def get_smi_and_parse(site_catalog_file):
"""Function to get the smi files from sftp server
The smi files are picked up according to the details in the site-catalog.xml
"""
if not os.path.exists(site_catalog_file):
raise GSMLogger().LogException(
"Error: site_catalog xml file not found at \
file not found at "
+ site_catalog_file
)
else:
catalog = open(site_catalog_file, "r")
site_data = etree.parse(site_catalog_file)
site_num = len(site_data.findall(".//site"))
gsmlogger.logger.info(str(site_num) + " total subject site entries read into tree.")
"""The reference site code is the current site on which
generate_subject_map.py is running.
As we need to get the only smi from the sftp to this site.
"""
for site in site_data.iter("site"):
site_name = site.findtext("site_name")
if site_name == "source":
host, port = gsm_lib.parse_host_and_port(site.findtext("site_URI"))
site_uname = site.findtext("site_uname")
site_password = site.findtext("site_password")
site_key_path = site.findtext("site_key_path")
site_contact_email = site.findtext("site_contact_email")
"""Pick up the smi file from the server and place it in the proj_root
"""
site_remotepath = site.findtext("site_remotepath")
file_name = site_remotepath.split("/")[-1]
site_localpath = configuration_directory + file_name
info = "Retrieving file: " + site_remotepath + " from " + host
print info
gsmlogger.logger.info(info)
info = "Errors will be reported to: " + site_contact_email
print info
gsmlogger.logger.info(info)
sftp_instance = SFTPClient(host, port, site_uname, site_password, site_key_path)
sftp_instance.get_file_from_uri(site_remotepath, site_localpath, site_contact_email)
catalog.close()
gsmlogger.logger.info("site catalog XML file closed.")
return site_localpath
def get_smi_and_parse(site_catalog_file, settings, logger):
'''Function to get the smi files from sftp server
The smi files are picked up according to the details in the site-catalog.xml
'''
dikt = gsm_lib.get_site_details_as_dict(site_catalog_file, 'data_source')
site_uri = dikt['site_URI']
host, port = gsm_lib.parse_host_and_port(site_uri)
site_uname = dikt['site_uname']
site_password = dikt['site_password']
site_remotepath = dikt['site_remotepath']
site_key_path = dikt['site_key_path']
site_contact_email = dikt['site_contact_email']
file_name = os.path.basename(site_remotepath)
site_localpath = os.path.join(configuration_directory, file_name)
# Pick up the smi file from the server and place it in the proj_root
logger.info('Retrieving file: %s from %s:%s', site_remotepath, host, port)
logger.info('Errors will be reported to: ' + site_contact_email)
email_props_sftp = EmailProps(
settings.smtp_host,
settings.smtp_port,
settings.sender_email,
[site_contact_email],
[],
'Research Subject Mapper Notification')
sftp_instance = SFTPClient(
host,
port,
site_uname,
site_password,
site_key_path)
sftp_instance.get_file_from_uri(site_remotepath, site_localpath, email_props_sftp)
return site_localpath
