meta-edc 0.3.15__py3-none-any.whl → 0.3.50__py3-none-any.whl

meta_subject/migrations/0214_historicalstudymedication_stock_codes_and_more.py

@@ -0,0 +1,44 @@
+# Generated by Django 5.1.2 on 2024-11-18 02:18
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0213_rename_bloodresultslipid_bloodresultslipids_and_more"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="historicalstudymedication",
+            name="stock_codes",
+            field=models.CharField(
+                blank=True,
+                help_text="Enter the medication bottle barcode or bacodes seperated by comma, no spaces",
+                max_length=30,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        regex="^([a-zA-Z0-9]{6})(,[a-zA-Z0-9]{6})*$"
+                    )
+                ],
+            ),
+        ),
+        migrations.AddField(
+            model_name="studymedication",
+            name="stock_codes",
+            field=models.CharField(
+                blank=True,
+                help_text="Enter the medication bottle barcode or bacodes seperated by comma, no spaces",
+                max_length=30,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        regex="^([a-zA-Z0-9]{6})(,[a-zA-Z0-9]{6})*$"
+                    )
+                ],
+            ),
+        ),
+    ]

meta_subject/migrations/0215_alter_historicalstudymedication_stock_codes_and_more.py

@@ -0,0 +1,46 @@
+# Generated by Django 5.1.2 on 2024-11-18 02:34
+
+import django.core.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_subject", "0214_historicalstudymedication_stock_codes_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalstudymedication",
+            name="stock_codes",
+            field=models.CharField(
+                blank=True,
+                help_text="Enter the medication bottle barcode or barcodes seperated by comma, no spaces",
+                max_length=30,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        message="Enter one or more valid codes separated by comma",
+                        regex="^([A-Z0-9]{6})(,[A-Z0-9]{6})*$",
+                    )
+                ],
+            ),
+        ),
+        migrations.AlterField(
+            model_name="studymedication",
+            name="stock_codes",
+            field=models.CharField(
+                blank=True,
+                help_text="Enter the medication bottle barcode or barcodes seperated by comma, no spaces",
+                max_length=30,
+                null=True,
+                validators=[
+                    django.core.validators.RegexValidator(
+                        message="Enter one or more valid codes separated by comma",
+                        regex="^([A-Z0-9]{6})(,[A-Z0-9]{6})*$",
+                    )
+                ],
+            ),
+        ),
+    ]

meta_subject/model_mixins/arv_history_model_mixin.py

@@ -44,7 +44,7 @@ class ArvHistoryModelMixin(models.Model):
         ArvRegimens,
         on_delete=models.PROTECT,
         related_name="current_arv_regimen",
-        verbose_name=("Which antiretroviral therapy regimen is the patient currently on?"),
+        verbose_name="Which antiretroviral therapy regimen is the patient currently on?",
         null=True,
         blank=False,
     )
@@ -69,7 +69,7 @@ class ArvHistoryModelMixin(models.Model):
         ArvRegimens,
         on_delete=models.PROTECT,
         related_name="previous_arv_regimen",
-        verbose_name=("Which antiretroviral therapy regimen was the patient previously on?"),
+        verbose_name="Which antiretroviral therapy regimen was the patient previously on?",
         null=True,
         blank=True,
     )
@@ -77,7 +77,7 @@ class ArvHistoryModelMixin(models.Model):
     other_previous_arv_regimen = OtherCharField(null=True, blank=True)
 
     on_oi_prophylaxis = models.CharField(
-        verbose_name=("Is the patient on any prophylaxis against opportunistic infections?"),
+        verbose_name="Is the patient on any prophylaxis against opportunistic infections?",
         max_length=15,
         choices=YES_NO,
     )

meta_subject/models/__init__.py

@@ -4,14 +4,14 @@ from .blood_results import (
     BloodResultsHba1c,
     BloodResultsIns,
     BloodResultsLft,
-    BloodResultsLipid,
+    BloodResultsLipids,
     BloodResultsRft,
 )
 from .complications import Complications
 from .complications_glycemia import ComplicationsGlycemia
 from .concomitant_medication import ConcomitantMedication
 from .delivery import Delivery
-from .diabetes import DmDiagnosis, DmDxResult, DmFollowup
+from .diabetes import DmEndpoint, DmFollowup
 from .diet_and_lifestyle import DietAndLifestyle
 from .egfr_drop_notification import EgfrDropNotification
 from .eq5d3l import Eq5d3l
@@ -36,6 +36,7 @@ from .pregnancy_update import PregnancyUpdate
 from .sf12 import Sf12
 from .signals import (
     study_medication_on_pre_save,
+    update_glucose_endpoints_for_subject_on_post_save,
     update_pregnancy_notification_on_delivery_post_save,
     update_schedule_on_delivery_post_save,
 )

meta_subject/models/birth_outcomes.py

@@ -1,6 +1,7 @@
 from django.db import models
 from django.db.models import PROTECT, Index
 from edc_consent.model_mixins import RequiresConsentFieldsModelMixin
+from edc_crf.model_mixins import CrfStatusModelMixin
 from edc_model.models import BaseUuidModel, HistoricalRecords
 from edc_offstudy.model_mixins import OffstudyCrfModelMixin
 from edc_sites.managers import CurrentSiteManager
@@ -35,7 +36,11 @@ class Manager(models.Manager):
 
 
 class BirthOutcomes(
-    SiteModelMixin, RequiresConsentFieldsModelMixin, OffstudyCrfModelMixin, BaseUuidModel
+    CrfStatusModelMixin,
+    SiteModelMixin,
+    RequiresConsentFieldsModelMixin,
+    OffstudyCrfModelMixin,
+    BaseUuidModel,
 ):
     """A user model to capture birth outcomes.
 

meta_subject/models/blood_results/__init__.py

@@ -2,5 +2,5 @@ from .blood_results_fbc import BloodResultsFbc
 from .blood_results_hba1c import BloodResultsHba1c
 from .blood_results_ins import BloodResultsIns
 from .blood_results_lft import BloodResultsLft
-from .blood_results_lipid import BloodResultsLipid
+from .blood_results_lipids import BloodResultsLipids
 from .blood_results_rft import BloodResultsRft

meta_subject/models/blood_results/{blood_results_lipid.py → blood_results_lipids.py}

@@ -2,7 +2,7 @@ from django.db import models
 from edc_crf.model_mixins import CrfStatusModelMixin
 from edc_lab.model_mixins import CrfWithRequisitionModelMixin, requisition_fk_options
 from edc_lab_panel.panels import lipids_panel
-from edc_lab_results import BLOOD_RESULTS_LIPID_ACTION
+from edc_lab_results import BLOOD_RESULTS_LIPIDS_ACTION
 from edc_lab_results.model_mixins import (
     BloodResultsModelMixin,
     CholModelMixin,
@@ -15,7 +15,7 @@ from edc_model.models import BaseUuidModel
 from ...model_mixins import CrfWithActionModelMixin
 
 
-class BloodResultsLipid(
+class BloodResultsLipids(
     CrfWithActionModelMixin,
     HdlModelMixin,
     LdlModelMixin,
@@ -26,7 +26,7 @@ class BloodResultsLipid(
     CrfStatusModelMixin,
     BaseUuidModel,
 ):
-    action_name = BLOOD_RESULTS_LIPID_ACTION
+    action_name = BLOOD_RESULTS_LIPIDS_ACTION
     tracking_identifier_prefix = "LP"
     lab_panel = lipids_panel
 

meta_subject/models/diabetes/__init__.py

@@ -1,3 +1,2 @@
-from .dm_diagnosis import DmDiagnosis
-from .dm_dx_result import DmDxResult
+from .dm_endpoint import DmEndpoint
 from .dm_followup import DmFollowup

meta_subject/models/diabetes/dm_endpoint.py

@@ -0,0 +1,61 @@
+from django.db import models
+from edc_constants.choices import YES_NO, YES_NO_RETIRED
+from edc_constants.constants import QUESTION_RETIRED
+from edc_model.models import BaseUuidModel
+from edc_model_fields.fields import OtherCharField
+
+from ...model_mixins import CrfModelMixin
+
+
+class DmEndpoint(CrfModelMixin, BaseUuidModel):
+    """A user model to enrolled patient onto the DM Referral
+    Schedule.
+    """
+
+    endpoint_reached = models.CharField(
+        verbose_name="Was the patient referred because the diabetes endpoint was reached?",
+        max_length=15,
+        choices=YES_NO,
+        null=True,
+        blank=False,
+        help_text="If YES, the EDC will check for the patient on the Endpoints report.",
+    )
+
+    # retired
+    dx_date = models.DateField(verbose_name="Date endpoint reached", null=True)
+
+    # retired
+    dx_initiated_by = models.CharField(
+        verbose_name="What initiated the diagnosis",
+        max_length=25,
+        default=QUESTION_RETIRED,
+    )
+
+    # retired
+    dx_initiated_by_other = OtherCharField(null=True, blank=True)
+
+    # retired
+    dx_tmg = models.CharField(
+        verbose_name="Was this case discussed with the TMG?",
+        max_length=25,
+        choices=YES_NO_RETIRED,
+        default=QUESTION_RETIRED,
+    )
+
+    # retired
+    dx_tmg_date = models.DateField(
+        verbose_name="If YES, provide the date of the TMG discussion", null=True, blank=True
+    )
+
+    # retired
+    dx_no_tmg_reason = models.TextField(
+        verbose_name="If NO, please explain why this case was not discussed with the TMG",
+        null=True,
+        blank=True,
+    )
+
+    comments = models.TextField(verbose_name="Any other comments", null=True, blank=True)
+
+    class Meta(CrfModelMixin.Meta, BaseUuidModel.Meta):
+        verbose_name = "Diabetes endpoint"
+        verbose_name_plural = "Diabetes endpoint"

meta_subject/models/glucose.py

@@ -31,7 +31,10 @@ class Glucose(
     ogtt_model_mixin_factory("ogtt"),
     BaseUuidModel,
 ):
-    """A user model to capture FBG/RBG and OGTT"""
+    """A user model to capture both FBG/RBG and OGTT
+
+    See also GlucoseFbg.
+    """
 
     fbg_performed = models.CharField(
         verbose_name="Was the FBG test performed?",

meta_subject/models/physical_exam.py

@@ -35,6 +35,7 @@ class PhysicalExam(
         validators=[MinValueValidator(50.0), MaxValueValidator(175.0)],
         help_text="in centimeters",
         null=True,
+        blank=True,
     )
 
     jaundice = models.CharField(verbose_name="Jaundice?", max_length=15, choices=YES_NO)

meta_subject/models/signals.py

@@ -11,6 +11,7 @@ from meta_edc.meta_version import get_meta_version
 from meta_pharmacy.constants import METFORMIN
 from meta_visit_schedule.constants import SCHEDULE_PREGNANCY
 
+from . import Glucose, GlucoseFbg
 from .delivery import Delivery
 from .study_medication import StudyMedication
 from .subject_visit import SubjectVisit
@@ -105,3 +106,21 @@ def update_schedule_on_delivery_post_save(sender, instance, raw, **kwargs):
                 subject_identifier=instance.subject_identifier,
                 offschedule_datetime=offschedule_datetime,
             )
+
+
+@receiver(
+    post_save,
+    weak=False,
+    dispatch_uid="update_glucose_endpoints_for_subject_on_post_save",
+)
+def update_glucose_endpoints_for_subject_on_post_save(
+    sender, instance, raw, update_fields, **kwargs
+):
+    if not raw and not update_fields and sender in [Glucose, GlucoseFbg]:
+        from meta_analytics.dataframes import GlucoseEndpointsByDate
+
+        cls = GlucoseEndpointsByDate(
+            subject_identifiers=[instance.subject_visit.subject_identifier]
+        )
+        cls.run()
+        cls.to_model()

meta_subject/models/todo.txt

@@ -5,4 +5,4 @@
 - remove hepatitis
 - remove hba1c venous
 
-- add missing other specify fields on followup examination
+- add missing other specify fields on followup examination

meta_subject/static/meta_subject/slider.css

@@ -43,4 +43,4 @@ https://www.w3schools.com/howto/howto_js_rangeslider.asp
   border-radius: 50%;
   background: #4CAF50; /* Green background */
   cursor: pointer; /* Cursor on hover */
-}
+}

meta_subject/templates/meta_subject/endpoint_review_instructions.html

@@ -3,4 +3,4 @@
 <BR>FBG≥7.0 and OGTT≥11.1: Yes, endpoint reached
 <BR>FBG<7v and OGTT≥11.1: Yes, endpoint reached
 <BR>FBG≥7.0 and OGTT<11.1: Not today, repeat FBG in 1 week<BR>
-</P>
+</P>

meta_subject/templates/meta_subject/widgets/slider.html

@@ -20,4 +20,3 @@ slider.oninput = function() {
   output.innerHTML = this.value;
 }
 </script>
-

meta_subject/tests/holidays.csv

@@ -12,4 +12,4 @@
 2019-12-01,Mawlid Day,tanzania
 2019-12-09,Independence Day,tanzania
 2019-12-25,Christmas Day,tanzania
-2019-12-26,Boxing Day,tanzania
+2019-12-26,Boxing Day,tanzania

meta_subject/tests/tests/test_medication_adherence.py

@@ -37,7 +37,11 @@ class TestMedicationAdherence(MetaTestCaseMixin, TestCase):
 
     def test_ok(self):
         subject_visit = self.get_next_subject_visit(self.subject_visit)
-        obj = make_recipe("meta_subject.medicationadherence", subject_visit=subject_visit)
+        obj = make_recipe(
+            "meta_subject.medicationadherence",
+            subject_visit=subject_visit,
+            report_datetime=subject_visit.report_datetime,
+        )
         form = MedicationAdherenceForm(instance=obj)
         form.is_valid()
         self.assertIsNone(form._errors)

meta_subject/tests/tests/test_metadata_rules.py

@@ -99,8 +99,8 @@ class TestMetadataRules(MetaTestCaseMixin, TestCase):
             subject_screening=subject_screening,
             subject_consent=subject_consent,
         )
-        self.assertEqual(
-            ["meta_subject.delivery"],
+        self.assertIn(
+            "meta_subject.delivery",
             [obj.model for obj in self.get_crf_metadata(subject_visit)],
         )