def testInsert_rightParticipantId(self):
self._make_summary()
summary = ParticipantSummaryDao().get(self.participant.participantId)
self.assertIsNone(summary.physicalMeasurementsStatus)
with FakeClock(TIME_2):
measurements = self.dao.insert(self._make_physical_measurements())
expected_measurements = PhysicalMeasurements(
physicalMeasurementsId=1,
participantId=self.participant.participantId,
resource=self._with_id(self.measurement_json, '1'),
created=TIME_2,
finalized=TIME_1,
final=True,
logPositionId=1,
createdSiteId=1,
finalizedSiteId=2)
self.assertEquals(expected_measurements.asdict(), measurements.asdict())
measurements = self.dao.get(measurements.physicalMeasurementsId)
self.assertEquals(expected_measurements.asdict(), measurements.asdict())
# Completing physical measurements changes the participant summary status
summary = ParticipantSummaryDao().get(self.participant.participantId)
self.assertEquals(PhysicalMeasurementsStatus.COMPLETED, summary.physicalMeasurementsStatus)
self.assertEquals(TIME_2, summary.physicalMeasurementsTime)
self.assertEquals(TIME_2, summary.lastModified)
def _make_physical_measurements(self, **kwargs):
"""Makes a new PhysicalMeasurements (same values every time) with valid/complete defaults.
Kwargs pass through to PM constructor, overriding defaults.
"""
for k, default_value in (('physicalMeasurementsId',
1), ('participantId',
self.participant.participantId),
('resource', self.pm_json),
('createdSiteId', self.site.siteId),
('finalizedSiteId', self.site.siteId)):
if k not in kwargs:
kwargs[k] = default_value
return PhysicalMeasurements(**kwargs)
def test_schema(self):
session = self.database.make_session()
hpo = HPO(hpoId=1,
name='UNSET',
displayName='No organization set',
organizationType=OrganizationType.UNSET)
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(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 from_client_json(resource_json, participant_id=None, **unused_kwargs):
#pylint: disable=unused-argument
measurements = []
observations = []
qualifier_map = {}
created_site_id = None
created_username = None
finalized_site_id = None
finalized_username = None
for entry in resource_json['entry']:
resource = entry.get('resource')
if resource:
resource_type = resource.get('resourceType')
if resource_type == _OBSERVATION_RESOURCE_TYPE:
observations.append(
(entry['fullUrl'],
fhirclient.models.observation.Observation(resource)))
elif resource_type == _COMPOSITION_RESOURCE_TYPE:
extensions = resource.get('extension', [])
if not extensions:
logging.warning(
'No extensions in composition resource (expected site info).'
)
for extension in extensions:
value_reference = extension.get('valueReference')
if value_reference:
url = extension.get('url')
if url == _CREATED_LOC_EXTENSION:
created_site_id = PhysicalMeasurementsDao.get_location_site_id(
value_reference)
elif url == _FINALIZED_LOC_EXTENSION:
finalized_site_id = PhysicalMeasurementsDao.get_location_site_id(
value_reference)
elif url not in _ALL_EXTENSIONS:
logging.warning(
'Unrecognized extension URL: %r (should be one of %s)',
url, _ALL_EXTENSIONS)
else:
logging.warning(
'No valueReference in extension, skipping: %r',
extension)
authors = resource.get('author')
for author in authors:
author_extension = author.get('extension')
reference = author.get('reference')
if author_extension and reference:
authoring_step = PhysicalMeasurementsDao.get_authoring_step(
author_extension)
if authoring_step == _FINALIZED_STATUS:
finalized_username = PhysicalMeasurementsDao.get_author_username(
reference)
elif authoring_step == _CREATED_STATUS:
created_username = PhysicalMeasurementsDao.get_author_username(
reference)
else:
logging.warning(
'Unrecognized resource type (expected %r or %r), skipping: %r',
_OBSERVATION_RESOURCE_TYPE, _COMPOSITION_RESOURCE_TYPE,
resource_type)
# Take two passes over the observations; once to find all the qualifiers and observations
# without related qualifiers, and a second time to find all observations with related
# qualifiers.
for first_pass in [True, False]:
for fullUrl, observation in observations:
measurement = PhysicalMeasurementsDao.from_observation(
observation, fullUrl, qualifier_map, first_pass)
if measurement:
measurements.append(measurement)
return PhysicalMeasurements(participantId=participant_id,
resource=json.dumps(resource_json),
measurements=measurements,
createdSiteId=created_site_id,
createdUsername=created_username,
finalizedSiteId=finalized_site_id,
finalizedUsername=finalized_username)