def get_access_token_util(auth_code):
"""
Given an auth code, retrieve and return the access token from BaseSpace
"""
app = current.db(current.db.app_data.id > 0).select().first()
bs_api = BaseSpaceAPI(app.client_id,app.client_secret,app.baseSpaceUrl,app.version,current.session.app_session_num)
bs_api.updatePrivileges(auth_code)
access_token = bs_api.getAccessToken()
# set token in session var
current.session.token = access_token
return access_token
class TestSDK(object):
'''
Compares objects from BaseSpace REST API to SDK objects, including pickled objects
'''
def __init__(self):
self.qp = {}
self.rest_method = 'GET'
self.postData = None
self.headerParams=None
self.list_request = False
# TODO change to unit_tests, but need to add projects/run to account?
self.myAPI = BaseSpaceAPI(profile="ps_native_hoth")
self.api = APIClient(self.myAPI.getAccessToken(), self.myAPI.apiServer)
def compare_dict_to_obj(self, rest_dict, p_obj):
"""
Compare a dictionary from a REST API response and a SDK object for identity.
"""
for r_key, r_val in rest_dict.iteritems():
# confirm that the key from REST api exists in stored object
try:
p_val = getattr(p_obj, r_key)
except AttributeError:
print "REST API attribute '" + r_key + "' doesn't exist in object"
else:
self.classify_rest_item(r_val, p_val, r_key)
def compare_list_to_obj(self, rest_list, p_obj, r_key):
"""
Compare a list from a REST API response and an SDK object for identity.
"""
if type(p_obj) != list:
print "Attribute '" + r_key + "' is a list in the REST API but not in the object"
elif len(p_obj) != len(rest_list):
print "Attribute '" + r_key + "' has different list length between REST API and object"
else:
for r_val, p_val in map(None, rest_list, p_obj):
self.classify_rest_item(r_val, p_val, r_key)
def compare_builtin_to_obj(self, rest_val, p_obj, r_key):
"""
Compare a built-in type from a REST API response and an SDK object for identity.
"""
# convert unicode to ascii for comparisons
if isinstance(rest_val, unicode):
rest_val = rest_val.encode('ascii','ignore')
# don't compare values for datetimes
if r_key in ['DateCreated', 'DateModified', 'DateUploadCompleted', 'DateUploadStarted']:
pass
elif rest_val != p_obj:
print "REST API attribute '" + r_key + "' has value '" + str(rest_val) + "' doesn't match object value '" + str(p_obj) + "'"
def classify_rest_item(self, r_val, p_val, r_key):
"""
Determine the input REST item's type and call method to compare to input object
"""
if type(r_val) in [ int, str, bool, float, unicode]:
self.compare_builtin_to_obj(r_val, p_val, r_key)
elif type(r_val) == dict:
self.compare_dict_to_obj(r_val, p_val)
elif type(r_val) == list:
self.compare_list_to_obj(r_val, p_val, r_key)
else:
print "REST API attribute'" + r_key + "' has an unrecognized attribute type"
def test_rest_vs_sdk(self):
"""
Compares REST API response and python SDK object for identify, for an API method
"""
sdk_obj = self.call_sdk()
rest_obj = self.call_rest_api()
# TODO passing Response here, SDK doesn't currently capture other items at this level (e.g. Notifications)
if self.list_request:
self.compare_list_to_obj(rest_obj['Response']['Items'], sdk_obj, "BASE")
else:
self.compare_dict_to_obj(rest_obj['Response'], sdk_obj)
def call_rest_api(self):
"""
Call the REST API for this object
"""
return self.api.callAPI(self.rest_path, self.rest_method, queryParams=self.qp, postData=self.postData, headerParams=self.headerParams)
def create_pickle_from_sdk(self, pickle_path):
"""
Stores a pickled object in the provided path (include file name) for the object returned for this SDK method
"""
sdk_obj = self.call_sdk()
with open(pickle_path, 'w') as f:
Pickle.dump(sdk_obj, f)
def get_pickle(self, pickle_path):
"""
Retrieves a pickled object from the provided path (include file name), for this API test
"""
with open(pickle_path, 'r') as f:
sdk_obj = Pickle.load(f)
return sdk_obj
def test_rest_vs_pickle(self, pickle_path):
"""
Compares REST API response and a stored object for identify, for an API method
"""
p_obj = self.get_pickle(pickle_path)
rest_obj = self.call_rest_api()
self.compare_dict_to_obj(rest_obj['Response'], p_obj)
# Have the user visit the verification uri to grant us access print "\nPlease visit the uri within 15 seconds and grant access" print deviceInfo['verification_with_code_uri'] webbrowser.open_new(deviceInfo['verification_with_code_uri']) time.sleep(15) ## PAUSE HERE # Once the user has granted us access to objects we requested, we can # get the basespace access token and start browsing simply by calling updatePriviliges # on the baseSpaceApi instance. code = deviceInfo['device_code'] myAPI.updatePrivileges(code) # As a reference the provided access-token can be obtained from the BaseSpaceApi object print "\nMy Access-token:" print myAPI.getAccessToken() # Let's try and grab all available genomes with our new api! allGenomes = myAPI.getAvailableGenomes() print "\nGenomes \n" + str(allGenomes) # If at a later stage we wish to initialize a BaseSpaceAPI object when we already have # an access-token from a previous sessions, this may simply be done by initializing the BaseSpaceAPI # object using the key-word AccessToken. myToken = myAPI.getAccessToken() myAPI.setAccessToken(myToken) print "\nA BaseSpaceAPI instance was updated with an access-token: " print myAPI #################### Web-based verification ################################# # The scenario where the authentication is done through a web-browser
class TestSDK(object):
'''
Compares objects from BaseSpace REST API to SDK objects, including pickled objects
'''
def __init__(self):
self.qp = {}
self.rest_method = 'GET'
self.postData = None
self.headerParams = None
self.list_request = False
# TODO change to unit_tests, but need to add projects/run to account?
self.myAPI = BaseSpaceAPI(profile="ps_native_hoth")
self.api = APIClient(self.myAPI.getAccessToken(), self.myAPI.apiServer)
def compare_dict_to_obj(self, rest_dict, p_obj):
"""
Compare a dictionary from a REST API response and a SDK object for identity.
"""
for r_key, r_val in six.iteritems(rest_dict):
# confirm that the key from REST api exists in stored object
try:
p_val = getattr(p_obj, r_key)
except AttributeError:
print("REST API attribute '" + r_key +
"' doesn't exist in object")
else:
self.classify_rest_item(r_val, p_val, r_key)
def compare_list_to_obj(self, rest_list, p_obj, r_key):
"""
Compare a list from a REST API response and an SDK object for identity.
"""
if type(p_obj) != list:
print("Attribute '" + r_key +
"' is a list in the REST API but not in the object")
elif len(p_obj) != len(rest_list):
print("Attribute '" + r_key +
"' has different list length between REST API and object")
else:
for r_val, p_val in map(None, rest_list, p_obj):
self.classify_rest_item(r_val, p_val, r_key)
def compare_builtin_to_obj(self, rest_val, p_obj, r_key):
"""
Compare a built-in type from a REST API response and an SDK object for identity.
"""
# convert unicode to ascii for comparisons
if isinstance(rest_val, six.text_type):
rest_val = rest_val.encode('ascii', 'ignore')
# don't compare values for datetimes
if r_key in [
'DateCreated', 'DateModified', 'DateUploadCompleted',
'DateUploadStarted'
]:
pass
elif rest_val != p_obj:
print("REST API attribute '" + r_key + "' has value '" +
str(rest_val) + "' doesn't match object value '" +
str(p_obj) + "'")
def classify_rest_item(self, r_val, p_val, r_key):
"""
Determine the input REST item's type and call method to compare to input object
"""
if type(r_val) in [int, str, bool, float, six.text_type]:
self.compare_builtin_to_obj(r_val, p_val, r_key)
elif type(r_val) == dict:
self.compare_dict_to_obj(r_val, p_val)
elif type(r_val) == list:
self.compare_list_to_obj(r_val, p_val, r_key)
else:
print("REST API attribute'" + r_key +
"' has an unrecognized attribute type")
def test_rest_vs_sdk(self):
"""
Compares REST API response and python SDK object for identify, for an API method
"""
sdk_obj = self.call_sdk()
rest_obj = self.call_rest_api()
# TODO passing Response here, SDK doesn't currently capture other items at this level (e.g. Notifications)
if self.list_request:
self.compare_list_to_obj(rest_obj['Response']['Items'], sdk_obj,
"BASE")
else:
self.compare_dict_to_obj(rest_obj['Response'], sdk_obj)
def call_rest_api(self):
"""
Call the REST API for this object
"""
return self.api.callAPI(self.rest_path,
self.rest_method,
queryParams=self.qp,
postData=self.postData,
headerParams=self.headerParams)
def create_pickle_from_sdk(self, pickle_path):
"""
Stores a pickled object in the provided path (include file name) for the object returned for this SDK method
"""
sdk_obj = self.call_sdk()
with open(pickle_path, 'w') as f:
Pickle.dump(sdk_obj, f)
def get_pickle(self, pickle_path):
"""
Retrieves a pickled object from the provided path (include file name), for this API test
"""
with open(pickle_path, 'r') as f:
sdk_obj = Pickle.load(f)
return sdk_obj
def test_rest_vs_pickle(self, pickle_path):
"""
Compares REST API response and a stored object for identify, for an API method
"""
p_obj = self.get_pickle(pickle_path)
rest_obj = self.call_rest_api()
self.compare_dict_to_obj(rest_obj['Response'], p_obj)
# Have the user visit the verification uri to grant us access print "\nPlease visit the uri within 15 seconds and grant access" print deviceInfo['verification_with_code_uri'] webbrowser.open_new(deviceInfo['verification_with_code_uri']) time.sleep(15) ## PAUSE HERE # Once the user has granted us access to objects we requested, we can # get the basespace access token and start browsing simply by calling updatePriviliges # on the baseSpaceApi instance. code = deviceInfo['device_code'] BSapi.updatePrivileges(code) # As a reference the provided access-token can be obtained from the BaseSpaceApi object print "\nMy Access-token:" print BSapi.getAccessToken() # Let's try and grab all available genomes with our new api! allGenomes = BSapi.getAvailableGenomes() print "\nGenomes \n" + str(allGenomes) # If at a later stage we wish to initialize a BaseSpaceAPI object when we already have # an access-token from a previous sessions, this may simply be done by initializing the BaseSpaceAPI # object using the key-word AccessToken. myToken = BSapi.getAccessToken() BSapi = BaseSpaceAPI(client_key, client_secret, BaseSpaceUrl, version, AppSessionId, AccessToken=myToken) print "\nA BaseSpaceAPI instance initialized with an access-token: " print BSapi
# Have the user visit the verification uri to grant us access
print("\nPlease visit the uri within 15 seconds and grant access")
print(deviceInfo['verification_with_code_uri'])
webbrowser.open_new(deviceInfo['verification_with_code_uri'])
time.sleep(15)
## PAUSE HERE
# Once the user has granted us access to objects we requested, we can
# get the basespace access token and start browsing simply by calling updatePriviliges
# on the baseSpaceApi instance.
code = deviceInfo['device_code']
myAPI.updatePrivileges(code)
# As a reference the provided access-token can be obtained from the BaseSpaceApi object
print("\nMy Access-token:")
print(myAPI.getAccessToken())
# Let's try and grab all available genomes with our new api!
allGenomes = myAPI.getAvailableGenomes()
print("\nGenomes \n" + str(allGenomes))
# If at a later stage we wish to initialize a BaseSpaceAPI object when we already have
# an access-token from a previous sessions, this may simply be done by initializing the BaseSpaceAPI
# object using the key-word AccessToken.
myToken = myAPI.getAccessToken()
myAPI.setAccessToken(myToken)
print("\nA BaseSpaceAPI instance was updated with an access-token: ")
print(myAPI)
#################### Web-based verification #################################
# The scenario where the authentication is done through a web-browser
# Have the user visit the verification uri to grant us access print "\nPlease visit the uri within 15 seconds and grant access" print deviceInfo['verification_with_code_uri'] webbrowser.open_new(deviceInfo['verification_with_code_uri']) time.sleep(15) ## PAUSE HERE # Once the user has granted us access to objects we requested, we can # get the basespace access token and start browsing simply by calling updatePriviliges # on the baseSpaceApi instance. code = deviceInfo['device_code'] myAPI.updatePrivileges(code) # As a reference the provided access-token can be obtained from the BaseSpaceApi object print "\nMy Access-token:" print myAPI.getAccessToken() # Let's try and grab all available genomes with our new api! allGenomes = myAPI.getAvailableGenomes() print "\nGenomes \n" + str(allGenomes) # If at a later stage we wish to initialize a BaseSpaceAPI object when we already have # an access-token from a previous sessions, this may simply be done by initializing the BaseSpaceAPI # object using the key-word AccessToken. myToken = myAPI.getAccessToken() myAPI.setAccessToken(myToken) print "\nA BaseSpaceAPI instance was updated with an access-token: " print myAPI
