def parse_site_details_and_send(site_catalog_file, subject_map_input, logger, settings, keep_files):
"""
Parses the site details from site catalog
Note: uses files generated by `write_element_tree_to_file` in the main
function.
"""
try:
site_data = etree.parse(site_catalog_file)
except IOError:
logger.exception("Could not open Site Catalog file: '%s'. "
"Check 'site_catalog' in your settings file.",
site_catalog_file)
raise
logger.info("Processing site details and uploading subject map input files")
site_num = len(site_data.findall(".//site"))
logger.debug("%s total subject site entries read into tree.", site_num)
for site in site_data.iter('site'):
site_code = site.findtext('site_code')
logger.debug("Processing site '%s'.", site_code)
if site_code not in subject_map_input.keys():
logger.warning('Site code "%s" defined in Site Catalog, but no '
'records found for that site.', site_code)
continue
host, port = gsm_lib.parse_host_and_port(site.findtext('site_URI'))
logger.debug("Server: %s:%s", host, port)
site_uname = site.findtext('site_uname')
logger.debug("Username: %s", site_uname)
site_key_path = site.findtext('site_key_path')
site_password = site.findtext('site_password')
site_contact_email = site.findtext('site_contact_email')
logger.debug("Site Contact Email: %s", site_contact_email)
# Pick up the correct smi file with the code and place in the
# destination as smi.xml at the specified remote path
site_remotepath = site.findtext('site_remotepath')
site_localpath = subject_map_input[site_code]
logger.info('Sending %s to %s: %s', site_localpath, host, site_remotepath)
logger.debug('Any errors will be emailed 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,
private_key = site_key_path)
sftp_instance.send_file_to_uri(
site_remotepath,
'smi.xml',
site_localpath,
email_props_sftp)
if keep_files:
logger.debug('Keeping the temporary file: ' + site_localpath)
else:
# remove the smi.xml from the folder
logger.debug('Removing the temporary file: ' + site_localpath)
try:
os.remove(site_localpath)
except OSError as error:
logger.warning(error)
def parse_site_details_and_send(site_catalog_file, local_file_path, action, settings, logger):
if not os.path.exists(local_file_path):
logging.error("subject map file " + local_file_path + " file not found")
raise IOError("subject map file " + local_file_path + " file not found")
dikt = gsm_lib.get_site_details_as_dict(site_catalog_file, 'data_destination')
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']
sender_email = settings.sender_email
# is it a file transfer or attachment email?
if action == 'sftp':
# Pick up the subject_map.csv and put it in the specified sftp server's remote path
info = '\nSending file: [ %s] to host %s:%s %s' % (local_file_path, host, port, site_remotepath)
logger.info(info)
info = 'Errors will be reported to: ' + site_contact_email
logger.info(info)
# put the subject map csv file
remote_directory = os.path.dirname(site_remotepath)
remote_file_name = os.path.basename(site_remotepath)
sftp_instance = SFTPClient(host,
port,
site_uname,
site_password,
site_key_path)
email_props_sftp = EmailProps(
settings.smtp_host,
settings.smtp_port,
settings.sender_email,
[site_contact_email],
[],
'Research Subject Mapper Notification')
sftp_instance.send_file_to_uri(
remote_directory,
remote_file_name,
local_file_path,
email_props_sftp)
elif action == 'email':
# Send the subject_map_exceptions.csv to the contact email address as an attachment
info = '\nSending file: [ %s ] as email attachement to: %s' % (local_file_path, site_contact_email)
logger.info(info)
mail_body = 'Hi, \n this mail contains attached exceptions.csv file.'
props = EmailProps(
settings.smtp_host,
settings.smtp_port,
settings.sender_email,
[site_contact_email],
[],
'Research Subject Mapper Notification',
mail_body,
[local_file_path])
EmailSender().send(props)
else:
info = 'Invalid option. Either sftp/email should be used.'
logger.warn(info)
return
def parse_site_details_and_send(site_catalog_file, smi_filenames, smi_ids, gsmlogger):
for smi_file_name in smi_filenames:
if not os.path.exists(smi_file_name):
raise GSMLogger().LogException("Error: smi file "+smi_file_name+" not found")
if not os.path.exists(site_catalog_file):
raise GSMLogger().LogException("Error: site_catalog xml file not found at "
+ site_catalog_file)
r2
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.")
for site in site_data.iter('site'):
site_code = site.findtext('site_code')
if site_code in smi_ids:
host, port = gsm_lib.parse_host_and_port(site.findtext('site_URI'))
site_uname = site.findtext('site_uname')
site_key_path = site.findtext('site_key_path')
site_password = site.findtext('site_password')
site_contact_email = site.findtext('site_contact_email')
'''Pick up the correct smi file with the code and place in the destination
as smi.xml at the specified remote path
'''
file_name = 'smi'+site_code+'.xml'
site_remotepath = site.findtext('site_remotepath')
site_localpath = tmp_folder + file_name
info = '\nSending '+site_localpath+' to '+host+':'+site_remotepath
print info
gsmlogger.logger.info(info)
info = 'Any error will be reported to '+site_contact_email
print info
gsmlogger.logger.info(info)
sftp_instance = SFTPClient(host, port, site_uname, site_password,
private_key=site_key_path)
sftp_instance.send_file_to_uri(site_remotepath, 'smi.xml',
site_localpath, site_contact_email)
if do_keep_gen_files:
print ' * Keeping the temporary file: ' + site_localpath
else :
# remove the smi.xml from the folder
try:
print ' * Removing the temporary file: ' + site_localpath
os.remove(site_localpath)
except OSError:
pass
else:
print 'Site code '+site_code+' does not exist'
gsmlogger.logger.info('Site code does not exist')
catalog.close()
gsmlogger.logger.info("site catalog XML file closed.")
pass
def parse_site_details_and_send(site_catalog_file, subject_map_input, logger,
settings, keep_files):
"""
Parses the site details from site catalog
Note: uses files generated by `write_element_tree_to_file` in the main
function.
"""
try:
site_data = etree.parse(site_catalog_file)
except IOError:
logger.exception(
"Could not open Site Catalog file: '%s'. "
"Check 'site_catalog' in your settings file.", site_catalog_file)
raise
logger.info(
"Processing site details and uploading subject map input files")
site_num = len(site_data.findall(".//site"))
logger.debug("%s total subject site entries read into tree.", site_num)
for site in site_data.iter('site'):
site_code = site.findtext('site_code')
logger.debug("Processing site '%s'.", site_code)
if site_code not in subject_map_input.keys():
logger.warning(
'Site code "%s" defined in Site Catalog, but no '
'records found for that site.', site_code)
continue
host, port = gsm_lib.parse_host_and_port(site.findtext('site_URI'))
logger.debug("Server: %s:%s", host, port)
site_uname = site.findtext('site_uname')
logger.debug("Username: %s", site_uname)
site_key_path = site.findtext('site_key_path')
site_password = site.findtext('site_password')
site_contact_email = site.findtext('site_contact_email')
logger.debug("Site Contact Email: %s", site_contact_email)
# Pick up the correct smi file with the code and place in the
# destination as smi.xml at the specified remote path
site_remotepath = site.findtext('site_remotepath')
site_localpath = subject_map_input[site_code]
logger.info('Sending %s to %s: %s', site_localpath, host,
site_remotepath)
logger.debug('Any errors will be emailed 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,
private_key=site_key_path)
sftp_instance.send_file_to_uri(site_remotepath, 'smi.xml',
site_localpath, email_props_sftp)
if keep_files:
logger.debug('Keeping the temporary file: ' + site_localpath)
else:
# remove the smi.xml from the folder
logger.debug('Removing the temporary file: ' + site_localpath)
try:
os.remove(site_localpath)
except OSError as error:
logger.warning(error)
def parse_site_details_and_send(site_catalog_file, local_file_path, action):
if not os.path.exists(local_file_path):
raise GSMLogger().LogException("Error: subject map file " + local_file_path + " file not found")
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.")
for site in site_data.iter("site"):
site_name = site.findtext("site_name")
if site_name == "destination":
host, port = gsm_lib.parse_host_and_port(site.findtext("site_URI"))
subjectmap_uname = site.findtext("site_uname")
subjectmap_password = site.findtext("site_password")
subjectmap_key_path = site.findtext("site_key_path")
subjectmap_contact_email = site.findtext("site_contact_email")
# is it a file transfer or attachment email?
if action == "sftp":
"""Pick up the subject_map.csv and put it in the specified
sftp server's remote path
"""
# remote path to send the file to
subjectmap_remotepath = site.findtext("site_remotepath")
info = "\nSending file [" + local_file_path + "] to " + host + ":" + subjectmap_remotepath
print info
gsmlogger.logger.info(info)
info = "Errors will be reported to: " + subjectmap_contact_email
print info
gsmlogger.logger.info(info)
# put the subject map csv file
subjectmap_remote_directory = subjectmap_remotepath.rsplit("/", 1)[0] + "/"
remote_file_name = subjectmap_remotepath.split("/")[-1]
sftp_instance = SFTPClient(host, port, subjectmap_uname, subjectmap_password, subjectmap_key_path)
sftp_instance.send_file_to_uri(
subjectmap_remote_directory, remote_file_name, local_file_path, subjectmap_contact_email
)
elif action == "email":
"""Send the subject_map_exceptions.csv to the contact
email address as an attachment
"""
print "\nSending file: [" + local_file_path + "] as email attachement to " + subjectmap_contact_email
gsmlogger.logger.info(
"Sending %s as email attachement to %s", local_file_path, subjectmap_contact_email
)
# TODO change the mail body as required
mail_body = "Hi, \n this mail contains attached exceptions.csv file."
email_transactions().send_mail(
setup["sender_email"], subjectmap_contact_email, mail_body, [local_file_path]
)
else:
print "Invalid option. either sftp/email should be used"
gsmlogger.logger.info("Invalid option. either sftp/email should be used")
catalog.close()
pass