def test_from_string_content(self):
with open(
os.path.join(os.path.dirname(__file__), 'fixtures',
'NCT00985114.xml'), 'rb') as fh:
content = fh.read()
study = ClinicalStudy.from_content(content)
self.assertEqual('NCT00985114', study.nct_id)
def test_local_file_remote_schema(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
study = ClinicalStudy.from_file(
os.path.join(os.path.dirname(__file__), 'fixtures',
'NCT00985114.xml'))
donk.assert_called()
self.assertEqual('NCT00985114', study.nct_id)
def get_study(self, nct_id):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get(nct_id)
study = ClinicalStudy.from_nctid(nct_id)
return study
def test_parsed_exclusion_534(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get('NCT02536534')
study = ClinicalStudy.from_nctid('NCT02536534')
content = study.eligibility.criteria
processed = process_eligibility(content)
self.assertEqual(4, len(processed.get('exclusion')))
def test_study_types(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
for study_id, study_type in (('NCT02348489', 'Interventional'),
('NCT01565668', 'Interventional'),
('NCT02536534', 'Observational')):
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get(study_id)
study = ClinicalStudy.from_nctid(study_id)
self.assertEqual(study.study_type, study_type)
def test_study_phases(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
for study_id, phase in (('NCT02348489', 'Phase 3'),
('NCT01565668', 'Phase 2'), ('NCT02536534',
'N/A')):
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get(study_id)
study = ClinicalStudy.from_nctid(study_id)
self.assertEqual(study.phase, phase)
def test_study_conditions(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
for study_id, condition in (('NCT02348489', [
'Leukemia, Myeloid, Acute'
]), ('NCT01565668', ['Leukemia, Myeloid, Acute']),
('NCT02536534',
['Hypertension, Pulmonary'])):
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get(study_id)
study = ClinicalStudy.from_nctid(study_id)
self.assertEqual(study.conditions(), condition)
def test_parsed_exclusion_668(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get('NCT01565668')
study = ClinicalStudy.from_nctid('NCT01565668')
content = study.eligibility.criteria
processed = process_eligibility(content)
self.assertEqual(18, len(processed.get('exclusion')))
criterion = '- Subject has any medical, psychiatric, addictive or other kind of disorder which compromises ' \
'the ability of the subject to give written informed consent and/or to comply with procedures'
self.assertEqual(criterion, processed.get('exclusion')[-1])
def test_brief_summary(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get('NCT02536534')
study = ClinicalStudy.from_nctid('NCT02536534')
desc = 'Evaluate the correlation between activity level (monitored by Fitbit Flex remote activity tracker) ' \
'and 6-minute walk distance (6MWD) (performed by investigator) in patients with Pulmonary Arterial ' \
'Hypertension (PAH) or Chronic Thromboembolic Pulmonary Hypertension (CTEPH) over 6 months in ' \
'routine clinical practice settings.'
content = study.brief_summary
self.assertEqual(desc, content)
def test_last_known_status(self):
"""
Test the last known status
"""
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
for study_id, overall_status in (('NCT02348489',
''), ('NCT01565668', ''),
('NCT02536534', '')):
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get(study_id)
study = ClinicalStudy.from_nctid(study_id)
self.assertEqual(study.last_known_status, overall_status)
def test_study_status(self):
"""
Test the Overall Status
"""
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
for study_id, overall_status in (('NCT02348489',
'Active, not recruiting'),
('NCT01565668', 'Completed'),
('NCT02536534', 'Completed')):
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get(study_id)
study = ClinicalStudy.from_nctid(study_id)
self.assertEqual(study.status, overall_status)
def test_detailed_description(self):
with mock.patch('clinical_trials.clinical_study.get_schema') as donk:
donk.return_value = self.schema
with mock.patch(
"clinical_trials.clinical_study.get_study") as dink:
dink.return_value = self.cache.get('NCT02536534')
study = ClinicalStudy.from_nctid('NCT02536534')
desc = "Remote patient monitoring can lead to improved patient outcomes, including improved quality of " \
"life, reduced readmissions, earlier treatment for symptoms detected prior to schedule in-office " \
"follow-up visits, improved communications with care providers, increased participation in " \
"self-management of disease, and an improved knowledge of their medical conditions . In patients " \
"with PAH, daily activity level, as measured using a physical activity monitor for seven " \
"consecutive days, correlated with 6-minute walk distance (6MWD). The monitor used in the " \
"aforementioned PAH study was positioned on the patients' right upper arm with an armband, " \
"as opposed to the more popular and more comfortable wristbands used today, such as the Fitbit " \
"Flex. Although the aforementioned PAH study did show a correlation between activity level " \
"monitoring and 6MWD, the patients were monitored for only seven days. " \
"It is still unknown whether " \
"this correlation would exist over a longer trial period and whether patients, their caregivers, " \
"and clinicians would find activity level monitoring useful in helping manage PH."
content = study.detailed_description
self.assertEqual(desc, content)
def build_status(status):
if status in ("Active, not recruiting", "Enrolling by invitation",
"Recruiting"):
return 'in-progress'
elif status in ("Completed"):
return 'completed'
elif status in ("Suspended", "Terminated"):
return 'suspended'
elif status in ("Terminated", "Withdrawn"):
return 'stopped'
else:
return 'draft'
if __name__ == "__main__":
ct = ClinicalStudy.from_file("examples/NCT02348489.xml", local_schema=True)
locations = [build_location(x) for x in ct.locations]
foci = build_focus(ct.mesh_terms)
print([x.as_json() for x in foci])
keywords = build_keyword(ct.keywords)
print([x.as_json() for x in keywords])
identifiers = build_identifiers(ct.nct_id, ct.study_id, ct.secondary_id)
print([x.as_json() for x in identifiers])
package = bundle.Bundle()
package.type = "document"
package.identifier = identifier.Identifier(
dict(use='official',
system="https://clinicaltrials.gov/ct2/show/",
value=ct.nct_id))
entries = []
for location in locations:
def test_missing_file(self):
with self.assertRaises(ValueError) as exc:
study = ClinicalStudy.from_file("Some/missing/path")
self.assertEqual("File Some/missing/path not found",
str(exc.exception))
def test_local_file_local_schema(self):
study = ClinicalStudy.from_file(os.path.join(os.path.dirname(__file__),
'fixtures',
'NCT00985114.xml'),
local_schema=True)
self.assertEqual('NCT00985114', study.nct_id)