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collectors.log
$ make test
pylama collectors
pylama migrations
py.test
============================================================================================== test session starts ==============================================================================================
platform linux2 -- Python 2.7.12+, pytest-2.9.2, py-1.4.31, pluggy-0.3.1
rootdir: /home/victor/Workbench/okfn/opentrials/collectors, inifile: pytest.ini
plugins: betamax-0.8.0, cov-2.3.1, pylama-7.0.9
collected 22 items
tests/test_euctr.py .
tests/test_fda_dap.py .F....FFFFF
tests/test_gsk.py .
tests/test_hra.py .......
tests/test_isrctn.py .
tests/test_pubmed.py F
=================================================================================================== FAILURES ====================================================================================================
_____________________________________________________________________________________ TestFDADAP.test_parse_search_results ______________________________________________________________________________________
self = <tests.test_fda_dap.TestFDADAP object at 0x7fcf7df04190>, get_url = <function _get_url at 0x7fcf7df0c398>
def test_parse_search_results(self, get_url):
url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.SearchResults_Browse&DrugInitial=A'
random_seed = '123'
> response = get_url(url)
tests/test_fda_dap.py:28:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/conftest.py:52: in _get_url
response = betamax_session.get(url)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:488: in get
return self.request('GET', url, **kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:475: in request
resp = self.send(prep, **send_kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:596: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <betamax.adapter.BetamaxAdapter object at 0x7fcf7df04710>, request = <PreparedRequest [GET]>, stream = False, timeout = None, verify = True, cert = None, proxies = OrderedDict()
def send(self, request, stream=False, timeout=None, verify=True,
cert=None, proxies=None):
"""Send request.
:param request request: request
:returns: A Response object
"""
interaction = None
current_cassette = self.cassette
if not current_cassette:
raise BetamaxError('No cassette was specified or found.')
if current_cassette.interactions:
interaction = current_cassette.find_match(request)
if not interaction and current_cassette.is_recording():
interaction = self.send_and_record(
request, stream, timeout, verify, cert, proxies
)
if not interaction:
raise BetamaxError(unhandled_request_message(request,
> current_cassette))
E BetamaxError: A request was made that could not be handled.
E
E A request was made to http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.SearchResults_Browse&DrugInitial=A that could not be found in tests.test_fda_dap.TestFDADAP.test_parse_search_results.
E
E The settings on the cassette are:
E
E - record_mode: once
E - match_options set([u'body', u'headers', u'uri', u'method']).
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/betamax/adapter.py:132: BetamaxError
______________________________________________________________________________________ TestFDADAP.test_parse_drug_details _______________________________________________________________________________________
self = <tests.test_fda_dap.TestFDADAP object at 0x7fcf7de69b90>, get_url = <function _get_url at 0x7fcf7de85848>
def test_parse_drug_details(self, get_url):
url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Overview&DrugName=EFFEXOR%20XR'
> response = get_url(url, request_kwargs={'meta': {'cookiejar': 123}})
tests/test_fda_dap.py:110:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/conftest.py:52: in _get_url
response = betamax_session.get(url)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:488: in get
return self.request('GET', url, **kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:475: in request
resp = self.send(prep, **send_kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:596: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <betamax.adapter.BetamaxAdapter object at 0x7fcf7de69150>, request = <PreparedRequest [GET]>, stream = False, timeout = None, verify = True, cert = None, proxies = OrderedDict()
def send(self, request, stream=False, timeout=None, verify=True,
cert=None, proxies=None):
"""Send request.
:param request request: request
:returns: A Response object
"""
interaction = None
current_cassette = self.cassette
if not current_cassette:
raise BetamaxError('No cassette was specified or found.')
if current_cassette.interactions:
interaction = current_cassette.find_match(request)
if not interaction and current_cassette.is_recording():
interaction = self.send_and_record(
request, stream, timeout, verify, cert, proxies
)
if not interaction:
raise BetamaxError(unhandled_request_message(request,
> current_cassette))
E BetamaxError: A request was made that could not be handled.
E
E A request was made to http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Overview&DrugName=EFFEXOR%20XR that could not be found in tests.test_fda_dap.TestFDADAP.test_parse_drug_details.
E
E The settings on the cassette are:
E
E - record_mode: once
E - match_options set([u'body', u'headers', u'uri', u'method']).
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/betamax/adapter.py:132: BetamaxError
______________________________________________________________________________________ TestFDADAP.test_parse_drug_overview ______________________________________________________________________________________
self = <tests.test_fda_dap.TestFDADAP object at 0x7fcf7de8e450>, get_url = <function _get_url at 0x7fcf7de94398>
def test_parse_drug_overview(self, get_url):
random_seed = '123'
search_url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.SearchResults_Browse&DrugInitial=E'
url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Overview&DrugName=E%2DBASE'
> get_url(search_url) # Needed to set up the session
tests/test_fda_dap.py:124:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/conftest.py:52: in _get_url
response = betamax_session.get(url)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:488: in get
return self.request('GET', url, **kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:475: in request
resp = self.send(prep, **send_kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:596: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <betamax.adapter.BetamaxAdapter object at 0x7fcf7de8eb10>, request = <PreparedRequest [GET]>, stream = False, timeout = None, verify = True, cert = None, proxies = OrderedDict()
def send(self, request, stream=False, timeout=None, verify=True,
cert=None, proxies=None):
"""Send request.
:param request request: request
:returns: A Response object
"""
interaction = None
current_cassette = self.cassette
if not current_cassette:
raise BetamaxError('No cassette was specified or found.')
if current_cassette.interactions:
interaction = current_cassette.find_match(request)
if not interaction and current_cassette.is_recording():
interaction = self.send_and_record(
request, stream, timeout, verify, cert, proxies
)
if not interaction:
raise BetamaxError(unhandled_request_message(request,
> current_cassette))
E BetamaxError: A request was made that could not be handled.
E
E A request was made to http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.SearchResults_Browse&DrugInitial=E that could not be found in tests.test_fda_dap.TestFDADAP.test_parse_drug_overview.
E
E The settings on the cassette are:
E
E - record_mode: once
E - match_options set([u'body', u'headers', u'uri', u'method']).
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/betamax/adapter.py:132: BetamaxError
__________________________________________________________________ TestFDADAP.test_parse_drug_overview_only_follow_links_to_drug_details_page ___________________________________________________________________
self = <tests.test_fda_dap.TestFDADAP object at 0x7fcf7de7b510>, get_url = <function _get_url at 0x7fcf7de94938>
def test_parse_drug_overview_only_follow_links_to_drug_details_page(self, get_url):
'''There might be tables with links in multiple columns. We're only
interested in links on the first column (Drug Name).
'''
search_url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.SearchResults_Browse&DrugInitial=F'
url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Overview&DrugName=FYCOMPA'
> get_url(search_url) # Needed to set up the session
tests/test_fda_dap.py:156:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/conftest.py:52: in _get_url
response = betamax_session.get(url)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:488: in get
return self.request('GET', url, **kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:475: in request
resp = self.send(prep, **send_kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:596: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <betamax.adapter.BetamaxAdapter object at 0x7fcf7ddae050>, request = <PreparedRequest [GET]>, stream = False, timeout = None, verify = True, cert = None, proxies = OrderedDict()
def send(self, request, stream=False, timeout=None, verify=True,
cert=None, proxies=None):
"""Send request.
:param request request: request
:returns: A Response object
"""
interaction = None
current_cassette = self.cassette
if not current_cassette:
raise BetamaxError('No cassette was specified or found.')
if current_cassette.interactions:
interaction = current_cassette.find_match(request)
if not interaction and current_cassette.is_recording():
interaction = self.send_and_record(
request, stream, timeout, verify, cert, proxies
)
if not interaction:
raise BetamaxError(unhandled_request_message(request,
> current_cassette))
E BetamaxError: A request was made that could not be handled.
E
E A request was made to http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.SearchResults_Browse&DrugInitial=F that could not be found in tests.test_fda_dap.TestFDADAP.test_parse_drug_overview_only_follow_links_to_drug_details_page.
E
E The settings on the cassette are:
E
E - record_mode: once
E - match_options set([u'body', u'headers', u'uri', u'method']).
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/betamax/adapter.py:132: BetamaxError
____________________________________________________________________________________ TestFDADAP.test_parse_approval_history _____________________________________________________________________________________
self = <tests.test_fda_dap.TestFDADAP object at 0x7fcf7ddc8690>, get_url = <function _get_url at 0x7fcf7ddab320>
def test_parse_approval_history(self, get_url):
search_overview_url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Overview&DrugName=EFFEXOR%20XR'
url = 'http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Label_ApprovalHistory#apphist'
> get_url(search_overview_url)
tests/test_fda_dap.py:169:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/conftest.py:52: in _get_url
response = betamax_session.get(url)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:488: in get
return self.request('GET', url, **kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:475: in request
resp = self.send(prep, **send_kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:596: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <betamax.adapter.BetamaxAdapter object at 0x7fcf7ddc8ad0>, request = <PreparedRequest [GET]>, stream = False, timeout = None, verify = True, cert = None, proxies = OrderedDict()
def send(self, request, stream=False, timeout=None, verify=True,
cert=None, proxies=None):
"""Send request.
:param request request: request
:returns: A Response object
"""
interaction = None
current_cassette = self.cassette
if not current_cassette:
raise BetamaxError('No cassette was specified or found.')
if current_cassette.interactions:
interaction = current_cassette.find_match(request)
if not interaction and current_cassette.is_recording():
interaction = self.send_and_record(
request, stream, timeout, verify, cert, proxies
)
if not interaction:
raise BetamaxError(unhandled_request_message(request,
> current_cassette))
E BetamaxError: A request was made that could not be handled.
E
E A request was made to http://www.accessdata.fda.gov/scripts/cder/drugsatfda/index.cfm?fuseaction=Search.Overview&DrugName=EFFEXOR%20XR that could not be found in tests.test_fda_dap.TestFDADAP.test_parse_approval_history.
E
E The settings on the cassette are:
E
E - record_mode: once
E - match_options set([u'body', u'headers', u'uri', u'method']).
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/betamax/adapter.py:132: BetamaxError
________________________________________________________________________________________ TestFDADAP.test_parse_dap_page _________________________________________________________________________________________
self = <tests.test_fda_dap.TestFDADAP object at 0x7fcf7ddde450>, get_url = <function _get_url at 0x7fcf7ddab758>
def test_parse_dap_page(self, get_url):
url = 'http://www.accessdata.fda.gov/drugsatfda_docs/nda/97/020699_effexorxr_toc.cfm'
mock_item = {
'documents': [
{'name': 'Foo', 'urls': ['http://foo.com/bar.pdf']},
]
}
> response = get_url(url)
tests/test_fda_dap.py:200:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/conftest.py:52: in _get_url
response = betamax_session.get(url)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:488: in get
return self.request('GET', url, **kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:475: in request
resp = self.send(prep, **send_kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:596: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <betamax.adapter.BetamaxAdapter object at 0x7fcf7dddeb10>, request = <PreparedRequest [GET]>, stream = False, timeout = None, verify = True, cert = None, proxies = OrderedDict()
def send(self, request, stream=False, timeout=None, verify=True,
cert=None, proxies=None):
"""Send request.
:param request request: request
:returns: A Response object
"""
interaction = None
current_cassette = self.cassette
if not current_cassette:
raise BetamaxError('No cassette was specified or found.')
if current_cassette.interactions:
interaction = current_cassette.find_match(request)
if not interaction and current_cassette.is_recording():
interaction = self.send_and_record(
request, stream, timeout, verify, cert, proxies
)
if not interaction:
raise BetamaxError(unhandled_request_message(request,
> current_cassette))
E BetamaxError: A request was made that could not be handled.
E
E A request was made to http://www.accessdata.fda.gov/drugsatfda_docs/nda/97/020699_effexorxr_toc.cfm that could not be found in tests.test_fda_dap.TestFDADAP.test_parse_dap_page.
E
E The settings on the cassette are:
E
E - record_mode: once
E - match_options set([u'body', u'headers', u'uri', u'method']).
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/betamax/adapter.py:132: BetamaxError
_____________________________________________________________________________________________ test_make_start_urls ______________________________________________________________________________________________
def test_make_start_urls():
result = _make_start_urls(
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi/',
'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi/?db=pubmed&id={pmid}&retmode=xml',
> '2016-01-01', '2016-01-01')
tests/test_pubmed.py:17:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
collectors/pubmed/spider.py:90: in _make_start_urls
response = session.get(url)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:488: in get
return self.request('GET', url, **kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:475: in request
resp = self.send(prep, **send_kwargs)
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/sessions.py:596: in send
r = adapter.send(request, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <requests.adapters.HTTPAdapter object at 0x7fcf7deb4c10>, request = <PreparedRequest [GET]>, stream = False, timeout = <requests.packages.urllib3.util.timeout.Timeout object at 0x7fcf7deb4650>
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
:param verify: (optional) Whether to verify SSL certificates.
: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
"""
conn = self.get_connection(request.url, proxies)
self.cert_verify(conn, request.url, verify, cert)
url = self.request_url(request, proxies)
self.add_headers(request)
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 {0}. Pass a (connect, read) "
"timeout tuple, or a single float to set "
"both timeouts to the same value".format(timeout))
raise ValueError(err)
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+ versions, use buffering of HTTP
# responses
r = low_conn.getresponse(buffering=True)
except TypeError:
# For compatibility with Python 2.6 versions and back
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)
E ConnectionError: ('Connection aborted.', BadStatusLine("''",))
../../../../.virtualenv/collectors/local/lib/python2.7/site-packages/requests/adapters.py:473: ConnectionError
--------------------------------------------------------------------------------------------- Captured stderr call ----------------------------------------------------------------------------------------------
INFO:requests.packages.urllib3.connectionpool:Starting new HTTP connection (1): eutils.ncbi.nlm.nih.gov
DEBUG:requests.packages.urllib3.connectionpool:"GET /entrez/eutils/esearch.fcgi/?db=pubmed&retmode=json&mindate=2016%2F01%2F01&maxdate=2016%2F01%2F01&term=trial+registration&datetype=pdat&retstart=0&retmax=50000 HTTP/1.1" 200 3238
INFO:requests.packages.urllib3.connectionpool:Resetting dropped connection: eutils.ncbi.nlm.nih.gov
DEBUG:requests.packages.urllib3.connectionpool:"GET /entrez/eutils/esearch.fcgi/?db=pubmed&retmode=json&mindate=2016%2F01%2F01&maxdate=2016%2F01%2F01&term=trial+registration&datetype=pdat&retstart=50000&retmax=50000 HTTP/1.1" 200 487
DEBUG:requests.packages.urllib3.connectionpool:"GET /entrez/eutils/esearch.fcgi/?db=pubmed&retmode=json&mindate=2016%2F01%2F01&maxdate=2016%2F01%2F01&term=trial+registration&datetype=mdat&retstart=0&retmax=50000 HTTP/1.1" 200 720
====================================================================================== 7 failed, 15 passed in 3.93 seconds ======================================================================================
Makefile:35: recipe for target 'test' failed
make: *** [test] Error 1
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