if isinstance(timeout, tuple):
try:
connect, read = timeout
timeout = TimeoutSauce(connect=connect, read=read)
except ValueError as e:
# this may raise a string formatting error.
err = ("Invalid timeout {}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
if not chunked:
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
)
# Send the request.
else:
if hasattr(conn, 'proxy_pool'):
conn = conn.proxy_pool
low_conn = conn._get_conn(timeout=DEFAULT_POOL_TIMEOUT)
try:
low_conn.putrequest(request.method,
url,
skip_accept_encoding=True)
for header, value in request.headers.items():
low_conn.putheader(header, value)
low_conn.endheaders()
for i in request.body:
low_conn.send(hex(len(i))[2:].encode('utf-8'))
low_conn.send(b'\r\n')
low_conn.send(i)
low_conn.send(b'\r\n')
low_conn.send(b'0\r\n\r\n')
# Receive the response from the server
try:
# For Python 2.7, use buffering of HTTP responses
r = low_conn.getresponse(buffering=True)
except TypeError:
# For compatibility with Python 3.3+
r = low_conn.getresponse()
resp = HTTPResponse.from_httplib(
r,
pool=conn,
connection=low_conn,
preload_content=False,
decode_content=False
)
except:
# If we hit any problems here, clean up the connection.
# Then, reraise so that we can handle the actual exception.
low_conn.close()
raise
except (ProtocolError, socket.error) 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 0x7f754a6fda30>: Failed to establish a new connection: [Errno 110] Connection timed out'))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:516: ConnectionError
_____________________________ test_scaffold_files ______________________________
self = <urllib3.connection.HTTPSConnection object at 0x7f754a370400>
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
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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)
return sock
except socket.error as e:
err = e
if sock is not None:
sock.close()
sock = None
if err is not None:
> raise err
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:96:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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 TimeoutError: [Errno 110] Connection timed out
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:86: TimeoutError
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754a2c70a0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"size": "30", "from": 0}'
headers = {'User-Agent': 'python-requests/2.25.1', '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_dev/_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,
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754a2c70a0>
conn = <urllib3.connection.HTTPSConnection object at 0x7f754a370400>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"size": "30", "from": 0}', 'headers': {'User-Agent': 'python-requests/2.25.1', 'Accept-Encoding': 'gzip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '25', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = timeout_obj.connect_timeout
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754a2c70a0>
conn = <urllib3.connection.HTTPSConnection object at 0x7f754a370400>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f754a370400>
def connect(self):
# Add certificate verification
> conn = self._new_conn()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:353:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f754a370400>
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 0x7f754a370400>: Failed to establish a new connection: [Errno 110] Connection timed out
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f754a2c73d0>
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 as e:
# this may raise a string formatting error.
err = ("Invalid timeout {}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
if not chunked:
> 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
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:439:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754a2c70a0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"size": "30", "from": 0}'
headers = {'User-Agent': 'python-requests/2.25.1', '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_dev/_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,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
if isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:755:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754a370400>: Failed to establish a new connection: [Errno 110] Connection timed out')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754a2c70a0>
_stacktrace = <traceback object at 0x7f754a2e5f40>
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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754a370400>: Failed to establish a new connection: [Errno 110] Connection timed out'))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open
return Client.open(
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise
raise value
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise
raise value
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:707: in filter_search
response = requests.post(
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:119: in post
return request('post', url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:61: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:542: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:655: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f754a2c73d0>
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 as e:
# this may raise a string formatting error.
err = ("Invalid timeout {}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
if not chunked:
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
)
# Send the request.
else:
if hasattr(conn, 'proxy_pool'):
conn = conn.proxy_pool
low_conn = conn._get_conn(timeout=DEFAULT_POOL_TIMEOUT)
try:
low_conn.putrequest(request.method,
url,
skip_accept_encoding=True)
for header, value in request.headers.items():
low_conn.putheader(header, value)
low_conn.endheaders()
for i in request.body:
low_conn.send(hex(len(i))[2:].encode('utf-8'))
low_conn.send(b'\r\n')
low_conn.send(i)
low_conn.send(b'\r\n')
low_conn.send(b'0\r\n\r\n')
# Receive the response from the server
try:
# For Python 2.7, use buffering of HTTP responses
r = low_conn.getresponse(buffering=True)
except TypeError:
# For compatibility with Python 3.3+
r = low_conn.getresponse()
resp = HTTPResponse.from_httplib(
r,
pool=conn,
connection=low_conn,
preload_content=False,
decode_content=False
)
except:
# If we hit any problems here, clean up the connection.
# Then, reraise so that we can handle the actual exception.
low_conn.close()
raise
except (ProtocolError, socket.error) 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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754a370400>: Failed to establish a new connection: [Errno 110] Connection timed out'))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:516: ConnectionError
_____________________ test_finding_contextual_information ______________________
self = <urllib3.connection.HTTPSConnection object at 0x7f754b649a60>
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
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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)
return sock
except socket.error as e:
err = e
if sock is not None:
sock.close()
sock = None
if err is not None:
> raise err
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:96:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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 TimeoutError: [Errno 110] Connection timed out
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:86: TimeoutError
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754b649220>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"size": 999, "query": {"terms": {"pennsieve.identifier": ["76"]}}}'
headers = {'User-Agent': 'python-requests/2.25.1', '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_dev/_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,
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754b649220>
conn = <urllib3.connection.HTTPSConnection object at 0x7f754b649a60>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"size": 999, "query": {"terms": {"pennsieve.identifier": ["76"]}}}', 'headers': {'User-Agent': 'python-req...ip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '67', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = timeout_obj.connect_timeout
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754b649220>
conn = <urllib3.connection.HTTPSConnection object at 0x7f754b649a60>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f754b649a60>
def connect(self):
# Add certificate verification
> conn = self._new_conn()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:353:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f754b649a60>
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 0x7f754b649a60>: Failed to establish a new connection: [Errno 110] Connection timed out
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f7550036c10>
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 as e:
# this may raise a string formatting error.
err = ("Invalid timeout {}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
if not chunked:
> 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
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:439:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754b649220>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"size": 999, "query": {"terms": {"pennsieve.identifier": ["76"]}}}'
headers = {'User-Agent': 'python-requests/2.25.1', '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_dev/_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,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
if isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:755:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754b649a60>: Failed to establish a new connection: [Errno 110] Connection timed out')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754b649220>
_stacktrace = <traceback object at 0x7f754a28c8c0>
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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754b649a60>: Failed to establish a new connection: [Errno 110] Connection timed out'))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open
return Client.open(
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise
raise value
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise
raise value
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:567: in get_dataset_info_discoverIds
return process_results(dataset_search(query))
app/main.py:663: in dataset_search
response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:119: in post
return request('post', url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:61: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:542: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:655: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f7550036c10>
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 as e:
# this may raise a string formatting error.
err = ("Invalid timeout {}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
if not chunked:
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
)
# Send the request.
else:
if hasattr(conn, 'proxy_pool'):
conn = conn.proxy_pool
low_conn = conn._get_conn(timeout=DEFAULT_POOL_TIMEOUT)
try:
low_conn.putrequest(request.method,
url,
skip_accept_encoding=True)
for header, value in request.headers.items():
low_conn.putheader(header, value)
low_conn.endheaders()
for i in request.body:
low_conn.send(hex(len(i))[2:].encode('utf-8'))
low_conn.send(b'\r\n')
low_conn.send(i)
low_conn.send(b'\r\n')
low_conn.send(b'0\r\n\r\n')
# Receive the response from the server
try:
# For Python 2.7, use buffering of HTTP responses
r = low_conn.getresponse(buffering=True)
except TypeError:
# For compatibility with Python 3.3+
r = low_conn.getresponse()
resp = HTTPResponse.from_httplib(
r,
pool=conn,
connection=low_conn,
preload_content=False,
decode_content=False
)
except:
# If we hit any problems here, clean up the connection.
# Then, reraise so that we can handle the actual exception.
low_conn.close()
raise
except (ProtocolError, socket.error) 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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754b649a60>: Failed to establish a new connection: [Errno 110] Connection timed out'))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:516: ConnectionError
____________________ test_undefined_version_dataset_search _____________________
self = <urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>
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
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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)
return sock
except socket.error as e:
err = e
if sock is not None:
sock.close()
sock = None
if err is not None:
> raise err
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:96:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
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 TimeoutError: [Errno 110] Connection timed out
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/util/connection.py:86: TimeoutError
During handling of the above exception, another exception occurred:
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754acba940>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"query": {"term": {"item.curie": "10.26275/mlua-o9oj"}}}'
headers = {'User-Agent': 'python-requests/2.25.1', '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_dev/_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,
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:699:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754acba940>
conn = <urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
timeout = Timeout(connect=None, read=None, total=None), chunked = False
httplib_request_kw = {'body': b'{"query": {"term": {"item.curie": "10.26275/mlua-o9oj"}}}', 'headers': {'User-Agent': 'python-requests/2.25...ip, deflate', 'Accept': '*/*', 'Connection': 'keep-alive', 'Content-Length': '57', 'Content-Type': 'application/json'}}
timeout_obj = Timeout(connect=None, read=None, total=None)
def _make_request(
self, conn, method, url, timeout=_Default, chunked=False, **httplib_request_kw
):
"""
Perform a request on a given urllib connection object taken from our
pool.
:param conn:
a connection from one of our connection pools
:param timeout:
Socket timeout in seconds for the request. This can be a
float or integer, which will set the same timeout value for
the socket connect and the socket read, or an instance of
:class:`urllib3.util.Timeout`, which gives you more fine-grained
control over your timeouts.
"""
self.num_requests += 1
timeout_obj = self._get_timeout(timeout)
timeout_obj.start_connect()
conn.timeout = timeout_obj.connect_timeout
# Trigger any extra validation we need to do.
try:
> self._validate_conn(conn)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:382:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754acba940>
conn = <urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>
def _validate_conn(self, conn):
"""
Called right before a request is made, after the socket is created.
"""
super(HTTPSConnectionPool, self)._validate_conn(conn)
# Force connect early to allow us to validate the connection.
if not getattr(conn, "sock", None): # AppEngine might not have `.sock`
> conn.connect()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:1010:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>
def connect(self):
# Add certificate verification
> conn = self._new_conn()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:353:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>
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 0x7f754a87e6a0>: Failed to establish a new connection: [Errno 110] Connection timed out
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connection.py:181: NewConnectionError
During handling of the above exception, another exception occurred:
self = <requests.adapters.HTTPAdapter object at 0x7f754acba670>
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 as e:
# this may raise a string formatting error.
err = ("Invalid timeout {}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
if not chunked:
> 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
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:439:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754acba940>
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
body = b'{"query": {"term": {"item.curie": "10.26275/mlua-o9oj"}}}'
headers = {'User-Agent': 'python-requests/2.25.1', '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_dev/_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,
)
# If we're going to release the connection in ``finally:``, then
# the response doesn't need to know about the connection. Otherwise
# it will also try to release it and we'll have a double-release
# mess.
response_conn = conn if not release_conn else None
# Pass method to Response for length checking
response_kw["request_method"] = method
# Import httplib's response into our own wrapper object
response = self.ResponseCls.from_httplib(
httplib_response,
pool=self,
connection=response_conn,
retries=retries,
**response_kw
)
# Everything went great!
clean_exit = True
except EmptyPoolError:
# Didn't get a connection from the pool, no need to clean up
clean_exit = True
release_this_conn = False
raise
except (
TimeoutError,
HTTPException,
SocketError,
ProtocolError,
BaseSSLError,
SSLError,
CertificateError,
) as e:
# Discard the connection for these exceptions. It will be
# replaced during the next _get_conn() call.
clean_exit = False
if isinstance(e, (BaseSSLError, CertificateError)):
e = SSLError(e)
elif isinstance(e, (SocketError, NewConnectionError)) and self.proxy:
e = ProxyError("Cannot connect to proxy.", e)
elif isinstance(e, (SocketError, HTTPException)):
e = ProtocolError("Connection aborted.", e)
> retries = retries.increment(
method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/urllib3/connectionpool.py:755:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = Retry(total=0, connect=None, read=False, redirect=None, status=None)
method = 'POST'
url = '/api/1/elastic/SPARC_PortalDatasets_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'
response = None
error = NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>: Failed to establish a new connection: [Errno 110] Connection timed out')
_pool = <urllib3.connectionpool.HTTPSConnectionPool object at 0x7f754acba940>
_stacktrace = <traceback object at 0x7f754a288b80>
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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>: Failed to establish a new connection: [Errno 110] Connection timed out'))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/testing.py:222: in open
return Client.open(
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise
raise value
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/_compat.py:39: in reraise
raise value
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:539: in get_dataset_info_doi
return reform_dataset_results(dataset_search(query))
app/main.py:663: in dataset_search
response = requests.post(f'{Config.SCI_CRUNCH_HOST}/_search',
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:119: in post
return request('post', url, data=data, json=json, **kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/api.py:61: in request
return session.request(method=method, url=url, **kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:542: in request
resp = self.send(prep, **send_kwargs)
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/sessions.py:655: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7f754acba670>
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 as e:
# this may raise a string formatting error.
err = ("Invalid timeout {}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
elif isinstance(timeout, TimeoutSauce):
pass
else:
timeout = TimeoutSauce(connect=timeout, read=timeout)
try:
if not chunked:
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
)
# Send the request.
else:
if hasattr(conn, 'proxy_pool'):
conn = conn.proxy_pool
low_conn = conn._get_conn(timeout=DEFAULT_POOL_TIMEOUT)
try:
low_conn.putrequest(request.method,
url,
skip_accept_encoding=True)
for header, value in request.headers.items():
low_conn.putheader(header, value)
low_conn.endheaders()
for i in request.body:
low_conn.send(hex(len(i))[2:].encode('utf-8'))
low_conn.send(b'\r\n')
low_conn.send(i)
low_conn.send(b'\r\n')
low_conn.send(b'0\r\n\r\n')
# Receive the response from the server
try:
# For Python 2.7, use buffering of HTTP responses
r = low_conn.getresponse(buffering=True)
except TypeError:
# For compatibility with Python 3.3+
r = low_conn.getresponse()
resp = HTTPResponse.from_httplib(
r,
pool=conn,
connection=low_conn,
preload_content=False,
decode_content=False
)
except:
# If we hit any problems here, clean up the connection.
# Then, reraise so that we can handle the actual exception.
low_conn.close()
raise
except (ProtocolError, socket.error) 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_dev/_search?api_key=xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f754a87e6a0>: Failed to establish a new connection: [Errno 110] Connection timed out'))
../../shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/requests/adapters.py:516: ConnectionError
=============================== warnings summary ===============================
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/apscheduler/__init__.py:1
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:19
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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(
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:36
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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(
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:53
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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(
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:70
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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(
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/pennsieve/cache/cache_segment_pb2.py:29
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/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(
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12
/home/cmiss/Jenkins/shiningpanda/jobs/7c726052/virtualenvs/d41d8cd9/lib/python3.9/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; 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-DEV/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead.
assert_equals("healthy", json_response.get("status"))
-- Docs: https://docs.pytest.org/en/latest/warnings.html
=========================== short test summary info ============================
FAILED tests/test_api.py::test_onto_term_lookup - requests.exceptions.Connect...
FAILED tests/test_api.py::test_non_existing_simulation_ui_file - requests.exc...
FAILED tests/test_api.py::test_simulation_ui_file_old_s3_bucket - requests.ex...
FAILED tests/test_api.py::test_simulation_ui_file_new_s3_bucket - requests.ex...
FAILED tests/test_dataset_info.py::test_current_doi_list - requests.exception...
FAILED tests/test_dataset_info.py::test_generic_mouse_colon_dataset_search - ...
FAILED tests/test_dataset_info.py::test_complex_title_dataset_search - reques...
FAILED tests/test_dataset_info.py::test_title_plot_annotation_dataset_search
FAILED tests/test_dataset_info.py::test_object_identifier_dataset_search - re...
FAILED tests/test_dataset_info.py::test_pennsieve_identifier_dataset_search
FAILED tests/test_scicrunch.py::test_scicrunch_keys - requests.exceptions.Con...
FAILED tests/test_scicrunch.py::test_scicrunch_versions_are_supported - reque...
FAILED tests/test_scicrunch.py::test_scicrunch_dataset_doi - requests.excepti...
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_doi - request...
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_ids - request...
FAILED tests/test_scicrunch.py::test_scicrunch_search - requests.exceptions.C...
FAILED tests/test_scicrunch.py::test_scicrunch_all_data - requests.exceptions...
FAILED tests/test_scicrunch.py::test_scicrunch_filter - requests.exceptions.C...
FAILED tests/test_scicrunch.py::test_scicrunch_filter_scaffolds - requests.ex...
FAILED tests/test_scicrunch.py::test_scicrunch_basic_search - requests.except...
FAILED tests/test_scicrunch.py::test_scicrunch_image_search - requests.except...
FAILED tests/test_scicrunch.py::test_scicrunch_boolean_logic - requests.excep...
FAILED tests/test_scicrunch.py::test_scicrunch_combined_facet_text - requests...
FAILED tests/test_scicrunch.py::test_getting_facets - requests.exceptions.Con...
FAILED tests/test_scicrunch.py::test_create_identifier_query - requests.excep...
FAILED tests/test_scicrunch.py::test_create_anatomy_query - requests.exceptio...
FAILED tests/test_scicrunch.py::test_response_version - requests.exceptions.C...
FAILED tests/test_scicrunch.py::test_response_abi_plot - requests.exceptions....
FAILED tests/test_scicrunch.py::test_response_abi_scaffold - requests.excepti...
FAILED tests/test_scicrunch.py::test_response_sample_subject_size - requests....
FAILED tests/test_scicrunch.py::test_raw_response_structure - requests.except...
FAILED tests/test_scicrunch.py::test_get_body_scaffold_info - requests.except...
FAILED tests/test_scicrunch.py::test_getting_curies - requests.exceptions.Con...
FAILED tests/test_scicrunch.py::test_get_related_terms - requests.exceptions....
FAILED tests/test_scicrunch.py::test_scaffold_files - requests.exceptions.Con...
FAILED tests/test_scicrunch.py::test_finding_contextual_information - request...
FAILED tests/test_scicrunch.py::test_undefined_version_dataset_search - reque...
====== 37 failed, 66 passed, 3 skipped, 10 warnings in 4977.89s (1:22:57) ======
Build step 'Virtualenv Builder' marked build as failure
[Slack Notifications] found #939 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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