def test_scrub(self):
samp1 = 'd8592c74-85f0-2135-e040-8a80115d6401' # 000001766
with Transaction() as t:
acct1, src1 = self._get_source_from_sample(t, samp1)
sr = SampleRepo(t)
# get original source associations
src1_sample = sr.get_samples_by_source(acct1, src1)[0]
res = sr.scrub(acct1, src1, src1_sample.id)
self.assertTrue(res)
obs_sample = sr.get_samples_by_source(acct1, src1)[0]
self.assertNotEqual(src1_sample.notes, obs_sample.notes)
def _remote_survey_url_polyphenol_ffq(transaction, account_id, source_id,
language_tag):
st_repo = SurveyTemplateRepo(transaction)
# right now, ID won't exist
# future plans to allow surveys to behave more flexibly will use this
# functionality to allow participants to re-join in-progress surveys
polyphenol_ffq_id, study = \
st_repo.get_polyphenol_ffq_id_if_exists(account_id, source_id)
if polyphenol_ffq_id is None:
# The Polyphenol FFQ belongs to Danone and they're interested in
# tracking results that come from their sponsored studies
# separately from other samples. We pass 'THDMI' as the study for
# THDMI samples and 'Microsetta' for all other samples. Therefore,
# we need to determine if the source has any THDMI-associated samples.
# Without investing significant developer effort to build a category
# system around projects, a basic text search is the best compromise.
study = 'Microsetta'
sample_repo = SampleRepo(transaction)
samples = sample_repo.get_samples_by_source(account_id, source_id)
for s in samples:
for s_p in s.sample_projects:
if s_p.startswith('THDMI'):
study = 'THDMI'
break
polyphenol_ffq_id = st_repo.create_polyphenol_ffq_entry(
account_id, source_id, language_tag, study)
return polyphenol_ffq.gen_ffq_url(polyphenol_ffq_id, study, language_tag)
def read_sample_associations(account_id, source_id, token_info):
_validate_account_access(token_info, account_id)
with Transaction() as t:
sample_repo = SampleRepo(t)
samples = sample_repo.get_samples_by_source(account_id, source_id)
api_samples = [x.to_api() for x in samples]
return jsonify(api_samples), 200
def test_update_sample_assocation_with_migration(self):
samp1 = 'd8592c74-85f0-2135-e040-8a80115d6401' # 000001766
samp2 = 'ceaa6fd6-0861-4335-aa35-da1857bd5294' # 000067789
with Transaction() as t:
acct1, src1 = self._get_source_from_sample(t, samp1)
acct2, src2 = self._get_source_from_sample(t, samp2)
sr = SampleRepo(t)
# get original source associations
src1_samples = sr.get_samples_by_source(acct1, src1)
src2_samples = sr.get_samples_by_source(acct2, src2)
# verify samples are part of the original source
self.assertTrue(self._sample_in_source(src1_samples, samp1))
self.assertTrue(self._sample_in_source(src2_samples, samp2))
# swap associations
sr._update_sample_association(samp1, src2, True)
sr._update_sample_association(samp2, src1, True)
# get new samples by source
src1_samples = sr.get_samples_by_source(acct1, src1)
src2_samples = sr.get_samples_by_source(acct2, src2)
# verify samples are part of the new source
self.assertTrue(self._sample_in_source(src1_samples, samp2))
self.assertTrue(self._sample_in_source(src2_samples, samp1))
# verify samples are not part of the original source
self.assertFalse(self._sample_in_source(src1_samples, samp1))
self.assertFalse(self._sample_in_source(src2_samples, samp2))
# fix associations
sr._update_sample_association(samp1, src1, True)
sr._update_sample_association(samp2, src2, True)
# ...and verify assocations are fixed
src1_samples = sr.get_samples_by_source(acct1, src1)
src2_samples = sr.get_samples_by_source(acct2, src2)
self.assertTrue(self._sample_in_source(src1_samples, samp1))
self.assertTrue(self._sample_in_source(src2_samples, samp2))
def delete_account(account_id, token_info):
validate_admin_access(token_info)
with Transaction() as t:
acct_repo = AccountRepo(t)
src_repo = SourceRepo(t)
samp_repo = SampleRepo(t)
sar_repo = SurveyAnswersRepo(t)
acct = acct_repo.get_account(account_id)
if acct is None:
return jsonify(message="Account not found", code=404), 404
else:
# the account is already scrubbed so let's stop early
if acct.account_type == 'deleted':
return None, 204
sample_count = 0
sources = src_repo.get_sources_in_account(account_id)
for source in sources:
samples = samp_repo.get_samples_by_source(account_id, source.id)
has_samples = len(samples) > 0
sample_count += len(samples)
for sample in samples:
# we scrub rather than disassociate in the event that the
# sample is in our freezers but not with an up-to-date scan
samp_repo.scrub(account_id, source.id, sample.id)
surveys = sar_repo.list_answered_surveys(account_id, source.id)
if has_samples:
# if we have samples, we need to scrub survey / source
# free text
for survey_id in surveys:
sar_repo.scrub(account_id, source.id, survey_id)
src_repo.scrub(account_id, source.id)
else:
# if we do not have associated samples, then the source
# is safe to delete
for survey_id in surveys:
sar_repo.delete_answered_survey(account_id, survey_id)
src_repo.delete_source(account_id, source.id)
# an account is safe to delete if there are no associated samples
if sample_count > 0:
acct_repo.scrub(account_id)
else:
acct_repo.delete_account(account_id)
t.commit()
return None, 204
def delete_dummy_accts():
all_sample_ids = []
acct_ids = [ACCT_ID_1, ACCT_ID_2]
with Transaction() as t:
acct_repo = AccountRepo(t)
source_repo = SourceRepo(t)
survey_answers_repo = SurveyAnswersRepo(t)
sample_repo = SampleRepo(t)
for curr_acct_id in acct_ids:
sources = source_repo.get_sources_in_account(curr_acct_id)
for curr_source in sources:
source_samples = sample_repo.get_samples_by_source(
curr_acct_id, curr_source.id)
sample_ids = [x.id for x in source_samples]
all_sample_ids.extend(sample_ids)
# Dissociate all samples linked to this source from all
# answered surveys linked to this source, then delete all
# answered surveys
delete_dummy_answered_surveys_from_source_with_t(
t, curr_acct_id, curr_source.id, sample_ids,
survey_answers_repo)
# Now dissociate all the samples from this source
for curr_sample_id in sample_ids:
sample_repo.dissociate_sample(curr_acct_id, curr_source.id,
curr_sample_id)
# Finally, delete the source
source_repo.delete_source(curr_acct_id, curr_source.id)
# Delete the account
acct_repo.delete_account(curr_acct_id)
# Belt and suspenders: these test emails are used by some tests outside
# of this module as well, so can't be sure they are paired with the
# above dummy account ids
acct_repo.delete_account_by_email(TEST_EMAIL)
acct_repo.delete_account_by_email(TEST_EMAIL_2)
# Delete the kit and all samples that were attached to any sources
# NB: This won't clean up any samples that were created but NOT
# attached to any sources ...
if len(all_sample_ids) == 0:
all_sample_ids = None
_remove_mock_kit(t, mock_sample_ids=all_sample_ids)
t.commit()
def test_migrate_sample(self):
samp1 = 'd8592c74-85f0-2135-e040-8a80115d6401' # 000001766
samp2 = 'ceaa6fd6-0861-4335-aa35-da1857bd5294' # 000067789
with Transaction() as t:
acct1, src1 = self._get_source_from_sample(t, samp1)
acct2, src2 = self._get_source_from_sample(t, samp2)
sr = SampleRepo(t)
sr.migrate_sample(samp1, src1, src2, True)
# get new samples by source
src1_samples = sr.get_samples_by_source(acct1, src1)
src2_samples = sr.get_samples_by_source(acct2, src2)
# verify samples are part of the new source
self.assertFalse(self._sample_in_source(src1_samples, samp1))
self.assertTrue(self._sample_in_source(src2_samples, samp1))
def query_email_stats(body, token_info):
validate_admin_access(token_info)
email_list = body.get("emails", [])
project = body.get("project")
results = []
with Transaction() as t:
account_repo = AccountRepo(t)
kit_repo = KitRepo(t)
source_repo = SourceRepo(t)
sample_repo = SampleRepo(t)
for email in email_list:
result = {'email': email, 'project': project}
results.append(result)
# can use internal lookup by email, because we have admin access
account = account_repo._find_account_by_email(email) # noqa
if account is None:
result['summary'] = "No Account"
continue
else:
result['account_id'] = account.id
result['creation_time'] = account.creation_time
result['kit_name'] = account.created_with_kit_id
if account.created_with_kit_id is not None:
unused = kit_repo.get_kit_unused_samples(
account.created_with_kit_id
)
if unused is None:
result['unclaimed-samples-in-kit'] = 0
else:
result['unclaimed-samples-in-kit'] = len(unused.samples)
sample_statuses = defaultdict(int)
sources = source_repo.get_sources_in_account(account.id)
samples_in_project = 0
for source in sources:
samples = sample_repo.get_samples_by_source(account.id,
source.id)
for sample in samples:
if project is not None and \
project != "" and \
project not in sample.sample_projects:
continue
samples_in_project += 1
sample_status = sample_repo.get_sample_status(
sample.barcode,
sample._latest_scan_timestamp # noqa
)
if sample_status is None:
sample_status = "never-scanned"
sample_statuses[sample_status] += 1
result.update(sample_statuses)
if result.get('unclaimed-samples-in-kit', 0) > 0:
result['summary'] = 'Possible Unreturned Samples'
elif samples_in_project == 0:
result['summary'] = "No Samples In Specified Project"
elif result.get('sample-is-valid') == samples_in_project:
result['summary'] = 'All Samples Valid'
else:
result['summary'] = 'May Require User Interaction'
return jsonify(results), 200
