meta-edc 0.3.33__tar.gz → 0.3.34__tar.gz

{meta_edc-0.3.33 → meta_edc-0.3.34}/.github/workflows/build.yml

@@ -6,9 +6,9 @@ on: [push, pull_request]
 jobs:
   build:
     name: >
-      ${{ matrix.codebase }}-
-      Py${{ matrix.python-version }}-
-      Dj${{ matrix.django-version }}-
+      ${{ matrix.codebase }} /
+      py${{ matrix.python-version }} /
+      dj${{ matrix.django-version }} /
       ${{ matrix.database-engine }}
     runs-on: ubuntu-latest
 
@@ -16,8 +16,8 @@ jobs:
       fail-fast: false
       matrix:
         codebase: ['Prod', 'Dev']
-        django-version: ['4.2', '5.1', 'dev']
         python-version: ['3.12']
+        django-version: ['4.2', '5.1', 'dev']
         database-engine: ["mysql", "postgres"]
         exclude:
           - codebase: 'Prod'
@@ -43,6 +43,7 @@ jobs:
           --health-retries 5
         ports:
           - 5432:5432
+
     steps:
       - name: Install pycups and words dependency
         run: |
@@ -75,7 +76,6 @@ jobs:
           python -m pip install --upgrade pip
           python -m pip install -r https://raw.githubusercontent.com/clinicedc/edc/develop/requirements.tests/tox.txt
 
-
       - name: Tox tests
         run: |
           tox -v

{meta_edc-0.3.33 → meta_edc-0.3.34}/.gitignore

@@ -1,3 +1,4 @@
+pg.load
 celerybeat*
 get_data*
 static/

{meta_edc-0.3.33 → meta_edc-0.3.34}/.pre-commit-config.yaml

@@ -3,20 +3,20 @@ exclude: tests/etc/user-*
 
 repos:
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.8
+    rev: 1.7.9
     hooks:
       - id: bandit
         args:
           - "-x *test*.py"
 
   - repo: https://github.com/psf/black
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
         language_version: python3.12
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         args:
@@ -30,21 +30,21 @@ repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.6.0
     hooks:
-      - id: requirements-txt-fixer
-        files: requirements/.*\.txt$
-      - id: trailing-whitespace
       - id: check-added-large-files
         args: ['--maxkb=1100']
-      - id: fix-byte-order-marker
       - id: check-docstring-first
       - id: check-executables-have-shebangs
       - id: check-merge-conflict
+      - id: check-toml
       - id: debug-statements
       - id: detect-private-key
-      - id: check-toml
+      - id: fix-byte-order-marker
+      - id: requirements-txt-fixer
+        files: requirements/.*\.txt$
+      - id: trailing-whitespace
 
   - repo: https://github.com/rstcheck/rstcheck
-    rev: v6.2.0
+    rev: v6.2.4
     hooks:
       - id: rstcheck
 

{meta_edc-0.3.33 → meta_edc-0.3.34}/CHANGES

@@ -1,6 +1,11 @@
 Changes
 -------
 
+0.3.34
+------
+- add IMP Substitutions model and report
+- bump edc 0.6.11
+
 0.3.33
 ------
 - fix issues with endpoint report / generate_endpoints command

{meta_edc-0.3.33 → meta_edc-0.3.34}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.33
+Version: 0.3.34
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -20,7 +20,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.6.10
+Requires-Dist: edc==0.6.11
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics
@@ -35,7 +35,10 @@ META Edc
 
 Metformin treatment in Africa- META
 
-https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
+* https://www.ucl.ac.uk/global-health/research/z-research/respond-africa/metformin-treatment-africa-meta
+* https://www.inteafrica.org/related-projects/meta-trial/
+* 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)
 

{meta_edc-0.3.33 → meta_edc-0.3.34}/README.rst

@@ -6,7 +6,10 @@ META Edc
 
 Metformin treatment in Africa- META
 
-https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
+* https://www.ucl.ac.uk/global-health/research/z-research/respond-africa/metformin-treatment-africa-meta
+* https://www.inteafrica.org/related-projects/meta-trial/
+* 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)
 

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_auth/auth_objects.py

@@ -3,6 +3,7 @@ from edc_auth.get_app_codenames import get_app_codenames
 
 META_REPORTS = "META_REPORTS"
 META_REPORTS_AUDIT = "META_REPORTS_AUDIT"
+META_PHARMACIST = "META_PHARMACIST"
 
 
 clinic_codenames = get_app_codenames(
@@ -10,6 +11,20 @@ clinic_codenames = get_app_codenames(
 )
 
 reports_codenames = get_app_codenames("meta_reports")
+reports_codenames.remove("meta_reports.view_impsubstitutions")
+
+meta_pharmacy_codenames = get_app_codenames("meta_pharmacy")
+meta_pharmacy_codenames.append("meta_reports.view_impsubstitutions")
+meta_pharmacy_codenames.append("meta_reports.viewallsites_impsubstitutions")
+excluded_meta_pharmacy_codenames = [
+    "meta_pharmacy.add_rx",
+    "meta_pharmacy.change_rx",
+    "meta_pharmacy.delete_rx",
+]
+
+meta_pharmacy_codenames = [
+    c for c in meta_pharmacy_codenames if c not in excluded_meta_pharmacy_codenames
+]
 
 add_perms = []
 if not settings.LIVE_SYSTEM:

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_auth/auths.py

@@ -28,15 +28,18 @@ from edc_subject_dashboard.auths import SUBJECT_VIEW
 from edc_unblinding.auth_objects import UNBLINDING_REQUESTORS
 
 from .auth_objects import (
+    META_PHARMACIST,
     META_REPORTS,
     META_REPORTS_AUDIT,
     clinic_codenames,
+    meta_pharmacy_codenames,
     reports_codenames,
     screening_codenames,
 )
 
 site_auths.add_group(*reports_codenames, name=META_REPORTS)
 site_auths.add_group(*reports_codenames, name=META_REPORTS_AUDIT, view_only=True)
+site_auths.add_group(*meta_pharmacy_codenames, name=META_PHARMACIST)
 
 # update edc_auth default groups
 site_auths.update_group(*clinic_codenames, name=AUDITOR, view_only=True)
@@ -69,8 +72,8 @@ site_auths.update_role(
     DATA_MANAGER_EXPORT,
     name=DATA_EXPORTER_ROLE,
 )
-site_auths.update_role(RANDO_UNBLINDED, PII, name=PHARMACIST_ROLE)
-site_auths.update_role(RANDO_BLINDED, PII, name=SITE_PHARMACIST_ROLE)
+site_auths.update_role(RANDO_UNBLINDED, PII, META_PHARMACIST, name=PHARMACIST_ROLE)
+site_auths.update_role(RANDO_BLINDED, PII, META_PHARMACIST, name=SITE_PHARMACIST_ROLE)
 site_auths.update_role(SUBJECT_VIEW, SCREENING_VIEW, name=DATA_MANAGER_ROLE)
 site_auths.update_role(
     SUBJECT_VIEW, SCREENING_VIEW, ACTION_ITEM, UNBLINDING_REQUESTORS, name=TMG_ROLE

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_edc/settings/debug.py

@@ -7,8 +7,8 @@ from .defaults import *  # noqa
 print(f"Settings file {__file__}")
 
 # TZ Sites:
-SITE_ID = SiteID(default=20)  # Amana
-# SITE_ID = SiteID(default=10)  # Hindu Mandal
+# 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

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_edc/settings/defaults.py

@@ -188,6 +188,7 @@ MIDDLEWARE = [
     "django.contrib.sites.middleware.CurrentSiteMiddleware",
     "django.middleware.csrf.CsrfViewMiddleware",
     "django.contrib.auth.middleware.AuthenticationMiddleware",
+    "django.contrib.auth.middleware.LoginRequiredMiddleware",
     "defender.middleware.FailedLoginMiddleware",
     "django.contrib.messages.middleware.MessageMiddleware",
     "django.middleware.clickjacking.XFrameOptionsMiddleware",
@@ -413,6 +414,9 @@ EDC_RANDOMIZATION_SKIP_VERIFY_CHECKS = True
 # edc-sites
 EDC_SITES_MODULE_NAME = env.str("EDC_SITES_MODULE_NAME")
 
+# meta_pharmacy
+META_PHARMACY_RX_SUBSTITUTION_FILE = env.str("META_PHARMACY_RX_SUBSTITUTION_FILE")
+
 # django-multisite
 CACHE_MULTISITE_KEY_PREFIX = "meta4"
 SILENCED_SYSTEM_CHECKS = ["sites.E101"]

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_edc/urls.py

@@ -62,6 +62,7 @@ urlpatterns = [
     *paths_for_urlpatterns("meta_consent"),
     *paths_for_urlpatterns("meta_export"),
     *paths_for_urlpatterns("meta_lists"),
+    *paths_for_urlpatterns("meta_pharmacy"),
     *paths_for_urlpatterns("meta_prn"),
     *paths_for_urlpatterns("meta_screening"),
     *paths_for_urlpatterns("meta_subject"),

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_edc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.33
+Version: 0.3.34
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -20,7 +20,7 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.6.10
+Requires-Dist: edc==0.6.11
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics
@@ -35,7 +35,10 @@ META Edc
 
 Metformin treatment in Africa- META
 
-https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
+* https://www.ucl.ac.uk/global-health/research/z-research/respond-africa/metformin-treatment-africa-meta
+* https://www.inteafrica.org/related-projects/meta-trial/
+* 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)
 

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_edc.egg-info/SOURCES.txt

@@ -168,7 +168,6 @@ meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py
 meta_analytics/dataframes/screening/__init__.py
 meta_analytics/dataframes/screening/get_glucose_tested_only_df.py
 meta_analytics/dataframes/screening/get_screening_df.py
-meta_analytics/notebooks/meta_endpoints.ipynb
 meta_analytics/tables/__init__.py
 meta_analytics/tables/eligible.py
 meta_analytics/tables/has_dm.py
@@ -368,11 +367,17 @@ meta_lists/migrations/__init__.py
 meta_lists/tests/__init__.py
 meta_lists/tests/test_lists.py
 meta_pharmacy/__init__.py
+meta_pharmacy/admin.py
+meta_pharmacy/admin_site.py
 meta_pharmacy/apps.py
 meta_pharmacy/constants.py
+meta_pharmacy/forms.py
 meta_pharmacy/models.py
 meta_pharmacy/prepare_meta_pharmacy.py
+meta_pharmacy/urls.py
 meta_pharmacy/migrations/0001_initial.py
+meta_pharmacy/migrations/0002_initial.py
+meta_pharmacy/migrations/0003_auto_20240909_2335.py
 meta_pharmacy/migrations/__init__.py
 meta_prn/__init__.py
 meta_prn/action_items.py
@@ -519,6 +524,7 @@ meta_reports/admin/list_filters.py
 meta_reports/admin/modeladmin_mixins.py
 meta_reports/admin/dbviews/__init__.py
 meta_reports/admin/dbviews/glucose_summary_admin.py
+meta_reports/admin/dbviews/imp_substitutions_admin.py
 meta_reports/admin/dbviews/patient_history_missing_baseline_cd4_admin.py
 meta_reports/admin/dbviews/unattended_three_in_row2_admin.py
 meta_reports/admin/dbviews/unattended_three_in_row_admin.py
@@ -581,6 +587,8 @@ meta_reports/migrations/0043_auto_20240828_2309.py
 meta_reports/migrations/0044_auto_20240828_2323.py
 meta_reports/migrations/0045_auto_20240829_0248.py
 meta_reports/migrations/0046_auto_20240829_0250.py
+meta_reports/migrations/0047_impsubstitutions.py
+meta_reports/migrations/0048_auto_20240909_2338.py
 meta_reports/migrations/__init__.py
 meta_reports/models/__init__.py
 meta_reports/models/endpoints.py
@@ -590,6 +598,9 @@ meta_reports/models/dbviews/__init__.py
 meta_reports/models/dbviews/glucose_summary/__init__.py
 meta_reports/models/dbviews/glucose_summary/unmanaged_model.py
 meta_reports/models/dbviews/glucose_summary/view_definition.py
+meta_reports/models/dbviews/imp_substitutions/__init__.py
+meta_reports/models/dbviews/imp_substitutions/unmanaged_model.py
+meta_reports/models/dbviews/imp_substitutions/view_definition.py
 meta_reports/models/dbviews/missing_screening_ogtt/__init__.py
 meta_reports/models/dbviews/missing_screening_ogtt/note_model.py
 meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_edc.egg-info/requires.txt

@@ -1,4 +1,4 @@
-edc==0.6.10
+edc==0.6.11
 edc-microscopy
 beautifulsoup4
 edc-analytics

meta_edc-0.3.34/meta_pharmacy/admin.py

@@ -0,0 +1,128 @@
+from django.contrib import admin
+from django_audit_fields.admin import audit_fieldset_tuple
+from edc_model_admin.dashboard import ModelAdminSubjectDashboardMixin
+from edc_model_admin.history import SimpleHistoryAdmin
+from edc_pharmacy.admin.list_filters import MedicationsListFilter
+from edc_sites.admin import SiteModelAdminMixin
+
+from .admin_site import meta_pharmacy_admin
+from .forms import RxForm, SubstitutionsForm
+from .models import Rx, Substitutions
+
+
+@admin.register(Substitutions, site=meta_pharmacy_admin)
+class SubstitutionsAdmin(
+    SiteModelAdminMixin,
+    ModelAdminSubjectDashboardMixin,
+    SimpleHistoryAdmin,
+):
+    """Admin class for meta_pharmacy.Substitutions"""
+
+    form = SubstitutionsForm
+
+    autocomplete_fields = ["rx"]
+
+    add_instructions = "This form is used to record any substitions made for IMP refills"
+
+    fieldsets = (
+        (
+            None,
+            {"fields": ("report_datetime",)},
+        ),
+        ("Original label on bottle", {"fields": ("sid", "visit_no")}),
+        (
+            "Substitution / Changed label",
+            {
+                "description": "The label on this bottle has been changed to the following",
+                "fields": ("dispensed_sid", "updated_visit_no"),
+            },
+        ),
+        (
+            "Subject",
+            {
+                "fields": ("rx",),
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    list_display = (
+        "sid",
+        "dispensed_sid",
+        "arm_match",
+        "subject_identifier",
+        "report_datetime",
+    )
+
+    radio_fields = {"arm_match": admin.VERTICAL}
+
+    list_filter = ("arm_match", "report_datetime")
+
+    search_fields = ["subject_identifier", "sid", "dispensed_sid"]
+
+
+@admin.register(Rx, site=meta_pharmacy_admin)
+class RxAdmin(ModelAdminSubjectDashboardMixin, admin.ModelAdmin):
+    """Admin class for proxy model of edc_pharmacy.Rx"""
+
+    show_object_tools = True
+
+    form = RxForm
+
+    fieldsets = (
+        (
+            None,
+            {
+                "fields": (
+                    "subject_identifier",
+                    "report_datetime",
+                    "rx_name",
+                    "rx_date",
+                    "medications",
+                    "clinician_initials",
+                    "notes",
+                )
+            },
+        ),
+        (
+            "Randomization",
+            {
+                "fields": ("rando_sid", "randomizer_name", "weight_in_kgs"),
+            },
+        ),
+        audit_fieldset_tuple,
+    )
+
+    filter_horizontal = ("medications",)
+
+    list_display = (
+        "subject_identifier",
+        "dashboard",
+        "rx_medications",
+        "rando_sid",
+        "rx_date",
+        "weight_in_kgs",
+        "rx_name",
+    )
+
+    list_filter = ("report_datetime", MedicationsListFilter, "site")
+
+    search_fields = (
+        "id",
+        "subject_identifier",
+        "rando_sid",
+        "registered_subject__initials",
+        "medications__name",
+        "site__id",
+        "rx_name",
+    )
+
+    readonly_fields = (
+        "rando_sid",
+        "weight_in_kgs",
+        "rx_name",
+    )
+
+    @admin.display
+    def rx_medications(self, obj):
+        return ", ".join([obj.display_name for obj in obj.medications.all()])

meta_edc-0.3.34/meta_pharmacy/admin_site.py

@@ -0,0 +1,5 @@
+from edc_model_admin.admin_site import EdcAdminSite
+
+from .apps import AppConfig
+
+meta_pharmacy_admin = EdcAdminSite(name="meta_pharmacy_admin", app_label=AppConfig.name)

{meta_edc-0.3.33 → meta_edc-0.3.34}/meta_pharmacy/apps.py

@@ -15,6 +15,9 @@ def post_migrate_populate_pharmacy_models(sender=None, **kwargs):  # noqa
 class AppConfig(DjangoAppConfig):
     name = "meta_pharmacy"
     verbose_name = "META Pharmacy"
+    include_in_administration_section = True
+    has_exportable_data = True
+    default_auto_field = "django.db.models.BigAutoField"
 
     def ready(self):
         post_migrate.connect(post_migrate_populate_pharmacy_models, sender=self)

meta_edc-0.3.34/meta_pharmacy/constants.py

@@ -0,0 +1,11 @@
+from edc_constants.constants import OK
+
+METFORMIN = "metformin"
+REVIEW = "REVIEW"
+MISSING_SUBJECT_IDENTIFIER = "MISSING_SUBJECT_IDENTIFIER"
+
+SUBSTITUTION_STATUS = (
+    (OK, "ok"),
+    (MISSING_SUBJECT_IDENTIFIER, "Missing Subject ID"),
+    (REVIEW, "review"),
+)

meta_edc-0.3.34/meta_pharmacy/forms.py

@@ -0,0 +1,65 @@
+from django import forms
+from django.core.exceptions import ObjectDoesNotExist
+from edc_form_validators.form_validator import FormValidator
+from edc_form_validators.form_validator_mixins import FormValidatorMixin
+from edc_model_form.mixins import BaseModelFormMixin
+from edc_offstudy.modelform_mixins import OffstudyNonCrfModelFormMixin
+from edc_prn.modelform_mixins import PrnFormValidatorMixin
+from edc_sites.forms import SiteModelFormMixin
+
+from .models import Rx, Substitutions
+
+
+class SubstitutionsFormValidator(PrnFormValidatorMixin, FormValidator):
+    pass
+
+
+class SubstitutionsForm(
+    SiteModelFormMixin,
+    OffstudyNonCrfModelFormMixin,
+    BaseModelFormMixin,
+    FormValidatorMixin,
+    forms.ModelForm,
+):
+    form_validator_cls = SubstitutionsFormValidator
+
+    def clean(self):
+        if self.cleaned_data.get("sid"):
+            try:
+                obj = Rx.objects.get(rando_sid=self.cleaned_data.get("sid"))
+            except ObjectDoesNotExist:
+                raise forms.ValidationError({"sid": "Unknown SID for this trial"})
+            else:
+                if obj.site.id != self.site.id:
+                    raise forms.ValidationError(
+                        {
+                            "sid": (
+                                "Unknown SID for this trial site. "
+                                f"Expected SITE {obj.site.id}."
+                            )
+                        }
+                    )
+        if self.cleaned_data.get("dispensed_sid"):
+            try:
+                Rx.objects.get(
+                    rando_sid=self.cleaned_data.get("dispensed_sid"),
+                )
+            except ObjectDoesNotExist:
+                raise forms.ValidationError({"dispensed_sid": "Unknown SID for this trial"})
+
+    class Meta:
+        model = Substitutions
+        fields = "__all__"
+
+
+class RxForm(forms.ModelForm):
+
+    subject_identifier = forms.CharField(
+        label="Subject Identifier",
+        required=False,
+        widget=forms.TextInput(attrs={"readonly": "readonly"}),
+    )
+
+    class Meta:
+        model = Rx
+        fields = "__all__"