def test_process_project_data_and_account(self):
fa=Find_and_register_new_project_data(projet_info_path=os.path.join('.','data/check_project_data'),\
dbconfig=self.dbconfig,\
user_account_template='template/email_notification/send_new_account_info.txt',\
log_slack=False,\
setup_irods=False,\
notify_user=False,\
check_hpc_user=False,\
)
fa.process_project_data_and_account()
dbparam = None
with open(self.dbconfig, 'r') as json_data:
dbparam = json.load(json_data)
base = BaseAdaptor(**dbparam)
base.start_session()
pa=ProjectAdaptor(**{'session':base.session})
project_exists=pa.check_project_records_igf_id(project_igf_id='IGFP0002_test_23-5-2017_rna')
self.assertTrue(project_exists)
ua=UserAdaptor(**{'session':base.session})
user_exists=ua.check_user_records_email_id(email_id='*****@*****.**')
self.assertTrue(user_exists)
user1=ua.fetch_user_records_email_id(user_email_id='*****@*****.**')
self.assertEqual(user1.name,'User2')
sa=SampleAdaptor(**{'session':base.session})
sample_exists=sa.check_sample_records_igf_id(sample_igf_id='IGF00006')
self.assertTrue(sample_exists)
project_user_exists=pa.check_existing_project_user(project_igf_id='IGFP0002_test_23-5-2017_rna',\
email_id='*****@*****.**')
self.assertTrue(project_user_exists)
project_user_exists=pa.check_existing_project_user(project_igf_id='IGFP0002_test_23-5-2017_rna',\
email_id='*****@*****.**')
self.assertTrue(project_user_exists)
base.close_session()
def _check_existing_data(self,
data,
dbsession,
table_name,
check_column='EXISTS'):
'''
An internal function for checking and registering project info
:param data: A pandas data series
:param dbsession: A sqlalchemy database session object
:param table_name: A database table name
:param check_column: Column name for existing data
'''
try:
if not isinstance(data, pd.Series):
raise ValueError('Expecting a data series and got {0}'.format(
type(data)))
if table_name == 'project':
if self.project_lookup_column in data and \
not pd.isnull(data[self.project_lookup_column]):
project_igf_id = data[self.project_lookup_column]
pa = ProjectAdaptor(**{'session': dbsession
}) # connect to project adaptor
project_exists = pa.check_project_records_igf_id(
project_igf_id)
if project_exists: # store data only if project is not existing
data[check_column] = True
else:
data[check_column] = False
return data
else:
raise ValueError('Missing or empty required column {0}'.\
format(self.project_lookup_column))
elif table_name == 'user':
if self.user_lookup_column in data and \
not pd.isnull(data[self.user_lookup_column]):
user_email = data[self.user_lookup_column]
ua = UserAdaptor(**{'session':
dbsession}) # connect to user adaptor
user_exists = ua.check_user_records_email_id(
email_id=user_email)
if user_exists: # store data only if user is not existing
data[check_column] = True
else:
data[check_column] = False
return data
else:
raise ValueError('Missing or empty required column {0}'.\
format(self.user_lookup_column))
elif table_name == 'sample':
if self.sample_lookup_column in data and \
not pd.isnull(data[self.sample_lookup_column]):
project_igf_id = data[self.project_lookup_column]
sample_igf_id = data[self.sample_lookup_column]
sa = SampleAdaptor(**{'session': dbsession
}) # connect to sample adaptor
sample_project_exists=sa.check_project_and_sample(project_igf_id=project_igf_id,\
sample_igf_id=sample_igf_id) # check for existing sample_id and project-id combination
if sample_project_exists: # store data only if sample is not existing
data[check_column] = True
else:
sample_exists = sa.check_sample_records_igf_id(
sample_igf_id) # check for existing sample
if sample_exists:
raise ValueError('Sample {0} exists in database but not associated with project {1}'.\
format(sample_igf_id,project_igf_id)) # inconsistency in sample project combination
data[check_column] = False
return data
else:
raise ValueError('Missing or empty required column {0}'.\
format(self.sample_lookup_column))
elif table_name == 'project_user':
if self.user_lookup_column in data and \
not pd.isnull(data[self.user_lookup_column]) and \
self.project_lookup_column in data and \
not pd.isnull(data[self.project_lookup_column]):
project_igf_id = data[self.project_lookup_column]
user_email = data[self.user_lookup_column]
pa = ProjectAdaptor(**{'session': dbsession
}) # connect to project adaptor
project_user_exists=pa.check_existing_project_user(project_igf_id,\
email_id=user_email)
if user_email != self.default_user_email and \
(self.data_authority_column not in data or \
pd.isnull(data[self.data_authority_column])):
data[
self.
data_authority_column] = True # set user as data authority, filter default user
if project_user_exists: # store data only if sample is not existing
data[check_column] = True
else:
data[check_column] = False
return data
else:
raise ValueError('Missing or empty required column {0}, {1}'.\
format(self.project_lookup_column,\
self.user_lookup_column))
else:
raise ValueError('table {0} not supported'.format(table_name))
except:
raise