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

meta_edc-1.4.0.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: uv 0.9.9
+Root-Is-Purelib: true
+Tag: py3-none-any

meta_labs/list_data.py

@@ -6,11 +6,11 @@ model_data = {
             "address": "NIMR Tanzania",
             "postal_code": "-",
             "city": "Dar es Salaam",
-            "state": None,
+            "state": "",
             "country": "Tanzania",
             "telephone": "+255763244779",
             "mobile": "+255763244779",
-            "fax": None,
+            "fax": "",
             "email": "sokoinele@yahoo.co.uk",
         }
     ]

meta_labs/reportables.py

@@ -1,16 +1,85 @@
-from edc_reportable import GRADE3, GRADE4, site_reportables
-from edc_reportable.grading_data.daids_july_2017 import chemistries, dummies, hematology
-from edc_reportable.normal_data.africa import normal_data
+from clinicedc_constants import (
+    FEMALE,
+    MALE,
+    MICRO_IU_MILLILITER,
+    MILLIGRAMS_PER_DECILITER,
+    MILLIMOLES_PER_LITER,
+)
+from edc_reportable.adult_age_options import adult_age_options
+from edc_reportable.data import africa, daids_july_2017
+from edc_reportable.formula import Formula
 
 grading_data = {}
-grading_data.update(**dummies)
-grading_data.update(**chemistries)
-grading_data.update(**hematology)
+grading_data.update(**daids_july_2017.dummies)
+grading_data.update(**daids_july_2017.chemistries)
+grading_data.update(**daids_july_2017.hematology)
+
+collection_name = "meta"
+normal_data = africa.normal_data
+reportable_grades = [3, 4]
+reportable_grades_exceptions = {}
+
+normal_data.update(
+    {
+        "glucose": [
+            Formula(
+                "0<=x<=99999",
+                units=MILLIMOLES_PER_LITER,
+                gender=[MALE, FEMALE],
+                **adult_age_options,
+            ),
+            Formula(
+                "0<=x<=99999",
+                units=MILLIGRAMS_PER_DECILITER,
+                gender=[MALE, FEMALE],
+                **adult_age_options,
+            ),
+        ],
+        "ins": [
+            Formula(
+                "0<=x<=99999",
+                units=MICRO_IU_MILLILITER,
+                gender=[MALE, FEMALE],
+                **adult_age_options,
+            ),
+        ],
+    }
+)
+
+grading_data.update(
+    {
+        "glucose": [
+            Formula(
+                "x<0",
+                grade=0,
+                units=MILLIMOLES_PER_LITER,
+                gender=[MALE, FEMALE],
+                **adult_age_options,
+            ),
+            Formula(
+                "x<0",
+                grade=0,
+                units=MILLIGRAMS_PER_DECILITER,
+                gender=[MALE, FEMALE],
+                **adult_age_options,
+            ),
+        ],
+        "ins": [
+            Formula(
+                "x<0",
+                grade=0,
+                units=MICRO_IU_MILLILITER,
+                gender=[MALE, FEMALE],
+                **adult_age_options,
+            ),
+        ],
+    }
+)
 
-site_reportables.register(
-    name="meta",
-    normal_data=normal_data,
+reference_range_options = dict(
+    collection_name=collection_name,
+    normal_data=africa.normal_data,
     grading_data=grading_data,
-    reportable_grades=[GRADE3, GRADE4],
-    reportable_grades_exceptions=None,
+    reportable_grades=reportable_grades,
+    reportable_grades_exceptions=reportable_grades_exceptions,
 )

meta_lists/list_data.py

@@ -1,18 +1,23 @@
-from edc_constants.constants import (
+from clinicedc_constants import (
+    CLINIC,
     DEAD,
     DELIVERY,
     DIABETES,
+    LTFU,
     NONE,
     OTHER,
     PREGNANCY,
     TOXICITY,
     UNKNOWN,
 )
-from edc_ltfu.constants import LOST_TO_FOLLOWUP
 from edc_offstudy.constants import COMPLETED_FOLLOWUP, WITHDRAWAL
 from edc_transfer.constants import TRANSFERRED
 
-from meta_prn.constants import CLINICAL_WITHDRAWAL, LATE_EXCLUSION
+from meta_prn.constants import (
+    CLINICAL_WITHDRAWAL,
+    COMPLETED_FOLLOWUP_48,
+    LATE_EXCLUSION,
+)
 
 list_data = {
     "meta_lists.dmmedications": [
@@ -197,6 +202,7 @@ list_data = {
     ],
     "meta_lists.offstudyreasons": [
         (COMPLETED_FOLLOWUP, "Patient completed 36 months of follow-up"),
+        (COMPLETED_FOLLOWUP_48, "Patient completed 48 months of follow-up"),
         (DELIVERY, "Delivered / Completed followup from pregnancy"),
         (PREGNANCY, "Pregnancy, declined further followup"),
         (DIABETES, "Patient developed diabetes"),
@@ -210,7 +216,7 @@ list_data = {
             "intercurrent_illness",
             "Intercurrent illness which prevents further treatment",  # see limit_choices_to
         ),
-        (LOST_TO_FOLLOWUP, "Patient lost to follow-up"),
+        (LTFU, "Patient lost to follow-up"),
         (DEAD, "Patient reported/known to have died"),
         (WITHDRAWAL, "Patient withdrew consent to participate further"),
         (
@@ -231,4 +237,7 @@ list_data = {
         ("stigma", "Concerned about stigma"),
         (OTHER, "Other reason (specify below)"),
     ],
+    "edc_facility.healthfacilitytypes": [
+        (CLINIC, "META Study Clinic"),
+    ],
 }

meta_lists/migrations/0008_auto_20200528_1517.py

@@ -2,7 +2,7 @@
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import migrations
 from django.db.migrations import RunPython
-from edc_ltfu.constants import LOST_TO_FOLLOWUP
+from clinicedc_constants import LTFU
 
 
 def update_ltfu(apps, schema_editor):
@@ -12,7 +12,7 @@ def update_ltfu(apps, schema_editor):
     except ObjectDoesNotExist:
         pass
     else:
-        obj.name = LOST_TO_FOLLOWUP
+        obj.name = LTFU
         obj.save_base(update_fields=["name"])
 
 

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_lists/migrations/0020_alter_abnormalfootappearanceobservations_extra_value_and_more.py

@@ -0,0 +1,404 @@
+# Generated by Django 5.2.6 on 2025-09-24 05:45
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_lists", "0019_auto_20250128_0143"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="abnormalfootappearanceobservations",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="abnormalfootappearanceobservations",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="abnormalfootappearanceobservations",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="arvregimens",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="arvregimens",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="arvregimens",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="baselinesymptoms",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="baselinesymptoms",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="baselinesymptoms",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="complications",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="complications",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="complications",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="diabetessymptoms",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="diabetessymptoms",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="diabetessymptoms",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dmmedications",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="dmmedications",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dmmedications",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dmtreatments",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="dmtreatments",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="dmtreatments",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthcareworkers",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="healthcareworkers",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthcareworkers",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="hypertensionmedications",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="hypertensionmedications",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="hypertensionmedications",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="investigations",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="investigations",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="investigations",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="missedreferralreasons",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="missedreferralreasons",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="missedreferralreasons",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="nonadherencereasons",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="nonadherencereasons",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="nonadherencereasons",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="offstudyreasons",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="offstudyreasons",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="offstudyreasons",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="oiprophylaxis",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="oiprophylaxis",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="oiprophylaxis",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectvisitmissedreasons",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="subjectvisitmissedreasons",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectvisitmissedreasons",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="symptoms",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="symptoms",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="symptoms",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="transferreasons",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="transferreasons",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="transferreasons",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+    ]

meta_pharmacy/admin/__init__.py

@@ -1,2 +1,7 @@
 from .rx_admin import RxAdmin
 from .substitutions_admin import SubstitutionsAdmin
+
+__all__ = [
+    "RxAdmin",
+    "SubstitutionsAdmin",
+]

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_pharmacy/admin/substitutions_admin.py

@@ -20,7 +20,7 @@ class SubstitutionsAdmin(
 
     form = SubstitutionsForm
 
-    autocomplete_fields = ["rx"]
+    autocomplete_fields = ("rx",)
 
     add_instructions = "This form is used to record any substitions made for IMP refills"
 
@@ -54,11 +54,11 @@ class SubstitutionsAdmin(
         "report_date",
     )
 
-    radio_fields = {"arm_match": admin.VERTICAL}
+    radio_fields = {"arm_match": admin.VERTICAL}  # noqa: RUF012
 
     list_filter = ("arm_match", ReportDateListFilter)
 
-    search_fields = ["subject_identifier", "sid", "dispensed_sid"]
+    search_fields = ("subject_identifier", "sid", "dispensed_sid")
 
     @admin.display(description="Report date", ordering="report_datetime")
     def report_date(self, obj) -> str | None:

meta_pharmacy/constants.py

@@ -1,4 +1,4 @@
-from edc_constants.constants import OK
+from clinicedc_constants import OK
 
 METFORMIN = "metformin"
 REVIEW = "REVIEW"

meta_pharmacy/forms/__init__.py

@@ -1,2 +1,4 @@
 from .rx_form import RxForm
 from .substitutions_form import SubstitutionsForm
+
+__all__ = ["RxForm", "SubstitutionsForm"]