def main():
args = cli.parse_args()
settings = args.settings
days_till_expiration = int(settings['days.tillexpiration'])
days_till_notify = int(settings['days.tillnotify'])
try:
results = sync_redcap.get_cts_results(settings)
if not args.dry:
Session.add_all(results)
Session.commit()
else:
log.info('Dry run, not commiting changes')
sync_site_codes = settings.get('site.codes').split()
ucsd_site_codes = settings.get('ucsd.site.codes').split()
emory_site_codes = settings.get('emory.site.codes').split()
gwu_site_codes = settings.get('gwu.site.codes').split()
rcs = json.loads(open(settings['redcap_json'], 'r').read())
redcap = RCProject(sync_site_codes, rcs)
# Refresh results
for site_code in sync_site_codes:
print 'site code'
print site_code
for type_ in models.TYPES:
#notify = settings.get('notify.%s.%s' % (site_code.lower(), type_.lower()), '').split()
notify = []
print type_
pnt = list(
r for r in results
if r.check(type_) is True and r.site_code == site_code)
neg = [
r for r in results
if r.check(type_) is False and r.site_code == site_code
]
odd = [
r for r in results
if r.check(type_) is None and r.site_code == site_code
]
if not (pnt):
continue
'clear'
if type_ == 'dhiv':
notify = get_receipients(redcap, 'hiv_pos', site_code,
ucsd_site_codes, emory_site_codes,
gwu_site_codes)
t_type = 'HIV'
elif type_ == 'dhcv':
notify = get_receipients(redcap, 'hcv_pos', site_code,
ucsd_site_codes, emory_site_codes,
gwu_site_codes)
t_type = 'HCV'
elif type_ == 'dhbv':
notify = get_receipients(redcap, 'hbv_pos', site_code,
ucsd_site_codes, emory_site_codes,
gwu_site_codes)
t_type = 'HBV'
print notify
if not notify:
continue
turbomail.send(
turbomail.Message(
to=notify,
subject='New %s+ NAT' % t_type,
plain=lookup.get_template('email/parse.mako').render(
**{
'timestamp': datetime.datetime.now(),
'type_': t_type,
'site_code': site_code,
'pnt': pnt,
'neg': neg,
'odd': odd
})))
log.info('Notified %s mailing lists of results for "%s"' %
(site_code, type_))
for code in sync_site_codes:
results_count = 0
shouldNotify = False
# Get number of site specific results in this upload
for r in results:
if r.site_code == code.upper():
results_count += 1
# Get list of results with missing draw dates
missing_draw = find_missing_draw(days_till_expiration, code)
missing_draw_count = len(missing_draw)
# Get list of draw dates with missing Red Cross results that are more than 7 days old
missing_results = find_missing_results(days_till_notify,
days_till_expiration,
redcap, code)
missing_results_count = len(missing_results)
# Notify recipients if there is anything to notify about
if results_count > 0 or missing_results_count > 0 or missing_draw_count > 0:
shouldNotify = True
if shouldNotify:
#notify = settings.get('notify.%s.sync' % code.lower()).split()
notify = get_receipients(redcap, 'date_missing', code,
ucsd_site_codes, emory_site_codes,
gwu_site_codes)
# Notify appropriate people about missing draw dates and Red Cross results
turbomail.send(
turbomail.Message(
to=notify,
subject=
'[The Early Test]: Red Cross Synchronize Report (%s)' %
code,
plain=lookup.get_template('email/sync.mako').render(
**{
'timestamp': datetime.datetime.now(),
'results_count': results_count,
'missing_draw_count': missing_draw_count,
'missing_draw': missing_draw,
'missing_results_count': missing_results_count,
'missing_results': missing_results,
'days_till_notify': days_till_notify,
'code': code
})))
log.info(
'Notified mailing lists of %s for missing draw dates' %
(code))
log.info(
'Notified mailing lists of %s diagnostic for missing Red Cross results'
% (code))
except:
# If an unexpected error occurs, let the developers know
turbomail.send(
turbomail.Message(
to=settings['notify.error'].split(),
subject='[The Early Test]: Parser failed execution',
plain=traceback.format_exc()))
raise
def main():
args = cli.parse_args()
settings = args.settings
days_till_expiration = int(settings['days.tillexpiration'])
days_till_notify = int(settings['days.tillnotify'])
try:
log.info('Called on %s' % args.srcfile)
results, duplicates = parser.parse(args.srcfile, settings)
if not args.dry:
if duplicates:
raise Exception('\n'.join(
['Already exists: %s%s' % (r.site_code, r.reference_number)
for r in duplicates]))
# Archive processed file
shutil.move(args.srcfile, settings['dir.raw'])
log.info('Moved encrypted file to %s' % settings['dir.raw'])
# Commit all changes now that we've successfully processed the file
map(lambda r: setattr(r, 'file', os.path.basename(args.srcfile)), results)
Session.add_all(results)
Session.commit()
else:
log.info('Dry run, not commiting changes')
sync_site_codes = settings.get('site.codes').split()
rcs = json.loads(open(settings['redcap_json'], 'r').read())
redcap = RCProject(sync_site_codes, rcs)
# Refresh results
for site_code in sync_site_codes:
for type_ in models.TYPES:
notify = settings.get('notify.%s.%s' % (site_code.lower(), type_.lower()), '').split()
if not notify:
continue
pnt = [r for r in results if r.check(type_) is True and r.site_code == site_code]
neg = [r for r in results if r.check(type_) is False and r.site_code == site_code]
odd = [r for r in results if r.check(type_) is None and r.site_code == site_code]
if not (pnt or odd):
continue
turbomail.send(turbomail.Message(
to=notify,
subject='[The Early Test]: New Records Notification (%s)' % type_,
plain=lookup.get_template('email/parse.mako').render(**{
'timestamp': datetime.datetime.now(),
'type_': type_,
'site_code': site_code,
'pnt': pnt,
'neg': neg,
'odd': odd})))
log.info('Notified %s mailing lists of results for "%s"' % (site_code, type_))
for code in sync_site_codes:
results_count = 0
shouldNotify = False
# Get number of site specific results in this upload
for r in results:
if r.site_code == code.upper():
results_count += 1
# Get list of results with missing draw dates
missing_draw = find_missing_draw(days_till_expiration, code)
missing_draw_count = len(missing_draw)
# Get list of draw dates with missing Red Cross results that are more than 7 days old
missing_results = find_missing_results(days_till_notify, days_till_expiration, redcap, code)
missing_results_count = len(missing_results)
# Notify recipients if there is anything to notify about
if results_count > 0 or missing_results_count > 0 or missing_draw_count > 0:
shouldNotify = True
if shouldNotify:
notify = settings.get('notify.%s.sync' % code.lower()).split()
# Notify appropriate people about missing draw dates and Red Cross results
turbomail.send(turbomail.Message(
to=notify,
subject='[The Early Test]: Red Cross Synchronize Report (%s)' % code,
plain=lookup.get_template('email/sync.mako').render(**{
'timestamp': datetime.datetime.now(),
'results_count': results_count,
'missing_draw_count': missing_draw_count,
'missing_draw': missing_draw,
'missing_results_count': missing_results_count,
'missing_results': missing_results,
'days_till_notify': days_till_notify,
'code': code})))
log.info('Notified mailing lists of %s for missing draw dates' % (code))
log.info('Notified mailing lists of %s diagnostic for missing Red Cross results' % (code))
except:
# If an unexpected error occurs, let the developers know
turbomail.send(turbomail.Message(
to=settings['notify.error'].split(),
subject='[The Early Test]: Parser failed execution',
plain=traceback.format_exc()))
raise