def __init__(self, config):
self.cwd = os.getcwd()
self.countries = config['countries'].split(',')
self.session = MolgenisConnector(config['target_server'], config['target_account'],
config['target_password']).session
model_maker = BbmriEricCountryModelMaker(self.countries, self.cwd)
os.chdir('data_model/countries')
model_maker.create_country_directories()
model_maker.create_meta_data_for_countries()
def main():
config = ConfigParser().config
molgenis_connector = MolgenisConnector(config['url'], config['account'],
config['password'])
qc = QualityChecker(molgenis_connector)
qc.check_collection_data()
qc.check_biobank_data()
qc.check_network_data()
qc.check_person_data()
qc.logs.close()
qc.breaking_logs.close()
pprint.pprint(qc.breaking_errors)
molgenis_connector.logout()
def __init__(self, config):
self.diseaseCorrections = ""
self.filter_rows = ""
self.collections = ""
self.biobanks = ""
self.networks = ""
self.persons = ""
self.server = config['target_server']
self.username = config['target_account']
self.password = config['target_password']
url = config['url']
molgenis_connector = MolgenisConnector(url, config['account'],
config['password'])
self.retrieve_data(molgenis_connector)
self.retrieve_country_data(config, molgenis_connector)
def upload_data(self, entity, entities, url, user, pwd):
new_server = MolgenisConnector(url, user, pwd)
print('Uploading {}...'.format(entity))
status = new_server.session.add_all(entity, entities)
class BbmriEricModelUploader():
def __init__(self, config):
self.cwd = os.getcwd()
self.countries = config['countries'].split(',')
self.session = MolgenisConnector(config['target_server'], config['target_account'],
config['target_password']).session
model_maker = BbmriEricCountryModelMaker(self.countries, self.cwd)
os.chdir('data_model/countries')
model_maker.create_country_directories()
model_maker.create_meta_data_for_countries()
def upload_all_countries(self):
for country in self.countries:
self.upload_country(country)
def upload_country(self, country):
response = self.session.upload_zip('{}/{}.zip'.format(country, country))
self.check_import_run(response, country)
def check_import_run(self, response, name):
response = response.split('/')
runEntityType = response[-2]
runId = response[-1]
statusInfo = self.session.getById(runEntityType, runId)
count = 1
print("\r{} uploading{}".format(name, count * "."), end='')
while statusInfo['status'] == 'RUNNING':
count += 1
print("\r{} uploading{}".format(name, count * "."), end='')
statusInfo = self.session.getById(runEntityType, runId)
if statusInfo["status"] == "FINISHED":
print("{} uploaded".format(name))
return "FINISHED"
if statusInfo["status"] == "FAILED":
print(statusInfo)
print("Failed: ", statusInfo['message'])
return "FAILED"
def upload_all(self):
zipFileName = self.cwd + '/data_model/meta_data.zip'
meta_data = zipfile.ZipFile(zipFileName, 'w')
packages = self.cwd + '/data_model/packages.csv'
attributes = self.cwd + '/data_model/attributes.csv'
entities = self.cwd + '/data_model/entities.csv'
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_age_units.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_biobank_size.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_body_parts.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_capabilities.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_countries.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_collection_types.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_data_types.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_disease_types.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_image_data_types.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_imaging_modality.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_lab_standards.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_material_types.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_ops_standards.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_sex_types.csv')
meta_data.write(self.cwd + '/data_model/eu_bbmri_eric_temp_types.csv')
meta_data.write(packages)
meta_data.write(attributes)
meta_data.write(entities)
meta_data.close()
response = self.session.upload_zip(zipFileName)
status = self.check_import_run(response, "general meta data")
if status == "FINISHED":
self.upload_all_countries()