def test_subject(self):
""" verify save and find operations """
added_date = datetime.today()
subject = SubjectEntity.create(
redcap_id="001",
added_at=added_date,
last_checked_at=added_date,
was_deleted=False)
self.assertEquals(1, subject.id)
self.assertEquals("001", subject.redcap_id)
self.assertIsNotNone(subject.added_at)
self.assertIsNotNone(subject.last_checked_at)
self.assertFalse(subject.was_deleted)
self.assertEqual(subject.added_at, subject.last_checked_at)
subjects = SubjectEntity.query.all()
self.assertEquals(1, len(subjects))
# test usage of CRUDMixin.get_by_id() and create()
subject = SubjectEntity.update(subject, redcap_id="002")
self.assertEquals("002", subject.redcap_id)
evt = EventEntity.create(redcap_arm='Arm 1', redcap_event='Event 1',
added_at=added_date)
fdata = {'name': 'a.png', 'size': '1MB', 'event': evt.id}
user = UserEntity.create(email="*****@*****.**",
first="",
last="",
minitial="",
added_at=added_date,
modified_at=added_date,
access_expires_at=added_date)
subject_file = SubjectFileEntity.create(
subject_id=subject.id,
event_id=fdata['event'],
file_name=fdata['name'],
file_check_sum=utils.compute_text_md5(fdata['name']),
file_size=fdata['size'],
uploaded_at=added_date,
user_id=user.get_id())
self.assertIsNotNone(subject_file.id)
actual_count = SubjectFileEntity.query.count()
self.assertEqual(1, actual_count)
actual_count = SubjectFileEntity.query.filter_by(
event_id=1).count()
self.assertEqual(1, actual_count)
sfile = SubjectFileEntity.query.first()
self.assertEqual(user.id, sfile.user_id)
def test_subject(self):
""" verify save and find operations """
added_date = datetime.today()
subject = SubjectEntity.create(redcap_id="001",
added_at=added_date,
last_checked_at=added_date,
was_deleted=False)
self.assertEquals(1, subject.id)
self.assertEquals("001", subject.redcap_id)
self.assertIsNotNone(subject.added_at)
self.assertIsNotNone(subject.last_checked_at)
self.assertFalse(subject.was_deleted)
self.assertEqual(subject.added_at, subject.last_checked_at)
subjects = SubjectEntity.query.all()
self.assertEquals(1, len(subjects))
# test usage of CRUDMixin.get_by_id() and create()
subject = SubjectEntity.update(subject, redcap_id="002")
self.assertEquals("002", subject.redcap_id)
evt = EventEntity.create(redcap_arm='Arm 1',
redcap_event='Event 1',
added_at=added_date)
fdata = {'name': 'a.png', 'size': '1MB', 'event': evt.id}
user = UserEntity.create(email="*****@*****.**",
first="",
last="",
minitial="",
added_at=added_date,
modified_at=added_date,
access_expires_at=added_date)
subject_file = SubjectFileEntity.create(
subject_id=subject.id,
event_id=fdata['event'],
file_name=fdata['name'],
file_check_sum=utils.compute_text_md5(fdata['name']),
file_size=fdata['size'],
uploaded_at=added_date,
user_id=user.get_id())
self.assertIsNotNone(subject_file.id)
actual_count = SubjectFileEntity.query.count()
self.assertEqual(1, actual_count)
actual_count = SubjectFileEntity.query.filter_by(event_id=1).count()
self.assertEqual(1, actual_count)
sfile = SubjectFileEntity.query.first()
self.assertEqual(user.id, sfile.user_id)
def create_sample_data(self):
""" Add some data """
# == Create users
added_date = datetime.today()
access_end_date = utils.get_expiration_date(180)
user = UserEntity.create(email="*****@*****.**",
first="First",
last="Last",
minitial="M",
added_at=added_date,
modified_at=added_date,
email_confirmed_at=added_date,
access_expires_at=access_end_date)
# == Create roles
role_admin = RoleEntity.create(name=ROLE_ADMIN, description='role')
role_tech = RoleEntity.create(name=ROLE_TECHNICIAN, description='role')
role_res1 = RoleEntity.create(name=ROLE_RESEARCHER_ONE, description='')
role_res2 = RoleEntity.create(name=ROLE_RESEARCHER_TWO, description='')
user.roles.extend([role_admin, role_tech, role_res1, role_res2])
# == Create subject
subject = SubjectEntity.create(
redcap_id="001",
added_at=added_date,
last_checked_at=added_date,
was_deleted=0)
# == Create events
evt = EventEntity.create(redcap_arm='Arm 1',
redcap_event='Event 1',
day_offset=1,
added_at=added_date)
evt2 = EventEntity.create(redcap_arm='Arm 1',
redcap_event='Event 2',
day_offset=2.3,
added_at=added_date)
self.assertIsNotNone(evt.id)
self.assertIsNotNone(evt2.id)
files = [
{'name': 'a.png', 'size': '123', 'event': evt.id},
{'name': 'b.png', 'size': '1234', 'event': evt.id},
{'name': 'c.png', 'size': '12345', 'event': evt2.id},
{'name': 'd.png', 'size': '123456', 'event': evt2.id},
{'name': 'e.png', 'size': '1234567', 'event': evt2.id},
]
# Create subject files
for fdata in files:
subject_file = SubjectFileEntity.create(
subject_id=subject.id,
event_id=fdata['event'],
file_name=fdata['name'],
file_check_sum=utils.compute_text_md5(fdata['name']),
file_size=fdata['size'],
uploaded_at=added_date,
user_id=user.id)
self.assertIsNotNone(subject_file.id)
def api_import_redcap_subjects():
"""
Refresh the list of subjects
"""
local_subjects = SubjectEntity.query.all()
url = app.config['REDCAP_API_URL']
redcap_subjects = utils.retrieve_redcap_subjects(
url=url,
token=app.config['REDCAP_API_TOKEN'],
fields=app.config['REDCAP_DEMOGRAPHICS_SUBJECT_ID'],
max_time=app.config['REDCAP_CURL_API_MAX_TIME'])
new_subjects = find_new_subjects(local_subjects, redcap_subjects)
added_date = datetime.today()
inserted_subjects = []
for id, redcap_subject in new_subjects.iteritems():
subject = SubjectEntity.create(
redcap_id=id,
added_at=added_date,
last_checked_at=added_date,
was_deleted=False)
inserted_subjects.append(subject)
details = [i for i in new_subjects]
LogEntity.redcap_subjects_imported(session['uuid'],
"Total: {} \n {}"
.format(len(details), details))
return utils.jsonify_success({
'local_subjects': [i.redcap_id for i in local_subjects],
'redcap_subjects': redcap_subjects,
'inserted_subjects': [i.redcap_id for i in inserted_subjects],
'api_url': url
})
def api_import_redcap_subjects():
"""
Refresh the list of subjects
"""
local_subjects = SubjectEntity.query.all()
url = app.config['REDCAP_API_URL']
redcap_subjects = utils.retrieve_redcap_subjects(
url=url,
token=app.config['REDCAP_API_TOKEN'],
fields=app.config['REDCAP_DEMOGRAPHICS_SUBJECT_ID'],
max_time=app.config['REDCAP_CURL_API_MAX_TIME'])
new_subjects = find_new_subjects(local_subjects, redcap_subjects)
added_date = datetime.today()
inserted_subjects = []
for id, redcap_subject in new_subjects.iteritems():
subject = SubjectEntity.create(redcap_id=id,
added_at=added_date,
last_checked_at=added_date,
was_deleted=False)
inserted_subjects.append(subject)
details = [i for i in new_subjects]
LogEntity.redcap_subjects_imported(
session['uuid'], "Total: {} \n {}".format(len(details), details))
return utils.jsonify_success({
'local_subjects': [i.redcap_id for i in local_subjects],
'redcap_subjects':
redcap_subjects,
'inserted_subjects': [i.redcap_id for i in inserted_subjects],
'api_url':
url
})
def create_sample_data(self):
""" Add some data """
# == Create users
added_date = datetime.today()
access_end_date = utils.get_expiration_date(180)
user = UserEntity.create(email="*****@*****.**",
first="First",
last="Last",
minitial="M",
added_at=added_date,
modified_at=added_date,
access_expires_at=access_end_date)
# == Create roles
role_admin = RoleEntity.create(name=ROLE_ADMIN, description='role')
role_tech = RoleEntity.create(name=ROLE_TECHNICIAN, description='role')
user.roles.extend([role_admin, role_tech])
# == Create subject
subject = SubjectEntity.create(
redcap_id="001",
added_at=added_date,
last_checked_at=added_date,
was_deleted=0)
# == Create events
evt = EventEntity.create(redcap_arm='Arm 1', redcap_event='Event 1',
added_at=added_date)
evt2 = EventEntity.create(redcap_arm='Arm 1', redcap_event='Event 2',
added_at=added_date)
assert evt.id is not None
files = [
{'name': 'a.png', 'size': '1MB', 'event': evt.id},
{'name': 'b.png', 'size': '2MB', 'event': evt.id},
{'name': 'c.png', 'size': '3MB', 'event': evt2.id},
{'name': 'd.png', 'size': '4MB', 'event': evt2.id},
{'name': 'e.png', 'size': '5MB', 'event': evt2.id},
]
# Create subject files
for fdata in files:
subject_file = SubjectFileEntity.create(
subject_id=subject.id,
event_id=fdata['event'],
file_name=fdata['name'],
file_check_sum=utils.compute_text_md5(fdata['name']),
file_size=fdata['size'],
uploaded_at=added_date,
user_id=user.id)
app.logger.debug("Init test case with: {}".format(subject_file))
def save_file_metadata(fchunk):
"""
Insert a row in SubjectFile table to preserve file details.
Called from api.py#api_upload() -> #save_uploaded_file() -> #merge_files()
@return SubjectFileEntity
"""
added_date = datetime.today()
subject = SubjectEntity.get_by_redcap_id(fchunk.redcap_id)
subject_file = SubjectFileEntity.create(subject_id=subject.id,
event_id=fchunk.event_id,
file_name=fchunk.file_name,
file_check_sum='pending',
file_size=fchunk.total_size,
uploaded_at=added_date,
user_id=current_user.id)
logger.debug("Saved metadata to the db: ".format(subject_file))
return subject_file
def save_file_metadata(fchunk):
"""
Insert a row in SubjectFile table to preserve file details.
Called from api.py#api_upload() -> #save_uploaded_file() -> #merge_files()
@return SubjectFileEntity
"""
added_date = datetime.today()
subject = SubjectEntity.get_by_redcap_id(fchunk.redcap_id)
subject_file = SubjectFileEntity.create(
subject_id=subject.id,
event_id=fchunk.event_id,
file_name=fchunk.file_name,
file_check_sum='pending',
file_size=fchunk.total_size,
uploaded_at=added_date,
user_id=current_user.id)
logger.debug("Saved metadata to the db: ".format(subject_file))
return subject_file
def create_sample_data(self):
""" Add some data """
# == Create users
added_date = datetime.today()
access_end_date = utils.get_expiration_date(180)
user = UserEntity.create(email="*****@*****.**",
first="First",
last="Last",
minitial="M",
added_at=added_date,
modified_at=added_date,
email_confirmed_at=added_date,
access_expires_at=access_end_date)
# == Create roles
role_admin = RoleEntity.create(name=ROLE_ADMIN, description='role')
role_tech = RoleEntity.create(name=ROLE_TECHNICIAN, description='role')
role_res1 = RoleEntity.create(name=ROLE_RESEARCHER_ONE, description='')
role_res2 = RoleEntity.create(name=ROLE_RESEARCHER_TWO, description='')
user.roles.extend([role_admin, role_tech, role_res1, role_res2])
# == Create subject
subject = SubjectEntity.create(redcap_id="001",
added_at=added_date,
last_checked_at=added_date,
was_deleted=0)
# == Create events
evt = EventEntity.create(redcap_arm='Arm 1',
redcap_event='Event 1',
day_offset=1,
added_at=added_date)
evt2 = EventEntity.create(redcap_arm='Arm 1',
redcap_event='Event 2',
day_offset=2.3,
added_at=added_date)
self.assertIsNotNone(evt.id)
self.assertIsNotNone(evt2.id)
files = [
{
'name': 'a.png',
'size': '123',
'event': evt.id
},
{
'name': 'b.png',
'size': '1234',
'event': evt.id
},
{
'name': 'c.png',
'size': '12345',
'event': evt2.id
},
{
'name': 'd.png',
'size': '123456',
'event': evt2.id
},
{
'name': 'e.png',
'size': '1234567',
'event': evt2.id
},
]
# Create subject files
for fdata in files:
subject_file = SubjectFileEntity.create(
subject_id=subject.id,
event_id=fdata['event'],
file_name=fdata['name'],
file_check_sum=utils.compute_text_md5(fdata['name']),
file_size=fdata['size'],
uploaded_at=added_date,
user_id=user.id)
self.assertIsNotNone(subject_file.id)
def create_sample_data(self):
""" Add some data """
# == Create users
added_date = datetime.today()
access_end_date = utils.get_expiration_date(180)
user = UserEntity.create(email="*****@*****.**",
first="First",
last="Last",
minitial="M",
added_at=added_date,
modified_at=added_date,
access_expires_at=access_end_date)
# == Create roles
role_admin = RoleEntity.create(name=ROLE_ADMIN, description='role')
role_tech = RoleEntity.create(name=ROLE_TECHNICIAN, description='role')
user.roles.extend([role_admin, role_tech])
# == Create subject
subject = SubjectEntity.create(redcap_id="001",
added_at=added_date,
last_checked_at=added_date,
was_deleted=0)
# == Create events
evt = EventEntity.create(redcap_arm='Arm 1',
redcap_event='Event 1',
added_at=added_date)
evt2 = EventEntity.create(redcap_arm='Arm 1',
redcap_event='Event 2',
added_at=added_date)
assert evt.id is not None
files = [
{
'name': 'a.png',
'size': '1MB',
'event': evt.id
},
{
'name': 'b.png',
'size': '2MB',
'event': evt.id
},
{
'name': 'c.png',
'size': '3MB',
'event': evt2.id
},
{
'name': 'd.png',
'size': '4MB',
'event': evt2.id
},
{
'name': 'e.png',
'size': '5MB',
'event': evt2.id
},
]
# Create subject files
for fdata in files:
subject_file = SubjectFileEntity.create(
subject_id=subject.id,
event_id=fdata['event'],
file_name=fdata['name'],
file_check_sum=utils.compute_text_md5(fdata['name']),
file_size=fdata['size'],
uploaded_at=added_date,
user_id=user.id)
app.logger.debug("Init test case with: {}".format(subject_file))