def test_post(self):
details = db.getAGBarcodeDetails('000004216')
payload = {
'barcode': '000004216',
'ag_kit_id': details['ag_kit_id'],
'site_sampled': details['site_sampled'],
'sample_date': details['sample_date'],
'sample_time': details['sample_time'],
'participant_name': details['participant_name'],
'notes': details['notes'],
'environment_sampled': details['environment_sampled'],
'refunded': details['refunded'] or 'N'
}
self.mock_login_admin()
# Missing a parameters ('withdrawn')
response = self.post('/ag_edit_barcode/', payload)
self.assertEqual(response.code, 400)
payload['withdrawn'] = details['withdrawn'] or 'N'
payload['notes'] = 'Some new notes'
response = self.post('/ag_edit_barcode/', payload)
self.assertEqual(response.code, 200)
self.assertIn("Barcode was updated successfully", response.body)
self.assertEqual(
db.getAGBarcodeDetails('000004216')['notes'], 'Some new notes')
payload['ag_kit_id'] = 'notInDB'
response = self.post('/ag_edit_barcode/', payload)
# TODO: think about returning a non-OK status code to better report
# this error, see issue #139
self.assertEqual(response.code, 200)
self.assertIn("Error Updating Barcode Info", response.body)
def test_edit_none_participant(self):
self.mock_login_admin()
barcode = '000023125' # current survey_id = "a4f1061f5bac9ae3"
details = db.getAGBarcodeDetails(barcode)
payload = {
'barcode': barcode,
'ag_kit_id': details['ag_kit_id'],
'site_sampled': details['site_sampled'],
'sample_date': details['sample_date'],
'sample_time': details['sample_time'],
'participant_name': details['participant_name'],
'notes': details['notes'],
'environment_sampled': details['environment_sampled'],
'refunded': details['refunded'] or 'N',
'withdrawn': details['withdrawn'] or 'N'
}
old_sourcename = payload['participant_name']
payload['participant_name'] = None
response = self.post('/ag_edit_barcode/', payload)
obs_details = db.getAGBarcodeDetails(barcode)
obs_surveys = db.get_barcode_survey(barcode)
# revert to old participant_name to leave a clean DB
payload['participant_name'] = old_sourcename
response = self.post('/ag_edit_barcode/', payload)
self.assertEqual(response.code, 200)
self.assertIsNone(obs_details['participant_name'])
self.assertIsNone(obs_surveys)
self.assertIsNotNone(db.get_barcode_survey(barcode))
def test_post(self):
details = db.getAGBarcodeDetails('000004216')
payload = {'barcode': '000004216',
'ag_kit_id': details['ag_kit_id'],
'site_sampled': details['site_sampled'],
'sample_date': details['sample_date'],
'sample_time': details['sample_time'],
'participant_name': details['participant_name'],
'notes': details['notes'],
'environment_sampled': details['environment_sampled'],
'refunded': details['refunded'] or 'N'}
self.mock_login_admin()
# Missing a parameters ('withdrawn')
response = self.post('/ag_edit_barcode/', payload)
self.assertEqual(response.code, 400)
payload['withdrawn'] = details['withdrawn'] or 'N'
payload['notes'] = 'Some new notes'
response = self.post('/ag_edit_barcode/', payload)
self.assertEqual(response.code, 200)
self.assertIn("Barcode was updated successfully", response.body)
self.assertEqual(db.getAGBarcodeDetails('000004216')['notes'],
'Some new notes')
payload['ag_kit_id'] = 'notInDB'
response = self.post('/ag_edit_barcode/', payload)
# TODO: think about returning a non-OK status code to better report
# this error, see issue #139
self.assertEqual(response.code, 200)
self.assertIn("Error Updating Barcode Info", response.body)
def test_getAGBarcodeDetails(self):
obs = db.getAGBarcodeDetails('000018046')
exp = {
'status': 'Received',
'ag_kit_id': '0060a301-e5c0-6a4e-e050-8a800c5d49b7',
'barcode': '000018046',
'environment_sampled': None,
# 'name': 'REMOVED',
'ag_kit_barcode_id': '0060a301-e5c1-6a4e-e050-8a800c5d49b7',
'sample_time': datetime.time(11, 15),
# 'notes': 'REMOVED',
'overloaded': 'N',
'withdrawn': None, # 'email': 'REMOVED',
'other': 'N',
# 'deposited': False,
# 'participant_name': 'REMOVED-0',
'refunded': None,
'moldy': 'N',
'sample_date': datetime.date(2014, 8, 13),
'date_of_last_email': datetime.date(2014, 8, 15),
# 'other_text': 'REMOVED',
'site_sampled': 'Stool'
}
# only look at those fields, that are not subject to scrubbing
self.assertEqual({k: obs[k] for k in exp}, exp)
def test_get_ag_details(self):
self.mock_login_admin()
# test if AGP data are rendered correctly
barcode = '000029153'
response = self.get('/barcode_util/', {'barcode': barcode})
self.assertEqual(response.code, 200)
self.assertIn('<h2>%s Details</h2>' % 'American Gut', response.body)
ag_details = db.getAGBarcodeDetails(barcode)
self.assertIn('<tr><td>Sample Date</td><td>%s</td></tr>'
% ag_details['sample_date'], response.body)
self.assertIn('<tr><td>Sample Time</td><td>%s</td></tr>'
% ag_details['sample_time'], response.body)
self.assertIn('<tr><td>Sample Site</td><td>%s</td></tr>'
% ag_details['site_sampled'], response.body)
self.assertIn('<label for="moldy"> moldy (current: %s) </label> <br />'
% ag_details['moldy'], response.body)
self.assertIn(('<label for="overloaded"> overloaded (current: %s) '
'</label> <br />') % ag_details['overloaded'],
response.body)
self.assertIn(('<label for="other"> other (current: %s) '
'</label> <br />') % ag_details['other'], response.body)
self.assertIn(('<textarea name="other_text" onclick="this.select()'
'">%s</textarea>') %
xhtml_escape(ag_details['other_text']),
response.body)
self.assertIn(('<label for="send_mail" style="display:block;">send kit'
' owner %s (%s) an email </label>')
% (xhtml_escape(ag_details['name']),
xhtml_escape(ag_details['email'])),
response.body)
def test_getAGBarcodeDetails(self):
obs = db.getAGBarcodeDetails("000018046")
exp = {
"status": "Received",
"ag_kit_id": "0060a301-e5c0-6a4e-e050-8a800c5d49b7",
"barcode": "000018046",
"environment_sampled": None,
"name": "REMOVED",
"ag_kit_barcode_id": "0060a301-e5c1-6a4e-e050-8a800c5d49b7",
"sample_time": datetime.time(11, 15),
"notes": "REMOVED",
"overloaded": "N",
"withdrawn": None,
"email": "REMOVED",
"other": "N",
"deposited": False,
"participant_name": "REMOVED-0",
"refunded": None,
"moldy": "N",
"sample_date": datetime.date(2014, 8, 13),
"date_of_last_email": datetime.date(2014, 8, 15),
"other_text": "REMOVED",
"site_sampled": "Stool",
}
self.assertEqual(obs, exp)
def test_get(self):
self.mock_login_admin()
# check that error is raised for unknown barcode
response = self.get("/ag_edit_barcode/", {"barcode": "unknown"})
self.assertEqual(response.code, 500)
# make sure return code 400 is returned, if barcode is not given
response = self.get("/ag_edit_barcode/", {})
self.assertEqual(response.code, 400)
# check if page is rendered properly
barcode = db.get_barcodes_with_results()[0]
response = self.get("/ag_edit_barcode/", {"barcode": barcode})
self.assertEqual(response.code, 200)
details = db.getAGBarcodeDetails(barcode)
l = db.search_kits(details["ag_kit_id"])[0]
self.assertIn('name="barcode" id="barcode" value="%s"' % barcode, response.body)
for s in db.human_sites:
if details["site_sampled"] == str(s):
self.assertIn('<option value="%s" selected>%s</option>' % (str(s), str(s)), response.body)
else:
self.assertIn('<option value="%s">%s</option>' % (str(s), str(s)), response.body)
for e in db.general_sites:
if details["environment_sampled"] == str(e):
self.assertIn('<option value="%s" selected>%s</option>' % (str(e), str(e)), response.body)
else:
self.assertIn('<option value="%s">%s</option>' % (str(e), str(e)), response.body)
for p in db.getHumanParticipants(l) + db.getAnimalParticipants(l):
if details["participant_name"] == str(p):
self.assertIn('<option value="%s" selected>%s</option>' % (str(p), str(p)), response.body)
else:
self.assertIn('<option value="%s" >%s</option>' % (str(p), str(p)), response.body)
def test_get_ag_details(self):
self.mock_login_admin()
# test if AGP data are rendered correctly
barcode = "000029153"
response = self.get("/barcode_util/", {"barcode": barcode})
self.assertEqual(response.code, 200)
self.assertIn("<h2>%s Details</h2>" % "American Gut", response.body)
ag_details = db.getAGBarcodeDetails(barcode)
self.assertIn("<tr><td>Sample Date</td><td>%s</td></tr>" % ag_details["sample_date"], response.body)
self.assertIn("<tr><td>Sample Time</td><td>%s</td></tr>" % ag_details["sample_time"], response.body)
self.assertIn("<tr><td>Sample Site</td><td>%s</td></tr>" % ag_details["site_sampled"], response.body)
self.assertIn('<label for="moldy"> moldy (current: %s) </label> <br />' % ag_details["moldy"], response.body)
self.assertIn(
('<label for="overloaded"> overloaded (current: %s) ' "</label> <br />") % ag_details["overloaded"],
response.body,
)
self.assertIn(
('<label for="other"> other (current: %s) ' "</label> <br />") % ag_details["other"], response.body
)
self.assertIn(
('<textarea name="other_text" onclick="this.select()' '">%s</textarea>') % ag_details["notes"],
response.body,
)
self.assertIn(
('<label for="send_mail" style="display:block;">send kit' " owner %s (%s) an email </label>")
% (ag_details["name"], ag_details["email"]),
response.body,
)
def test_get(self):
self.mock_login_admin()
# check that error is raised for unknown barcode
response = self.get('/ag_edit_barcode/', {'barcode': 'unknown'})
self.assertEqual(response.code, 500)
# make sure return code 400 is returned, if barcode is not given
response = self.get('/ag_edit_barcode/', {})
self.assertEqual(response.code, 400)
# check if page is rendered properly
barcode = '000004216'
response = self.get('/ag_edit_barcode/', {'barcode': barcode})
self.assertEqual(response.code, 200)
self.assertIn('name="barcode" id="barcode" value="%s"' %
barcode, response.body)
self.assertIn('<option value="Stool" selected>Stool</option>',
response.body)
self.assertIn('2013-10-15', response.body)
hs = db.human_sites
hs.remove('Stool')
for s in hs:
self.assertIn('<option value="%s">%s</option>' %
(str(s), str(s)), response.body)
for e in db.general_sites:
self.assertIn('<option value="%s">%s</option>' %
(str(e), str(e)), response.body)
pname = xhtml_escape(
db.getAGBarcodeDetails(barcode)['participant_name'])
self.assertIn('<option value="%s" selected>%s</option>' %
(pname, pname), response.body)
def test_getAGBarcodeDetails(self):
obs = db.getAGBarcodeDetails('000018046')
exp = {
'status': 'Received',
'ag_kit_id': '0060a301-e5c0-6a4e-e050-8a800c5d49b7',
'barcode': '000018046',
'environment_sampled': None,
'name': 'REMOVED',
'ag_kit_barcode_id': '0060a301-e5c1-6a4e-e050-8a800c5d49b7',
'sample_time': datetime.time(11, 15),
'notes': 'REMOVED',
'overloaded': 'N',
'withdrawn': None,
'email': 'REMOVED',
'other': 'N',
'deposited': False,
'participant_name': 'REMOVED-0',
'refunded': None,
'moldy': 'N',
'sample_date': datetime.date(2014, 8, 13),
'date_of_last_email': datetime.date(2014, 8, 15),
'other_text': 'REMOVED',
'site_sampled': 'Stool'
}
self.assertEqual(obs, exp)
def get_ag_details(self, barcode):
ag_details = db.getAGBarcodeDetails(barcode)
_, failures = db.pulldown([barcode], [])
if len(ag_details) == 0 and failures:
div_id = "no_metadata"
message = "Cannot retrieve metadata: %s" % failures[barcode]
elif len(ag_details) > 0:
for col, val in ag_details.iteritems():
if val is None:
ag_details[col] = ''
ag_details['other_checked'] = ''
ag_details['overloaded_checked'] = ''
ag_details['moldy_checked'] = ''
ag_details['login_user'] = ag_details['name']
if ag_details['moldy'] == 'Y':
ag_details['moldy_checked'] = 'checked'
if ag_details['overloaded'] == 'Y':
ag_details['overloaded_checked'] = 'checked'
if ag_details['other'] == 'Y':
ag_details['other_checked'] = 'checked'
survey_id = db.get_barcode_survey(barcode)
# it has all sample details
# (sample time, date, site)
if failures:
div_id = "no_metadata"
message = "Cannot retrieve metadata: %s" % failures[barcode]
ag_details['email_type'] = "-1"
elif (survey_id is None and ag_details['environment_sampled']) \
or survey_id in survey_type:
div_id = "verified"
message = "All good"
ag_details['email_type'] = "1"
else:
# should never get here (this would happen
# if the metadata
# pulldown returned more than one row for a
# single barcode)
div_id = "md_pulldown_error"
message = ("This barcode has multiple entries "
"in the database, which should "
"never happen. Please notify "
"someone on the database crew.")
ag_details['email_type'] = "-1"
else:
# TODO: Stefan Janssen: I cannot see how this case should ever be
# reached, since failures will be set to 'Unknown reason' at the
# outmost.
div_id = "not_assigned"
message = ("In American Gut project group but no "
"American Gut info for barcode")
ag_details['email_type'] = "-1"
return div_id, message, ag_details
def get_ag_details(self, barcode):
ag_details = db.getAGBarcodeDetails(barcode)
_, failures = db.pulldown([barcode], [])
if len(ag_details) == 0 and failures:
div_id = "no_metadata"
message = "Cannot retrieve metadata: %s" % failures[barcode]
elif len(ag_details) > 0:
for col, val in ag_details.iteritems():
if val is None:
ag_details[col] = ''
ag_details['other_checked'] = ''
ag_details['overloaded_checked'] = ''
ag_details['moldy_checked'] = ''
ag_details['login_user'] = ag_details['name']
if ag_details['moldy'] == 'Y':
ag_details['moldy_checked'] = 'checked'
if ag_details['overloaded'] == 'Y':
ag_details['overloaded_checked'] = 'checked'
if ag_details['other'] == 'Y':
ag_details['other_checked'] = 'checked'
survey_id = db.get_barcode_survey(barcode)
# it has all sample details
# (sample time, date, site)
if failures:
div_id = "no_metadata"
message = "Cannot retrieve metadata: %s" % failures[barcode]
ag_details['email_type'] = "-1"
elif (survey_id is None and ag_details['environment_sampled']) \
or survey_id in survey_type:
div_id = "verified"
message = "All good"
ag_details['email_type'] = "1"
else:
# should never get here (this would happen
# if the metadata
# pulldown returned more than one row for a
# single barcode)
div_id = "md_pulldown_error"
message = ("This barcode has multiple entries "
"in the database, which should "
"never happen. Please notify "
"someone on the database crew.")
ag_details['email_type'] = "-1"
else:
# TODO: Stefan Janssen: I cannot see how this case should ever be
# reached, since failures will be set to 'Unknown reason' at the
# outmost.
div_id = "not_assigned"
message = ("In American Gut project group but no "
"American Gut info for barcode")
ag_details['email_type'] = "-1"
return div_id, message, ag_details
def get(self):
barcode = self.get_argument('barcode', None)
if barcode is not None:
details = db.getAGBarcodeDetails(barcode)
site_sampled = db.human_sites
environment_sampled = db.general_sites
logins = db.getAGKitsByLogin()
self.render("ag_edit_barcode.html", response=None, barcode=barcode,
sites_sampled=site_sampled, details=details,
environments_sampled=environment_sampled,
logins=logins, currentuser=self.current_user)
def test_post_update_ag(self):
db.alter_access_levels("test", [3])
notes = "".join([choice(ascii_letters) for x in range(40)])
self.data["other_text"] = notes
self.mock_login()
response = self.post("/barcode_util/", data=self.data)
self.assertEqual(response.code, 200)
self.assertIn("Barcode %s general details updated" % self.ag_good, response.body)
self.assertIn("Barcode %s AG info was successfully updated" % self.ag_good, response.body)
obs = db.getAGBarcodeDetails(self.ag_good)
self.assertEqual(obs["other_text"], notes)
def test_post_update_ag(self):
db.alter_access_levels('test', [3])
notes = ''.join([choice(ascii_letters) for x in range(40)])
self.data['other_text'] = notes
self.mock_login()
response = self.post('/barcode_util/', data=self.data)
self.assertEqual(response.code, 200)
self.assertIn('Barcode %s general details updated' % self.ag_good,
response.body)
self.assertIn(
'Barcode %s AG info was successfully updated' % self.ag_good,
response.body)
obs = db.getAGBarcodeDetails(self.ag_good)
self.assertEqual(obs['other_text'], notes)
def get(self):
barcode = self.get_argument('barcode', None)
if barcode is not None:
details = db.getAGBarcodeDetails(barcode)
ag_login_id = db.search_kits(details['ag_kit_id'])[0]
site_sampled = db.human_sites
environment_sampled = db.general_sites
participants = db.getHumanParticipants(ag_login_id) + \
db.getAnimalParticipants(ag_login_id)
self.render("ag_edit_barcode.html", response=None, barcode=barcode,
sites_sampled=site_sampled, details=details,
environments_sampled=environment_sampled,
participants=participants,
currentuser=self.current_user)
def get(self):
barcode = self.get_argument('barcode', None)
if barcode is not None:
details = db.getAGBarcodeDetails(barcode)
site_sampled = db.human_sites
environment_sampled = db.general_sites
logins = db.getAGKitsByLogin()
self.render("ag_edit_barcode.html",
response=None,
barcode=barcode,
sites_sampled=site_sampled,
details=details,
environments_sampled=environment_sampled,
logins=logins,
currentuser=self.current_user)
def get(self):
barcode = self.get_argument('barcode', None)
if barcode is not None:
details = db.getAGBarcodeDetails(barcode)
ag_login_id = db.search_kits(details['ag_kit_id'])[0]
site_sampled = db.human_sites
environment_sampled = db.general_sites
participants = db.getHumanParticipants(ag_login_id) + \
db.getAnimalParticipants(ag_login_id)
self.render("ag_edit_barcode.html", response=None, barcode=barcode,
sites_sampled=site_sampled, details=details,
environments_sampled=environment_sampled,
participants=participants,
currentuser=self.current_user)
else:
self.set_status(400)
def test_getAGBarcodeDetails(self):
obs = db.getAGBarcodeDetails('000018046')
exp = {'status': 'Received',
'ag_kit_id': '0060a301-e5c0-6a4e-e050-8a800c5d49b7',
'barcode': '000018046',
'environment_sampled': None,
'name': 'REMOVED',
'ag_kit_barcode_id': '0060a301-e5c1-6a4e-e050-8a800c5d49b7',
'sample_time': datetime.time(11, 15),
'notes': 'REMOVED',
'overloaded': 'N',
'withdrawn': None, 'email': 'REMOVED',
'other': 'N', 'deposited': False,
'participant_name': 'REMOVED-0',
'refunded': None, 'moldy': 'N',
'sample_date': datetime.date(2014, 8, 13),
'date_of_last_email': datetime.date(2014, 8, 15),
'other_text': 'REMOVED',
'site_sampled': 'Stool'}
self.assertEqual(obs, exp)
def test_getAGBarcodeDetails(self):
obs = db.getAGBarcodeDetails('000018046')
exp = {'status': 'Received',
'ag_kit_id': '0060a301-e5c0-6a4e-e050-8a800c5d49b7',
'barcode': '000018046',
'environment_sampled': None,
# 'name': 'REMOVED',
'ag_kit_barcode_id': '0060a301-e5c1-6a4e-e050-8a800c5d49b7',
'sample_time': datetime.time(11, 15),
# 'notes': 'REMOVED',
'overloaded': 'N',
'withdrawn': None, # 'email': 'REMOVED',
'other': 'N',
# 'deposited': False,
# 'participant_name': 'REMOVED-0',
'refunded': None, 'moldy': 'N',
'sample_date': datetime.date(2014, 8, 13),
'date_of_last_email': datetime.date(2014, 8, 15),
# 'other_text': 'REMOVED',
'site_sampled': 'Stool'}
# only look at those fields, that are not subject to scrubbing
self.assertEqual({k: obs[k] for k in exp}, exp)
def test_get_ag_details(self):
self.mock_login_admin()
# test if AGP data are rendered correctly
barcode = '000029153'
response = self.get('/barcode_util/', {'barcode': barcode})
self.assertEqual(response.code, 200)
self.assertIn('<h2>%s Details</h2>' % 'American Gut', response.body)
ag_details = db.getAGBarcodeDetails(barcode)
self.assertIn(
'<tr><td>Sample Date</td><td>%s</td></tr>' %
ag_details['sample_date'], response.body)
self.assertIn(
'<tr><td>Sample Time</td><td>%s</td></tr>' %
ag_details['sample_time'], response.body)
self.assertIn(
'<tr><td>Sample Site</td><td>%s</td></tr>' %
ag_details['site_sampled'], response.body)
self.assertIn(
'<label for="moldy"> moldy (current: %s) </label> <br />' %
ag_details['moldy'], response.body)
self.assertIn(('<label for="overloaded"> overloaded (current: %s) '
'</label> <br />') % ag_details['overloaded'],
response.body)
self.assertIn(('<label for="other"> other (current: %s) '
'</label> <br />') % ag_details['other'], response.body)
self.assertIn(
('<textarea name="other_text" onclick="this.select()'
'">%s</textarea>') % xhtml_escape(ag_details['other_text']),
response.body)
self.assertIn(
('<label for="send_mail" style="display:block;">send kit'
' owner %s (%s) an email </label>') % (xhtml_escape(
ag_details['name']), xhtml_escape(ag_details['email'])),
response.body)
def test_get(self):
self.mock_login_admin()
# check that error is raised for unknown barcode
response = self.get('/ag_edit_barcode/', {'barcode': 'unknown'})
self.assertEqual(response.code, 500)
# make sure return code 400 is returned, if barcode is not given
response = self.get('/ag_edit_barcode/', {})
self.assertEqual(response.code, 400)
# check if page is rendered properly
barcode = '000004216'
response = self.get('/ag_edit_barcode/', {'barcode': barcode})
self.assertEqual(response.code, 200)
self.assertIn('name="barcode" id="barcode" value="%s"' % barcode,
response.body)
self.assertIn('<option value="Stool" selected>Stool</option>',
response.body)
self.assertIn('2013-10-15', response.body)
hs = db.human_sites
hs.remove('Stool')
for s in hs:
self.assertIn('<option value="%s">%s</option>' % (str(s), str(s)),
response.body)
for e in db.general_sites:
self.assertIn('<option value="%s">%s</option>' % (str(e), str(e)),
response.body)
pname = xhtml_escape(
db.getAGBarcodeDetails(barcode)['participant_name'])
self.assertIn(
'<option value="%s" selected>%s</option>' % (pname, pname),
response.body)
def get_ag_details(self, barcode):
ag_details = db.getAGBarcodeDetails(barcode)
if len(ag_details) > 0:
for col, val in ag_details.iteritems():
if val is None:
ag_details[col] = ''
ag_details['other_checked'] = ''
ag_details['overloaded_checked'] = ''
ag_details['moldy_checked'] = ''
ag_details['login_user'] = ag_details['name']
if ag_details['moldy'] == 'Y':
ag_details['moldy_checked'] = 'checked'
if ag_details['overloaded'] == 'Y':
ag_details['overloaded_checked'] = 'checked'
if ag_details['other'] == 'Y':
ag_details['other_checked'] = 'checked'
survey_id = db.get_barcode_survey(barcode)
_, failures = db.pulldown([barcode])
if not (ag_details['sample_date'] == ag_details['site_sampled'] ==
ag_details['sample_time'] == ''):
# it has all sample details
# (sample time, date, site)
if survey_id is None:
div_id = "not_assigned"
message = "Missing info"
ag_details['email_type'] = "0"
elif barcode in failures:
div_id = "no_metadata"
message = "Cannot retrieve metadata"
ag_details['email_type'] = "-1"
elif survey_type[survey_id] == 'Human':
# and we can successfully retrieve sample
# metadata
div_id = "verified"
message = "All good"
ag_details['email_type'] = "1"
elif survey_type[survey_id] == 'Animal':
div_id = "verified_animal"
message = "All good"
ag_details['email_type'] = "1"
else:
# should never get here (this would happen
# if the metadata
# pulldown returned more than one row for a
# single barcode)
div_id = "md_pulldown_error"
message = ("This barcode has multiple entries "
"in the database, which should "
"never happen. Please notify "
"someone on the database crew.")
ag_details['email_type'] = "-1"
else:
div_id = "not_assigned"
message = ("In American Gut project group but No "
"American Gut info for barcode")
ag_details['email_type'] = "-1"
else:
div_id = "not_assigned"
message = ("In American Gut project group but No "
"American Gut info for barcode")
ag_details['email_type'] = "-1"
return div_id, message, ag_details
def test_source_reassignment(self):
# Elaine Wolfe found this bug, May 13th:
# Manually changing the survey a sample is assigned to is not saved
# even after getting the "barcode has successfully been updated"
# message. All other field changes (time, sample type, etc.) are
# saving properly.
self.mock_login_admin()
# this is a barcode that belongs to a set of ag_kits which has multiple
# participant_names, i.e. sources
# SELECT barcode
# FROM barcodes.barcode
# JOIN ag.ag_kit_barcodes USING (barcode)
# JOIN ag.ag_kit USING (ag_kit_id)
# WHERE ag_login_id IN
# (SELECT ag_login_id
# FROM (SELECT array_agg(participant_name) as sources,
# count(participant_name) as numsources,
# ag_login_id FROM ag.ag_login_surveys
# GROUP BY ag_login_id) as foo
# WHERE numsources > 2);
barcode = '000023125' # current survey_id = "a4f1061f5bac9ae3"
details = db.getAGBarcodeDetails(barcode)
payload = {
'barcode': barcode,
'ag_kit_id': details['ag_kit_id'],
'site_sampled': details['site_sampled'],
'sample_date': details['sample_date'],
'sample_time': details['sample_time'],
'participant_name': details['participant_name'],
'notes': details['notes'],
'environment_sampled': details['environment_sampled'],
'refunded': details['refunded'] or 'N',
'withdrawn': details['withdrawn'] or 'N'
}
response = self.post('/ag_edit_barcode/', payload)
self.assertEqual(response.code, 200)
# check that no actual change has happened
dbinfo = db.getAGBarcodeDetails(barcode)
for field in payload.keys():
if field in self.none_fields:
if details[field] in [None, 'N', 'None', '']:
details[field] = None
if dbinfo[field] in [None, 'N', 'None', '']:
dbinfo[field] = None
self.assertEqual(details[field], dbinfo[field])
# obtain all participant_names
sql = """SELECT DISTINCT participant_name
FROM ag.ag_kit_barcodes
LEFT JOIN ag.ag_kit USING (ag_kit_id)
LEFT JOIN ag.ag_login_surveys USING (ag_login_id)
WHERE barcode = %s"""
sourcenames = db._con.execute_fetchall(sql, [barcode])
self.assertIsNotNone(sourcenames)
sourcenames = [x[0] for x in sourcenames]
# changing source for the barcode
old_sourcename = payload['participant_name']
new_sourcename = list(set(sourcenames) - set(old_sourcename))[0]
payload['participant_name'] = new_sourcename
response = self.post('/ag_edit_barcode/', payload)
obs_details = db.getAGBarcodeDetails(barcode)
# revert to old participant_name to leave a clean DB
payload['participant_name'] = old_sourcename
response = self.post('/ag_edit_barcode/', payload)
self.assertEqual(response.code, 200)
self.assertEqual(obs_details['participant_name'], new_sourcename)
self.assertTrue(obs_details['participant_name'] != old_sourcename)
def get_ag_details(self, barcode):
ag_details = db.getAGBarcodeDetails(barcode)
if len(ag_details) > 0:
for col, val in ag_details.iteritems():
if val is None:
ag_details[col] = ''
ag_details['other_checked'] = ''
ag_details['overloaded_checked'] = ''
ag_details['moldy_checked'] = ''
ag_details['login_user'] = ag_details['name']
if ag_details['moldy'] == 'Y':
ag_details['moldy_checked'] = 'checked'
if ag_details['overloaded'] == 'Y':
ag_details['overloaded_checked'] = 'checked'
if ag_details['other'] == 'Y':
ag_details['other_checked'] = 'checked'
survey_id = db.get_barcode_survey(barcode)
_, failures = db.pulldown([barcode])
if not (ag_details['sample_date'] ==
ag_details['site_sampled'] ==
ag_details['sample_time'] == ''):
# it has all sample details
# (sample time, date, site)
if survey_id is None:
div_id = "not_assigned"
message = "Missing info"
ag_details['email_type'] = "0"
elif barcode in failures:
div_id = "no_metadata"
message = "Cannot retrieve metadata"
ag_details['email_type'] = "-1"
elif survey_type[survey_id] == 'Human':
# and we can successfully retrieve sample
# metadata
div_id = "verified"
message = "All good"
ag_details['email_type'] = "1"
elif survey_type[survey_id] == 'Animal':
div_id = "verified_animal"
message = "All good"
ag_details['email_type'] = "1"
else:
# should never get here (this would happen
# if the metadata
# pulldown returned more than one row for a
# single barcode)
div_id = "md_pulldown_error"
message = ("This barcode has multiple entries "
"in the database, which should "
"never happen. Please notify "
"someone on the database crew.")
ag_details['email_type'] = "-1"
else:
div_id = "not_assigned"
message = ("In American Gut project group but No "
"American Gut info for barcode")
ag_details['email_type'] = "-1"
else:
div_id = "not_assigned"
message = ("In American Gut project group but No "
"American Gut info for barcode")
ag_details['email_type'] = "-1"
return div_id, message, ag_details
