return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:689: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
_____________________________ test_scicrunch_keys ______________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_keys(client):
> r = client.get('/search/')
tests/test_scicrunch.py:26:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:779: in kb_search
return process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
____________________ test_scicrunch_versions_are_supported _____________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
def test_scicrunch_versions_are_supported():
# Lines below are to allow the test to be run from the root dir or sparc-api/tests
current_directory = os.path.dirname(os.path.abspath(__file__))
app_directory = os.path.join(current_directory, '..', 'app')
# List the contents of the 'app' directory, to find which versions we have files for
available_versions = os.listdir(app_directory)
r = requests.get(f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}&q=""')
> results = r.json()
tests/test_scicrunch.py:39:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
__________________________ test_scicrunch_dataset_doi __________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_dataset_doi(client):
# Testing with dataset 55
identifier = "55"
> run_doi_test = check_doi_status(client, identifier, '10.26275/pzek-91wx')
tests/test_scicrunch.py:68:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_scicrunch.py:53: in check_doi_status
r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id})
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:689: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
_____________________ test_scicrunch_multiple_dataset_doi ______________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_multiple_dataset_doi(client):
# Testing with dataset 55 and 68
> run_doi_test_1 = check_doi_status(client, "55", '10.26275/pzek-91wx')
tests/test_scicrunch.py:84:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_scicrunch.py:53: in check_doi_status
r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id})
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:689: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
_____________________ test_scicrunch_multiple_dataset_ids ______________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_multiple_dataset_ids(client):
# Testing with dataset 55 and 68
> r = client.get('/dataset_info/using_multiple_discoverIds/?discoverIds=55&discoverIds=68')
tests/test_scicrunch.py:102:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:654: in get_dataset_info_discoverIds
return process_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
____________________________ test_scicrunch_search _____________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_search(client):
> r = client.get('/search/heart')
tests/test_scicrunch.py:113:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:779: in kb_search
return process_results(response.json())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
___________________________ test_scicrunch_all_data ____________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_all_data(client):
r = client.get('/filter-search/')
> assert json.loads(r.data)['numberOfHits'] > 40
E KeyError: 'numberOfHits'
tests/test_scicrunch.py:120: KeyError
____________________________ test_scicrunch_filter _____________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_filter(client):
r = client.get('/filter-search/', query_string={'term': 'organ', 'facet': 'heart'})
> assert json.loads(r.data)['numberOfHits'] > 4
E KeyError: 'numberOfHits'
tests/test_scicrunch.py:125: KeyError
_______________________ test_scicrunch_filter_scaffolds ________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_filter_scaffolds(client):
r = client.get('/filter-search/?facet=scaffolds&term=datasets')
> assert json.loads(r.data)['numberOfHits'] > 10
E KeyError: 'numberOfHits'
tests/test_scicrunch.py:130: KeyError
_________________________ test_scicrunch_basic_search __________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_basic_search(client):
r = client.get('/filter-search/Heart/?facet=All+Species&term=species')
> assert json.loads(r.data)['numberOfHits'] > 10
E KeyError: 'numberOfHits'
tests/test_scicrunch.py:135: KeyError
_________________________ test_scicrunch_image_search __________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_image_search(client):
> r = client.get('/multiple_dataset_info/using_multiple_mimetype/?q="*jp2*+OR+*vnd.ome.xml*+OR+*jpx*"')
tests/test_scicrunch.py:138:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:645: in get_file_info_from_mimetype
return process_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
_________________________ test_scicrunch_boolean_logic _________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_boolean_logic(client):
r = client.get('/filter-search/?facet=All+Species&term=species&facet=male&term=gender&facet=female&term=gender')
> assert json.loads(r.data)['numberOfHits'] > 20
E KeyError: 'numberOfHits'
tests/test_scicrunch.py:143: KeyError
______________________ test_scicrunch_combined_facet_text ______________________
client = <FlaskClient <Flask 'app.main'>>
def test_scicrunch_combined_facet_text(client):
r = client.get('/filter-search/heart/?facet=All+Species&term=species&facet=male&term=gender&facet=female&term=gender')
> assert json.loads(r.data)['numberOfHits'] > 1
E KeyError: 'numberOfHits'
tests/test_scicrunch.py:148: KeyError
_____________________________ test_getting_facets ______________________________
client = <FlaskClient <Flask 'app.main'>>
def test_getting_facets(client):
r = client.get('/get-facets/organ')
facet_results = json.loads(r.data)
> facets = [facet_result['key'] for facet_result in facet_results]
tests/test_scicrunch.py:154:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
.0 = <dict_keyiterator object at 0x7f99084acb30>
> facets = [facet_result['key'] for facet_result in facet_results]
E TypeError: string indices must be integers
tests/test_scicrunch.py:154: TypeError
_________________________ test_create_identifier_query _________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_create_identifier_query(client):
> r = client.get('/dataset_info/using_object_identifier?identifier=package:e6435710-dd9c-46b7-9dfd-932103469733')
tests/test_scicrunch.py:159:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:670: in get_dataset_info_object_identifier
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
__________________________ test_create_anatomy_query ___________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_create_anatomy_query(client):
> r = client.get('/dataset_info/anatomy?identifier=90')
tests/test_scicrunch.py:176:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:681: in get_dataset_info_anatomy
return reform_anatomy_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
____________________________ test_response_version _____________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_response_version(client):
# Testing with dataset 44
identifier = "44"
doi = "10.26275/duz8-mq3n"
> run_doi_test = check_doi_status(client, identifier, doi)
tests/test_scicrunch.py:206:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_scicrunch.py:53: in check_doi_status
r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id})
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:689: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
____________________________ test_response_abi_plot ____________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_response_abi_plot(client):
# Testing abi-plot with dataset 212
identifier = "212"
doi = "10.26275/lok5-wje6"
> run_doi_test = check_doi_status(client, identifier, doi)
tests/test_scicrunch.py:221:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_scicrunch.py:53: in check_doi_status
r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id})
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:689: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
__________________________ test_response_abi_scaffold __________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_response_abi_scaffold(client):
# Testing abi-scaffold with dataset 76
identifier = "76"
doi = "10.26275/jarb-s8jw"
> run_doi_test = check_doi_status(client, identifier, doi)
tests/test_scicrunch.py:255:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
tests/test_scicrunch.py:53: in check_doi_status
r = client.get('/dataset_info/using_pennsieve_identifier', query_string={'identifier': dataset_id})
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:689: in get_dataset_info_pennsieve_identifier
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
______________________ test_response_sample_subject_size _______________________
client = <FlaskClient <Flask 'app.main'>>
def test_response_sample_subject_size(client):
# Only filter search returns the sample and subjectSuze
r = client.get('/filter-search/?facet=liver&term=organ')
data = r.data.decode('utf-8')
json_data = json.loads(data)
print(json_data)
> assert len(json_data['results']) == 1
E KeyError: 'results'
tests/test_scicrunch.py:315: KeyError
----------------------------- Captured stdout call -----------------------------
{'error': 'JSONDecodeError', 'message': 'Could not parse SciCrunch output, please try again later'}
_________________________ test_raw_response_structure __________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_raw_response_structure(client):
# 10.26275/zdxd-84xz
# 10.26275/duz8-mq3n
query = create_query_string("computational")
> data = dataset_search(query)
tests/test_scicrunch.py:428:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
_________________________ test_get_body_scaffold_info __________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_get_body_scaffold_info(client):
# Test if we get a shorter list of uberons with species specified
> r = client.get('/get_body_scaffold_info/human')
tests/test_scicrunch.py:458:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:1185: in get_body_scaffold_info
result = process_get_first_scaffold_info(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
_____________________________ test_getting_curies ______________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
@app.route("/get-organ-curies/")
def get_available_uberonids():
species = request.args.getlist('species')
requestBody = create_request_body_for_curies(species)
result = {}
try:
response = requests.post(
f'{Config.SCI_CRUNCH_HOST}/_search?api_key={Config.KNOWLEDGEBASE_KEY}',
json=requestBody)
> result = reform_curies_results(response.json())
app/main.py:2187:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_getting_curies(client):
# Test if we get a shorter list of uberons with species specified
> r = client.get('/get-organ-curies/')
tests/test_scicrunch.py:467:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:2189: in get_available_uberonids
logging.error("Failed getting Uberon IDs", ex)
/usr/lib/python3.10/logging/__init__.py:2105: in error
root.error(msg, *args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1506: in error
self._log(ERROR, msg, args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1624: in _log
self.handle(record)
/usr/lib/python3.10/logging/__init__.py:1634: in handle
self.callHandlers(record)
/usr/lib/python3.10/logging/__init__.py:1696: in callHandlers
hdlr.handle(record)
/usr/lib/python3.10/logging/__init__.py:968: in handle
self.emit(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:384: in emit
super().emit(record)
/usr/lib/python3.10/logging/__init__.py:1108: in emit
self.handleError(record)
/usr/lib/python3.10/logging/__init__.py:1100: in emit
msg = self.format(record)
/usr/lib/python3.10/logging/__init__.py:943: in format
return fmt.format(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:137: in format
return super().format(record)
/usr/lib/python3.10/logging/__init__.py:678: in format
record.message = record.getMessage()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/main.py, 2189, "Failed getting Uberon IDs">
def getMessage(self):
"""
Return the message for this LogRecord.
Return the message for this LogRecord after merging any user-supplied
arguments with the message.
"""
msg = str(self.msg)
if self.args:
> msg = msg % self.args
E TypeError: not all arguments converted during string formatting
/usr/lib/python3.10/logging/__init__.py:368: TypeError
____________________________ test_get_related_terms ____________________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
query = 'UBERON:0002084'
@app.route("/get-related-terms/<query>")
def get_related_terms(query):
payload = {
'direction': request.args.get('direction', default='OUTGOING'),
'relationshipType': request.args.get('relationshipType', default='BFO:0000050'),
'entail': request.args.get('entail', default='true'),
'api_key': Config.KNOWLEDGEBASE_KEY
}
result = {}
try:
response = requests.get(
f'{Config.SCI_CRUNCH_SCIGRAPH_HOST}/graph/neighbors/{query}',
params=payload)
> result = reform_related_terms(response.json())
app/main.py:2214:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_get_related_terms(client):
# Test if we can get the uberon term of heart using the uberon term
# of left ventricle
> r = client.get('/get-related-terms/UBERON:0002084')
tests/test_scicrunch.py:484:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:2216: in get_related_terms
logging.error(f"Failed getting related terms with payload {payload}", ex)
/usr/lib/python3.10/logging/__init__.py:2105: in error
root.error(msg, *args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1506: in error
self._log(ERROR, msg, args, **kwargs)
/usr/lib/python3.10/logging/__init__.py:1624: in _log
self.handle(record)
/usr/lib/python3.10/logging/__init__.py:1634: in handle
self.callHandlers(record)
/usr/lib/python3.10/logging/__init__.py:1696: in callHandlers
hdlr.handle(record)
/usr/lib/python3.10/logging/__init__.py:968: in handle
self.emit(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:384: in emit
super().emit(record)
/usr/lib/python3.10/logging/__init__.py:1108: in emit
self.handleError(record)
/usr/lib/python3.10/logging/__init__.py:1100: in emit
msg = self.format(record)
/usr/lib/python3.10/logging/__init__.py:943: in format
return fmt.format(record)
../../../python3.10.venv/lib/python3.10/site-packages/_pytest/logging.py:137: in format
return super().format(record)
/usr/lib/python3.10/logging/__init__.py:678: in format
record.message = record.getMessage()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <LogRecord: root, 40, /home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/main.py, 2216, "Failed getting related terms wit...ion': 'OUTGOING', 'relationshipType': 'BFO:0000050', 'entail': 'true', 'api_key': 'xBOrIfnZTvJQtobGo8XHRvThdMYGTxtf'}">
def getMessage(self):
"""
Return the message for this LogRecord.
Return the message for this LogRecord after merging any user-supplied
arguments with the message.
"""
msg = str(self.msg)
if self.args:
> msg = msg % self.args
E TypeError: not all arguments converted during string formatting
/usr/lib/python3.10/logging/__init__.py:368: TypeError
_____________________________ test_scaffold_files ______________________________
client = <FlaskClient <Flask 'app.main'>>
def test_scaffold_files(client):
r = client.get('/filter-search/?size=30')
results = json.loads(r.data)
> assert results['numberOfHits'] > 0
E KeyError: 'numberOfHits'
tests/test_scicrunch.py:500: KeyError
_____________________ test_finding_contextual_information ______________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_finding_contextual_information(client):
> r = client.get('/dataset_info/using_multiple_discoverIds/?discoverIds=76')
tests/test_scicrunch.py:514:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:654: in get_dataset_info_discoverIds
return process_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
____________________ test_undefined_version_dataset_search _____________________
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
> return complexjson.loads(self.text, **kwargs)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:971:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
/usr/lib/python3.10/json/__init__.py:346: in loads
return _default_decoder.decode(s)
/usr/lib/python3.10/json/decoder.py:337: in decode
obj, end = self.raw_decode(s, idx=_w(s, 0).end())
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <json.decoder.JSONDecoder object at 0x7f991261dcf0>, s = '', idx = 0
def raw_decode(self, s, idx=0):
"""Decode a JSON document from ``s`` (a ``str`` beginning with
a JSON document) and return a 2-tuple of the Python
representation and the index in ``s`` where the document ended.
This can be used to decode a JSON document from a string that may
have extraneous data at the end.
"""
try:
obj, end = self.scan_once(s, idx)
except StopIteration as err:
> raise JSONDecodeError("Expecting value", s, err.value) from None
E json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
/usr/lib/python3.10/json/decoder.py:355: JSONDecodeError
During handling of the above exception, another exception occurred:
client = <FlaskClient <Flask 'app.main'>>
def test_undefined_version_dataset_search(client):
# Testing with dataset 17 which is not versioned
identifier = "17"
doi = "10.26275/mlua-o9oj"
> r = client.get('/dataset_info/using_doi', query_string={'doi': doi})
tests/test_scicrunch.py:525:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1029: in get
return self.open(*args, **kw)
../../../python3.10.venv/lib/python3.10/site-packages/flask/testing.py:222: in open
return Client.open(
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:993: in open
response = self.run_wsgi_app(environ.copy(), buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:884: in run_wsgi_app
rv = run_wsgi_app(self.application, environ, buffered=buffered)
../../../python3.10.venv/lib/python3.10/site-packages/werkzeug/test.py:1119: in run_wsgi_app
app_rv = app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2463: in __call__
return self.wsgi_app(environ, start_response)
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2449: in wsgi_app
response = self.handle_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1866: in handle_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:2446: in wsgi_app
response = self.full_dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1951: in full_dispatch_request
rv = self.handle_user_exception(e)
../../../python3.10.venv/lib/python3.10/site-packages/flask_cors/extension.py:161: in wrapped_function
return cors_after_request(app.make_response(f(*args, **kwargs)))
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1820: in handle_user_exception
reraise(exc_type, exc_value, tb)
../../../python3.10.venv/lib/python3.10/site-packages/flask/_compat.py:39: in reraise
raise value
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1949: in full_dispatch_request
rv = self.dispatch_request()
../../../python3.10.venv/lib/python3.10/site-packages/flask/app.py:1935: in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
app/main.py:624: in get_dataset_info_doi
return reform_dataset_results(dataset_search(query))
app/main.py:758: in dataset_search
return response.json()
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <Response [200]>, kwargs = {}
def json(self, **kwargs):
r"""Returns the json-encoded content of a response, if any.
:param \*\*kwargs: Optional arguments that ``json.loads`` takes.
:raises requests.exceptions.JSONDecodeError: If the response body does not
contain valid json.
"""
if not self.encoding and self.content and len(self.content) > 3:
# No encoding set. JSON RFC 4627 section 3 states we should expect
# UTF-8, -16 or -32. Detect which one to use; If the detection or
# decoding fails, fall back to `self.text` (using charset_normalizer to make
# a best guess).
encoding = guess_json_utf(self.content)
if encoding is not None:
try:
return complexjson.loads(self.content.decode(encoding), **kwargs)
except UnicodeDecodeError:
# Wrong UTF codec detected; usually because it's not UTF-8
# but some other 8-bit codec. This is an RFC violation,
# and the server didn't bother to tell us what codec *was*
# used.
pass
except JSONDecodeError as e:
raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
try:
return complexjson.loads(self.text, **kwargs)
except JSONDecodeError as e:
# Catch JSON-related errors and raise as requests.JSONDecodeError
# This aliases json.JSONDecodeError and simplejson.JSONDecodeError
> raise RequestsJSONDecodeError(e.msg, e.doc, e.pos)
E requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
../../../python3.10.venv/lib/python3.10/site-packages/requests/models.py:975: JSONDecodeError
=============================== warnings summary ===============================
scripts/monthly_db.py:9
/home/cmiss/Jenkins/workspace/SPARC-API-DEV/scripts/monthly_db.py:9: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
base = declarative_base()
../../../python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/apscheduler/__init__.py:1: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
from pkg_resources import get_distribution, DistributionNotFound
../../../python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/marshmallow/__init__.py:17: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/flask_marshmallow/__init__.py:34: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
__version_info__ = tuple(LooseVersion(__version__).version)
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:19: DeprecationWarning: Call to deprecated create function FileDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
DESCRIPTOR = _descriptor.FileDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:36: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:53: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:70: DeprecationWarning: Call to deprecated create function FieldDescriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_descriptor.FieldDescriptor(
../../../python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/pennsieve/cache/cache_segment_pb2.py:29: DeprecationWarning: Call to deprecated create function Descriptor(). Note: Create unlinked descriptors is going to go away. Please use get/find descriptors from generated code or query the descriptor_pool.
_CACHESEGMENT = _descriptor.Descriptor(
app/dbtable.py:12
/home/cmiss/Jenkins/workspace/SPARC-API-DEV/app/dbtable.py:12: MovedIn20Warning: The ``declarative_base()`` function is now available as sqlalchemy.orm.declarative_base(). (deprecated since: 2.0) (Background on SQLAlchemy 2.0 at: https://sqlalche.me/e/b8d9)
base = declarative_base()
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: 3 warnings
tests/test_api.py: 33 warnings
tests/test_biolucida.py: 13 warnings
tests/test_dataset_info.py: 6 warnings
tests/test_monthly_stats.py: 11 warnings
tests/test_osparc.py: 17 warnings
tests/test_plot.py: 1 warning
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 28 warnings
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/util/ssl_.py:281: DeprecationWarning: ssl.PROTOCOL_TLS is deprecated
context = SSLContext(ssl_version or PROTOCOL_TLS)
../../../python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: 3 warnings
tests/test_api.py: 36 warnings
tests/test_biolucida.py: 13 warnings
tests/test_dataset_info.py: 7 warnings
tests/test_monthly_stats.py: 14 warnings
tests/test_osparc.py: 17 warnings
tests/test_plot.py: 1 warning
tests/test_pmr.py: 4 warnings
tests/test_scicrunch.py: 28 warnings
tests/test_segmentation_info.py: 1 warning
tests/test_thumbnails.py: 2 warnings
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/urllib3/connection.py:512: DeprecationWarning: ssl.match_hostname() is deprecated
match_hostname(cert, asserted_hostname)
../../../python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12
/home/cmiss/python3.10.venv/lib/python3.10/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib and slated for removal in Python 3.12; see the module's documentation for alternative uses
from imp import find_module, load_module, acquire_lock, release_lock
tests/test_health.py::test_request_response
/home/cmiss/Jenkins/workspace/SPARC-API-DEV/tests/test_health.py:13: DeprecationWarning: Please use assertEqual instead.
assert_equals("healthy", json_response.get("status"))
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED tests/test_api.py::test_non_existing_simulation_ui_file - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_api.py::test_simulation_ui_file_old_s3_bucket - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_api.py::test_simulation_ui_file_new_s3_bucket - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_dataset_info.py::test_current_doi_list - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_dataset_info.py::test_generic_mouse_colon_dataset_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_dataset_info.py::test_complex_title_dataset_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_dataset_info.py::test_title_plot_annotation_dataset_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_dataset_info.py::test_object_identifier_dataset_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_dataset_info.py::test_pennsieve_identifier_dataset_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_plot.py::test_abi_plot - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_keys - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_versions_are_supported - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_dataset_doi - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_doi - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_multiple_dataset_ids - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_all_data - KeyError: 'numberOfHits'
FAILED tests/test_scicrunch.py::test_scicrunch_filter - KeyError: 'numberOfHits'
FAILED tests/test_scicrunch.py::test_scicrunch_filter_scaffolds - KeyError: 'numberOfHits'
FAILED tests/test_scicrunch.py::test_scicrunch_basic_search - KeyError: 'numberOfHits'
FAILED tests/test_scicrunch.py::test_scicrunch_image_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_scicrunch_boolean_logic - KeyError: 'numberOfHits'
FAILED tests/test_scicrunch.py::test_scicrunch_combined_facet_text - KeyError: 'numberOfHits'
FAILED tests/test_scicrunch.py::test_getting_facets - TypeError: string indices must be integers
FAILED tests/test_scicrunch.py::test_create_identifier_query - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_create_anatomy_query - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_response_version - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_response_abi_plot - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_response_abi_scaffold - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_response_sample_subject_size - KeyError: 'results'
FAILED tests/test_scicrunch.py::test_raw_response_structure - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_get_body_scaffold_info - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_getting_curies - TypeError: not all arguments converted during string formatting
FAILED tests/test_scicrunch.py::test_get_related_terms - TypeError: not all arguments converted during string formatting
FAILED tests/test_scicrunch.py::test_scaffold_files - KeyError: 'numberOfHits'
FAILED tests/test_scicrunch.py::test_finding_contextual_information - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
FAILED tests/test_scicrunch.py::test_undefined_version_dataset_search - requests.exceptions.JSONDecodeError: Expecting value: line 1 column 1 (char 0)
====== 37 failed, 82 passed, 3 skipped, 256 warnings in 241.96s (0:04:01) ======
Build step 'Execute shell' marked build as failure
[Slack Notifications] found #1307 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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