def test_insert_second_codebook_same_system_same_version(self):
code_book_1 = CodeBook(name="pmi", version="v1", system="a")
self.code_book_dao.insert(code_book_1)
code_book_2 = CodeBook(name="pmi", version="v1", system="a")
with self.assertRaises(BadRequest):
self.code_book_dao.insert(code_book_2)
def test_insert_second_codebook_different_system(self):
code_book_1 = CodeBook(name="pmi", version="v1", system="a")
with FakeClock(TIME):
self.code_book_dao.insert(code_book_1)
code_book_2 = CodeBook(name="pmi", version="v2", system="b")
with FakeClock(TIME_2):
self.code_book_dao.insert(code_book_2)
expected_code_book = CodeBook(codeBookId=1,
latest=True,
created=TIME,
name="pmi",
version="v1",
system="a")
self.assertEquals(expected_code_book.asdict(),
self.code_book_dao.get(1).asdict())
expected_code_book_2 = CodeBook(codeBookId=2,
latest=True,
created=TIME_2,
name="pmi",
version="v2",
system="b")
self.assertEquals(expected_code_book_2.asdict(),
self.code_book_dao.get(2).asdict())
def import_codebook(self, codebook_json):
"""Imports a codebook and all codes inside it. Returns (new_codebook, imported_code_count)."""
version = codebook_json['version']
num_concepts = len(codebook_json['concept'])
logging.info('Importing %d concepts into new CodeBook version %r...',
num_concepts, version)
system = codebook_json['url']
codebook = CodeBook(name=codebook_json['name'],
version=version,
system=system)
code_count = 0
with self.session() as session:
# Pre-fetch all Codes. This avoids any potential race conditions, and keeps a persistent
# cache even though updates below invalidate the cache repeatedly.
# Fetch within the session so later merges are faster.
existing_codes = {
(code.system, code.value): code
for code in session.query(self.code_dao.model_type).all()
}
self.insert_with_session(session, codebook)
session.flush()
for i, concept in enumerate(codebook_json['concept'], start=1):
logging.info('Importing root concept %d of %d (%s).', i,
num_concepts, concept.get('display'))
code_count += self._import_concept(session, existing_codes,
concept, system,
codebook.codeBookId, None)
logging.info('Finished, %d codes imported.', code_count)
return codebook, code_count
def test_update_codes_no_codebook_id(self):
code_book_1 = CodeBook(name="pmi", version="v1", system="c")
with FakeClock(TIME):
self.code_book_dao.insert(code_book_1)
code_1 = Code(codeBookId=1,
system="a",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True)
with FakeClock(TIME_2):
self.code_dao.insert(code_1)
new_code_1 = Code(codeId=1,
system="x",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True)
with self.assertRaises(BadRequest):
self.code_dao.update(new_code_1)
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 test_insert_with_codebook_and_parent(self):
code_book_1 = CodeBook(name="pmi", version="v1", system="a")
with FakeClock(TIME):
self.code_book_dao.insert(code_book_1)
expected_code_book = CodeBook(codeBookId=1,
latest=True,
created=TIME,
name="pmi",
version="v1",
system="a")
self.assertEquals(expected_code_book.asdict(),
self.code_book_dao.get(1).asdict())
code_1 = Code(codeBookId=1,
system="a",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True)
with FakeClock(TIME_2):
self.code_dao.insert(code_1)
expected_code = Code(codeBookId=1,
codeId=1,
system="a",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=TIME_2)
self.assertEquals(expected_code.asdict(),
self.code_dao.get(1).asdict())
expected_code_history = CodeHistory(codeBookId=1,
codeHistoryId=1,
codeId=1,
system="a",
value=u"b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=TIME_2)
self.assertEquals(expected_code_history.asdict(),
self.code_history_dao.get(1).asdict())
code_2 = Code(codeBookId=1,
system="x",
value="y",
display=u"z",
topic=u"q",
codeType=CodeType.QUESTION,
mapped=False,
parentId=1)
with FakeClock(TIME_3):
self.code_dao.insert(code_2)
expected_code_2 = Code(codeBookId=1,
codeId=2,
system="x",
value="y",
display=u"z",
topic=u"q",
codeType=CodeType.QUESTION,
mapped=False,
created=TIME_3,
parentId=1)
self.assertEquals(expected_code_2.asdict(),
self.code_dao.get(2).asdict())
def test_import_codebook(self):
answer_1 = _make_concept(u"t1", "Answer", "c1", u"d1")
answer_2 = _make_concept(u"t2", "Answer", "c2", u"d2")
answer_3 = _make_concept(u"t2", "Answer", "c3", u"d3")
question_1 = _make_concept(u"t1", "Question", "q1", u"d4", [answer_1])
question_2 = _make_concept(u"t2", "Question", "q2", u"d5",
[answer_2, answer_3])
topic_1 = _make_concept(u"t1", "Topic", "t1", u"d6", [question_1])
module_1 = _make_concept(u"mt1", "Module Name", "m1", u"d7", [topic_1])
module_2 = _make_concept(u"mt2", "Module Name", "m2", u"d8",
[question_2])
system = 'http://blah/foo'
codebook = {
'name': 'pmi',
'version': 'v1',
'url': system,
'concept': [module_1, module_2]
}
with FakeClock(TIME):
self.code_book_dao.import_codebook(codebook)
expectedCodeBook = CodeBook(codeBookId=1,
latest=True,
created=TIME,
name="pmi",
version="v1",
system=system)
self.assertEquals(expectedCodeBook.asdict(),
self.code_book_dao.get(1).asdict())
expectedModule1 = Code(codeBookId=1,
codeId=1,
system=system,
value="m1",
shortValue="m1",
display=u"d7",
topic=u"mt1",
codeType=CodeType.MODULE,
mapped=True,
created=TIME)
self.assertEquals(expectedModule1.asdict(),
self.code_dao.get(1).asdict())
expectedModuleHistory1 = CodeHistory(codeHistoryId=1,
codeBookId=1,
codeId=1,
system=system,
value="m1",
shortValue="m1",
display=u"d7",
topic=u"mt1",
codeType=CodeType.MODULE,
mapped=True,
created=TIME)
self.assertEquals(expectedModuleHistory1.asdict(),
self.code_history_dao.get(1).asdict())
expectedTopic1 = Code(codeBookId=1,
codeId=2,
system=system,
value="t1",
shortValue="t1",
display=u"d6",
topic=u"t1",
codeType=CodeType.TOPIC,
mapped=True,
created=TIME,
parentId=1)
self.assertEquals(expectedTopic1.asdict(),
self.code_dao.get(2).asdict())
expectedQuestion1 = Code(codeBookId=1,
codeId=3,
system=system,
value="q1",
shortValue="q1",
display=u"d4",
topic=u"t1",
codeType=CodeType.QUESTION,
mapped=True,
created=TIME,
parentId=2)
self.assertEquals(expectedQuestion1.asdict(),
self.code_dao.get(3).asdict())
expectedAnswer1 = Code(codeBookId=1,
codeId=4,
system=system,
value="c1",
shortValue="c1",
display=u"d1",
topic=u"t1",
codeType=CodeType.ANSWER,
mapped=True,
created=TIME,
parentId=3)
self.assertEquals(expectedAnswer1.asdict(),
self.code_dao.get(4).asdict())
def test_update_codes_new_codebook_id(self):
code_book_1 = CodeBook(name="pmi", version="v1", system="a")
with FakeClock(TIME):
self.code_book_dao.insert(code_book_1)
code_1 = Code(codeBookId=1,
system="a",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True)
with FakeClock(TIME_2):
self.code_dao.insert(code_1)
code_book_2 = CodeBook(name="pmi", version="v2", system="a")
with FakeClock(TIME_3):
self.code_book_dao.insert(code_book_2)
new_code_1 = Code(codeBookId=2,
codeId=1,
system="x",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True)
with FakeClock(TIME_4):
self.code_dao.update(new_code_1)
expected_code = Code(codeBookId=2,
codeId=1,
system="x",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=TIME_2)
self.assertEquals(expected_code.asdict(),
self.code_dao.get(1).asdict())
expected_code_history = CodeHistory(codeBookId=1,
codeHistoryId=1,
codeId=1,
system="a",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=TIME_2)
self.assertEquals(expected_code_history.asdict(),
self.code_history_dao.get(1).asdict())
expected_code_history_2 = CodeHistory(codeHistoryId=2,
codeBookId=2,
codeId=1,
system="x",
value="b",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=TIME_2)
self.assertEquals(expected_code_history_2.asdict(),
self.code_history_dao.get(2).asdict())