def _sample_overview_renderer(self):
barcode = self.get_argument('barcode', None)
if barcode is None:
self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
return
has_access = ag_data.check_access(self.current_user, barcode)
if not has_access:
self.set_status(403)
self.render("403.html", skid=self.current_user)
return
sample_data = ag_data.getAGBarcodeDetails(barcode)
if not sample_data:
self.set_status(404)
self.render("404.html", skid=self.current_user)
return
web_barcode_pdf, web_barcode_txt = _get_data_path(barcode)
unidentified_results = _get_per_sample_results(barcode)
per_sample_data = _get_per_sample_data(barcode)
sample_time = sample_data['sample_time']
sample_date = sample_data['sample_date']
status = sample_data['status']
if status is None:
bgcolor = '#FFF'
status = 'Submitted'
elif status == 'Received':
bgcolor = '#AFA'
else:
bgcolor = '#FFF'
sample_origin = sample_data['site_sampled']
if sample_origin is None:
sample_origin = sample_data['environment_sampled']
notes = sample_data['notes']
if notes is None:
notes = ''
self.render('sample_overview.html', skid=self.current_user,
barcode_pdf=web_barcode_pdf, barcode_txt=web_barcode_txt,
bgcolor=bgcolor, status=status, barcode=barcode,
sample_origin=sample_origin, sample_date=sample_date,
sample_time=sample_time, notes=notes,
unidentified_results=unidentified_results,
per_sample_data=per_sample_data)
def _sample_overview_renderer(self):
barcode = self.get_argument('barcode', None)
if barcode is None:
self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
return
sample_data = ag_data.getAGBarcodeDetails(barcode)
fs_base = AMGUT_CONFIG.base_data_dir
web_base = "%s/results" % media_locale['SITEBASE']
fs_barcode_pdf = _format_data_path(fs_base, 'pdfs', barcode, 'pdf')
fs_barcode_txt = _format_data_path(fs_base, 'taxa-summaries', barcode,
'txt')
web_barcode_pdf = _format_data_path(web_base, 'pdfs', barcode, 'pdf')
web_barcode_txt = _format_data_path(web_base, 'taxa-summaries',
barcode, 'txt')
if not os.path.exists(fs_barcode_pdf):
web_barcode_pdf = None
if not os.path.exists(fs_barcode_txt):
web_barcode_txt = None
sample_time = sample_data['sample_time']
sample_date = sample_data['sample_date']
status = sample_data['status']
if status is None:
bgcolor = '#FFF'
status = 'Submitted'
elif status == 'Received':
bgcolor = '#AFA'
else:
bgcolor = '#FFF'
sample_origin = sample_data['site_sampled']
if sample_origin is None:
sample_origin = sample_data['environment_sampled']
notes = sample_data['notes']
if notes is None:
notes = ''
self.render('sample_overview.html', skid=self.current_user,
barcode_pdf=web_barcode_pdf, barcode_txt=web_barcode_txt,
bgcolor=bgcolor, status=status, barcode=barcode,
sample_origin=sample_origin, sample_date=sample_date,
sample_time=sample_time, notes=notes)
def test_post_general(self):
self.mock_login(
ag_data.ut_get_supplied_kit_id(
'd8592c74-9694-2135-e040-8a80115d6401'))
# make sure barcode properly removed
self.assertIn(
'000005628',
ag_data.getAvailableBarcodes(
'd8592c74-9694-2135-e040-8a80115d6401'))
# Run test
response = self.post(
'/authed/add_sample_general/', {
'participant_name': 'environmental',
'barcode': '000005628',
'sample_site': 'Biofilm',
'sample_date': '12/11/2014',
'sample_time': '10:12 PM',
'notes': 'TESTING TORNADO LOGGING GENERAL'
})
self.assertEqual(response.code, 200)
self.assertTrue(response.effective_url.endswith('/authed/portal/'))
obs = ag_data.getAGBarcodeDetails('000005628')
exp = {
'status': '',
'ag_kit_barcode_id': 'db447092-620e-54d8-e040-8a80115d3637',
'ag_kit_id': 'db447092-6209-54d8-e040-8a80115d3637',
'barcode': '000005628',
'site_sampled': None,
'environment_sampled': 'Biofilm',
'sample_date': datetime.date(2014, 12, 11),
'sample_time': datetime.time(22, 12),
'notes': 'TESTING TORNADO LOGGING GENERAL',
'overloaded': None,
'withdrawn': None,
'other': None,
'moldy': None,
'refunded': None,
'date_of_last_email': None
}
# only look at those fields, that are not subject to scrubbing
self.assertEqual({k: obs[k] for k in exp}, exp)
def test_post_general(self):
self.mock_login('tst_LbxUH')
# make sure barcode properly removed
self.assertIn('000005628', ag_data.getAvailableBarcodes(
'd8592c74-9694-2135-e040-8a80115d6401'))
# Run test
response = self.post('/authed/add_sample_general/',
{'participant_name': 'environmental',
'barcode': '000005628',
'sample_site': 'Biofilm',
'sample_date': '12/11/2014',
'sample_time': '10:12 PM',
'notes': 'TESTING TORNADO LOGGING GENERAL'})
self.assertEqual(response.code, 200)
self.assertTrue(
response.effective_url.endswith('/authed/portal/'))
obs = ag_data.getAGBarcodeDetails('000005628')
exp = {
'status': None,
'ag_kit_barcode_id': 'db447092-620e-54d8-e040-8a80115d3637',
'ag_kit_id': 'db447092-6209-54d8-e040-8a80115d3637',
'barcode': '000005628',
'site_sampled': None,
'environment_sampled': 'Biofilm',
'name': 'REMOVED',
'sample_date': datetime.date(2014, 12, 11),
'sample_time': datetime.time(22, 12),
'notes': 'TESTING TORNADO LOGGING GENERAL',
'overloaded': None,
'withdrawn': None,
'email': 'REMOVED',
'other': None,
'moldy': None,
'participant_name': None,
'refunded': None,
'date_of_last_email': None,
'other_text': 'REMOVED'
}
self.assertDictEqual(obs, exp)
def test_post_human(self):
ag_login_id = 'd8592c74-9694-2135-e040-8a80115d6401'
self.mock_login(ag_data.ut_get_supplied_kit_id(ag_login_id))
# make sure barcode properly removed
self.assertIn('000005628', ag_data.getAvailableBarcodes(ag_login_id))
# Run test
names = ag_data.ut_get_participant_names_from_ag_login_id(ag_login_id)
response = self.post('/authed/add_sample_human/',
{'participant_name': names[0],
'barcode': '000005628',
'sample_site': 'Stool',
'sample_date': '12/13/2014',
'sample_time': '11:12 PM',
'notes': 'TESTING TORNADO LOGGING HUMAN'})
self.assertEqual(response.code, 200)
self.assertTrue(
response.effective_url.endswith('/authed/portal/'))
obs = ag_data.getAGBarcodeDetails('000005628')
exp = {
'status': '',
'ag_kit_barcode_id': 'db447092-620e-54d8-e040-8a80115d3637',
'ag_kit_id': 'db447092-6209-54d8-e040-8a80115d3637',
'barcode': '000005628',
'site_sampled': 'Stool',
'environment_sampled': None,
'sample_date': datetime.date(2014, 12, 13),
'sample_time': datetime.time(23, 12),
'notes': 'TESTING TORNADO LOGGING HUMAN',
'overloaded': None,
'withdrawn': None,
'other': None,
'moldy': None,
'refunded': None,
'date_of_last_email': None,
}
# only look at those fields, that are not subject to scrubbing
self.assertEqual({k: obs[k] for k in exp}, exp)
def _sample_overview_renderer(self):
barcode = self.get_argument('barcode', None)
if barcode is None:
self.redirect(media_locale['SITEBASE'] + '/authed/portal/')
return
has_access = ag_data.check_access(self.current_user, barcode)
if not has_access:
self.set_status(403)
self.render("403.html", skid=self.current_user)
return
sample_data = ag_data.getAGBarcodeDetails(barcode)
if not sample_data:
self.set_status(404)
self.render("404.html", skid=self.current_user)
return
web_barcode_pdf, web_barcode_txt = _get_data_path(barcode)
sequence_url = None
biomv1_url = None
classic_url = None
sequence_url = None
api_base = 'http://api.microbio.me/americangut/1/'
req = requests.get(api_base + 'sample/%s' % barcode)
if req.status_code == 200 and req.content != "(null)":
bc_with_suf = json.loads(req.content)[0]
biomv1_url = api_base + 'otu/%s/json' % bc_with_suf
classic_url = api_base + 'otu/%s/txt' % bc_with_suf
seq_req = requests.get(api_base + 'sequence/%s' % bc_with_suf)
if seq_req.status_code == 200:
sequence_url = json.loads(seq_req.content)[0]['fastq_url']
sample_time = sample_data['sample_time']
sample_date = sample_data['sample_date']
status = sample_data['status']
if status is None:
bgcolor = '#FFF'
status = 'Submitted'
elif status == 'Received':
bgcolor = '#AFA'
else:
bgcolor = '#FFF'
sample_origin = sample_data['site_sampled']
if sample_origin is None:
sample_origin = sample_data['environment_sampled']
notes = sample_data['notes']
if notes is None:
notes = ''
self.render('sample_overview.html', skid=self.current_user,
barcode_pdf=web_barcode_pdf, barcode_txt=web_barcode_txt,
bgcolor=bgcolor, status=status, barcode=barcode,
sample_origin=sample_origin, sample_date=sample_date,
sample_time=sample_time, notes=notes,
sequence_url=sequence_url, biomv1_url=biomv1_url,
classic_url=classic_url)
