def test_generate_metadata_files(self):
debug = True
live = LiveEBISRARestServices(self.study_id, self.web_app_user_id, self.root_dir, debug)
live.host_name = ''
#live.generate_metadata_files(debug = True, action_type = 'VALIDATE')
live.generate_metadata_files(debug = True, action_type = 'ADD')
#live.generate_metadata_files(debug = True, action_type = 'MODIFY')
#live.submit_files(debug = True)
pass
def main():
option_parser, opts, args = parse_command_line_parameters(**script_info)
# Some needed variables
study_id = opts.study_id
debug = opts.debug
action = opts.action
web_app_user_id = 12169
root_dir = '/home/wwwuser/user_data/studies'
study_dir = root_dir + '/study_{0}'.format(str(study_id))
ebi_export_log_fp = join(study_dir, 'ebi_export_log.txt')
curl_output_fp = join(study_dir, 'curl_output.xml')
curl_command_fp = join(study_dir, 'ebi_curl_command_{0}.sh'.format(study_id))
# Get the live EBI function reference
live = LiveEBISRARestServices(study_id, web_app_user_id, root_dir, debug)
live.host_name = ''
# Make one pass through metadata to generate files to validate. Also
# necessary to populate the list of sequence files to send.
live.generate_metadata_files(debug = True, action_type = 'VALIDATE')
if len(live.errors):
print 'Errors found while generating metadata files. Aborting. Errors are:'
for error in live.errors:
print 'Error: {0}'.format(error)
return
# Send the sequence files first - required for metadata to validate. If files have already been
# sent then skip this step.
data_access = data_access_factory(ServerConfig.data_access_type)
statement = 'select case when ebi_files_sent is null then 0 else ebi_files_sent end as ebi_files_sent from study where study_id = {0}'.format(study_id)
ebi_files_sent = data_access.dynamicMetadataSelect(statement).fetchone()[0]
if ebi_files_sent != 1:
try:
live.submit_files(debug = True)
except Exception, e:
print 'Error encountered while submitting files. Aborting. Error was:'
print str(e)
return
