def setUp(self, **kwargs):
super(MetricsEhrMultiEndpointTest, self).setUp(**kwargs)
#
# insert some test data
#
for date in iter_dates(datetime.date(2017, 12, 30),
datetime.date(2018, 2, 1)):
calendar_day = Calendar(day=date)
CalendarDao().insert(calendar_day)
# noinspection PyArgumentList
participant_1 = Participant(participantId=1, biobankId=4)
summary_1 = self._make_participant(
participant_1,
'Alice',
'Aardvark',
self.hpo_foo,
self.org_foo_a,
time_int=datetime.datetime(2018, 1, 2),
time_mem=datetime.datetime(2018, 1, 3),
time_fp=datetime.datetime(2018, 1, 4))
# noinspection PyArgumentList
participant_2 = Participant(participantId=2, biobankId=5)
summary_2 = self._make_participant(
participant_2,
'Bo',
'Badger',
self.hpo_bar,
self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5))
self._update_ehr(summary_1, update_time=datetime.datetime(2018, 1, 5))
self._update_ehr(summary_2, update_time=datetime.datetime(2018, 1, 6))
def GET(self):
params = web.input()
if not params.has_key('location'):
raise web.seeother('../')
location_id = params.location
length_update = Dbevent.updateDb(location_id)
length_delete = Dbevent.deleteDb(location_id)
Calendar.deleteMemcacheCity(location_id)
db.put(SyncQueue(key_name=location_id,
location_id=location_id,
update_at=datetime.utcnow()))
logging.info('update %s %d' %(location_id, length_update))
logging.info('delete %s %d' %(location_id, length_delete))
return 'ok'
def GET(self, location):
web.header('Content-Type', 'text/plain;charset=UTF-8')
params = web.input(type='all', length=None) # web.py post/get默认值
category = params.type # 活动类型
length = params.length # 活动长度
if length is not None and length.isdigit() and length > 0:
length = int(length)
else:
length = None
calendar = Calendar.getCalendar(location, category, length)
try:
return calendar.getICalendarStr()
except ValueError, e:
raise web.notfound()
def GET(self, location):
web.header("Content-Type", "text/plain;charset=UTF-8")
params = web.input(type="all", length=None) # web.py post/get默认值
category = params.type # 活动类型
length = params.length # 活动长度
if length is not None and length.isdigit() and length > 0:
length = int(length)
else:
length = None
calendar = Calendar.getCalendar(location, category, length)
try:
return calendar.getICalendarStr()
except ValueError, e:
raise web.notfound()
def test_consented_counts(self):
# Set up data
for date in iter_dates(
datetime.date(2017, 12, 30),
datetime.date(2018, 2, 1)
):
calendar_day = Calendar(day=date)
CalendarDao().insert(calendar_day)
# noinspection PyArgumentList
participant_1 = Participant(participantId=1, biobankId=4)
self._make_participant(
participant_1, 'Alice', 'Aardvark', self.hpo_foo, self.org_foo_a,
time_int=datetime.datetime(2018, 1, 2),
time_mem=datetime.datetime(2018, 1, 3),
time_study=datetime.datetime(2018, 1, 3),
time_fp=datetime.datetime(2018, 1, 4),
)
# noinspection PyArgumentList
participant_2 = Participant(participantId=2, biobankId=5)
self._make_participant(
participant_2, 'Bo', 'Badger', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
# Begin testing
response = self.send_get('MetricsEHR')
self.assertEqual(response['metrics']['EHR_CONSENTED'], 2)
self.assertEqual(
response['metrics']['EHR_CONSENTED'],
sum([o['total_ehr_consented'] for o in response['organization_metrics'].values()])
)
# test with organization filtering
response = self.send_get('MetricsEHR', query_string=urllib.urlencode({
'organization': 'foo_a',
}))
self.assertEqual(response['metrics']['EHR_CONSENTED'], 1)
self.assertEqual(
response['metrics']['EHR_CONSENTED'],
sum([o['total_ehr_consented'] for o in response['organization_metrics'].values()])
)
def setUp(self):
super(ParticipantCountsOverTimeApiTest, self).setUp(use_mysql=True)
self.dao = ParticipantDao()
self.ps_dao = ParticipantSummaryDao()
self.ps = ParticipantSummary()
self.calendar_dao = CalendarDao()
self.hpo_dao = HPODao()
# Needed by ParticipantCountsOverTimeApi
self.hpo_dao.insert(HPO(hpoId=TEST_HPO_ID, name=TEST_HPO_NAME, displayName='Test',
organizationType=OrganizationType.UNSET))
self.time1 = datetime.datetime(2017, 12, 31)
self.time2 = datetime.datetime(2018, 1, 1)
self.time3 = datetime.datetime(2018, 1, 2)
self.time4 = datetime.datetime(2018, 1, 3)
# Insert 2 weeks of dates
curr_date = datetime.date(2017, 12, 22)
for _ in xrange(0, 14):
calendar_day = Calendar(day=curr_date )
CalendarDao().insert(calendar_day)
curr_date = curr_date + datetime.timedelta(days=1)
def index():
content = read_static('view/index.html')
p = Calendar('nanjing')
current_time = p.current
content = content.replace("@@abc", current_time)
return content
def test_schema(self):
session = self.database.make_session()
hpo = HPO(hpoId=1,
name='UNSET',
displayName='No organization set',
organizationType=OrganizationType.UNSET)
calendar = Calendar(day=datetime.date(2018, 1, 1))
code_book = CodeBook(codeBookId=1,
created=datetime.datetime.now(),
latest=True,
name="pmi",
system="http://foo/bar",
version="v0.1.1")
session.add(hpo)
session.add(calendar)
session.add(code_book)
session.commit()
organization = Organization(organizationId=1,
externalId='org',
displayName='Organization',
hpoId=1)
session.add(organization)
session.commit()
site = Site(siteId=1,
siteName='site',
googleGroup='*****@*****.**',
mayolinkClientNumber=12345,
organizationId=1)
code1 = Code(codeId=1,
codeBookId=1,
system="a",
value="b",
shortValue="q",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=datetime.datetime.now())
codeHistory1 = CodeHistory(codeId=1,
codeBookId=1,
system="a",
value="b",
shortValue="q",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=datetime.datetime.now())
session.add(site)
session.add(code1)
session.add(codeHistory1)
session.commit()
code2 = Code(codeId=2,
codeBookId=1,
parentId=1,
system="a",
value="c",
display=u"X",
topic=u"d",
codeType=CodeType.QUESTION,
mapped=True,
created=datetime.datetime.now())
codeHistory2 = CodeHistory(codeId=2,
codeBookId=1,
parentId=1,
system="a",
value="c",
display=u"X",
topic=u"d",
codeType=CodeType.QUESTION,
mapped=True,
created=datetime.datetime.now())
session.add(code2)
session.add(codeHistory2)
session.commit()
code3 = Code(codeId=3,
codeBookId=1,
parentId=2,
system="a",
value="d",
display=u"Y",
topic=u"d",
codeType=CodeType.ANSWER,
mapped=False,
created=datetime.datetime.now())
codeHistory3 = CodeHistory(codeId=3,
codeBookId=1,
parentId=2,
system="a",
value="d",
display=u"Y",
topic=u"d",
codeType=CodeType.ANSWER,
mapped=False,
created=datetime.datetime.now())
session.add(code3)
session.add(codeHistory3)
session.commit()
session.commit()
p = self._participant_with_defaults(
participantId=1,
version=1,
biobankId=2,
clientId='*****@*****.**',
hpoId=hpo.hpoId,
signUpTime=datetime.datetime.now(),
lastModified=datetime.datetime.now())
ps = self._participant_summary_with_defaults(
participantId=1,
biobankId=2,
lastModified=datetime.datetime.now(),
hpoId=hpo.hpoId,
firstName=self.fake.first_name(),
middleName=self.fake.first_name(),
lastName=self.fake.last_name(),
email=self.fake.email(),
zipCode='78751',
dateOfBirth=datetime.date.today(),
genderIdentityId=1,
consentForStudyEnrollment=QuestionnaireStatus.SUBMITTED,
consentForStudyEnrollmentTime=datetime.datetime.now(),
numBaselineSamplesArrived=2)
p.participantSummary = ps
session.add(p)
ph = self._participant_history_with_defaults(
participantId=1,
biobankId=2,
clientId='*****@*****.**',
hpoId=hpo.hpoId,
signUpTime=datetime.datetime.now(),
lastModified=datetime.datetime.now())
session.add(ph)
session.commit()
session.add(
BiobankStoredSample(biobankStoredSampleId='WEB1234542',
biobankId=p.biobankId,
biobankOrderIdentifier='KIT',
test='1UR10',
confirmed=datetime.datetime.utcnow()))
session.add(
BiobankStoredSample(
biobankStoredSampleId='WEB99999', # Sample ID must be unique.
biobankId=p.
biobankId, # Participant ID and test may be duplicated.
biobankOrderIdentifier='KIT',
test='1UR10',
confirmed=datetime.datetime.utcnow()))
pm = PhysicalMeasurements(physicalMeasurementsId=1,
participantId=1,
created=datetime.datetime.now(),
resource='blah',
final=False,
logPosition=LogPosition())
pm2 = PhysicalMeasurements(physicalMeasurementsId=2,
participantId=1,
created=datetime.datetime.now(),
resource='blah',
final=True,
amendedMeasurementsId=1,
logPosition=LogPosition())
session.add(pm)
session.add(pm2)
session.commit()
q1 = Measurement(measurementId=3,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
valueCodeSystem='valueCodeSystem',
valueCodeValue='value3')
session.add(q1)
session.commit()
m1 = Measurement(measurementId=1,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
bodySiteCodeSystem='bodySiteCodeSystem',
bodySiteCodeValue='bodySiteCodeValue',
valueString='a',
valueDecimal=1.2,
valueUnit='cm',
valueCodeSystem='valueCodeSystem',
valueCodeValue='value',
valueDateTime=datetime.datetime.now(),
qualifierId=q1.measurementId)
session.add(m1)
session.commit()
m2 = Measurement(measurementId=2,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
valueCodeSystem='valueCodeSystem',
valueCodeValue='value2',
parentId=m1.measurementId,
qualifierId=q1.measurementId)
session.add(m2)
session.commit()
q = Questionnaire(questionnaireId=1,
version=1,
created=datetime.datetime.now(),
lastModified=datetime.datetime.now(),
resource='what?')
qh = QuestionnaireHistory(questionnaireId=1,
version=1,
created=datetime.datetime.now(),
lastModified=datetime.datetime.now(),
resource='what?')
qh.questions.append(
QuestionnaireQuestion(questionnaireQuestionId=1,
questionnaireId=1,
questionnaireVersion=1,
linkId="1.2.3",
codeId=2,
repeats=True))
qh.concepts.append(
QuestionnaireConcept(questionnaireConceptId=1,
questionnaireId=1,
questionnaireVersion=1,
codeId=1))
session.add(q)
session.add(qh)
session.commit()
qr = QuestionnaireResponse(questionnaireResponseId=1,
questionnaireId=1,
questionnaireVersion=1,
participantId=1,
created=datetime.datetime.now(),
resource='blah')
qr.answers.append(
QuestionnaireResponseAnswer(questionnaireResponseAnswerId=1,
questionnaireResponseId=1,
questionId=1,
endTime=datetime.datetime.now(),
valueSystem='a',
valueCodeId=3,
valueDecimal=123,
valueString=self.fake.first_name(),
valueDate=datetime.date.today()))
session.add(qr)
session.commit()
mv = MetricsVersion(metricsVersionId=1,
inProgress=False,
complete=True,
date=datetime.datetime.utcnow(),
dataVersion=1)
session.add(mv)
session.commit()
mb = MetricsBucket(metricsVersionId=1,
date=datetime.date.today(),
hpoId='PITT',
metrics='blah')
session.add(mb)
session.commit()
def test_organization_counts(self):
# Set up data
for date in iter_dates(datetime.date(2017, 12, 30),
datetime.date(2018, 2, 1)):
calendar_day = Calendar(day=date)
CalendarDao().insert(calendar_day)
# noinspection PyArgumentList
participant_1 = Participant(participantId=1, biobankId=4)
summary_1 = self._make_participant(
participant_1,
'A',
'Aardvark',
self.hpo_foo,
self.org_foo_a,
time_int=datetime.datetime(2018, 1, 2),
time_mem=datetime.datetime(2018, 1, 3),
time_fp=datetime.datetime(2018, 1, 4))
self._update_ehr(summary_1, update_time=datetime.datetime(2018, 1, 5))
# noinspection PyArgumentList
participant_2 = Participant(participantId=2, biobankId=5)
summary_2 = self._make_participant(
participant_2,
'B',
'Badger',
self.hpo_foo,
self.org_foo_a,
time_int=datetime.datetime(2018, 1, 2),
time_mem=datetime.datetime(2018, 1, 3),
time_fp=datetime.datetime(2018, 1, 4))
self._update_ehr(summary_2, update_time=datetime.datetime(2018, 1, 5))
# noinspection PyArgumentList
participant_3 = Participant(participantId=3, biobankId=6)
summary_3 = self._make_participant(
participant_3,
'C',
'Chicken',
self.hpo_foo,
self.org_foo_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5))
self._update_ehr(summary_3, update_time=datetime.datetime(2018, 1, 6))
# noinspection PyArgumentList
participant_4 = Participant(participantId=4, biobankId=7)
summary_4 = self._make_participant(
participant_4,
'D',
'Dog',
self.hpo_bar,
self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5))
self._update_ehr(summary_4, update_time=datetime.datetime(2018, 1, 6))
self._update_ehr(summary_4, update_time=datetime.datetime(2018, 1, 7))
# Begin testing
response = self.send_get('MetricsEHR',
query_string=urllib.urlencode({
'start_date':
'2018-01-01',
'end_date':
'2018-01-08',
'interval':
'day'
}))
counts_by_date = {
day['date']: day['metrics']['ORGANIZATIONS_ACTIVE']
for day in response['metrics_over_time']
}
self.assertEqual(
counts_by_date, {
u'2018-01-01': 0,
u'2018-01-02': 0,
u'2018-01-03': 0,
u'2018-01-04': 0,
u'2018-01-05': 1,
u'2018-01-06': 2,
u'2018-01-07': 1,
u'2018-01-08': 0,
})
# test with organization filtering
response = self.send_get('MetricsEHR',
query_string=urllib.urlencode({
'start_date':
'2018-01-01',
'end_date':
'2018-01-08',
'interval':
'day',
'organization':
'FOO_A',
}))
counts_by_date = {
day['date']: day['metrics']['ORGANIZATIONS_ACTIVE']
for day in response['metrics_over_time']
}
self.assertEqual(
counts_by_date, {
u'2018-01-01': 0,
u'2018-01-02': 0,
u'2018-01-03': 0,
u'2018-01-04': 0,
u'2018-01-05': 1,
u'2018-01-06': 1,
u'2018-01-07': 0,
u'2018-01-08': 0,
})
# test organization filter multiple
response = self.send_get('MetricsEHR',
query_string=urllib.urlencode({
'start_date':
'2018-01-01',
'end_date':
'2018-01-08',
'interval':
'day',
'organization':
'FOO_A,BAR_A',
}))
counts_by_date = {
day['date']: day['metrics']['ORGANIZATIONS_ACTIVE']
for day in response['metrics_over_time']
}
self.assertEqual(
counts_by_date, {
u'2018-01-01': 0,
u'2018-01-02': 0,
u'2018-01-03': 0,
u'2018-01-04': 0,
u'2018-01-05': 1,
u'2018-01-06': 2,
u'2018-01-07': 1,
u'2018-01-08': 0,
})
def test_consented_counts(self):
# Set up data
for date in iter_dates(datetime.date(2017, 12, 30),
datetime.date(2018, 2, 1)):
calendar_day = Calendar(day=date)
CalendarDao().insert(calendar_day)
# noinspection PyArgumentList
participant_1 = Participant(participantId=1, biobankId=4)
self._make_participant(
participant_1,
'Alice',
'Aardvark',
self.hpo_foo,
self.org_foo_a,
time_int=datetime.datetime(2018, 1, 2),
time_mem=datetime.datetime(2018, 1, 3),
time_fp=datetime.datetime(2018, 1, 4),
)
# noinspection PyArgumentList
participant_2 = Participant(participantId=2, biobankId=5)
self._make_participant(participant_2,
'Bo',
'Badger',
self.hpo_bar,
self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5))
# Begin testing
response = self.send_get('MetricsEHR',
query_string=urllib.urlencode({
'start_date':
'2018-01-01',
'end_date':
'2018-01-06',
'interval':
'day'
}))
counts_by_date = {
day['date']: day['metrics']['EHR_CONSENTED']
for day in response['metrics_over_time']
}
self.assertEqual(
counts_by_date, {
u'2018-01-01': 0,
u'2018-01-02': 0,
u'2018-01-03': 1,
u'2018-01-04': 2,
u'2018-01-05': 2,
u'2018-01-06': 2,
})
# test with organization filtering
response = self.send_get('MetricsEHR',
query_string=urllib.urlencode({
'start_date':
'2018-01-01',
'end_date':
'2018-01-06',
'interval':
'day',
'organization':
'foo_a',
}))
counts_by_date = {
day['date']: day['metrics']['EHR_CONSENTED']
for day in response['metrics_over_time']
}
self.assertEqual(
counts_by_date, {
u'2018-01-01': 0,
u'2018-01-02': 0,
u'2018-01-03': 1,
u'2018-01-04': 1,
u'2018-01-05': 1,
u'2018-01-06': 1,
})
from model.calendar import Calendar
year, month = 0, 0
while year <= 0:
year = int(input("Enter a year: "))
while not 1 <= month <= 12:
month = int(input("Enter a month: "))
print()
c = Calendar(year, month)
c.show_calendar()
def _fill_calendar_range(self, start, end):
for date in self._iter_dates_in_range(start, end):
self.calendar_dao.insert(Calendar(day=date))
def setUp(self, **kwargs):
super(MetricsEhrMultiEndpointTest, self).setUp(**kwargs)
#
# insert some test data
#
for date in iter_dates(
datetime.date(2017, 12, 30),
datetime.date(2018, 2, 1)
):
calendar_day = Calendar(day=date)
CalendarDao().insert(calendar_day)
# noinspection PyArgumentList
participant_1 = Participant(participantId=1, biobankId=1)
summary_1 = self._make_participant(
participant_1, 'Alice', 'Aardvark', self.hpo_foo, self.org_foo_a,
time_int=datetime.datetime(2018, 1, 2),
time_mem=datetime.datetime(2018, 1, 3),
time_study=datetime.datetime(2018, 1, 3),
time_fp=datetime.datetime(2018, 1, 4)
)
self._update_ehr(
summary_1,
update_time=datetime.datetime(2018, 1, 5)
)
# noinspection PyArgumentList
participant_2 = Participant(participantId=2, biobankId=2)
summary_2 = self._make_participant(
participant_2, 'Bo', 'Badger', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
self._update_ehr(
summary_2,
update_time=datetime.datetime(2018, 1, 6)
)
# noinspection PyArgumentList
participant_3 = Participant(participantId=3, biobankId=3)
self._make_participant(
participant_3, 'Cheryl', 'Caterpillar', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
participant_3.withdrawalStatus = WithdrawalStatus.NO_USE
self.dao.update(participant_3)
# noinspection PyArgumentList
participant_4 = Participant(participantId=4, biobankId=4)
self._make_participant(
participant_4, 'Dan', 'Donkey', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
participant_4.isGhostId = True
self.dao.update(participant_4)
# noinspection PyArgumentList
participant_5 = Participant(participantId=5, biobankId=5)
self._make_participant(
participant_5, 'Elia', 'Elephant', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_study=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
# noinspection PyArgumentList
participant_6 = Participant(participantId=6, biobankId=6)
self._make_participant(
participant_6, 'Elia', 'Elephant', self.hpo_bar, self.org_bar_a,
time_int=datetime.datetime(2018, 1, 3),
time_mem=datetime.datetime(2018, 1, 4),
time_fp=datetime.datetime(2018, 1, 5)
)
