def test_set_curate(self):
trial = set_curated(self.trial)
assert 'curated_on' in trial, trial
trial = self._check_trial_post(trial)
# send again
trial = set_curated(trial)
assert 'curated_on' in trial, trial
assert 'last_updated' in trial and trial['last_updated'] == self.today, trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'], field)
self._check_trial_post(trial)
# update
trial = set_updated(trial)
assert 'curated_on' in trial, trial
assert 'last_updated' in trial and trial['last_updated'], trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'], field)
self._check_trial_post(trial)
def test_set_curate(self):
trial = set_curated(self.trial)
assert 'curated_on' in trial, trial
build_trial_elasticsearch_fields([trial])
# send again
trial = set_curated(trial)
assert 'curated_on' in trial, trial
assert 'last_updated' in trial and trial[
'last_updated'] == self.today, trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'],
field)
build_trial_elasticsearch_fields([trial])
# update
trial = set_updated(trial)
assert 'curated_on' in trial, trial
assert 'last_updated' in trial and trial['last_updated'], trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'],
field)
def test_set_curate(self):
trial = set_curated(self.trial)
assert 'curated_on' in trial, trial
trial = self._check_trial_post(trial)
# send again
trial = set_curated(trial)
assert 'curated_on' in trial, trial
assert 'last_updated' in trial and trial[
'last_updated'] == self.today, trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'],
field)
self._check_trial_post(trial)
# update
trial = set_updated(trial)
assert 'curated_on' in trial, trial
assert 'last_updated' in trial and trial['last_updated'], trial
for field in self.trial_status_fields:
assert field in trial['_summary'], '%s\n\n%s' % (trial['_summary'],
field)
self._check_trial_post(trial)
def test_updatedt_with_curatedt(self):
# set up
today = dt.datetime.now().strftime('%B %d, %Y')
old = 'October 27, 2016'
on_trial['_genomic'] = {'hugo_symbol': [{'value': 'TEST'}]}
on_trial['_clinical'] = {'disease_status': [{'value': ['TEST']}]}
# set both dates to OLD
on_trial['curated_on'] = old
on_trial['last_updated'] = old
assert on_trial['curated_on'] == old, self._debug(
on_trial, 'curated_on')
assert on_trial['last_updated'] == old, self._debug(
on_trial, 'last_updated')
# set "last_updated" to TODAY
trial = set_updated(on_trial)
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
# check dates are preserved after trial_insert is called
trial['protocol_no'] = '01-001'
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
# check the other way around
on_trial['curated_on'] = old
trial['last_updated'] = old
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == old, self._debug(trial, 'last_updated')
trial = set_curated(on_trial)
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(
trial, 'last_updated')
def test_updatedt_with_curatedt(self):
# set up
today = dt.datetime.now().strftime('%B %d, %Y')
old = 'October 27, 2016'
on_trial['_genomic'] = {'hugo_symbol': [{'value': 'TEST'}]}
on_trial['_clinical'] = {'disease_status': [{'value': ['TEST']}]}
# set both dates to OLD
on_trial['curated_on'] = old
on_trial['last_updated'] = old
assert on_trial['curated_on'] == old, self._debug(on_trial, 'curated_on')
assert on_trial['last_updated'] == old, self._debug(on_trial, 'last_updated')
# set "last_updated" to TODAY
trial = set_updated(on_trial)
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
# check dates are preserved after trial_insert is called
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
# check the other way around
on_trial['curated_on'] = old
trial['last_updated'] = old
assert trial['curated_on'] == old, self._debug(trial, 'curated_on')
assert trial['last_updated'] == old, self._debug(trial, 'last_updated')
trial = set_curated(on_trial)
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
trial = trial_insert([trial])
trial = trial[0]
assert trial['curated_on'] == today, self._debug(trial, 'curated_on')
assert trial['last_updated'] == today, self._debug(trial, 'last_updated')
def index():
# set headers.
headers = {
'Content-Type':
'application/json',
'Authorization':
'Basic ' +
base64.b64encode(f'{API_TOKEN}:'.encode('utf-8')).decode('utf-8'),
}
# render the form.
if request.method == 'GET':
# render the page
return _render_trials()
# render the response
else:
# check if the post request has the file part
if 'file' not in request.files:
return "no file"
#return redirect(request.url)
# ensure file is present.
file = request.files['file']
if file.filename == '':
return "empty filename"
if file:
# create trial.
try:
# load the trial.
trial_new = yaml.load(file)
except yaml.YAMLError as exc:
# set yaml error.
r_code = 512
r_text = exc
return "%s</br></br>%s" % (r_code, r_text)
# Deal with "disease_site_code" type exception
trial_new = _handle_exc(trial_new)
# create the request.
qstr = "where=%s" % json.dumps(
({
"protocol_no": trial_new['protocol_no']
}))
# get the trial list from db.
url = '%s/trial?%s' % (API_ADDRESS, qstr)
r = requests.get(url, headers=headers)
output = r.json()
# set curated on field
trial_new = set_curated(trial_new)
# detected a new trial.
if len(output['_items']) == 0:
# post the trial.
url = '%s/trial' % (API_ADDRESS)
r = requests.post(url, json=trial_new, headers=headers)
r_code = r.status_code
r_text = r.text
else:
# get info.
trial = output['_items'][0]
trial_id = str(trial['_id'])
etag = trial['_etag']
# strip meta
for key in list(trial.keys()):
if key[0] == "_":
del trial[key]
trial['_id'] = trial_id
# add the defaults
headers['If-Match'] = etag
# post the trial.
url = '%s/trial/%s' % (API_ADDRESS, trial_id)
r = requests.put(url, json=trial_new, headers=headers)
r_code = r.status_code
r_text = json.dumps(r.json(), indent=4)
# render index if good.
if r_code > 199 and r_code < 300:
return _render_trials()
# render the error
return "%s</br></br>%s" % (r_code, r_text)