meta-edc 1.0.3__tar.gz → 1.0.5__tar.gz

{meta_edc-1.0.3 → meta_edc-1.0.5}/.pre-commit-config.yaml

@@ -3,20 +3,20 @@ exclude: tests/etc/user-*
 
 repos:
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.10
+    rev: 1.8.3
     hooks:
       - id: bandit
         args:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 24.10.0
+    rev: 25.1.0
     hooks:
       - id: black
         language_version: python3.12
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
+    rev: 7.1.2
     hooks:
       - id: flake8
         args:

{meta_edc-1.0.3 → meta_edc-1.0.5}/CHANGES

@@ -1,6 +1,14 @@
 Changes
 -------
 
+1.0.5
+-----
+- bump edc-pharmacy, edc=1.0.7
+- add django-admin-rangefilter as requirement
+
+1.0.4
+-----
+
 1.0.3
 -----
 - edc 1.0.2

{meta_edc-1.0.3 → meta_edc-1.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: meta-edc
-Version: 1.0.3
+Version: 1.0.5
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -693,7 +693,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==1.0.2
+Requires-Dist: edc==1.0.8
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: celery[redis]
@@ -712,7 +712,7 @@ Metformin treatment in Africa- META
 * https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
 * http://www.isrctn.com/ISRCTN76157257
 
-py 3.12 / DJ 5.1 / edc 0.6.0 (META3)
+py 3.12 / DJ 5.1.5 / edc 1.0.3 (META3)
 
 This codebase is used for two randomized clinical trials:
 

{meta_edc-1.0.3 → meta_edc-1.0.5}/README.rst

@@ -11,7 +11,7 @@ Metformin treatment in Africa- META
 * https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
 * http://www.isrctn.com/ISRCTN76157257
 
-py 3.12 / DJ 5.1 / edc 0.6.0 (META3)
+py 3.12 / DJ 5.1.5 / edc 1.0.3 (META3)
 
 This codebase is used for two randomized clinical trials:
 

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_analytics/dataframes/get_eos_df.py

@@ -14,7 +14,7 @@ def get_eos_df() -> pd.DataFrame:
     df_visit = get_subject_visit("meta_subject.subjectvisit")
     df_last_visit = (
         df_visit.groupby(["subject_identifier", "site"])
-        .agg({"last_visit_code": "max", "last_visit_datetime": "max"})
+        .agg({"endline_visit_code": "max", "endline_visit_datetime": "max"})
         .reset_index()
     )
     df_last_visit = df_last_visit.rename(columns={"site": "site_id"})

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_analytics/dataframes/get_last_imp_visits_df.py

@@ -37,11 +37,14 @@ def get_last_imp_visits_df(
     df_meds = (
         df_meds[(df_meds.refill == "Yes") & (site_cond(df_meds, site_id))]
         .groupby(by=["subject_identifier", "site_id"])
-        .agg({"last_visit_code": "max", "last_visit_datetime": "max"})
+        .agg({"endline_visit_code": "max", "endline_visit_datetime": "max"})
         .reset_index()
     )
     df_meds = df_meds.rename(
-        columns={"last_visit_code": "imp_visit_code", "last_visit_datetime": "imp_visit_date"}
+        columns={
+            "endline_visit_code": "imp_visit_code",
+            "endline_visit_datetime": "imp_visit_date",
+        }
     )
     df_meds.reset_index()
 

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_analytics/dataframes/screening/get_screening_df.py

@@ -110,7 +110,8 @@ def get_screening_df(df: pd.DataFrame | None = None) -> pd.DataFrame:
 
     # bmi
     # subject SR9E8B4D has eligible part two == No but subject has a glucose value
-    df.loc[(df["screening_identifier"] == "SR9E8B4D"), "eligible_part_two"] = "Yes"
+    # NOTE: update 10-02-2025: subject is not eligible by congestive_heart_failure
+    # df.loc[(df["screening_identifier"] == "SR9E8B4D"), "eligible_part_two"] = "Yes"
 
     # merge with physical exam to get waist circumference if taken at baseline
     subject_identifiers = list(df["subject_identifier"])

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_edc/settings/debug.py

@@ -7,11 +7,11 @@ from .defaults import *  # noqa
 print(f"Settings file {__file__}")
 
 # TZ Sites:
-SITE_ID = SiteID(default=20)  # Amana
+# SITE_ID = SiteID(default=20)  # Amana
 # SITE_ID = SiteID(default=10)  # Hindu Mandal
 # SITE_ID = SiteID(default=40)  # Mwananyamala
 # SITE_ID = SiteID(default=50)  # Mbagala
-# SITE_ID = SiteID(default=60)  # Mnazi-Moja
+SITE_ID = SiteID(default=60)  # Mnazi-Moja
 # SITE_ID = SiteID(default=30)  # Temeke
 INDEX_PAGE = "http://localhost:8000"
 EDC_SITES_UAT_DOMAIN = False

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_edc/settings/defaults.py

@@ -94,6 +94,7 @@ INSTALLED_APPS = [
     # "django_celery_results",
     "django_db_views",
     "fontawesomefree",
+    "rangefilter",
     "django_crypto_fields.apps.AppConfig",
     "django_revision.apps.AppConfig",
     # "django_extensions",

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_edc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: meta-edc
-Version: 1.0.3
+Version: 1.0.5
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -693,7 +693,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==1.0.2
+Requires-Dist: edc==1.0.8
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: celery[redis]
@@ -712,7 +712,7 @@ Metformin treatment in Africa- META
 * https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
 * http://www.isrctn.com/ISRCTN76157257
 
-py 3.12 / DJ 5.1 / edc 0.6.0 (META3)
+py 3.12 / DJ 5.1.5 / edc 1.0.3 (META3)
 
 This codebase is used for two randomized clinical trials:
 

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_edc.egg-info/SOURCES.txt

@@ -385,6 +385,7 @@ meta_lists/migrations/0015_abnormalfootappearanceobservations_extra_value_and_mo
 meta_lists/migrations/0016_alter_abnormalfootappearanceobservations_options_and_more.py
 meta_lists/migrations/0017_complications_dmmedications_dmtreatments_and_more.py
 meta_lists/migrations/0018_missedreferralreasons.py
+meta_lists/migrations/0019_auto_20250128_0143.py
 meta_lists/migrations/__init__.py
 meta_lists/tests/__init__.py
 meta_lists/tests/test_lists.py
@@ -866,6 +867,7 @@ meta_subject/admin/malaria_test_admin.py
 meta_subject/admin/medication_adherence_admin.py
 meta_subject/admin/mnsi_admin.py
 meta_subject/admin/modeladmin.py
+meta_subject/admin/next_appointment_admin.py
 meta_subject/admin/other_arv_regimens_admin.py
 meta_subject/admin/patient_history_admin.py
 meta_subject/admin/physical_exam_admin.py
@@ -915,6 +917,7 @@ meta_subject/forms/malaria_test_form.py
 meta_subject/forms/medication_adherence_form.py
 meta_subject/forms/mixins.py
 meta_subject/forms/mnsi_form.py
+meta_subject/forms/next_appointment_form.py
 meta_subject/forms/other_arv_regimens_detail_form.py
 meta_subject/forms/other_arv_regimens_form.py
 meta_subject/forms/patient_history_form.py
@@ -1164,6 +1167,11 @@ meta_subject/migrations/0212_auto_20240827_2222.py
 meta_subject/migrations/0213_rename_bloodresultslipid_bloodresultslipids_and_more.py
 meta_subject/migrations/0214_historicalstudymedication_stock_codes_and_more.py
 meta_subject/migrations/0215_alter_historicalstudymedication_stock_codes_and_more.py
+meta_subject/migrations/0216_historicalnextappointment_nextappointment.py
+meta_subject/migrations/0217_alter_historicalnextappointment_appt_datetime_and_more.py
+meta_subject/migrations/0218_alter_historicalnextappointment_appt_date_and_more.py
+meta_subject/migrations/0219_remove_historicalnextappointment_allow_create_interim_and_more.py
+meta_subject/migrations/0220_historicalbloodresultsgludummy_bloodresultsgludummy.py
 meta_subject/migrations/__init__.py
 meta_subject/model_mixins/__init__.py
 meta_subject/model_mixins/arv_history_model_mixin.py
@@ -1189,6 +1197,7 @@ meta_subject/models/hepatitis_test.py
 meta_subject/models/malaria_test.py
 meta_subject/models/medication_adherence.py
 meta_subject/models/mnsi.py
+meta_subject/models/next_appointment.py
 meta_subject/models/off_study_drug.py
 meta_subject/models/other_arv_regimens.py
 meta_subject/models/other_arv_regimens_detail.py
@@ -1206,6 +1215,7 @@ meta_subject/models/urine_dipstick_test.py
 meta_subject/models/urine_pregnancy.py
 meta_subject/models/blood_results/__init__.py
 meta_subject/models/blood_results/blood_results_fbc.py
+meta_subject/models/blood_results/blood_results_glu.py
 meta_subject/models/blood_results/blood_results_hba1c.py
 meta_subject/models/blood_results/blood_results_ins.py
 meta_subject/models/blood_results/blood_results_lft.py
@@ -1233,6 +1243,7 @@ meta_subject/tests/tests/test_manager_order.py
 meta_subject/tests/tests/test_medication_adherence.py
 meta_subject/tests/tests/test_metadata_rules.py
 meta_subject/tests/tests/test_mnsi.py
+meta_subject/tests/tests/test_next_appointment.py
 meta_subject/tests/tests/test_patient_history_form.py
 meta_subject/tests/tests/test_physical_exam.py
 meta_subject/tests/tests/test_sf12.py

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_edc.egg-info/requires.txt

@@ -1,4 +1,4 @@
-edc==1.0.2
+edc==1.0.8
 edc-microscopy
 beautifulsoup4
 celery[redis]

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_lists/list_data.py

@@ -1,4 +1,5 @@
 from edc_constants.constants import (
+    CLINIC,
     DEAD,
     DELIVERY,
     DIABETES,
@@ -236,4 +237,7 @@ list_data = {
         ("stigma", "Concerned about stigma"),
         (OTHER, "Other reason (specify below)"),
     ],
+    "edc_facility.healthfacilitytypes": [
+        (CLINIC, "META Study Clinic"),
+    ],
 }

meta_edc-1.0.5/meta_lists/migrations/0019_auto_20250128_0143.py

@@ -0,0 +1,48 @@
+# Generated by Django 6.0 on 2025-01-27 22:43
+from django.apps import apps as django_apps
+from django.core.exceptions import ObjectDoesNotExist
+from django.db import migrations
+from edc_facility.utils import get_health_facility_model_cls
+from edc_sites.site import sites as site_sites
+from edc_sites.utils import get_site_model_cls
+
+from meta_lists.list_data import list_data
+
+
+def update_healthfacility(apps, schema_editor):
+    health_facility_model_cls = get_health_facility_model_cls()
+
+    name, display_name = list_data.get("edc_facility.healthfacilitytypes")[0]
+    try:
+        health_facility_type = django_apps.get_model(
+            "edc_facility.healthfacilitytypes"
+        ).objects.get(name=name)
+    except ObjectDoesNotExist:
+        health_facility_type = django_apps.get_model(
+            "edc_facility.healthfacilitytypes"
+        ).objects.create(name=name, display_name=display_name)
+
+    for site_obj in get_site_model_cls().objects.all():
+        single_site = site_sites.get(site_obj.id)
+        health_facility_model_cls.objects.create(
+            name=single_site.name,
+            title=single_site.title,
+            mon=True,
+            tue=True,
+            wed=True,
+            thu=True,
+            fri=True,
+            sat=False,
+            sun=False,
+            site_id=site_obj.id,
+            health_facility_type=health_facility_type,
+        )
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_lists", "0018_missedreferralreasons"),
+    ]
+
+    operations = [migrations.RunPython(update_healthfacility)]

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_pharmacy/admin/rx_admin.py

@@ -50,6 +50,7 @@ class RxAdmin(ModelAdminSubjectDashboardMixin, admin.ModelAdmin):
         "rx_date",
         "weight_in_kgs",
         "rx_name",
+        "rx_expiration_date",
     )
 
     list_filter = ("report_datetime", MedicationsListFilter, "site")

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_subject/action_items.py

@@ -4,8 +4,11 @@ from edc_action_item.site_action_items import AlreadyRegistered
 from edc_adverse_event.constants import AE_INITIAL_ACTION
 from edc_constants.constants import HIGH_PRIORITY, NEW, NONE, POS, YES
 from edc_egfr.constants import EGFR_DROP_NOTIFICATION_ACTION
+from edc_lab_results.action_items import BloodResultsFbcAction
+from edc_lab_results.action_items import (
+    BloodResultsGluAction as BaseBloodResultsGluAction,
+)
 from edc_lab_results.action_items import (
-    BloodResultsFbcAction,
     BloodResultsHba1cAction,
     BloodResultsLftAction,
     BloodResultsLipidsAction,
@@ -122,6 +125,10 @@ class BloodResultsRftAction(BaseBloodResultsRftAction):
         return next_actions
 
 
+class BloodResultsGluAction(BaseBloodResultsGluAction):
+    reference_model = "meta_subject.bloodresultsgludummy"
+
+
 class DeliveryAction(ActionWithNotification):
     name = DELIVERY_ACTION
     display_name = "Submit Delivery Form"

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_subject/admin/__init__.py

@@ -22,6 +22,7 @@ from .hepatitis_test_admin import HepatitisTestAdmin
 from .malaria_test_admin import MalariaTestAdmin
 from .medication_adherence_admin import MedicationAdherenceAdmin
 from .mnsi_admin import MnsiAdmin
+from .next_appointment_admin import NextAppointmentAdmin
 from .other_arv_regimens_admin import OtherArvRegimensAdmin
 from .patient_history_admin import PatientHistoryAdmin
 from .physical_exam_admin import PhysicalExamAdmin

meta_edc-1.0.5/meta_subject/admin/next_appointment_admin.py

@@ -0,0 +1,20 @@
+from __future__ import annotations
+
+from django.contrib import admin
+from edc_appointment.modeladmin_mixins import NextAppointmentCrfModelAdminMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+
+from ..admin_site import meta_subject_admin
+from ..forms import NextAppointmentForm
+from ..models import NextAppointment
+from .modeladmin import CrfModelAdminMixin
+
+__all__ = ["NextAppointmentAdmin"]
+
+
+@admin.register(NextAppointment, site=meta_subject_admin)
+class NextAppointmentAdmin(
+    CrfModelAdminMixin, NextAppointmentCrfModelAdminMixin, SimpleHistoryAdmin
+):
+
+    form = NextAppointmentForm

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_subject/forms/__init__.py

@@ -22,6 +22,7 @@ from .hepatitis_test_form import HepatitisTestForm
 from .malaria_test_form import MalariaTestForm
 from .medication_adherence_form import MedicationAdherenceForm
 from .mnsi_form import MnsiForm
+from .next_appointment_form import NextAppointmentForm
 from .other_arv_regimens_detail_form import OtherArvRegimensDetailForm
 from .other_arv_regimens_form import OtherArvRegimensForm
 from .patient_history_form import PatientHistoryForm

meta_edc-1.0.5/meta_subject/forms/next_appointment_form.py

@@ -0,0 +1,37 @@
+from __future__ import annotations
+
+from django import forms
+from edc_appointment.form_validator_mixins import NextAppointmentCrfFormValidatorMixin
+from edc_crf.crf_form_validator import CrfFormValidator
+from edc_crf.modelform_mixins import CrfModelFormMixin
+
+from ..models import NextAppointment
+
+__all__ = ["NextAppointmentForm"]
+
+
+class NextAppointmentCrfFormValidator(
+    NextAppointmentCrfFormValidatorMixin,
+    CrfFormValidator,
+):
+    pass
+
+
+class NextAppointmentForm(CrfModelFormMixin, forms.ModelForm):
+
+    form_validator_cls = NextAppointmentCrfFormValidator
+
+    class Meta:
+        model = NextAppointment
+        fields = "__all__"
+        labels = {
+            "appt_date": "Next scheduled appointment date",
+            "visitschedule": "Next scheduled appointment",
+        }
+        help_texts = {
+            "appt_date": (
+                "Default recommended. If changed, should be within "
+                "the window period of the next appointment"
+            ),
+            "visitschedule": "Default recommended. Can only be the next visit",
+        }

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_subject/metadata_rules/metadata_rules.py

@@ -160,3 +160,17 @@ class Eq53dlRuleGroup(CrfRuleGroup):
     class Meta:
         app_label = "meta_subject"
         source_model = "meta_subject.subjectvisit"
+
+
+@register()
+class NextAppointmentRuleGroup(CrfRuleGroup):
+    next_appt = CrfRule(
+        predicate=pc.next_appt_required,
+        consequence=REQUIRED,
+        alternative=NOT_REQUIRED,
+        target_models=["nextappointment"],
+    )
+
+    class Meta:
+        app_label = "meta_subject"
+        source_model = "meta_subject.subjectvisit"

{meta_edc-1.0.3 → meta_edc-1.0.5}/meta_subject/metadata_rules/predicates.py

@@ -3,6 +3,7 @@ from zoneinfo import ZoneInfo
 
 from django.apps import apps as django_apps
 from django.core.exceptions import ObjectDoesNotExist
+from edc_appointment.constants import NEW_APPT
 from edc_constants.constants import YES
 from edc_lab_panel.panels import hba1c_panel, insulin_panel
 from edc_metadata.metadata_rules import PersistantSingletonMixin
@@ -69,6 +70,12 @@ def hba1c_requisition_required_at_baseline(visit):
 class Predicates(PersistantSingletonMixin):
     app_label = "meta_subject"
 
+    @staticmethod
+    def next_appt_required(visit, **kwargs):
+        if visit.appointment.next and visit.appointment.next.appt_status == NEW_APPT:
+            return True
+        return False
+
     @staticmethod
     def glucose_required(visit, **kwargs):
         if visit.visit_code in [MONTH12, MONTH24, MONTH36, MONTH48]:
@@ -213,7 +220,10 @@ class Predicates(PersistantSingletonMixin):
         """
         model_cls = django_apps.get_model(f"{self.app_label}.mnsi")
         required = True
-        if visit.visit_code_sequence != 0:
+
+        if self.offschedule_today(visit):
+            return True
+        elif visit.visit_code_sequence != 0:
             required = False
         elif visit.visit_code not in [
             MONTH1,
@@ -250,7 +260,9 @@ class Predicates(PersistantSingletonMixin):
 
     def sf12_required(self, visit, **kwargs):
         model = f"{self.app_label}.sf12"
-        if visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
+        if self.offschedule_today(visit):
+            return True
+        elif visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
             return True
         return self.persistant_singleton_required(
             visit, model=model, exclude_visit_codes=[DAY1]
@@ -258,8 +270,22 @@ class Predicates(PersistantSingletonMixin):
 
     def eq5d3l_required(self, visit, **kwargs):
         model = f"{self.app_label}.eq5d3l"
-        if visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
+        if self.offschedule_today(visit):
+            return True
+        elif visit.visit_code_sequence == 0 and visit.visit_code in [MONTH36, MONTH48]:
             return True
         return self.persistant_singleton_required(
             visit, model=model, exclude_visit_codes=[DAY1]
         )
+
+    def offschedule_today(self, visit):
+        try:
+            obj = django_apps.get_model(f"{self.app_label}.nextappointment").objects.get(
+                subject_visit=visit
+            )
+        except ObjectDoesNotExist:
+            pass
+        else:
+            if obj.offschedule_today == YES:
+                return True
+        return False