def test_get_counts_for_unconsented_individuals(self):
    # Those who have signed up but not consented should be INTERESTED

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'UNSET', unconsented=True, time_int=self.time1)

    p2 = Participant(participantId=2, biobankId=5)
    self._insert(p2, 'Bob', 'Builder', 'AZ_TUCSON', time_int=self.time1)

    p3 = Participant(participantId=3, biobankId=6)
    self._insert(p3, 'Chad', 'Caterpillar', 'AZ_TUCSON', time_int=self.time1)

    qs = """
          bucketSize=1
          &stratification=ENROLLMENT_STATUS
          &startDate=2017-12-30
          &endDate=2018-01-04
          """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    total_count_day_1 = response[0]['metrics']['INTERESTED']
    total_count_day_2 = response[1]['metrics']['INTERESTED']

    self.assertEquals(total_count_day_1, 0)
    self.assertEquals(total_count_day_2, 3)
  def test_get_counts_excluding_interested_participants(self):
    # When filtering only for MEMBER, no INTERESTED (neither consented nor unconsented) should be counted

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'UNSET', unconsented=True, time_int=self.time1)

    p2 = Participant(participantId=2, biobankId=5)
    self._insert(p2, 'Bob', 'Builder', 'AZ_TUCSON', time_int=self.time1)

    p3 = Participant(participantId=3, biobankId=6)
    self._insert(p3, 'Chad', 'Caterpillar', 'AZ_TUCSON', time_int=self.time1, time_mem=self.time1)

    qs = """
        bucketSize=1
        &stratification=ENROLLMENT_STATUS
        &startDate=2017-12-30
        &endDate=2018-01-04
        &enrollmentStatus=MEMBER
        """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    interested_count_day_2 = response[1]['metrics']['INTERESTED']
    member_count_day_2 = response[1]['metrics']['MEMBER']

    self.assertEquals(interested_count_day_2, 0)
    self.assertEquals(member_count_day_2, 1)
  def test_get_counts_excluding_withdrawn_participants(self):
    # Withdrawn participants should not appear in counts

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'PITT', time_int=self.time1)

    p2 = Participant(participantId=2, biobankId=5)
    self._insert(p2, 'Bob', 'Builder', 'AZ_TUCSON', time_int=self.time1)

    p3 = Participant(participantId=3, biobankId=6)
    ps3 = self._insert(p3, 'Chad', 'Caterpillar', 'AZ_TUCSON', time_int=self.time1)
    ps3.withdrawalStatus = WithdrawalStatus.NO_USE  # Chad withdrew from the study
    self.ps_dao.update(ps3)

    qs = """
        bucketSize=1
        &stratification=TOTAL
        &startDate=2017-12-30
        &endDate=2018-01-04
        """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    total_count_day_1 = response[0]['metrics']['TOTAL']
    total_count_day_2 = response[1]['metrics']['TOTAL']

    self.assertEquals(total_count_day_1, 0)
    self.assertEquals(total_count_day_2, 2)
  def test_get_counts_with_multiple_various_filters(self):
    # Do the awardee and enrollment status filters work when passed multiple values?

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'PITT', time_int=self.time1)

    p2 = Participant(participantId=2, biobankId=5)
    self._insert(p2, 'Bob', 'Builder', 'AZ_TUCSON', time_int=self.time1)

    p3 = Participant(participantId=3, biobankId=6)
    self._insert(p3, 'Chad', 'Caterpillar', 'AZ_TUCSON', time_int=self.time1)

    qs = """
        bucketSize=1
        &stratification=ENROLLMENT_STATUS
        &startDate=2017-12-30
        &endDate=2018-01-04
        &awardee=AZ_TUCSON,PITT
        &enrollmentStatus=INTERESTED,MEMBER,FULL_PARTICIPANT
        """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    interested_count_day_1 = response[0]['metrics']['INTERESTED']
    interested_count_day_2 = response[1]['metrics']['INTERESTED']

    self.assertEquals(interested_count_day_1, 0)
    self.assertEquals(interested_count_day_2, 3)
  def test_get_counts_with_total_stratification_unfiltered(self):

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'PITT', time_int=self.time1)

    p2 = Participant(participantId=2, biobankId=5)
    self._insert(p2, 'Bob', 'Builder', 'AZ_TUCSON', time_int=self.time1)

    p3 = Participant(participantId=3, biobankId=6)
    self._insert(p3, 'Chad', 'Caterpillar', 'AZ_TUCSON', time_int=self.time1)

    qs = """
      bucketSize=1
      &stratification=TOTAL
      &startDate=2017-12-30
      &endDate=2018-01-04
      """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    total_count_day_1 = response[0]['metrics']['TOTAL']
    total_count_day_2 = response[1]['metrics']['TOTAL']

    self.assertEquals(total_count_day_1, 0)
    self.assertEquals(total_count_day_2, 3)
コード例 #6
0
  def test_update_from_samples(self):
    # baseline_tests = ['BASELINE1', 'BASELINE2']
    baseline_tests = ["1PST8", "2PST8"]

    config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
    self.dao.update_from_biobank_stored_samples()  # safe noop

    p_baseline_samples = self._insert(Participant(participantId=1, biobankId=11))
    p_mixed_samples = self._insert(Participant(participantId=2, biobankId=22))
    p_no_samples = self._insert(Participant(participantId=3, biobankId=33))
    p_unconfirmed = self._insert(Participant(participantId=4, biobankId=44))
    self.assertEquals(self.dao.get(p_baseline_samples.participantId).numBaselineSamplesArrived, 0)

    def get_p_baseline_last_modified():
      return self.dao.get(p_baseline_samples.participantId).lastModified
    p_baseline_last_modified1 = get_p_baseline_last_modified()

    sample_dao = BiobankStoredSampleDao()

    def add_sample(participant, test_code, sample_id):
      TIME = datetime.datetime(2018, 3, 2)
      sample_dao.insert(BiobankStoredSample(
          biobankStoredSampleId=sample_id, biobankId=participant.biobankId,
        biobankOrderIdentifier='KIT', test=test_code, confirmed=TIME))

    add_sample(p_baseline_samples, baseline_tests[0], '11111')
    add_sample(p_baseline_samples, baseline_tests[1], '22223')
    add_sample(p_mixed_samples, baseline_tests[0], '11112')
    add_sample(p_mixed_samples, 'NOT1', '44441')
    # add unconfirmed sample
    sample_dao.insert(BiobankStoredSample(biobankStoredSampleId=55555,
                                          biobankId=p_unconfirmed.biobankId,
                                          biobankOrderIdentifier='KIT', test=baseline_tests[1],
                                          confirmed=None))
    # sleep 1 sec to make lastModified different
    time.sleep(1)
    self.dao.update_from_biobank_stored_samples()

    p_baseline_last_modified2 = get_p_baseline_last_modified()
    self.assertNotEquals(p_baseline_last_modified2, p_baseline_last_modified1)

    self.assertEquals(self.dao.get(p_baseline_samples.participantId).numBaselineSamplesArrived, 2)
    self.assertEquals(self.dao.get(p_mixed_samples.participantId).numBaselineSamplesArrived, 1)
    self.assertEquals(self.dao.get(p_no_samples.participantId).numBaselineSamplesArrived, 0)
    self.assertEquals(self.dao.get(p_unconfirmed.participantId).numBaselineSamplesArrived, 0)

    M_baseline_samples = self._insert(Participant(participantId=9, biobankId=99))
    add_sample(M_baseline_samples, baseline_tests[0], '999')
    M_first_update = self.dao.get(M_baseline_samples.participantId)
    # sleep 1 sec to make lastModified different
    time.sleep(1)
    self.dao.update_from_biobank_stored_samples()
    add_sample(M_baseline_samples, baseline_tests[1], '9999')
    M_second_update = self.dao.get(M_baseline_samples.participantId)
    # sleep 1 sec to make lastModified different
    time.sleep(1)
    self.dao.update_from_biobank_stored_samples()

    self.assertNotEqual(M_first_update.lastModified, M_second_update.lastModified)
    self.assertEquals(get_p_baseline_last_modified(), p_baseline_last_modified2)
コード例 #7
0
    def test_pairing_at_different_levels(self):
        p = Participant()
        time = datetime.datetime(2016, 1, 1)
        with random_ids([1, 2]):
            with FakeClock(time):
                self.dao.insert(p)

        p.version = 1
        p.siteId = 1
        time2 = datetime.datetime(2016, 1, 2)
        with FakeClock(time2):
            self.dao.update(p)

        p2 = self.dao.get(1)
        ep = self._participant_with_defaults(participantId=1,
                                             version=2,
                                             biobankId=2,
                                             lastModified=time2,
                                             signUpTime=time,
                                             hpoId=PITT_HPO_ID,
                                             siteId=1,
                                             organizationId=PITT_ORG_ID,
                                             providerLink=p2.providerLink)
        self.assertEquals(ep.siteId, p2.siteId)
        # ensure that p2 get paired with expected awardee and organization from update().
        self.assertEquals(ep.hpoId, p2.hpoId)
        self.assertEquals(ep.organizationId, p2.organizationId)
コード例 #8
0
    def test_insert_with_external_id(self):
        p = Participant(externalId=3)
        time = datetime.datetime(2016, 1, 1)
        with random_ids([1, 2]):
            with FakeClock(time):
                self.dao.insert(p)
        expected_participant = self._participant_with_defaults(
            participantId=1,
            externalId=3,
            version=1,
            biobankId=2,
            lastModified=time,
            signUpTime=time)
        self.assertEquals(expected_participant.asdict(), p.asdict())

        p2 = self.dao.get(1)
        self.assertEquals(p.asdict(), p2.asdict())

        # Creating a participant also creates a ParticipantHistory row, but not a ParticipantSummary row
        ps = self.participant_summary_dao.get(1)
        self.assertIsNone(ps)
        ph = self.participant_history_dao.get([1, 1])
        expected_ph = self._participant_history_with_defaults(
            participantId=1,
            externalId=3,
            biobankId=2,
            lastModified=time,
            signUpTime=time)
        self.assertEquals(expected_ph.asdict(), ph.asdict())
コード例 #9
0
    def test_update_from_samples(self):
        # baseline_tests = ['BASELINE1', 'BASELINE2']
        baseline_tests = ["1PST8", "2PST8"]

        config.override_setting(config.BASELINE_SAMPLE_TEST_CODES,
                                baseline_tests)
        self.dao.update_from_biobank_stored_samples()  # safe noop

        p_baseline_samples = self._insert(
            Participant(participantId=1, biobankId=11))
        p_mixed_samples = self._insert(
            Participant(participantId=2, biobankId=22))
        p_no_samples = self._insert(Participant(participantId=3, biobankId=33))
        self.assertEquals(
            self.dao.get(
                p_baseline_samples.participantId).numBaselineSamplesArrived, 0)

        sample_dao = BiobankStoredSampleDao()

        def add_sample(participant, test_code, sample_id):
            TIME = datetime.datetime(2018, 3, 2)
            sample_dao.insert(
                BiobankStoredSample(biobankStoredSampleId=sample_id,
                                    biobankId=participant.biobankId,
                                    biobankOrderIdentifier='KIT',
                                    test=test_code,
                                    confirmed=TIME))

        add_sample(p_baseline_samples, baseline_tests[0], '11111')
        add_sample(p_baseline_samples, baseline_tests[1], '22223')
        add_sample(p_mixed_samples, baseline_tests[0], '11112')
        add_sample(p_mixed_samples, 'NOT1', '44441')

        self.dao.update_from_biobank_stored_samples()
        test_last_modified_doesnt_change_below = self.dao.get(1).lastModified
        self.assertEquals(
            self.dao.get(
                p_baseline_samples.participantId).numBaselineSamplesArrived, 2)
        self.assertEquals(
            self.dao.get(
                p_mixed_samples.participantId).numBaselineSamplesArrived, 1)
        self.assertEquals(
            self.dao.get(p_no_samples.participantId).numBaselineSamplesArrived,
            0)

        M_baseline_samples = self._insert(
            Participant(participantId=9, biobankId=99))
        add_sample(M_baseline_samples, baseline_tests[0], '999')
        M_first_update = self.dao.get(M_baseline_samples.participantId)

        self.dao.update_from_biobank_stored_samples()
        add_sample(M_baseline_samples, baseline_tests[1], '9999')
        M_second_update = self.dao.get(M_baseline_samples.participantId)
        self.dao.update_from_biobank_stored_samples()

        p_baseline_update = self.dao.get(p_baseline_samples.participantId)
        self.assertNotEqual(M_first_update.lastModified,
                            M_second_update.lastModified)
        self.assertEquals(p_baseline_update.lastModified,
                          test_last_modified_doesnt_change_below)
コード例 #10
0
    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))
コード例 #11
0
  def testQuery_threeSummaries_paginate(self):
    participant_1 = Participant(participantId=1, biobankId=4)
    self._insert(participant_1, 'Alice', 'Aardvark')
    participant_2 = Participant(participantId=2, biobankId=1)
    self._insert(participant_2, 'Bob', 'Builder')
    participant_3 = Participant(participantId=3, biobankId=3)
    self._insert(participant_3, 'Chad', 'Caterpillar')
    ps_1 = self.dao.get(1)
    ps_2 = self.dao.get(2)
    ps_3 = self.dao.get(3)
    self.assert_results(self.no_filter_query, [ps_1, ps_2],
                        _make_pagination_token(['Builder', 'Bob', None, 2]))
    self.assert_results(self.one_filter_query, [ps_1])
    self.assert_no_results(self.two_filter_query)
    self.assert_results(self.ascending_biobank_id_query, [ps_2, ps_3],
                        _make_pagination_token([3, 'Caterpillar', 'Chad', None, 3]))
    self.assert_results(self.descending_biobank_id_query, [ps_1, ps_3],
                        _make_pagination_token([3, 'Caterpillar', 'Chad', None, 3]))

    self.assert_results(_with_token(self.no_filter_query,
                                    _make_pagination_token(['Builder', 'Bob', None, 2])), [ps_3])
    self.assert_results(_with_token(self.ascending_biobank_id_query,
                                    _make_pagination_token([3, 'Caterpillar', 'Chad', None, 3])),
                        [ps_1])
    self.assert_results(_with_token(self.descending_biobank_id_query,
                                    _make_pagination_token([3, 'Caterpillar', 'Chad', None, 3])),
                        [ps_2])
  def test_get_counts_with_enrollment_status_member_filter(self):

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'PITT', time_int=self.time1)

    p2 = Participant(participantId=2, biobankId=5)
    self._insert(p2, 'Bob', 'Builder', 'AZ_TUCSON', time_int=self.time1, time_mem=self.time2)

    p3 = Participant(participantId=3, biobankId=6)
    self._insert(p3, 'Chad', 'Caterpillar', 'AZ_TUCSON', time_int=self.time1, time_mem=self.time2)

    p4 = Participant(participantId=4, biobankId=7)
    self._insert(p4, 'Debra', 'Dinosaur', 'PITT', time_int=self.time1, time_mem=self.time3)

    # awardee param intentionally left blank to test we can handle it
    qs = """
      bucketSize=1
      &stratification=ENROLLMENT_STATUS
      &startDate=2017-12-30
      &endDate=2018-01-04
      &awardee=
      &enrollmentStatus=MEMBER
      """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    member_count_day_1 = response[0]['metrics']['MEMBER']
    member_count_day_2 = response[1]['metrics']['MEMBER']
    member_count_day_3 = response[2]['metrics']['MEMBER']
    member_count_day_4 = response[3]['metrics']['MEMBER']
    interested_count_day_4 = response[1]['metrics']['INTERESTED']

    self.assertEquals(member_count_day_1, 0)
    self.assertEquals(member_count_day_2, 0)
    self.assertEquals(member_count_day_3, 2)
    self.assertEquals(member_count_day_4, 3)
    self.assertEquals(interested_count_day_4, 0)

    qs = """
      bucketSize=1
      &stratification=TOTAL
      &startDate=2017-12-30
      &endDate=2018-01-04
      &enrollmentStatus=MEMBER
      """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    total_count_day_1 = response[0]['metrics']['TOTAL']
    total_count_day_2 = response[1]['metrics']['TOTAL']

    self.assertEquals(total_count_day_1, 0)
    self.assertEquals(total_count_day_2, 3)
コード例 #13
0
    def test_bad_hpo_update(self):
        p = Participant(participantId=1, biobankId=2)
        time = datetime.datetime(2016, 1, 1)
        with FakeClock(time):
            self.dao.insert(p)

        p.providerLink = make_primary_provider_link_for_name('FOO')
        with self.assertRaises(BadRequest):
            self.dao.update(p)
コード例 #14
0
 def _setup_participants(self):
     self.participant1 = Participant(participantId=1, biobankId=1)
     self.participant2 = Participant(participantId=2, biobankId=2)
     self.participant_dao.insert(self.participant1)
     self.participant_dao.insert(self.participant2)
     self.assertEqual(self.participant1.isGhostId, None)
     self.assertEqual(self.participant1.dateAddedGhost, None)
     self.assertEqual(self.participant2.isGhostId, None)
     self.assertEqual(self.participant2.dateAddedGhost, None)
コード例 #15
0
    def test_update_no_expected_version_with_ps(self):
        p = Participant()
        time = datetime.datetime(2016, 1, 1)
        with random_ids([1, 2]):
            with FakeClock(time):
                self.dao.insert(p)

        p.providerLink = make_primary_provider_link_for_name('PITT')
        time2 = datetime.datetime(2016, 1, 2)
        with FakeClock(time2):
            self.dao.update(p)

        summary = self.participant_summary(p)
        self.participant_summary_dao.insert(summary)

        # lastModified, hpoId, version is updated on p after being passed in
        p2 = self.dao.get(1)
        expected_participant = self._participant_with_defaults(
            participantId=1,
            version=2,
            biobankId=2,
            lastModified=time2,
            signUpTime=time,
            hpoId=PITT_HPO_ID,
            providerLink=p2.providerLink)
        self.assertEquals(expected_participant.asdict(), p2.asdict())
        self.assertEquals(p.asdict(), p2.asdict())

        # Updating the participant provider link also updates the HPO ID on the participant summary.
        ps = self.participant_summary_dao.get(1)
        expected_ps = self._participant_summary_with_defaults(
            participantId=1,
            biobankId=2,
            signUpTime=time,
            hpoId=PITT_HPO_ID,
            firstName=summary.firstName,
            lastName=summary.lastName,
            email=summary.email)
        self.assertEquals(expected_ps.asdict(), ps.asdict())

        expected_ph = self._participant_history_with_defaults(
            participantId=1, biobankId=2, lastModified=time, signUpTime=time)
        # And updating the participant adds a new ParticipantHistory row.
        ph = self.participant_history_dao.get([1, 1])
        self.assertEquals(expected_ph.asdict(), ph.asdict())
        ph2 = self.participant_history_dao.get([1, 2])
        expected_ph2 = self._participant_history_with_defaults(
            participantId=1,
            version=2,
            biobankId=2,
            lastModified=time2,
            signUpTime=time,
            hpoId=PITT_HPO_ID,
            providerLink=p2.providerLink)
        self.assertEquals(expected_ph2.asdict(), ph2.asdict())
コード例 #16
0
 def test_insert_duplicate_biobank_id_give_up(self):
     p = Participant()
     with random_ids([1, 2]):
         self.dao.insert(p)
     rand_ints = []
     for i in range(0, MAX_INSERT_ATTEMPTS):
         rand_ints.append(i + 2)
         rand_ints.append(2)
     p2 = Participant()
     with random_ids(rand_ints):
         with self.assertRaises(ServiceUnavailable):
             self.dao.insert(p2)
コード例 #17
0
 def testQuery_twoSummaries(self):
     participant_1 = Participant(participantId=1, biobankId=2)
     self._insert(participant_1, 'Alice', 'Smith')
     participant_2 = Participant(participantId=2, biobankId=1)
     self._insert(participant_2, 'Zed', 'Zebra')
     ps_1 = self.dao.get(1)
     ps_2 = self.dao.get(2)
     self.assert_results(self.no_filter_query, [ps_1, ps_2])
     self.assert_results(self.one_filter_query, [ps_1])
     self.assert_no_results(self.two_filter_query)
     self.assert_results(self.ascending_biobank_id_query, [ps_2, ps_1])
     self.assert_results(self.descending_biobank_id_query, [ps_1, ps_2])
コード例 #18
0
    def test_update_wrong_expected_version(self):
        p = Participant()
        time = datetime.datetime(2016, 1, 1)
        with random_ids([1, 2]):
            with FakeClock(time):
                self.dao.insert(p)

        p.version = 2
        p.providerLink = make_primary_provider_link_for_name('PITT')
        time2 = datetime.datetime(2016, 1, 2)
        with FakeClock(time2):
            with self.assertRaises(PreconditionFailed):
                self.dao.update(p)
  def test_get_counts_with_single_awardee_filter(self):
    # Does the awardee filter work?

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'PITT', time_int=self.time1)

    p1 = Participant(participantId=2, biobankId=5)
    self._insert(p1, 'Bob', 'Builder', 'AZ_TUCSON', time_int=self.time1)

    p1 = Participant(participantId=3, biobankId=6)
    self._insert(p1, 'Chad', 'Caterpillar', 'AZ_TUCSON', time_int=self.time1)

    # enrollmentStatus param left blank to test we can handle it
    qs = """
      bucketSize=1
      &stratification=ENROLLMENT_STATUS
      &startDate=2017-12-30
      &endDate=2018-01-04
      &awardee=PITT
      &enrollmentStatus=
      """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    interested_count_day_1 = response[0]['metrics']['INTERESTED']
    interested_count_day_2 = response[1]['metrics']['INTERESTED']

    self.assertEquals(interested_count_day_1, 0)
    self.assertEquals(interested_count_day_2, 1)

    qs = """
      bucketSize=1
      &stratification=ENROLLMENT_STATUS
      &startDate=2017-12-30
      &endDate=2018-01-04
      &awardee=AZ_TUCSON
      """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    interested_count_day_1 = response[0]['metrics']['INTERESTED']
    interested_count_day_2 = response[1]['metrics']['INTERESTED']

    self.assertEquals(interested_count_day_1, 0)
    self.assertEquals(interested_count_day_2, 2)
コード例 #20
0
    def test_end_to_end(self):
        dao = BiobankStoredSampleDao()
        self.assertEquals(dao.count(), 0)

        # Create 3 participants and pass their (random) IDs into sample rows.
        summary_dao = ParticipantSummaryDao()
        biobank_ids = []
        participant_ids = []
        for _ in xrange(3):
            participant = self.participant_dao.insert(Participant())
            summary_dao.insert(self.participant_summary(participant))
            participant_ids.append(participant.participantId)
            biobank_ids.append(participant.biobankId)
            self.assertEquals(
                summary_dao.get(
                    participant.participantId).numBaselineSamplesArrived, 0)
        test1, test2, test3 = random.sample(_BASELINE_TESTS, 3)
        samples_file = test_data.open_biobank_samples(*biobank_ids,
                                                      test1=test1,
                                                      test2=test2,
                                                      test3=test3)
        input_filename = 'cloud%s.csv' % self._naive_utc_to_naive_central(
            clock.CLOCK.now()).strftime(
                biobank_samples_pipeline.INPUT_CSV_TIME_FORMAT)
        self._write_cloud_csv(input_filename, samples_file.read())

        biobank_samples_pipeline.upsert_from_latest_csv()

        self.assertEquals(dao.count(), 3)
        self._check_summary(participant_ids[0], test1, '2016-11-29T12:19:32')
        self._check_summary(participant_ids[1], test2, '2016-11-29T12:38:58')
        self._check_summary(participant_ids[2], test3, '2016-11-29T12:41:26')
コード例 #21
0
 def from_client_json(self, resource_json, id_=None, expected_version=None, client_id=None):
   parse_json_enum(resource_json, 'withdrawalStatus', WithdrawalStatus)
   parse_json_enum(resource_json, 'withdrawalReason', WithdrawalReason)
   parse_json_enum(resource_json, 'suspensionStatus', SuspensionStatus)
   if 'withdrawalTimeStamp' in resource_json and resource_json['withdrawalTimeStamp'] is not None:
     try:
       resource_json['withdrawalTimeStamp'] = datetime.datetime\
         .utcfromtimestamp(float(resource_json['withdrawalTimeStamp'])/1000)
     except (ValueError, TypeError):
       raise ValueError("Could not parse {} as TIMESTAMP"
                        .format(resource_json['withdrawalTimeStamp']))
   # biobankId, lastModified, signUpTime are set by DAO.
   return Participant(
     participantId=id_,
     externalId=resource_json.get('externalId'),
     version=expected_version,
     providerLink=json.dumps(resource_json.get('providerLink')),
     clientId=client_id,
     withdrawalStatus=resource_json.get('withdrawalStatus'),
     withdrawalReason=resource_json.get('withdrawalReason'),
     withdrawalAuthored=resource_json.get('withdrawalTimeStamp'),
     withdrawalReasonJustification=resource_json.get('withdrawalReasonJustification'),
     suspensionStatus=resource_json.get('suspensionStatus'),
     organizationId=get_organization_id_from_external_id(resource_json, self.organization_dao),
     hpoId=get_awardee_id_from_name(resource_json, self.hpo_dao),
     siteId=get_site_id_from_google_group(resource_json, self.site_dao))
コード例 #22
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 def test_insert_duplicate_participant_id_retry(self):
     p = Participant()
     with random_ids([1, 2]):
         self.dao.insert(p)
     p2 = Participant()
     time = datetime.datetime(2016, 1, 1)
     with random_ids([1, 3, 2, 3]):
         with FakeClock(time):
             p2 = self.dao.insert(p2)
     expected_participant = self._participant_with_defaults(
         participantId=2,
         version=1,
         biobankId=3,
         lastModified=time,
         signUpTime=time)
     self.assertEquals(expected_participant.asdict(), p2.asdict())
コード例 #23
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 def test_insert_duplicate(self):
     self.insert_codes()
     p = Participant(participantId=1, biobankId=2)
     self.participant_dao.insert(p)
     self._setup_questionnaire()
     qr = QuestionnaireResponse(questionnaireResponseId=1,
                                questionnaireId=1,
                                questionnaireVersion=1,
                                participantId=1,
                                resource=QUESTIONNAIRE_RESPONSE_RESOURCE)
     qr.answers.extend(self._names_and_email_answers())
     self.questionnaire_response_dao.insert(qr)
     qr2 = QuestionnaireResponse(questionnaireResponseId=1,
                                 questionnaireId=1,
                                 questionnaireVersion=1,
                                 participantId=1,
                                 resource=QUESTIONNAIRE_RESPONSE_RESOURCE_2)
     qr2.answers.append(
         QuestionnaireResponseAnswer(questionnaireResponseAnswerId=2,
                                     questionnaireResponseId=1,
                                     questionId=2,
                                     valueSystem='c',
                                     valueCodeId=4))
     with self.assertRaises(IntegrityError):
         self.questionnaire_response_dao.insert(qr2)
コード例 #24
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 def test_get_after_withdrawal_fails(self):
     self.insert_codes()
     p = Participant(participantId=1, biobankId=2)
     self.participant_dao.insert(p)
     self._setup_questionnaire()
     qr = QuestionnaireResponse(questionnaireResponseId=1,
                                questionnaireId=1,
                                questionnaireVersion=1,
                                participantId=1,
                                resource=QUESTIONNAIRE_RESPONSE_RESOURCE)
     qr.answers.extend(self._names_and_email_answers())
     self.questionnaire_response_dao.insert(qr)
     p.withdrawalStatus = WithdrawalStatus.NO_USE
     self.participant_dao.update(p)
     with self.assertRaises(Forbidden):
         self.questionnaire_response_dao.get(qr.questionnaireResponseId)
コード例 #25
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    def test_overwrite_existing_pairing(self):
        participant_id = 99
        created = self.dao.insert(
            Participant(participantId=participant_id,
                        biobankId=2,
                        hpoId=self._test_db.hpo_id,
                        providerLink=make_primary_provider_link_for_id(
                            self._test_db.hpo_id)))
        self.participant_summary_dao.insert(self.participant_summary(created))
        self.assertEquals(created.hpoId, self._test_db.hpo_id)  # sanity check

        other_hpo = HPODao().insert(
            HPO(hpoId=PITT_HPO_ID + 1, name='DIFFERENT_HPO'))
        other_site = SiteDao().insert(
            Site(hpoId=other_hpo.hpoId,
                 siteName='Arbitrary Site',
                 googleGroup='*****@*****.**'))

        with self.dao.session() as session:
            self.dao.add_missing_hpo_from_site(session, participant_id,
                                               other_site.siteId)

        # Original Participant + summary is affected.
        refetched = self.dao.get(participant_id)

        self.assertEquals(refetched.hpoId, other_hpo.hpoId)
        self.assertEquals(refetched.providerLink,
                          make_primary_provider_link_for_id(other_hpo.hpoId))
        self.assertEquals(
            self.participant_summary_dao.get(participant_id).hpoId,
            other_hpo.hpoId)
  def test_get_counts_with_default_parameters(self):
    # The most basic test in this class

    p1 = Participant(participantId=1, biobankId=4)
    self._insert(p1, 'Alice', 'Aardvark', 'PITT', time_int=self.time1)

    # TODO: remove bucketSize from these parameters in all tests
    qs = """
      bucketSize=1
      &stratification=ENROLLMENT_STATUS
      &startDate=2017-12-30
      &endDate=2018-01-04
      """

    qs = ''.join(qs.split())  # Remove all whitespace

    response = self.send_get('ParticipantCountsOverTime', query_string=qs)

    # You can debug API responses easily by uncommenting the lines below
    # print('response')
    # print(response)

    interested_count_day_1 = response[0]['metrics']['INTERESTED']
    interested_count_day_2 = response[1]['metrics']['INTERESTED']

    self.assertEquals(interested_count_day_1, 0)
    self.assertEquals(interested_count_day_2, 1)
コード例 #27
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    def test_dv_order_sample_update(self):
        """
    Test Biobank Direct Volunteer order
    """
        participant = self.participant_dao.insert(Participant())
        self.summary_dao.insert(self.participant_summary(participant))

        created_ts = datetime.datetime(2019, 03, 22, 18, 30, 45)
        confirmed_ts = datetime.datetime(2019, 03, 23, 12, 13, 00)

        bo = self._make_biobank_order(participantId=participant.participantId)
        BiobankOrderDao().insert(bo)

        boi = bo.identifiers[0]

        bss = BiobankStoredSample(biobankStoredSampleId=u'23523523',
                                  biobankId=participant.biobankId,
                                  test=u'1SAL2',
                                  created=created_ts,
                                  biobankOrderIdentifier=boi.value,
                                  confirmed=confirmed_ts)

        with self.participant_dao.session() as session:
            session.add(bss)

        ps = self.summary_dao.get(participant.participantId)
        self.assertIsNone(ps.sampleStatusDV1SAL2)
        self.assertIsNone(ps.sampleStatusDV1SAL2Time)

        self.summary_dao.update_from_biobank_stored_samples()
        ps = self.summary_dao.get(participant.participantId)
        self.assertEqual(ps.sampleStatus1SAL2, SampleStatus.RECEIVED)
        self.assertEqual(ps.sampleStatus1SAL2Time, confirmed_ts)
コード例 #28
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  def test_amending_biobank_order_distinct_visit_count(self):
    self.participant = self._insert(Participant(participantId=9, biobankId=13))
    with clock.FakeClock(TIME_5):
      order = self.order_dao.insert(self._make_biobank_order(biobankOrderId='2', identifiers=[
        BiobankOrderIdentifier(system='b', value='d')], samples=[BiobankOrderedSample(
                                                        biobankOrderId='2',
                                                        finalized=TIME_5,
                                                        test=BIOBANK_TESTS[0],
                                                        description='description',
                                                        processingRequired=True)]))

      summary = self.dao.get(self.participant.participantId)
      self.assertEquals(summary.numberDistinctVisits, 1)

    with clock.FakeClock(TIME_7):
      amend_order = self._get_amended_info(order)
      with self.order_dao.session() as session:
        self.order_dao._do_update(session, amend_order, order)

      # Shouldn't change on a simple amendment (unless finalized time on samples change)
      summary = self.dao.get(self.participant.participantId)
      self.assertEquals(summary.numberDistinctVisits, 1)

    with clock.FakeClock(TIME_7_5):
      cancel_request = cancel_biobank_order()
      order = self.order_dao.update_with_patch(order.biobankOrderId, cancel_request, order.version)

    # A cancelled order (even after amending) should reduce count (unless some other valid order on same day)
    summary = self.dao.get(self.participant.participantId)
    self.assertEquals(summary.numberDistinctVisits, 0)
コード例 #29
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  def test_only_update_dna_sample(self):
    dna_tests = ["1ED10", "1SAL2"]

    config.override_setting(config.DNA_SAMPLE_TEST_CODES, dna_tests)
    self.dao.update_from_biobank_stored_samples()  # safe noop

    p_dna_samples = self._insert(Participant(participantId=1, biobankId=11))

    self.assertEquals(self.dao.get(p_dna_samples.participantId).samplesToIsolateDNA, None)
    self.assertEquals(
      self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreStoredSampleTime, None)
    self.assertEquals(
      self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreOrderedSampleTime, None)

    sample_dao = BiobankStoredSampleDao()

    def add_sample(participant, test_code, sample_id, confirmed_time):
      sample_dao.insert(BiobankStoredSample(
          biobankStoredSampleId=sample_id, biobankId=participant.biobankId,
          biobankOrderIdentifier='KIT', test=test_code, confirmed=confirmed_time))

    confirmed_time_0 = datetime.datetime(2018, 3, 1)
    add_sample(p_dna_samples, dna_tests[0], '11111', confirmed_time_0)

    self.dao.update_from_biobank_stored_samples()

    self.assertEquals(self.dao.get(p_dna_samples.participantId).samplesToIsolateDNA,
                      SampleStatus.RECEIVED)
    # only update dna sample will not update enrollmentStatusCoreStoredSampleTime
    self.assertEquals(
      self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreStoredSampleTime, None)
    self.assertEquals(
      self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreOrderedSampleTime, None)
コード例 #30
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  def test_update_from_samples_changed_tests(self):
    baseline_tests = ["1PST8", "2PST8"]
    config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
    self.dao.update_from_biobank_stored_samples()  # safe noop

    participant = self._insert(Participant(participantId=1, biobankId=11))
    self.assertEquals(self.dao.get(participant.participantId).numBaselineSamplesArrived, 0)

    sample_dao = BiobankStoredSampleDao()
    def add_sample(test_code, sample_id):
      TIME = datetime.datetime(2018, 3, 2)
      sample_dao.insert(BiobankStoredSample(
          biobankStoredSampleId=sample_id, biobankId=participant.biobankId,
          biobankOrderIdentifier='KIT', test=test_code, confirmed=TIME))

    add_sample(baseline_tests[0], '11111')
    add_sample(baseline_tests[1], '22223')
    self.dao.update_from_biobank_stored_samples()
    summary = self.dao.get(participant.participantId)
    init_last_modified = summary.lastModified
    self.assertEquals(summary.numBaselineSamplesArrived, 2)
    # sleep 1 sec to make lastModified different
    time.sleep(1)
    # Simulate removal of one of the baseline tests from config.json.
    baseline_tests.pop()
    config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
    self.dao.update_from_biobank_stored_samples()

    summary = self.dao.get(participant.participantId)
    self.assertEquals(summary.numBaselineSamplesArrived, 1)
    self.assertNotEqual(init_last_modified, summary.lastModified)
コード例 #31
0
ファイル: participant.py プロジェクト: sanjuro/RCGAEO
 def show(self):
     r = Participant.get(self.params.get('id'))
コード例 #32
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ファイル: participant.py プロジェクト: sanjuro/RCGAEO
 def index(self):
     query = Participant.all()
     self.result = query.fetch(limit=1000)