Merge branch 'develop' into feat/521-add-sodium-blood-results-chem

CHANGES

@@ -3,7 +3,9 @@ Changes
 
 unreleased
 ------
+- add QA reports for Missing Lab Values
 - add Sodium field to Blood Result: Chemistry form (#521)
+- bump to edc 0.6.12
 
 0.1.55
 ------

effect_edc/settings/defaults.py

@@ -82,8 +82,9 @@
     "multisite",
     "fontawesomefree",
     "django_crypto_fields.apps.AppConfig",
-    "django_revision.apps.AppConfig",
+    "django_db_views",
     "django_extensions",
+    "django_revision.apps.AppConfig",
     "logentry_admin",
     "simple_history",
     "storages",
@@ -482,7 +483,7 @@
     AWS_S3_OBJECT_PARAMETERS = {"CacheControl": "max-age=86400"}
     AWS_LOCATION = env.str("AWS_LOCATION")
     AWS_IS_GZIPPED = True
-    STATICFILES_STORAGE = "storages.backends.s3boto3.S3Boto3Storage"
+    STORAGES = {"staticfiles": {"BACKEND": "storages.backends.s3boto3.S3Boto3Storage"}}
     STATIC_URL = f"{os.path.join(AWS_S3_CUSTOM_DOMAIN, AWS_LOCATION)}/"
     STATIC_ROOT = ""
 else:

effect_labs/constants.py

@@ -0,0 +1,3 @@
+BLOOD_CULTURE = "blood_culture"
+CHEMISTRY = "chemistry"
+CSF_CULTURE = "csf_culture"

effect_labs/panels.py

@@ -1,5 +1,7 @@
 from edc_lab import RequisitionPanel
+from edc_lab_panel.constants import FBC
 
+from .constants import BLOOD_CULTURE, CHEMISTRY, CSF_CULTURE
 from .processing_profiles import (
     blood_culture_processing,
     chemistry_processing,
@@ -10,7 +12,7 @@
 )
 
 chemistry_panel = RequisitionPanel(
-    name="chemistry",
+    name=CHEMISTRY,
     verbose_name="Chemistry: RFT, LFT, Electrolytes",
     abbreviation="CHEM",
     processing_profile=chemistry_processing,
@@ -41,7 +43,7 @@
     ],
 )
 csf_culture_panel = RequisitionPanel(
-    name="csf_culture",
+    name=CSF_CULTURE,
     verbose_name="CSF culture",
     abbreviation="CSFC",
     processing_profile=csf_culture_processing,
@@ -65,7 +67,7 @@
 )
 
 blood_culture_panel = RequisitionPanel(
-    name="blood_culture",
+    name=BLOOD_CULTURE,
     verbose_name="Blood culture",
     abbreviation="BLE",
     processing_profile=blood_culture_processing,
@@ -74,7 +76,7 @@
 
 # TODO: update fbc_panel
 fbc_panel = RequisitionPanel(
-    name="fbc",
+    name=FBC,
     verbose_name="Full Blood Count",
     processing_profile=fbc_processing,
     abbreviation="FBC",

effect_reports/admin/__init__.py

@@ -1,3 +1,4 @@
+from .dbviews import OnStudyMissingLabValuesAdmin
 from .serum_crag_date_admin import SerumCragDateAdmin, SerumCragDateNoteAdmin
 from .unmanaged import (
     Rm792KwInCurrentSxGteG3OtherAdmin,

effect_reports/admin/dbviews/__init__.py

@@ -0,0 +1 @@
+from .on_study_missing_lab_values_admin import OnStudyMissingLabValuesAdmin

effect_reports/admin/dbviews/on_study_missing_lab_values_admin/__init__.py

@@ -0,0 +1 @@
+from .unmanaged_model_admin import OnStudyMissingLabValuesAdmin

effect_reports/admin/dbviews/on_study_missing_lab_values_admin/unmanaged_model_admin.py

@@ -0,0 +1,13 @@
+from django.contrib import admin
+from edc_qareports.modeladmin_mixins import OnStudyMissingValuesModelAdminMixin
+
+from ....admin_site import effect_reports_admin
+from ....models import OnStudyMissingLabValues
+
+
+@admin.register(OnStudyMissingLabValues, site=effect_reports_admin)
+class OnStudyMissingLabValuesAdmin(OnStudyMissingValuesModelAdminMixin, admin.ModelAdmin):
+
+    include_note_column: bool = True
+
+    instructions = ["ello"]

effect_reports/migrations/0004_onstudymissinglabvalues_and_more.py

@@ -0,0 +1,50 @@
+# Generated by Django 5.1.1 on 2024-09-12 09:55
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("effect_reports", "0003_serumcragdate_historicalserumcragdatenote_and_more"),
+        ("sites", "0002_alter_domain_unique"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="OnStudyMissingLabValues",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("original_id", models.UUIDField(null=True)),
+                ("label_lower", models.CharField(max_length=150, null=True)),
+                ("subject_visit_id", models.UUIDField(null=True)),
+                ("report_datetime", models.DateTimeField(null=True)),
+                ("label", models.CharField(max_length=50, null=True)),
+                ("visit_code", models.CharField(max_length=25, null=True)),
+                ("visit_code_sequence", models.IntegerField(null=True)),
+                ("schedule_name", models.CharField(max_length=25, null=True)),
+                ("modified", models.DateTimeField(null=True)),
+                ("report_model", models.CharField(max_length=50)),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("created", models.DateTimeField()),
+            ],
+            options={
+                "verbose_name": "Missing lab values for on-study patient",
+                "verbose_name_plural": "Missing lab values for on-study patients",
+                "db_table": "onstudy_missing_lab_values_view",
+                "managed": False,
+                "default_permissions": ("view", "export", "viewallsites"),
+            },
+        ),
+        migrations.AddIndex(
+            model_name="serumcragdate",
+            index=models.Index(
+                fields=["subject_identifier", "site"], name="effect_repo_subject_24c4b3_idx"
+            ),
+        ),
+    ]