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

meta_visit_schedule/visit_schedules/phase_three/crfs.py

@@ -9,6 +9,7 @@ crfs_prn = CrfCollection(
     Crf(show_order=255, model="meta_subject.bloodresultslft"),
     Crf(show_order=265, model="meta_subject.bloodresultslipids"),
     Crf(show_order=268, model="meta_subject.bloodresultsins"),
+    Crf(show_order=321, model="meta_subject.hivexitreview"),
     Crf(show_order=461, model="meta_subject.eq5d3l"),
     Crf(show_order=466, model="meta_subject.sf12"),
     Crf(show_order=471, model="meta_subject.mnsi"),
@@ -48,6 +49,7 @@ crfs_d1 = CrfCollection(
     Crf(show_order=360, model="meta_subject.malariatest"),
     Crf(show_order=370, model="meta_subject.urinedipsticktest"),
     Crf(show_order=400, model="meta_subject.studymedication"),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="day1",
 )
 
@@ -61,6 +63,7 @@ crfs_w2 = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l"),
     Crf(show_order=465, model="meta_subject.sf12"),
     Crf(show_order=480, model="meta_subject.healtheconomicssimple"),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="week2",
 )
 
@@ -75,6 +78,7 @@ crfs_1m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=480, model="meta_subject.healtheconomicssimple", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="1m",
 )
 
@@ -91,6 +95,7 @@ crfs_3m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate"),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="3m",
 )
 
@@ -108,6 +113,7 @@ crfs_6m = CrfCollection(
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="6m",
 )
 
@@ -121,6 +127,7 @@ crfs_9m = CrfCollection(
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="9m",
 )
 
@@ -135,9 +142,11 @@ crfs_12m = CrfCollection(
     Crf(show_order=250, model="meta_subject.bloodresultslipids"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="12m",
 )
 
@@ -148,9 +157,11 @@ crfs_15m = CrfCollection(
     Crf(show_order=200, model="meta_subject.glucosefbg"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="15m",
 )
 
@@ -162,9 +173,11 @@ crfs_18m = CrfCollection(
     Crf(show_order=220, model="meta_subject.bloodresultsfbc"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="18m",
 )
 
@@ -175,9 +188,11 @@ crfs_21m = CrfCollection(
     Crf(show_order=200, model="meta_subject.glucosefbg"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="21m",
 )
 
@@ -189,13 +204,15 @@ crfs_24m = CrfCollection(
     Crf(show_order=220, model="meta_subject.bloodresultsrft"),
     Crf(show_order=230, model="meta_subject.bloodresultslft"),
     Crf(show_order=240, model="meta_subject.bloodresultsfbc"),
-    Crf(show_order=250, model="meta_subject.bloodresultslipids"),
+    # Crf(show_order=250, model="meta_subject.bloodresultslipids"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="24m",
 )
 
@@ -205,10 +222,12 @@ crfs_27m = CrfCollection(
     Crf(show_order=155, model="meta_subject.glucose", required=False),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="27m",
 )
 
@@ -219,10 +238,12 @@ crfs_30m = CrfCollection(
     Crf(show_order=205, model="meta_subject.glucosefbg"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="30m",
 )
 
@@ -232,10 +253,12 @@ crfs_33m = CrfCollection(
     Crf(show_order=155, model="meta_subject.glucose", required=False),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="33m",
 )
 
@@ -250,10 +273,12 @@ crfs_36m = CrfCollection(
     Crf(show_order=250, model="meta_subject.bloodresultslipids"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l"),
     Crf(show_order=465, model="meta_subject.sf12"),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="36m",
 )
 
@@ -263,10 +288,12 @@ crfs_39m = CrfCollection(
     Crf(show_order=155, model="meta_subject.glucose", required=False),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="39m",
 )
 
@@ -277,10 +304,12 @@ crfs_42m = CrfCollection(
     Crf(show_order=200, model="meta_subject.glucosefbg"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="42m",
 )
 
@@ -290,10 +319,12 @@ crfs_45m = CrfCollection(
     Crf(show_order=155, model="meta_subject.glucose", required=False),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview", required=False),
     Crf(show_order=460, model="meta_subject.eq5d3l", required=False),
     Crf(show_order=465, model="meta_subject.sf12", required=False),
     Crf(show_order=470, model="meta_subject.mnsi", required=False),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="45m",
 )
 
@@ -308,9 +339,11 @@ crfs_48m = CrfCollection(
     Crf(show_order=250, model="meta_subject.bloodresultslipids"),
     Crf(show_order=300, model="meta_subject.studymedication"),
     Crf(show_order=310, model="meta_subject.medicationadherence"),
+    Crf(show_order=320, model="meta_subject.hivexitreview"),
     Crf(show_order=460, model="meta_subject.eq5d3l"),
     Crf(show_order=465, model="meta_subject.sf12"),
     Crf(show_order=470, model="meta_subject.mnsi"),
     Crf(show_order=500, model="meta_subject.healtheconomicsupdate", required=False),
+    Crf(show_order=600, model="meta_subject.nextappointment", required=False),
     name="48m",
 )

meta_visit_schedule/visit_schedules/phase_three/schedule.py

@@ -47,10 +47,10 @@ from .crfs import (
     crfs_48m,
     crfs_d1,
     crfs_missed,
+    crfs_w2,
 )
 from .crfs import crfs_prn as default_crfs_prn
 from .crfs import crfs_unscheduled as default_crfs_unscheduled
-from .crfs import crfs_w2
 from .requisitions import (
     requisitions_1m,
     requisitions_3m,
@@ -70,10 +70,10 @@ from .requisitions import (
     requisitions_45m,
     requisitions_48m,
     requisitions_d1,
+    requisitions_w2,
 )
 from .requisitions import requisitions_prn as default_requisitions_prn
 from .requisitions import requisitions_unscheduled as default_requisitions_unscheduled
-from .requisitions import requisitions_w2
 
 
 class Visit(BaseVisit):
@@ -101,7 +101,7 @@ class Visit(BaseVisit):
 # schedule for new participants
 schedule = Schedule(
     name=SCHEDULE,
-    verbose_name="Day 1 to Month 12 Follow-up",
+    verbose_name="Day 1 to Month 36/48 Follow-up",
     onschedule_model="meta_prn.onschedule",
     offschedule_model="meta_prn.offschedule",
     consent_definitions=[consent_v1],
@@ -286,7 +286,7 @@ visit36 = Visit(
     timepoint=14,
     rbase=relativedelta(months=36),
     rlower=relativedelta(months=1),
-    rupper=relativedelta(months=1),
+    rupper=relativedelta(months=2),
     requisitions=requisitions_36m,
     crfs=crfs_36m,
     facility_name=FIVE_DAY_CLINIC,

meta_visit_schedule/visit_schedules/phase_three/schedule_dm_referral.py

@@ -6,8 +6,7 @@ from edc_visit_schedule.visit import Crf, CrfCollection, Visit
 from meta_consent.consents import consent_v1
 
 from ...constants import DM_BASELINE, DM_FOLLOWUP, SCHEDULE_DM_REFERRAL
-from .crfs import crfs_missed
-from .crfs import crfs_prn
+from .crfs import crfs_missed, crfs_prn
 from .crfs import crfs_prn as default_crfs_prn
 
 crfs_baseline = CrfCollection(

meta_visit_schedule/visit_schedules/phase_three/schedule_pregnancy.py

@@ -6,8 +6,7 @@ from edc_visit_schedule.visit import Visit
 from meta_consent.consents import consent_v1
 
 from ...constants import DELIVERY, SCHEDULE_PREGNANCY
-from .crfs import crfs_missed
-from .crfs import crfs_prn
+from .crfs import crfs_missed, crfs_prn
 from .crfs import crfs_prn as default_crfs_prn
 from .crfs_pregnancy import crfs_pregnancy
 
@@ -28,7 +27,7 @@ visit = Visit(
     timepoint=200,
     rbase=relativedelta(days=0),
     rlower=relativedelta(days=0),
-    rupper=relativedelta(months=12),
+    rupper=relativedelta(months=24),
     crfs=crfs_pregnancy,
     crfs_prn=crfs_prn or default_crfs_prn,
     crfs_missed=crfs_missed,

meta_ae/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_ae/tests/tests/test_actions.py

@@ -1,127 +0,0 @@
-from django.core.exceptions import ObjectDoesNotExist
-from django.test import TestCase, override_settings
-from edc_action_item.models import ActionItem
-from edc_adverse_event.constants import (
-    AE_FOLLOWUP_ACTION,
-    AE_TMG_ACTION,
-    DEATH_REPORT_ACTION,
-    DEATH_REPORT_TMG_ACTION,
-)
-from edc_constants.constants import CLOSED, NEW
-from edc_reportable.constants import GRADE4, GRADE5
-from model_bakery import baker
-
-from meta_screening.tests.meta_test_case_mixin import MetaTestCaseMixin
-
-
-class TestActions(MetaTestCaseMixin, TestCase):
-    def test_ae_initial_creates_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        ae_initial = baker.make_recipe(
-            "meta_ae.aeinitial", subject_identifier=subject_consent.subject_identifier
-        )
-
-        try:
-            action_item = ActionItem.objects.get(
-                action_identifier=ae_initial.action_identifier
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-        else:
-            self.assertEqual(action_item.status, CLOSED)
-            self.assertEqual(
-                action_item.subject_identifier, subject_consent.subject_identifier
-            )
-
-    def test_ae_initial_creates_ae_followup_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        ae_initial = baker.make_recipe(
-            "meta_ae.aeinitial", subject_identifier=subject_consent.subject_identifier
-        )
-
-        action_item = ActionItem.objects.get(action_identifier=ae_initial.action_identifier)
-        try:
-            action_item = ActionItem.objects.get(
-                parent_action_item=action_item,
-                action_type__name=AE_FOLLOWUP_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-        else:
-            self.assertEqual(action_item.status, NEW)
-
-    @override_settings(EDC_RANDOMIZATION_REGISTER_DEFAULT_RANDOMIZER=False)
-    def test_ae_initial_G4_creates_ae_tmg_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        baker.make_recipe(
-            "meta_ae.aeinitial",
-            subject_identifier=subject_consent.subject_identifier,
-            ae_grade=GRADE4,
-        )
-
-        try:
-            ActionItem.objects.get(
-                action_type__name=AE_TMG_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-
-    def test_ae_initial_G5_creates_death_report_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        baker.make_recipe(
-            "meta_ae.aeinitial",
-            subject_identifier=subject_consent.subject_identifier,
-            ae_grade=GRADE5,
-        )
-        try:
-            ActionItem.objects.get(
-                action_type__name=DEATH_REPORT_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-
-        self.assertRaises(
-            ObjectDoesNotExist,
-            ActionItem.objects.get,
-            action_type__name=DEATH_REPORT_TMG_ACTION,
-            subject_identifier=subject_consent.subject_identifier,
-        )
-
-    def test_death_report_create_death_report_tmg_action(self):
-        subject_screening = self.get_subject_screening()
-        subject_consent = self.get_subject_consent(subject_screening)
-        baker.make_recipe(
-            "meta_ae.aeinitial",
-            subject_identifier=subject_consent.subject_identifier,
-            ae_grade=GRADE5,
-        )
-        action_item = ActionItem.objects.get(
-            action_type__name=DEATH_REPORT_ACTION,
-            subject_identifier=subject_consent.subject_identifier,
-        )
-
-        baker.make_recipe(
-            "meta_ae.deathreport",
-            subject_identifier=subject_consent.subject_identifier,
-            action_identifier=action_item.action_identifier,
-        )
-
-        action_item.refresh_from_db()
-        self.assertEqual(action_item.status, CLOSED)
-
-        try:
-            action_item = ActionItem.objects.get(
-                action_type__name=DEATH_REPORT_TMG_ACTION,
-                subject_identifier=subject_consent.subject_identifier,
-            )
-        except ObjectDoesNotExist:
-            self.fail("ObjectDoesNotExist unexpectedly raised.")
-        else:
-            self.assertEqual(action_item.status, NEW)

meta_ae/tests/urls.py

@@ -1,10 +0,0 @@
-from django.contrib import admin
-from django.urls.conf import include, path
-
-from meta_ae.admin_site import meta_ae_admin
-
-urlpatterns = [
-    path("ae/", include("meta_ae.urls")),
-    path("admin/", meta_ae_admin.urls),
-    path("admin/", admin.site.urls),
-]

meta_analytics/dataframes/enrolled/__init__.py

@@ -1 +0,0 @@
-from .get_glucose_df import get_glucose_df

meta_analytics/dataframes/enrolled/get_glucose_df.py

@@ -1,122 +0,0 @@
-import numpy as np
-import pandas as pd
-from django_pandas.io import read_frame
-from edc_pdutils.dataframes import get_eos, get_subject_consent, get_subject_visit
-
-from meta_subject.models import Glucose, GlucoseFbg
-
-
-def get_glucose_df() -> pd.DataFrame:
-    qs_glucose_fbg = GlucoseFbg.objects.all()
-    df_glucose_fbg = read_frame(qs_glucose_fbg)
-    df_glucose_fbg.rename(
-        columns={"fbg_fasting": "fasting", "subject_visit": "subject_visit_id"},
-        inplace=True,
-    )
-
-    df_glucose_fbg.loc[(df_glucose_fbg["fasting"] == "fasting"), "fasting"] = "Yes"
-    df_glucose_fbg.loc[(df_glucose_fbg["fasting"] == "non_fasting"), "fasting"] = "No"
-    df_glucose_fbg["fasting_hrs"] = np.nan
-    df_glucose_fbg["fasting_hrs"] = df_glucose_fbg["fasting_duration_delta"].apply(
-        lambda x: x.total_seconds() / 3600
-    )
-    df_glucose_fbg["fasting_hrs"] = df_glucose_fbg["fasting_hrs"].apply(
-        lambda x: 8.05 if not x else x
-    )
-    # df_glucose_fbg = df_glucose_fbg.loc[df_glucose_fbg["fasting_hrs"] >= 8.0]
-    # df_glucose_fbg.reset_index(drop=True, inplace=True)
-    df_glucose_fbg.loc[
-        :,
-        ["ogtt_value", "ogtt_units", "ogtt_datetime"],
-    ] = [np.nan, None, pd.NaT]
-    df_glucose_fbg["source"] = "meta_subject.glucosefbg"
-
-    qs_glucose = Glucose.objects.all()
-    df_glucose = read_frame(qs_glucose)
-    df_glucose.rename(columns={"subject_visit": "subject_visit_id"}, inplace=True)
-    df_glucose.loc[(df_glucose["fasting"] == "fasting"), "fasting"] = "Yes"
-    df_glucose.loc[(df_glucose["fasting"] == "non_fasting"), "fasting"] = "No"
-    df_glucose["fasting_hrs"] = np.nan
-    df_glucose["fasting_hrs"] = df_glucose[df_glucose["fasting"] == "Yes"][
-        "fasting_duration_delta"
-    ].apply(lambda x: x.total_seconds() / 3600)
-    df_glucose["fasting_hrs"] = df_glucose["fasting_hrs"].apply(lambda x: 8.05 if not x else x)
-    # df_glucose = df_glucose.loc[df_glucose["fasting_hrs"] >= 8.0]
-    # df_glucose.reset_index(drop=True, inplace=True)
-    df_glucose["source"] = "meta_subject.glucose"
-
-    keep_cols = [
-        "subject_visit_id",
-        "fasting",
-        "fasting_hrs",
-        "fbg_value",
-        "fbg_units",
-        "fbg_datetime",
-        "ogtt_value",
-        "ogtt_units",
-        "ogtt_datetime",
-        "source",
-        "revision",
-        "report_datetime",
-    ]
-    df_glucose = df_glucose[keep_cols]
-    df_glucose_fbg = df_glucose_fbg[keep_cols]
-    # df = pd.concat([df_glucose_fbg, df_glucose])
-    df = pd.merge(
-        df_glucose,
-        df_glucose_fbg,
-        on="subject_visit_id",
-        how="outer",
-        indicator=True,
-        suffixes=("", "_2"),
-    )
-
-    for suffix in ["", "_2"]:
-        cols = [f"fasting_hrs{suffix}", f"fbg_value{suffix}", f"ogtt_value{suffix}"]
-        df[cols] = df[cols].apply(pd.to_numeric)
-        cols = [f"fbg_datetime{suffix}", f"ogtt_datetime{suffix}"]
-        df[cols] = df[cols].apply(pd.to_datetime)
-        df.loc[
-            (df[f"fbg_units{suffix}"] != "mmol/L (millimoles/L)")
-            & (df[f"fbg_value{suffix}"] >= 0),
-            f"fbg_units{suffix}",
-        ] = "mmol/L (millimoles/L)"
-        df.loc[
-            (df[f"ogtt_units{suffix}"] != "mmol/L (millimoles/L)")
-            & (df[f"ogtt_value{suffix}"] >= 0),
-            f"ogtt_units{suffix}",
-        ] = "mmol/L (millimoles/L)"
-        # remove values if not fasted
-        # df.loc[(df[f"fasting{suffix}"] != YES), f"fbg_value{suffix}"] = np.nan
-        # df.loc[(df[f"fasting{suffix}"] != YES), f"ogtt_value{suffix}"] = np.nan
-
-    # reconcile all to single column
-    df.loc[(df["fbg_value"].isna()) & (df["fbg_value_2"].notna()), "fbg_value"] = df[
-        "fbg_value_2"
-    ]
-    df.loc[(df["ogtt_value"].isna()) & (df["ogtt_value_2"].notna()), "ogtt_value"] = df[
-        "ogtt_value_2"
-    ]
-    cols = [col for col in list(df.columns) if col.endswith("_2")]
-    df.drop(columns=cols, inplace=True)
-    cols = [col for col in list(df.columns) if col.endswith("_3")]
-    df.drop(columns=cols, inplace=True)
-
-    df_subject_visit = get_subject_visit("meta_subject.subjectvisit")
-    df_consent = get_subject_consent("meta_consent.subjectconsent")
-    df_eos = get_eos("meta_prn.endofstudy")
-
-    df = pd.merge(df_subject_visit, df, on="subject_visit_id", how="left")
-    df = pd.merge(df, df_consent, on="subject_identifier", how="left")
-    df = pd.merge(df, df_eos, on="subject_identifier", how="left")
-
-    df["visit_days"] = df["baseline_datetime"].rsub(df["visit_datetime"]).dt.days
-    df["fgb_days"] = df["baseline_datetime"].rsub(df["fbg_datetime"]).dt.days
-    df["ogtt_days"] = df["baseline_datetime"].rsub(df["ogtt_datetime"]).dt.days
-    df["visit_days"] = pd.to_numeric(df["visit_days"], downcast="integer")
-    df["fgb_days"] = pd.to_numeric(df["fgb_days"], downcast="integer")
-    df["ogtt_days"] = pd.to_numeric(df["ogtt_days"], downcast="integer")
-
-    df = df.sort_values(by=["subject_identifier", "visit_code"])
-    df.reset_index(drop=True, inplace=True)
-    return df

meta_analytics/tests/test_endpoints_by_date.py

@@ -1,94 +0,0 @@
-from datetime import datetime
-
-import numpy as np
-import pandas as pd
-from dateutil.relativedelta import relativedelta
-from django.test import TestCase
-from edc_constants.constants import YES
-
-from meta_analytics.dataframes import EndpointByDate
-
-
-class TestEndpointsByDate(TestCase):
-    def test_case_one(self):
-        def d(m: int, w: int | None = None):
-            if w:
-                return datetime.now() - relativedelta(months=m, weeks=w)
-            return datetime.now() - relativedelta(months=m)
-
-        def append_to(subject_df, endpoint_df):
-            if endpoint_df.empty:
-                endpoint_df = subject_df.copy()
-            elif subject_df.empty:
-                pass
-            else:
-                endpoint_df = pd.concat([endpoint_df, subject_df])
-                endpoint_df = self.endpoint_df.sort_values(
-                    by=["subject_identifier", "visit_code"]
-                )
-                endpoint_df.reset_index(drop=True, inplace=True)
-
-        subject_identifier = "101-1"
-        data = {
-            "subject_identifier": [subject_identifier] * 10,
-            "visit_code": [
-                1000.0,
-                1005.0,
-                1010.0,
-                1030.0,
-                1060.0,
-                1090.0,
-                1120.0,
-                1115.0,
-                1118.0,
-                1210.0,
-            ],
-            "fasting": [YES] * 10,
-            "fbg_datetime": [
-                d(0),
-                d(0, 2),
-                d(1),
-                d(3),
-                d(6),
-                d(9),
-                d(12),
-                d(15),
-                d(18),
-                d(21),
-            ],
-            "fbg_value": [np.nan, 6.9, 6.9, 7.1, 7.1, 6.4, 7.0, np.nan, 8.1, np.nan],
-            "ogtt_value": [
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                np.nan,
-                7.9,
-                np.nan,
-            ],
-        }
-
-        fbgs = [np.nan, 6.9, 6.9, 7.1, 7.1, 6.4, 7.0, np.nan, 8.1, np.nan]
-        ogtts = [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, 7.9, np.nan]
-
-        fbgs = [np.nan, 6.9, 6.9, 7.1, 7.1, 6.4, 7.0, 8.1, np.nan, np.nan]
-        ogtts = [np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, np.nan, 7.9, np.nan, np.nan]
-
-        data.update(fbg_values=fbgs, ogtt_values=ogtts)
-        subject_df = pd.DataFrame(data)
-        subject_df["fasting"] = subject_df.apply(
-            lambda r: np.nan if pd.isna(r.fbg_value) else r.fbg_value, axis=1
-        )
-        subject_df["fbg_datetime"] = subject_df.apply(
-            lambda r: np.nan if pd.isna(r.fbg_value) else r.fbg_datetime, axis=1
-        )
-
-        endpoint_df = pd.DataFrame()
-        for index, row in subject_df.iterrows():
-            cls = EndpointByDate(index, row, fbg_threshhold=7.0, ogtt_threshhold=11.1)
-            append_to(cls.subject_df, endpoint_df)
-
-        endpoint_df