984: in get_related_terms
logging.error(f"Failed getting related terms with payload {payload}", ex)
/usr/lib/python3.10/logging/__init__.py:2105: in error
root.error(msg, *args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1506: in error
self._log(ERROR, msg, args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1624: in _log
self.handle(record)
/usr/lib/python3.10/logging/__init__.py:1634: in handle
self.callHandlers(record)
/usr/lib/python3.10/logging/__init__.py:1696: in callHandlers
hdlr.handle(record)
/usr/lib/python3.10/logging/__init__.py:968: in handle
self.emit(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:386: in emit
super().emit(record)
/usr/lib/python3.10/logging/__init__.py:1108: in emit
self.handleError(record)
/usr/lib/python3.10/logging/__init__.py:1100: in emit
msg = self.format(record)
/usr/lib/python3.10/logging/__init__.py:943: in format
return fmt.format(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:139: in format
return super().format(record)
/usr/lib/python3.10/logging/__init__.py:678: in format
record.message = record.getMessage()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API/app/main.py, 1984, "Failed getting related terms with pa...ion': 'OUTGOING', 'relationshipType': 'BFO:0000050', 'entail': 'true', 'api_key': 'xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'}">
def getMessage(self):
"""
Return the message for this LogRecord.
Return the message for this LogRecord after merging any user-supplied
arguments with the message.
"""
msg = str(self.msg)
if self.args:
> msg = msg % self.args
E TypeError: not all arguments converted during string formatting
/usr/lib/python3.10/logging/__init__.py:368: TypeError
_____________________________ test_scaffold_files ______________________________
self = <urllib3.connection.HTTPSConnection object at 0x7f0928a5b490>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
> conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection
raise err
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
address = ('scicrunch.org', 443), timeout = None, source_address = None
socket_options = [(6, 1, 1)]
def create_connection(
address,
timeout=socket._GLOBAL_DEFAULT_TIMEOUT,
source_address=None,
socket_options=None,
):
"""Connect to *address* and return the socket object.
Convenience function. Connect to *address* (a 2-tuple ``(host,
port)``) and return the socket object. Passing the optional
*timeout* parameter will set the timeout on the socket instance
before attempting to connect. If no *timeout* is supplied, the
global default timeout setting returned by :func:`socket.getdefaulttimeout`
is used. If *source_address* is set it must be a tuple of (host, port)
for the socket to bind as a source address before making the connection.
An host of '' or port 0 tells the OS to use the default.
"""
host, port = address
if host.startswith("["):
host = host.strip("[]")
err = None
# Using the value from allowed_gai_family() in the context of getaddrinfo lets
# us select whether to work with IPv4 DNS records, IPv6 records, or both.
# The original create_connection function always returns all records.
family = allowed_gai_family()
try:
host.encode("idna")
except UnicodeError:
return six.raise_from(
LocationParseError(u"'%s', label empty or too long" % host), None
)
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
af, socktype, proto, canonname, sa = res
sock = None
try:
sock = socket.socket(af, socktype, proto)
# If provided, set socket level options before connecting.
_set_socket_options(sock, socket_options)
if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT:
sock.settimeout(timeout)
if source_address:
sock.bind(source_address)
> sock.connect(sa)
E OSError: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f0928a5bd30>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"size": "30", "from": 0}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '25', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_pr/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request
self._validate_conn(conn)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn
conn.connect()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect
conn = self._new_conn()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f0928a5b490>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
except SocketTimeout:
raise ConnectTimeoutError(
self,
"Connection to %s timed out. (connect timeout=%s)"
% (self.host, self.timeout),
)
except SocketError as e:
> raise NewConnectionError(
self, "Failed to establish a new connection: %s" % e
)
E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f0928a5b490>: Failed to establish a new connection: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f0928a5bfd0>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen
retries = retries.increment(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928a5b490>: Failed to establish a new connection: [Errno 113] No route to host')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f0928a5bd30>
_stacktrace = <traceback object at 0x7f0928c92800>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928a5b490>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_scaffold_files(client):
> r = client.get('/filter-search/?size=30')
tests/test_scicrunch.py:498:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:779: in filter_search
response = requests.post(
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f0928a5bfd0>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
raise SSLError(e, request=request)
> raise ConnectionError(e, request=request)
E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928a5b490>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError
_____________________ test_finding_contextual_information ______________________
self = <urllib3.connection.HTTPSConnection object at 0x7f09294930d0>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
> conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection
raise err
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
address = ('scicrunch.org', 443), timeout = None, source_address = None
socket_options = [(6, 1, 1)]
def create_connection(
address,
timeout=socket._GLOBAL_DEFAULT_TIMEOUT,
source_address=None,
socket_options=None,
):
"""Connect to *address* and return the socket object.
Convenience function. Connect to *address* (a 2-tuple ``(host,
port)``) and return the socket object. Passing the optional
*timeout* parameter will set the timeout on the socket instance
before attempting to connect. If no *timeout* is supplied, the
global default timeout setting returned by :func:`socket.getdefaulttimeout`
is used. If *source_address* is set it must be a tuple of (host, port)
for the socket to bind as a source address before making the connection.
An host of '' or port 0 tells the OS to use the default.
"""
host, port = address
if host.startswith("["):
host = host.strip("[]")
err = None
# Using the value from allowed_gai_family() in the context of getaddrinfo lets
# us select whether to work with IPv4 DNS records, IPv6 records, or both.
# The original create_connection function always returns all records.
family = allowed_gai_family()
try:
host.encode("idna")
except UnicodeError:
return six.raise_from(
LocationParseError(u"'%s', label empty or too long" % host), None
)
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
af, socktype, proto, canonname, sa = res
sock = None
try:
sock = socket.socket(af, socktype, proto)
# If provided, set socket level options before connecting.
_set_socket_options(sock, socket_options)
if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT:
sock.settimeout(timeout)
if source_address:
sock.bind(source_address)
> sock.connect(sa)
E OSError: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f0929491a50>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"size": 999, "query": {"terms": {"pennsieve.identifier": ["76"]}}}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '67', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_pr/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request
self._validate_conn(conn)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn
conn.connect()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect
conn = self._new_conn()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f09294930d0>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
except SocketTimeout:
raise ConnectTimeoutError(
self,
"Connection to %s timed out. (connect timeout=%s)"
% (self.host, self.timeout),
)
except SocketError as e:
> raise NewConnectionError(
self, "Failed to establish a new connection: %s" % e
)
E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f09294930d0>: Failed to establish a new connection: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f0929492140>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen
retries = retries.increment(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09294930d0>: Failed to establish a new connection: [Errno 113] No route to host')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f0929491a50>
_stacktrace = <traceback object at 0x7f0928b49440>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09294930d0>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_finding_contextual_information(client):
> r = client.get('/dataset_info/using_multiple_discoverIds/?discoverIds=76')
tests/test_scicrunch.py:514:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:634: in get_dataset_info_discoverIds
return process_results(dataset_search(query))
app/main.py:735: in dataset_search
response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f0929492140>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
raise SSLError(e, request=request)
> raise ConnectionError(e, request=request)
E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09294930d0>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError
____________________ test_undefined_version_dataset_search _____________________
self = <urllib3.connection.HTTPSConnection object at 0x7f092a28bc10>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
> conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:96: in create_connection
raise err
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
address = ('scicrunch.org', 443), timeout = None, source_address = None
socket_options = [(6, 1, 1)]
def create_connection(
address,
timeout=socket._GLOBAL_DEFAULT_TIMEOUT,
source_address=None,
socket_options=None,
):
"""Connect to *address* and return the socket object.
Convenience function. Connect to *address* (a 2-tuple ``(host,
port)``) and return the socket object. Passing the optional
*timeout* parameter will set the timeout on the socket instance
before attempting to connect. If no *timeout* is supplied, the
global default timeout setting returned by :func:`socket.getdefaulttimeout`
is used. If *source_address* is set it must be a tuple of (host, port)
for the socket to bind as a source address before making the connection.
An host of '' or port 0 tells the OS to use the default.
"""
host, port = address
if host.startswith("["):
host = host.strip("[]")
err = None
# Using the value from allowed_gai_family() in the context of getaddrinfo lets
# us select whether to work with IPv4 DNS records, IPv6 records, or both.
# The original create_connection function always returns all records.
family = allowed_gai_family()
try:
host.encode("idna")
except UnicodeError:
return six.raise_from(
LocationParseError(u"'%s', label empty or too long" % host), None
)
for res in socket.getaddrinfo(host, port, family, socket.SOCK_STREAM):
af, socktype, proto, canonname, sa = res
sock = None
try:
sock = socket.socket(af, socktype, proto)
# If provided, set socket level options before connecting.
_set_socket_options(sock, socket_options)
if timeout is not socket._GLOBAL_DEFAULT_TIMEOUT:
sock.settimeout(timeout)
if source_address:
sock.bind(source_address)
> sock.connect(sa)
E OSError: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/connection.py:86: OSError
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f092a289f30>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"query": {"term": {"item.curie": "10.26275/mlua-o9oj"}}}'
headers = {'User-Agent': 'python-requests/2.31.0', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '57', 'Content-Type': 'application/json'}
retries = Retry(total=0, connect=None, read=False, redirect=None, status=None)
redirect = False, assert_same_host = False
timeout = Timeout(connect=None, read=None, total=None), pool_timeout = None
release_conn = False, chunked = False, body_pos = None
response_kw = {'decode_content': False, 'preload_content': False}
parsed_url = Url(scheme=None, auth=None, host=None, port=None, path='/api/1/elastic/SPARC_PortalDatasets_pr/_search', query='api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf', fragment=None)
destination_scheme = None, conn = None, release_this_conn = True
http_tunnel_required = False, err = None, clean_exit = False
def urlopen(
self,
method,
url,
body=None,
headers=None,
retries=None,
redirect=True,
assert_same_host=True,
timeout=_Default,
pool_timeout=None,
release_conn=None,
chunked=False,
body_pos=None,
**response_kw
):
"""
Get a connection from the pool and perform an HTTP request. This is the
lowest level call for making a request, so you'll need to specify all
the raw details.
.. note::
More commonly, it's appropriate to use a convenience method provided
by :class:`.RequestMethods`, such as :meth:`request`.
.. note::
`release_conn` will only behave as expected if
`preload_content=False` because we want to make
`preload_content=False` the default behaviour someday soon without
breaking backwards compatibility.
:param method:
HTTP request method (such as GET, POST, PUT, etc.)
:param url:
The URL to perform the request on.
:param body:
Data to send in the request body, either :class:`str`, :class:`bytes`,
an iterable of :class:`str`/:class:`bytes`, or a file-like object.
:param headers:
Dictionary of custom headers to send, such as User-Agent,
If-None-Match, etc. If None, pool headers are used. If provided,
these headers completely replace any pool-specific headers.
:param retries:
Configure the number of retries to allow before raising a
:class:`~urllib3.exceptions.MaxRetryError` exception.
Pass ``None`` to retry until you receive a response. Pass a
:class:`~urllib3.util.retry.Retry` object for fine-grained control
over different types of retries.
Pass an integer number to retry connection errors that many times,
but no other types of errors. Pass zero to never retry.
If ``False``, then retries are disabled and any exception is raised
immediately. Also, instead of raising a MaxRetryError on redirects,
the redirect response will be returned.
:type retries: :class:`~urllib3.util.retry.Retry`, False, or an int.
:param redirect:
If True, automatically handle redirects (status codes 301, 302,
303, 307, 308). Each redirect counts as a retry. Disabling retries
will disable redirect, too.
:param assert_same_host:
If ``True``, will make sure that the host of the pool requests is
consistent else will raise HostChangedError. When ``False``, you can
use the pool on an HTTP proxy and request foreign hosts.
:param timeout:
If specified, overrides the default timeout for this one
request. It may be a float (in seconds) or an instance of
:class:`urllib3.util.Timeout`.
:param pool_timeout:
If set and the pool is set to block=True, then this method will
block for ``pool_timeout`` seconds and raise EmptyPoolError if no
connection is available within the time period.
:param release_conn:
If False, then the urlopen call will not release the connection
back into the pool once a response is received (but will release if
you read the entire contents of the response such as when
`preload_content=True`). This is useful if you're not preloading
the response's content immediately. You will need to call
``r.release_conn()`` on the response ``r`` to return the connection
back into the pool. If None, it takes the value of
``response_kw.get('preload_content', True)``.
:param chunked:
If True, urllib3 will send the body using chunked transfer
encoding. Otherwise, urllib3 will send the body using the standard
content-length form. Defaults to False.
:param int body_pos:
Position to seek to in file-like body in the event of a retry or
redirect. Typically this won't need to be set because urllib3 will
auto-populate the value when needed.
:param \\**response_kw:
Additional parameters are passed to
:meth:`urllib3.response.HTTPResponse.from_httplib`
"""
parsed_url = parse_url(url)
destination_scheme = parsed_url.scheme
if headers is None:
headers = self.headers
if not isinstance(retries, Retry):
retries = Retry.from_int(retries, redirect=redirect, default=self.retries)
if release_conn is None:
release_conn = response_kw.get("preload_content", True)
# Check host
if assert_same_host and not self.is_same_host(url):
raise HostChangedError(self, url, retries)
# Ensure that the URL we're connecting to is properly encoded
if url.startswith("/"):
url = six.ensure_str(_encode_target(url))
else:
url = six.ensure_str(parsed_url.url)
conn = None
# Track whether `conn` needs to be released before
# returning/raising/recursing. Update this variable if necessary, and
# leave `release_conn` constant throughout the function. That way, if
# the function recurses, the original value of `release_conn` will be
# passed down into the recursive call, and its value will be respected.
#
# See issue #651 [1] for details.
#
# [1] <https://github.com/urllib3/urllib3/issues/651>
release_this_conn = release_conn
http_tunnel_required = connection_requires_http_tunnel(
self.proxy, self.proxy_config, destination_scheme
)
# Merge the proxy headers. Only done when not using HTTP CONNECT. We
# have to copy the headers dict so we can safely change it without those
# changes being reflected in anyone else's copy.
if not http_tunnel_required:
headers = headers.copy()
headers.update(self.proxy_headers)
# Must keep the exception bound to a separate variable or else Python 3
# complains about UnboundLocalError.
err = None
# Keep track of whether we cleanly exited the except block. This
# ensures we do proper cleanup in finally.
clean_exit = False
# Rewind body position, if needed. Record current position
# for future rewinds in the event of a redirect/retry.
body_pos = set_file_position(body, body_pos)
try:
# Request a connection from the queue.
timeout_obj = self._get_timeout(timeout)
conn = self._get_conn(timeout=pool_timeout)
conn.timeout = timeout_obj.connect_timeout
is_new_proxy_conn = self.proxy is not None and not getattr(
conn, "sock", None
)
if is_new_proxy_conn and http_tunnel_required:
self._prepare_proxy(conn)
# Make the request on the httplib connection object.
> httplib_response = self._make_request(
conn,
method,
url,
timeout=timeout_obj,
body=body,
headers=headers,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:382: in _make_request
self._validate_conn(conn)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:1010: in _validate_conn
conn.connect()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:353: in connect
conn = self._new_conn()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f092a28bc10>
def _new_conn(self):
"""Establish a socket connection and set nodelay settings on it.
:return: New socket connection.
"""
extra_kw = {}
if self.source_address:
extra_kw["source_address"] = self.source_address
if self.socket_options:
extra_kw["socket_options"] = self.socket_options
try:
conn = connection.create_connection(
(self._dns_host, self.port), self.timeout, **extra_kw
)
except SocketTimeout:
raise ConnectTimeoutError(
self,
"Connection to %s timed out. (connect timeout=%s)"
% (self.host, self.timeout),
)
except SocketError as e:
> raise NewConnectionError(
self, "Failed to establish a new connection: %s" % e
)
E urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x7f092a28bc10>: Failed to establish a new connection: [Errno 113] No route to host
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f092a28ab30>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
> resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:486:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connectionpool.py:755: in urlopen
retries = retries.increment(
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092a28bc10>: Failed to establish a new connection: [Errno 113] No route to host')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f092a289f30>
_stacktrace = <traceback object at 0x7f0928be3580>
def increment(
self,
method=None,
url=None,
response=None,
error=None,
_pool=None,
_stacktrace=None,
):
"""Return a new Retry object with incremented retry counters.
:param response: A response object, or None, if the server did not
return a response.
:type response: :class:`~urllib3.response.HTTPResponse`
:param Exception error: An error encountered during the request, or
None if the response was received successfully.
:return: A new ``Retry`` object.
"""
if self.total is False and error:
# Disabled, indicate to re-raise the error.
raise six.reraise(type(error), error, _stacktrace)
total = self.total
if total is not None:
total -= 1
connect = self.connect
read = self.read
redirect = self.redirect
status_count = self.status
other = self.other
cause = "unknown"
status = None
redirect_location = None
if error and self._is_connection_error(error):
# Connect retry?
if connect is False:
raise six.reraise(type(error), error, _stacktrace)
elif connect is not None:
connect -= 1
elif error and self._is_read_error(error):
# Read retry?
if read is False or not self._is_method_retryable(method):
raise six.reraise(type(error), error, _stacktrace)
elif read is not None:
read -= 1
elif error:
# Other retry?
if other is not None:
other -= 1
elif response and response.get_redirect_location():
# Redirect retry?
if redirect is not None:
redirect -= 1
cause = "too many redirects"
redirect_location = response.get_redirect_location()
status = response.status
else:
# Incrementing because of a server error like a 500 in
# status_forcelist and the given method is in the allowed_methods
cause = ResponseError.GENERIC_ERROR
if response and response.status:
if status_count is not None:
status_count -= 1
cause = ResponseError.SPECIFIC_ERROR.format(status_code=response.status)
status = response.status
history = self.history + (
RequestHistory(method, url, error, status, redirect_location),
)
new_retry = self.new(
total=total,
connect=connect,
read=read,
redirect=redirect,
status=status_count,
other=other,
history=history,
)
if new_retry.is_exhausted():
> raise MaxRetryError(_pool, url, error or ResponseError(cause))
E urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092a28bc10>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/retry.py:574: MaxRetryError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_undefined_version_dataset_search(client):
# Testing with dataset 17 which is not versioned
identifier = "17"
doi = "10.26275/mlua-o9oj"
> r = client.get('/dataset_info/using_doi', query_string={'doi': doi})
tests/test_scicrunch.py:525:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:604: in get_dataset_info_doi
return reform_dataset_results(dataset_search(query))
app/main.py:735: in dataset_search
response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:115: in post
return request("post", url, data=data, json=json, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/api.py:59: in request
return session.request(method=method, url=url, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:589: in request
resp = self.send(prep, **send_kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/sessions.py:703: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f092a28ab30>
request = <PreparedRequest [POST]>, stream = False
timeout = Timeout(connect=None, read=None, total=None), verify = True
cert = None, proxies = OrderedDict()
def send(
self, request, stream=False, timeout=None, verify=True, cert=None, proxies=None
):
"""Sends PreparedRequest object. Returns Response object.
:param request: The :class:`PreparedRequest <PreparedRequest>` being sent.
:param stream: (optional) Whether to stream the request content.
:param timeout: (optional) How long to wait for the server to send
data before giving up, as a float, or a :ref:`(connect timeout,
read timeout) <timeouts>` tuple.
:type timeout: float or tuple or urllib3 Timeout object
:param verify: (optional) Either a boolean, in which case it controls whether
we verify the server's TLS certificate, or a string, in which case it
must be a path to a CA bundle to use
:param cert: (optional) Any user-provided SSL certificate to be trusted.
:param proxies: (optional) The proxies dictionary to apply to the request.
:rtype: requests.Response
"""
try:
conn = self.get_connection(request.url, proxies)
except LocationValueError as e:
raise InvalidURL(e, request=request)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(
request,
stream=stream,
timeout=timeout,
verify=verify,
cert=cert,
proxies=proxies,
)
chunked = not (request.body is None or "Content-Length" in request.headers)
if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError:
raise ValueError(
f"Invalid timeout {timeout}. Pass a (connect, read) timeout tuple, "
f"or a single float to set both timeouts to the same value."
)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
resp = conn.urlopen(
method=request.method,
url=url,
body=request.body,
headers=request.headers,
redirect=False,
assert_same_host=False,
preload_content=False,
decode_content=False,
retries=self.max_retries,
timeout=timeout,
chunked=chunked,
)
except (ProtocolError, OSError) as err:
raise ConnectionError(err, request=request)
except MaxRetryError as e:
if isinstance(e.reason, ConnectTimeoutError):
# TODO: Remove this in 3.0.0: see #2811
if not isinstance(e.reason, NewConnectionError):
raise ConnectTimeout(e, request=request)
if isinstance(e.reason, ResponseError):
raise RetryError(e, request=request)
if isinstance(e.reason, _ProxyError):
raise ProxyError(e, request=request)
if isinstance(e.reason, _SSLError):
# This branch is for urllib3 v1.22 and later.
raise SSLError(e, request=request)
> raise ConnectionError(e, request=request)
E requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092a28bc10>: Failed to establish a new connection: [Errno 113] No route to host'))
../../../python3.10.venv/lib/python3.10/site-packages/requests/adapters.py:519: ConnectionError
=============================== warnings summary ===============================
scripts/monthly_db.py:9
/home/cmiss/Jenkins/workspace/SPARC-API/scripts/monthly_db.py:9: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
base = declarative_base()
../../../python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import get_distribution, DistributionNotFound
../../../python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
DESCRIPTOR = _descriptor.FileDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_CACHESEGMENT = _descriptor.Descriptor(
app/dbtable.py:12
/home/cmiss/Jenkins/workspace/SPARC-API/app/dbtable.py:12: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
base = declarative_base()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: 3 warnings
tests/test_api.py: 20 warnings
tests/test_biolucida.py: 13 warnings
tests/test_monthly_stats.py: 11 warnings
tests/test_osparc.py: 17 warnings
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 1 warning
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: DeprecationWarning: ssl.PROTOCOL_TLS is deprecated
context = SSLContext(ssl_version or PROTOCOL_TLS)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: 2 warnings
tests/test_api.py: 24 warnings
tests/test_biolucida.py: 13 warnings
tests/test_dataset_info.py: 1 warning
tests/test_monthly_stats.py: 14 warnings
tests/test_osparc.py: 17 warnings
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 1 warning
tests/test_segmentation_info.py: 1 warning
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: DeprecationWarning: ssl.match_hostname() is deprecated
match_hostname(cert, asserted_hostname)
../../../python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
tests/test_health.py::test_request_response
/home/cmiss/Jenkins/workspace/SPARC-API/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead.
assert_equals("healthy", json_response.get("status"))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_api.py::test_onto_term_lookup - TypeError: not all arguments converted during string formatting
FAILED tests/test_api.py::test_non_existing_simulation_ui_file - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09291f3dc0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_api.py::test_simulation_ui_file_old_s3_bucket - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0929391990>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_api.py::test_simulation_ui_file_new_s3_bucket - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928fbafb0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_dataset_info.py::test_current_doi_list - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0929359480>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_dataset_info.py::test_generic_mouse_colon_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09291d01f0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_dataset_info.py::test_complex_title_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928f3ac50>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_dataset_info.py::test_title_plot_annotation_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09293c9450>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_dataset_info.py::test_object_identifier_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0929798c40>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_dataset_info.py::test_pennsieve_identifier_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0929236f20>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_plot.py::test_abi_plot - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09291d9240>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_keys - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?q=&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928f0e410>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_versions_are_supported - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf&q=%22%22 (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09295fd420>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_dataset_doi - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09294a4910>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_doi - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092914fac0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_ids - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0929316ce0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?q=heart&size=10&from=0&api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092a1f77f0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_all_data - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928f0dcf0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_filter - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092913d270>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_filter_scaffolds - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928e6ee90>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_basic_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092901abf0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_image_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09291d3010>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_boolean_logic - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09295068c0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_scicrunch_combined_facet_text - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09291390c0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_getting_facets - TypeError: not all arguments converted during string formatting
FAILED tests/test_scicrunch.py::test_create_identifier_query - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928dfbd60>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_create_anatomy_query - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092a1ac490>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_response_version - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092914e6e0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_response_abi_plot - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092909d480>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_response_abi_scaffold - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09293c9150>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_response_sample_subject_size - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0929159690>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_raw_response_structure - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092ac342e0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_get_body_scaffold_info - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092a1ac2e0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_getting_curies - TypeError: not all arguments converted during string formatting
FAILED tests/test_scicrunch.py::test_get_related_terms - TypeError: not all arguments converted during string formatting
FAILED tests/test_scicrunch.py::test_scaffold_files - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f0928a5b490>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_finding_contextual_information - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f09294930d0>: Failed to establish a new connection: [Errno 113] No route to host'))
FAILED tests/test_scicrunch.py::test_undefined_version_dataset_search - requests.exceptions.ConnectionError: HTTPSConnectionPool(host='scicrunch.org', port=443): Max retries exceeded with url: /api/1/elastic/SPARC_PortalDatasets_pr/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f092a28bc10>: Failed to establish a new connection: [Errno 113] No route to host'))
====== 38 failed, 78 passed, 3 skipped, 162 warnings in 265.44s (0:04:25) ======
Build step 'Execute shell' marked build as failure
[Slack Notifications] found #1496 as previous completed, non-aborted build
[Slack Notifications] will send OnEveryFailureNotification because build matches and user preferences allow it
Finished: FAILURE
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