meta-edc 0.2.24__py3-none-any.whl → 1.4.0__py3-none-any.whl

meta_subject/migrations/0115_historicalegfrnotification_egfrnotification.py

@@ -7,7 +7,7 @@ import django.db.models.deletion
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
-import django_audit_fields.models.audit_model_mixin
+import django.utils.timezone
 import django_revision.revision_field
 import edc_utils.date
 import edc_visit_tracking.managers
@@ -16,7 +16,6 @@ import uuid
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("sites", "0002_alter_domain_unique"),
         ("edc_action_item", "0028_auto_20210203_0706"),
@@ -41,15 +40,11 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "created",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",
@@ -272,15 +267,11 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "created",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(
-                        blank=True, default=django_audit_fields.models.audit_model_mixin.utcnow
-                    ),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",

meta_subject/migrations/0116_egfrnotification_report_status_and_more.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0115_historicalegfrnotification_egfrnotification"),
     ]

meta_subject/migrations/0117_alter_egfrnotification_managers_and_more.py

@@ -6,7 +6,6 @@ import edc_visit_tracking.managers
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0116_egfrnotification_report_status_and_more"),
     ]

meta_subject/migrations/0118_delivery_crf_status_delivery_crf_status_comments_and_more.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0117_alter_egfrnotification_managers_and_more"),
     ]

meta_subject/migrations/0119_historicalstudymedication_roundup_divisible_by_and_more.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0118_delivery_crf_status_delivery_crf_status_comments_and_more"),
     ]

meta_subject/migrations/0120_alter_birthoutcomes_managers_and_more.py

@@ -6,7 +6,6 @@ import meta_subject.models.birth_outcomes
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0119_historicalstudymedication_roundup_divisible_by_and_more"),
     ]

meta_subject/migrations/0121_auto_20220704_1841.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0120_alter_birthoutcomes_managers_and_more"),
     ]

meta_subject/migrations/0122_auto_20220708_2144.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0121_auto_20220704_1841"),
     ]

meta_subject/migrations/0123_auto_20220714_2136.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0122_auto_20220708_2144"),
     ]

meta_subject/migrations/0124_auto_20220714_2303.py

@@ -34,7 +34,6 @@ def update_bloodresults(apps, schema_editor):
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0123_auto_20220714_2136"),
     ]

meta_subject/migrations/0125_auto_20220719_2134.py

@@ -5,7 +5,6 @@ from django.db import migrations
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("sites", "0002_alter_domain_unique"),
         migrations.swappable_dependency(settings.AUTH_USER_MODEL),

meta_subject/migrations/0126_auto_20220719_2142.py

@@ -4,18 +4,17 @@ from django.db import migrations
 
 
 def update_egfr_drop_action(apps, schema_editor):
-    action_item_model_cls = apps.get_model("edc_action_item.actionitem")
+    # action_item_model_cls = apps.get_model("edc_action_item.actionitem")
     crf_metadata_model_cls = apps.get_model("edc_metadata.crfmetadata")
-    action_item_model_cls.objects.filter(
-        reference_model="meta_subject.egfrnotification"
-    ).update(reference_model="meta_subject.egfrdropnotification")
+    # action_item_model_cls.objects.filter(
+    #     reference_model="meta_subject.egfrnotification"
+    # ).update(reference_model="meta_subject.egfrdropnotification")
     crf_metadata_model_cls.objects.filter(model="meta_subject.egfrnotification").update(
         model="meta_subject.egfrdropnotification"
     )
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0125_auto_20220719_2134"),
     ]

meta_subject/migrations/0127_auto_20220720_0053.py

@@ -5,7 +5,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0126_auto_20220719_2142"),
     ]

meta_subject/migrations/0128_auto_20220720_0055.py

@@ -2,7 +2,7 @@
 
 from django.db import migrations
 from django.db.models import F
-from edc_reportable import PERCENT
+from clinicedc_constants import PERCENT
 
 
 def update_new_egfr_drop_field(apps, schema_editor):
@@ -17,7 +17,6 @@ def update_new_egfr_drop_field(apps, schema_editor):
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0127_auto_20220720_0053"),
     ]

meta_subject/migrations/0129_auto_20220720_0108.py

@@ -4,7 +4,6 @@ from django.db import migrations
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0128_auto_20220720_0055"),
     ]

meta_subject/migrations/0130_auto_20220720_0216.py

@@ -12,7 +12,6 @@ def update_egfr_drop_field_to_percent(apps, schema_editor):
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0129_auto_20220720_0108"),
     ]

meta_subject/migrations/0131_auto_20220722_0411.py

@@ -1,8 +1,8 @@
 # Generated by Django 3.2.11 on 2022-07-22 01:11
-
+from django.core.exceptions import ObjectDoesNotExist
 from django.db import migrations
 from edc_action_item.identifiers import ActionIdentifier
-from edc_constants.constants import CLOSED, HIGH_PRIORITY
+from clinicedc_constants import CLOSED, HIGH_PRIORITY
 from tqdm import tqdm
 
 from meta_subject.constants import MISSED_VISIT_ACTION
@@ -13,32 +13,36 @@ def update_missing_action_items_for_missed_visits(apps, schema_editor):
     actionitem_model_cls = apps.get_model("edc_action_item.actionitem")
     subjectvisitmissed_model_cls = apps.get_model("meta_subject.subjectvisitmissed")
     subjectvisit_model_cls = apps.get_model("meta_subject.subjectvisit")
-    action_type = actiontype_model_cls.objects.get(name=MISSED_VISIT_ACTION)
-
-    total = subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True).count()
-    for obj in tqdm(
-        subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True),
-        total=total,
-    ):
-        subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
-        action_item = actionitem_model_cls.objects.create(
-            subject_identifier=subject_visit.subject_identifier,
-            action_identifier=ActionIdentifier(site_id=subject_visit.site_id).identifier,
-            report_datetime=subject_visit.report_datetime,
-            action_type=action_type,
-            reference_model="meta_subject.subjectvisitmissed",
-            linked_to_reference=True,
-            priority=HIGH_PRIORITY,
-            status=CLOSED,
-            auto_created=True,
-            site_id=subject_visit.site_id,
-        )
-        obj.action_identifier = action_item.action_identifier
-        obj.save_base(update_fields=["action_identifier"])
+    try:
+        action_type = actiontype_model_cls.objects.get(name=MISSED_VISIT_ACTION)
+    except ObjectDoesNotExist:
+        pass
+    else:
+        total = subjectvisitmissed_model_cls.objects.filter(
+            action_identifier__isnull=True
+        ).count()
+        for obj in tqdm(
+            subjectvisitmissed_model_cls.objects.filter(action_identifier__isnull=True),
+            total=total,
+        ):
+            subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
+            action_item = actionitem_model_cls.objects.create(
+                subject_identifier=subject_visit.subject_identifier,
+                action_identifier=ActionIdentifier(site_id=subject_visit.site_id).identifier,
+                report_datetime=subject_visit.report_datetime,
+                action_type=action_type,
+                reference_model="meta_subject.subjectvisitmissed",
+                linked_to_reference=True,
+                priority=HIGH_PRIORITY,
+                status=CLOSED,
+                auto_created=True,
+                site_id=subject_visit.site_id,
+            )
+            obj.action_identifier = action_item.action_identifier
+            obj.save_base(update_fields=["action_identifier"])
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0130_auto_20220720_0216"),
     ]

meta_subject/migrations/0132_auto_20220722_1825.py

@@ -1,5 +1,5 @@
 # Generated by Django 3.2.11 on 2022-07-22 15:25
-
+from django.core.exceptions import ObjectDoesNotExist
 from django.db import migrations
 from tqdm import tqdm
 
@@ -9,15 +9,18 @@ from meta_pharmacy.constants import METFORMIN
 def update_rx_missing_medication(apps, schema_editor):
     medication_model_cls = apps.get_model("edc_pharmacy.medication")
     rx_model_cls = apps.get_model("edc_pharmacy.rx")
-    medication = medication_model_cls.objects.get(name=METFORMIN)
-    total = rx_model_cls.objects.filter(medications__isnull=True).count()
-    for obj in tqdm(rx_model_cls.objects.filter(medications__isnull=True), total=total):
-        if not obj.medications.all().exists():
-            obj.medications.add(medication)
+    try:
+        medication = medication_model_cls.objects.get(name=METFORMIN)
+    except ObjectDoesNotExist:
+        pass
+    else:
+        total = rx_model_cls.objects.filter(medications__isnull=True).count()
+        for obj in tqdm(rx_model_cls.objects.filter(medications__isnull=True), total=total):
+            if not obj.medications.all().exists():
+                obj.medications.add(medication)
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0131_auto_20220722_0411"),
     ]

meta_subject/migrations/0133_auto_20220722_2140.py

@@ -5,7 +5,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0132_auto_20220722_1825"),
     ]

meta_subject/migrations/0134_auto_20220722_2211.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0133_auto_20220722_2140"),
     ]

meta_subject/migrations/0135_auto_20220722_2212.py

@@ -1,54 +1,58 @@
 # Generated by Django 3.2.11 on 2022-07-22 19:12
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import migrations
-from edc_egfr.calculators import EgfrCkdEpi, egfr_percent_change
 from edc_visit_schedule.constants import DAY1
 from tqdm import tqdm
+from clinicedc_utils import EgfrCkdEpi2009 as EgfrCkdEpi
+from clinicedc_utils import egfr_percent_change
 
 
 def update_revised_egrf(apps, schema_editor):
     bloodresultrft_model_cls = apps.get_model("meta_subject.bloodresultsrft")
     subjectvisit_model_cls = apps.get_model("meta_subject.subjectvisit")
-    subjectscreening_model_cls = apps.get_model("meta_screening.subjectscreening")
-    total = bloodresultrft_model_cls.objects.all().count()
-    for obj in tqdm(bloodresultrft_model_cls.objects.all(), total=total):
-        subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
-        subject_screening = subjectscreening_model_cls.objects.get(
-            subject_identifier=subject_visit.subject_identifier
-        )
-        try:
-            baseline_obj = bloodresultrft_model_cls.objects.get(
-                subject_visit__subject_identifier=subject_visit.subject_identifier,
-                subject_visit__visit_code=DAY1,
-                subject_visit__visit_code_sequence=0,
-            )
-        except ObjectDoesNotExist:
-            pass
-        else:
-            obj.old_egfr_value = obj.egfr_value
-            obj.old_egfr_drop_value = obj.egfr_drop_value
-            obj.egfr_value = EgfrCkdEpi(
-                gender=subject_screening.gender,
-                ethnicity=subject_screening.ethnicity,
-                age_in_years=subject_screening.age_in_years,
-                creatinine_value=obj.creatinine_value,
-                creatinine_units=obj.creatinine_units,
-            ).value
-            obj.egfr_drop_value = egfr_percent_change(
-                float(obj.egfr_value), float(baseline_obj.egfr_value)
-            )
-            obj.save_base(
-                update_fields=[
-                    "egfr_value",
-                    "egfr_drop_value",
-                    "old_egfr_value",
-                    "old_egfr_drop_value",
-                ]
+    try:
+        subjectscreening_model_cls = apps.get_model("meta_screening.subjectscreening")
+    except LookupError:
+        pass
+    else:
+        total = bloodresultrft_model_cls.objects.all().count()
+        for obj in tqdm(bloodresultrft_model_cls.objects.all(), total=total):
+            subject_visit = subjectvisit_model_cls.objects.get(id=obj.subject_visit_id)
+            subject_screening = subjectscreening_model_cls.objects.get(
+                subject_identifier=subject_visit.subject_identifier
             )
+            try:
+                baseline_obj = bloodresultrft_model_cls.objects.get(
+                    subject_visit__subject_identifier=subject_visit.subject_identifier,
+                    subject_visit__visit_code=DAY1,
+                    subject_visit__visit_code_sequence=0,
+                )
+            except ObjectDoesNotExist:
+                pass
+            else:
+                obj.old_egfr_value = obj.egfr_value
+                obj.old_egfr_drop_value = obj.egfr_drop_value
+                obj.egfr_value = EgfrCkdEpi(
+                    gender=subject_screening.gender,
+                    ethnicity=subject_screening.ethnicity,
+                    age_in_years=subject_screening.age_in_years,
+                    creatinine_value=obj.creatinine_value,
+                    creatinine_units=obj.creatinine_units,
+                ).value
+                obj.egfr_drop_value = egfr_percent_change(
+                    float(obj.egfr_value), float(baseline_obj.egfr_value)
+                )
+                obj.save_base(
+                    update_fields=[
+                        "egfr_value",
+                        "egfr_drop_value",
+                        "old_egfr_value",
+                        "old_egfr_drop_value",
+                    ]
+                )
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0134_auto_20220722_2211"),
     ]

meta_subject/migrations/0136_egfrdropnotification_creatinine_quantifier_and_more.py

@@ -9,7 +9,6 @@ import edc_vitals.models.fields.weight
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0135_auto_20220722_2212"),
     ]

meta_subject/migrations/0137_alter_egfrdropnotification_egfr_percent_change_and_more.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0136_egfrdropnotification_creatinine_quantifier_and_more"),
     ]

meta_subject/migrations/0138_alter_glucose_fbg_datetime_and_more.py

@@ -5,7 +5,6 @@ import edc_model.validators.date
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0137_alter_egfrdropnotification_egfr_percent_change_and_more"),
     ]

meta_subject/migrations/0139_alter_bloodresultsins_ins_units_and_more.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0138_alter_glucose_fbg_datetime_and_more"),
     ]

meta_subject/migrations/0140_alter_bloodresultsfbc_action_identifier_and_more.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0139_alter_bloodresultsins_ins_units_and_more"),
     ]

meta_subject/migrations/0141_auto_20220826_0258.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0140_alter_bloodresultsfbc_action_identifier_and_more"),
     ]

meta_subject/migrations/0142_auto_20220826_0322.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0141_auto_20220826_0258"),
     ]

meta_subject/migrations/0143_auto_20220826_0406.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0142_auto_20220826_0322"),
     ]

meta_subject/migrations/0144_auto_20220907_0157.py

@@ -7,7 +7,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0143_auto_20220826_0406"),
     ]

meta_subject/migrations/0145_auto_20220907_0202.py

@@ -6,7 +6,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0144_auto_20220907_0157"),
     ]

meta_subject/migrations/0146_auto_20220907_0207.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0145_auto_20220907_0202"),
     ]

meta_subject/migrations/0147_auto_20220907_1505.py

@@ -38,7 +38,6 @@ def update_refill_end_datetimes(apps, schema_editor):
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0146_auto_20220907_0207"),
     ]

meta_subject/migrations/0148_auto_20220908_1826.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0147_auto_20220907_1505"),
     ]

meta_subject/migrations/0149_auto_20220913_2139.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0148_auto_20220908_1826"),
     ]

meta_subject/migrations/0150_auto_20220914_0039.py

@@ -4,24 +4,26 @@ from tqdm import tqdm
 
 
 def update_rs_missing_ethnicity(apps, schema_editor):
-
     register_subject_model_cls = apps.get_model("edc_registration.registeredsubject")
-    subject_screening_model_cls = apps.get_model("meta_screening.subjectscreening")
     subject_consent_model_cls = apps.get_model("meta_consent.subjectconsent")
-    total = subject_consent_model_cls.objects.all().count()
-    for subject_consent in tqdm(subject_consent_model_cls.objects.all(), total=total):
-        subject_screening = subject_screening_model_cls.objects.get(
-            subject_identifier=subject_consent.subject_identifier
-        )
-        register_subject = register_subject_model_cls.objects.get(
-            subject_identifier=subject_consent.subject_identifier
-        )
-        register_subject.ethnicity = subject_screening.ethnicity
-        register_subject.save(update_fields=["ethnicity"])
+    try:
+        subject_screening_model_cls = apps.get_model("meta_screening.subjectscreening")
+    except LookupError:
+        pass
+    else:
+        total = subject_consent_model_cls.objects.all().count()
+        for subject_consent in tqdm(subject_consent_model_cls.objects.all(), total=total):
+            subject_screening = subject_screening_model_cls.objects.get(
+                subject_identifier=subject_consent.subject_identifier
+            )
+            register_subject = register_subject_model_cls.objects.get(
+                subject_identifier=subject_consent.subject_identifier
+            )
+            register_subject.ethnicity = subject_screening.ethnicity
+            register_subject.save(update_fields=["ethnicity"])
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_consent", "0014_alter_subjectconsent_managers"),
         ("meta_subject", "0149_auto_20220913_2139"),

meta_subject/migrations/0151_auto_20220918_0508.py

@@ -5,7 +5,6 @@ import edc_crf.model_mixins.crf_status_model_mixin
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0150_auto_20220914_0039"),
     ]

meta_subject/migrations/0152_auto_20220925_0509.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0151_auto_20220918_0508"),
     ]

meta_subject/migrations/0153_auto_20220928_0250.py

@@ -4,7 +4,6 @@ from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0152_auto_20220925_0509"),
     ]

meta_subject/migrations/0154_auto_20220928_0419.py

@@ -4,7 +4,6 @@ from django.db import migrations
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0153_auto_20220928_0250"),
     ]

meta_subject/migrations/0155_auto_20220929_1742.py

@@ -5,7 +5,6 @@ import edc_visit_tracking.managers
 
 
 class Migration(migrations.Migration):
-
     dependencies = [
         ("meta_subject", "0154_auto_20220928_0419"),
     ]