meta-edc 0.3.39__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_screening/offline_models.py

@@ -1,3 +0,0 @@
-from django_collect_offline.site_offline_models import site_offline_models
-
-site_offline_models.register_for_app("meta_screening")

meta_screening/tests/holidays.csv

@@ -1,15 +0,0 @@
-2019-01-01,New Year's Day,tanzania
-2019-01-12,Zanzibar Revolution Day,tanzania
-2019-04-07,The Sheikh Abeid Amani Karume Day,tanzania
-2019-04-17,Easter Monday,tanzania
-2019-04-26,Union Day,tanzania
-2019-05-01,Labour Day,tanzania
-2019-06-26,Eid al-Fitr,tanzania
-2019-07-07,Saba Saba Day,tanzania
-2019-07-14,Good Friday,tanzania
-2019-08-08,Nane Nane Day,tanzania
-2019-10-14,Nyerere Day,tanzania
-2019-12-01,Mawlid Day,tanzania
-2019-12-09,Independence Day,tanzania
-2019-12-25,Christmas Day,tanzania
-2019-12-26,Boxing Day,tanzania

meta_screening/tests/meta_test_case_mixin.py

@@ -1,216 +0,0 @@
-from __future__ import annotations
-
-from copy import deepcopy
-from datetime import date, datetime
-
-from dateutil.relativedelta import relativedelta
-from django.conf import settings
-from django.contrib.sites.models import Site
-from edc_appointment.constants import IN_PROGRESS_APPT, INCOMPLETE_APPT
-from edc_appointment.tests.test_case_mixins import AppointmentTestCaseMixin
-from edc_constants.constants import YES
-from edc_facility.import_holidays import import_holidays
-from edc_list_data.site_list_data import site_list_data
-from edc_metadata import REQUIRED
-from edc_metadata.models import CrfMetadata
-from edc_randomization.site_randomizers import site_randomizers
-from edc_sites.site import sites
-from edc_sites.utils import add_or_update_django_sites
-from edc_visit_tracking.constants import SCHEDULED
-from model_bakery import baker
-
-from meta_edc.meta_version import PHASE_THREE
-from meta_pharmacy.prepare_meta_pharmacy import prepare_meta_pharmacy
-from meta_sites.sites import domain_suffix
-from meta_subject.models import SubjectVisit
-from meta_visit_schedule.constants import DAY1
-
-from ..models import (
-    ScreeningPartOne,
-    ScreeningPartThree,
-    ScreeningPartTwo,
-    SubjectScreening,
-)
-from .options import (
-    get_part_one_eligible_options,
-    get_part_three_eligible_options,
-    get_part_two_eligible_options,
-    now,
-)
-
-
-class MetaTestCaseMixin(AppointmentTestCaseMixin):
-    fqdn = domain_suffix
-
-    default_sites = sites.get_by_country("tanzania", aslist=True)
-
-    site_names = [s.name for s in default_sites]
-
-    import_randomization_list = True
-
-    sid_count_for_tests = 5
-
-    @classmethod
-    def setUpTestData(cls):
-        import_holidays(test=True)
-        add_or_update_django_sites(single_sites=sites.get_by_country("tanzania", aslist=True))
-        if cls.import_randomization_list:
-            randomizer_cls = site_randomizers.get(PHASE_THREE)
-            randomizer_cls.import_list(
-                verbose=False, sid_count_for_tests=cls.sid_count_for_tests
-            )
-        site_list_data.initialize()
-        site_list_data.autodiscover()
-        prepare_meta_pharmacy()
-
-    def get_subject_screening(
-        self,
-        report_datetime: datetime | None = None,
-        eligibility_datetime: datetime | None = None,
-        gender: str | None = None,
-        ethnicity: str | None = None,
-        age_in_years: int | None = None,
-    ):
-        part_one_eligible_options = deepcopy(get_part_one_eligible_options())
-        part_two_eligible_options = deepcopy(get_part_two_eligible_options())
-        part_three_eligible_options = deepcopy(get_part_three_eligible_options())
-        if report_datetime:
-            part_one_eligible_options.update(report_datetime=report_datetime)
-        part_one_eligible_options["age_in_years"] = (
-            age_in_years or part_one_eligible_options["age_in_years"]
-        )
-        part_one_eligible_options["gender"] = gender or part_one_eligible_options["gender"]
-        part_one_eligible_options["ethnicity"] = (
-            ethnicity or part_one_eligible_options["ethnicity"]
-        )
-        part_one = ScreeningPartOne.objects.create(
-            user_created="erikvw",
-            user_modified="erikvw",
-            **part_one_eligible_options,
-        )
-        screening_identifier = part_one.screening_identifier
-        self.assertEqual(part_one.reasons_ineligible_part_one, None)
-        self.assertEqual(part_one.eligible_part_one, YES)
-
-        screening_part_two = ScreeningPartTwo.objects.get(
-            screening_identifier=screening_identifier
-        )
-        for k, v in part_two_eligible_options.items():
-            setattr(screening_part_two, k, v)
-        screening_part_two.save()
-        self.assertEqual(screening_part_two.reasons_ineligible_part_two, None)
-        self.assertEqual(screening_part_two.eligible_part_two, YES)
-
-        screening_part_three = ScreeningPartThree.objects.get(
-            screening_identifier=screening_identifier
-        )
-        for k, v in part_three_eligible_options.items():
-            setattr(screening_part_three, k, v)
-        screening_part_three.save()
-        self.assertEqual(screening_part_three.reasons_ineligible_part_three, None)
-        self.assertEqual(screening_part_three.eligible_part_three, YES)
-
-        subject_screening = SubjectScreening.objects.get(
-            screening_identifier=screening_identifier
-        )
-
-        self.assertTrue(subject_screening.eligible)
-
-        if eligibility_datetime:
-            screening_part_three.eligibility_datetime = eligibility_datetime
-            screening_part_three.save()
-            subject_screening = SubjectScreening.objects.get(
-                screening_identifier=screening_identifier
-            )
-        return subject_screening
-
-    @staticmethod
-    def get_subject_consent(
-        subject_screening: SubjectScreening,
-        consent_datetime: datetime = None,
-        dob: date = None,
-        site_id: int = None,
-    ):
-        return baker.make_recipe(
-            "meta_consent.subjectconsentv1",
-            user_created="erikvw",
-            user_modified="erikvw",
-            screening_identifier=subject_screening.screening_identifier,
-            initials=subject_screening.initials,
-            gender=subject_screening.gender,
-            dob=dob or (now.date() - relativedelta(years=subject_screening.age_in_years)),
-            site=Site.objects.get(id=site_id or settings.SITE_ID),
-            consent_datetime=consent_datetime or subject_screening.report_datetime,
-        )
-
-    def get_subject_visit(
-        self,
-        visit_code: str | None = None,
-        visit_code_sequence: int | None = None,
-        subject_screening=None,
-        subject_consent=None,
-        reason: str | None = None,
-        appt_datetime: datetime | None = None,
-        gender: str | None = None,
-        ethnicity: str | None = None,
-        age_in_years: int | None = None,
-        screening_datetime: datetime | None = None,
-        eligibility_datetime: datetime | None = None,
-    ):
-        reason = reason or SCHEDULED
-        subject_screening = subject_screening or self.get_subject_screening(
-            gender=gender,
-            ethnicity=ethnicity,
-            age_in_years=age_in_years,
-            report_datetime=screening_datetime,
-            eligibility_datetime=eligibility_datetime,
-        )
-        subject_consent = subject_consent or self.get_subject_consent(subject_screening)
-        options = dict(
-            subject_identifier=subject_consent.subject_identifier,
-            visit_code=visit_code or DAY1,
-            visit_code_sequence=(
-                visit_code_sequence if visit_code_sequence is not None else 0
-            ),
-            reason=reason,
-        )
-        if appt_datetime:
-            options.update(appt_datetime=appt_datetime)
-        appointment = self.get_appointment(**options)
-        subject_visit = SubjectVisit(
-            appointment=appointment,
-            reason=SCHEDULED,
-            report_datetime=appointment.appt_datetime,
-        )
-        subject_visit.save()
-        subject_visit.refresh_from_db()
-        return subject_visit
-
-    @staticmethod
-    def get_next_subject_visit(subject_visit):
-        appointment = subject_visit.appointment
-        appointment.appt_status = INCOMPLETE_APPT
-        appointment.save()
-        appointment.refresh_from_db()
-        next_appointment = appointment.next_by_timepoint
-        next_appointment.appt_status = IN_PROGRESS_APPT
-        next_appointment.save()
-        subject_visit = SubjectVisit(
-            appointment=next_appointment,
-            reason=SCHEDULED,
-            report_datetime=next_appointment.appt_datetime,
-            visit_code=next_appointment.visit_code,
-            visit_code_sequence=next_appointment.visit_code_sequence,
-        )
-        subject_visit.save()
-        subject_visit.refresh_from_db()
-        return subject_visit
-
-    @staticmethod
-    def get_crf_metadata(subject_visit):
-        return CrfMetadata.objects.filter(
-            subject_identifier=subject_visit.subject_identifier,
-            visit_code=subject_visit.visit_code,
-            visit_code_sequence=subject_visit.visit_code_sequence,
-            entry_status=REQUIRED,
-        )

meta_screening/tests/options.py

@@ -1,127 +0,0 @@
-from datetime import datetime
-from random import sample
-from secrets import choice
-from string import ascii_uppercase
-from zoneinfo import ZoneInfo
-
-from dateutil.relativedelta import relativedelta
-from django.conf import settings
-from django.contrib.sites.models import Site
-from edc_constants.constants import (
-    BLACK,
-    FEMALE,
-    NO,
-    NOT_APPLICABLE,
-    RANDOM_SAMPLING,
-    YES,
-)
-from edc_reportable.units import MICROMOLES_PER_LITER, MILLIMOLES_PER_LITER
-from faker import Faker
-
-from meta_edc.meta_version import get_meta_version
-from meta_screening.forms import part_one_fields, part_three_fields, part_two_fields
-
-fake = Faker()
-now = datetime(2019, 5, 1).astimezone(ZoneInfo("UTC"))
-tomorrow = now + relativedelta(days=1)
-
-
-def get_part_one_eligible_options():
-    options = dict(
-        age_in_years=25,
-        art_six_months=YES,
-        continue_part_two=YES,
-        ethnicity=BLACK,
-        gender=FEMALE,
-        hiv_pos=YES,
-        hospital_identifier="".join(map(str, sample(range(0, 10), 10))),
-        initials=f"{choice(ascii_uppercase)}{choice(ascii_uppercase)}",
-        lives_nearby=YES,
-        on_rx_stable=YES,
-        pregnant=NOT_APPLICABLE,
-        report_datetime=now,
-        screening_consent=YES,
-        selection_method=RANDOM_SAMPLING,
-        staying_nearby_12=YES,
-        vl_undetectable=YES,
-        meta_phase_two=NO,
-        site=Site.objects.get(id=settings.SITE_ID),
-    )
-    if fld := [f for f in part_one_fields if f not in options]:
-        raise TypeError(
-            f"Missing part one fields for meta phase {get_meta_version()}. Got {fld}."
-        )
-    return options
-
-
-def get_part_two_eligible_options(report_datetime: datetime = None) -> dict:
-    options = dict(
-        acute_condition=NO,
-        acute_metabolic_acidosis=NO,
-        advised_to_fast=YES,
-        alcoholism=NO,
-        already_fasted=NO,
-        appt_datetime=report_datetime or (now + relativedelta(days=10)),
-        congestive_heart_failure=NO,
-        liver_disease=NO,
-        metformin_sensitivity=NO,
-        part_two_report_datetime=report_datetime or now,
-        renal_function_condition=NO,
-        tissue_hypoxia_condition=NO,
-        has_dm=NO,
-        on_dm_medication=NO,
-        agree_to_p3=YES,
-        p3_ltfu=NOT_APPLICABLE,
-        p3_ltfu_date=None,
-        p3_ltfu_comment=None,
-        contact_number=None,
-    )
-    if fld := [f for f in part_two_fields if f not in options]:
-        raise TypeError(
-            f"Missing part two fields for meta phase {get_meta_version()}. Got {fld}."
-        )
-    return options
-
-
-def get_part_three_eligible_options(report_datetime: datetime = None):
-    options = dict(
-        creatinine_performed=YES,
-        creatinine_units=MICROMOLES_PER_LITER,
-        creatinine_value=50,
-        dia_blood_pressure=65,
-        dia_blood_pressure_one=65,
-        dia_blood_pressure_two=65,
-        fasting=YES,
-        fasting_duration_str="8h",
-        hba1c_performed=YES,
-        hba1c_datetime=report_datetime or now,
-        hba1c_value=7.0,
-        height=110,
-        fbg_datetime=tomorrow,
-        fbg_units=MILLIMOLES_PER_LITER,
-        fbg_value=6.9,
-        ogtt_base_datetime=tomorrow + relativedelta(minutes=5),
-        ogtt_datetime=tomorrow + relativedelta(hours=2),
-        ogtt_units=MILLIMOLES_PER_LITER,
-        ogtt_value=7.8,
-        repeat_glucose_opinion=NO,
-        ogtt2_performed=NOT_APPLICABLE,
-        part_three_report_datetime=report_datetime or now,
-        reasons_unsuitable=None,
-        sys_blood_pressure=120,
-        sys_blood_pressure_one=120,
-        sys_blood_pressure_two=120,
-        unsuitable_agreed=NOT_APPLICABLE,
-        unsuitable_for_study=NO,
-        urine_bhcg_date=None,
-        urine_bhcg_performed=NOT_APPLICABLE,
-        urine_bhcg_value=NOT_APPLICABLE,
-        waist_circumference=130,
-        weight=65,
-        severe_htn=NO,
-    )
-    if fld := [f for f in part_three_fields if f not in options]:
-        raise TypeError(
-            f"Missing part three fields for meta phase {get_meta_version()}. Got {fld}."
-        )
-    return options