meta-edc 0.3.20__tar.gz → 0.3.22__tar.gz

{meta_edc-0.3.20 → meta_edc-0.3.22}/.gitignore

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

{meta_edc-0.3.20 → meta_edc-0.3.22}/CHANGES

@@ -1,7 +1,7 @@
 Changes
 -------
 
-0.3.20
+0.3.21
 ------
 - bump edc 0.6.0, django-crypto-fields 0.4.2, Django 5.1
 

{meta_edc-0.3.20 → meta_edc-0.3.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.20
+Version: 0.3.22
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -19,10 +19,11 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.5.60
+Requires-Dist: edc==0.6.1
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics
+Requires-Dist: celery[redis]
 Requires-Dist: Django==5.1
 
 |pypi| |actions| |codecov| |downloads|
@@ -35,7 +36,7 @@ Metformin treatment in Africa- META
 
 https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
 
-py 3.11 / DJ 4.2.7 / edc 0.5.37 (META3)
+py 3.12 / DJ 5.1 / edc 0.6.0 (META3)
 
 This codebase is used for two randomized clinical trials:
 

{meta_edc-0.3.20 → meta_edc-0.3.22}/README.rst

@@ -8,7 +8,7 @@ Metformin treatment in Africa- META
 
 https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
 
-py 3.11 / DJ 4.2.7 / edc 0.5.37 (META3)
+py 3.12 / DJ 5.1 / edc 0.6.0 (META3)
 
 This codebase is used for two randomized clinical trials:
 

meta_edc-0.3.22/bin/celery/celery.live.conf

@@ -0,0 +1,27 @@
+# Name of nodes to start
+CELERYD_NODES="w1 w2"
+
+# Absolute or relative path to the 'celery' command:
+CELERY_BIN="/home/live/miniconda3/envs/edc/bin/celery"
+
+# App instance to use
+CELERY_APP="meta_edc.celery.live:app"
+
+# Where to chdir at start.
+CELERYD_CHDIR="/home/live/app/"
+
+# How to call manage.py
+CELERYD_MULTI="multi"
+
+# Extra command-line arguments to the worker
+CELERYD_OPTS="--time-limit=300 --concurrency=8"
+
+# - %n will be replaced with the first part of the nodename.
+# - %I will be replaced with the current child process index
+#   and is important when using the prefork pool to avoid race conditions.
+CELERYD_PID_FILE="/opt/celery/%n.live.pid"
+CELERYD_LOG_FILE="/var/log/celery/%n%I.live.log"
+CELERYD_LOG_LEVEL="INFO"
+
+CELERYD_USER="celery"
+CELERYD_GROUP="celery"

meta_edc-0.3.22/bin/celery/celery.uat.conf

@@ -0,0 +1,27 @@
+# Name of nodes to start
+CELERYD_NODES="w1 w2"
+
+# Absolute or relative path to the 'celery' command:
+CELERY_BIN="/home/uat/miniconda3/envs/edc/bin/celery"
+
+# App instance to use
+CELERY_APP="meta_edc.celery.uat:app"
+
+# Where to chdir at start.
+CELERYD_CHDIR="/home/uat/app/"
+
+# How to call manage.py
+CELERYD_MULTI="multi"
+
+# Extra command-line arguments to the worker
+CELERYD_OPTS="--time-limit=300 --concurrency=8"
+
+# - %n will be replaced with the first part of the nodename.
+# - %I will be replaced with the current child process index
+#   and is important when using the prefork pool to avoid race conditions.
+CELERYD_PID_FILE="/opt/celery/%n.uat.pid"
+CELERYD_LOG_FILE="/var/log/celery/%n%I.uat.log"
+CELERYD_LOG_LEVEL="INFO"
+
+CELERYD_USER="celery"
+CELERYD_GROUP="celery"

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_analytics/dataframes/glucose_endpoints/glucose_endpoints_by_date.py

@@ -32,11 +32,15 @@ class GlucoseEndpointsByDate:
     ogtt_threshhold = 11.1
     endpoint_cls = EndpointByDate
 
-    def __init__(self, case_list: list[int] | None = None):
+    def __init__(
+        self, subject_identifiers: list[str] | None = None, case_list: list[int] | None = None
+    ):
         self.case_list = case_list or [CASE_OGTT, 2, 3, CASE_EOS]
         self.endpoint_cases = {k: v for k, v in endpoint_cases.items() if k in self.case_list}
         self.endpoint_only_df = None
-        self.fbg_only_df = get_crf(model="meta_subject.glucosefbg")
+        self.fbg_only_df = get_crf(
+            model="meta_subject.glucosefbg", subject_identifiers=subject_identifiers
+        )
         self.fbg_only_df["source"] = "meta_subject.glucosefbg"
         self.fbg_only_df.rename(
             columns={"fbg_fasting": "fasting", "subject_visit": "subject_visit_id"},
@@ -45,7 +49,9 @@ class GlucoseEndpointsByDate:
         self.fbg_only_df.loc[(self.fbg_only_df["fasting"] == "fasting"), "fasting"] = YES
         self.fbg_only_df.loc[(self.fbg_only_df["fasting"] == "non_fasting"), "fasting"] = NO
 
-        self.df = get_crf(model="meta_subject.glucose")
+        self.df = get_crf(
+            model="meta_subject.glucose", subject_identifiers=subject_identifiers
+        )
         self.df["source"] = "meta_subject.glucose"
 
         for dftmp in [self.fbg_only_df, self.df]:
@@ -112,7 +118,9 @@ class GlucoseEndpointsByDate:
         for col, null_value in cols.items():
             self.df.loc[self.df["_merge"] == "right_only", col] = self.df[f"{col}2"]
 
-        df_subject_visit = get_subject_visit("meta_subject.subjectvisit")
+        df_subject_visit = get_subject_visit(
+            "meta_subject.subjectvisit", subject_identifiers=subject_identifiers
+        )
         visit_cols = [
             "subject_visit_id",
             "subject_identifier",
@@ -127,12 +135,14 @@ class GlucoseEndpointsByDate:
         self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
         self.df.reset_index(drop=True, inplace=True)
 
-        df_consent = get_subject_consent("meta_consent.subjectconsent")
+        df_consent = get_subject_consent(
+            "meta_consent.subjectconsent", subject_identifiers=subject_identifiers
+        )
         self.df = pd.merge(self.df, df_consent, on="subject_identifier", how="left")
         self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
         self.df.reset_index(drop=True, inplace=True)
 
-        df_eos = get_eos("meta_prn.endofstudy")
+        df_eos = get_eos("meta_prn.endofstudy", subject_identifiers=subject_identifiers)
         self.df = pd.merge(self.df, df_eos, on="subject_identifier", how="left")
         self.df = self.df.sort_values(by=["subject_identifier", "fbg_datetime"])
         self.df.reset_index(drop=True, inplace=True)
@@ -298,7 +308,7 @@ class GlucoseEndpointsByDate:
             self.endpoint_df["fbg_datetime"] - self.endpoint_df["baseline_datetime"]
         ).dt.days
 
-        print(f"Before dedup = {len(self.endpoint_df)}")
+        # print(f"Before dedup = {len(self.endpoint_df)}")
 
         df1 = self.endpoint_df.copy()
         df1 = df1[(df1["endpoint_type"] == CASE_EOS) & (df1["endpoint"] == 1)]
@@ -318,7 +328,7 @@ class GlucoseEndpointsByDate:
 
         self.endpoint_only_df = pd.concat([df1, df2])
         self.endpoint_only_df = self.endpoint_only_df.reset_index(drop=True)
-        print(f"After dedup = {len(self.endpoint_df)}")
+        # print(f"After dedup = {len(self.endpoint_df)}")
 
         self.df = pd.merge(
             self.df,
@@ -375,12 +385,15 @@ class GlucoseEndpointsByDate:
         df_counts = pd.concat([df_counts, sums_df], ignore_index=True)
         return df_counts
 
-    def to_model(self, model: str | None = None):
+    def to_model(self, model: str | None = None, subject_identifiers: list[str] | None = None):
         df = self.endpoint_only_df
         model = model or "meta_reports.endpoints"
         now = get_utcnow()
         model_cls = django_apps.get_model(model)
-        model_cls.objects.all().delete()
+        if subject_identifiers:
+            model_cls.objects.filter(subject_identifier__in=subject_identifiers).delete()
+        else:
+            model_cls.objects.all().delete()
         data = [
             model_cls(
                 subject_identifier=row["subject_identifier"],
@@ -407,4 +420,4 @@ class GlucoseEndpointsByDate:
             )
             for _, row in df.iterrows()
         ]
-        model_cls.objects.bulk_create(data)
+        return len(model_cls.objects.bulk_create(data))

meta_edc-0.3.22/meta_edc/__init__.py

@@ -0,0 +1,14 @@
+import os
+from importlib.metadata import PackageNotFoundError, version
+
+from .celery.debug import app as celery_debug
+from .celery.live import app as celery_live
+from .celery.uat import app as celery_uat
+
+try:
+    __version__ = version(os.getcwd().split(os.sep)[-1])
+except PackageNotFoundError:
+    __version__ = None
+
+
+__all__ = ["celery_live", "celery_uat", "celery_debug", "__version__"]

meta_edc-0.3.22/meta_edc/celery/debug.py

@@ -0,0 +1,17 @@
+import os
+
+from celery import Celery
+
+# load settings
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "meta_edc.settings.debug")
+
+# config celery
+# remember to include additional apps with tasks
+app = Celery("meta_edc", include=["meta_reports"])
+app.config_from_object("django.conf:settings", namespace="CELERY")
+app.autodiscover_tasks()
+
+
+@app.task(bind=True)
+def debug_task(self):
+    print("Request: {0!r}".format(self.request))

meta_edc-0.3.22/meta_edc/celery/live.py

@@ -0,0 +1,17 @@
+import os
+
+from celery import Celery
+
+# load settings
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "meta_edc.settings.live")
+
+# config celery
+# remember to include additional apps with tasks
+app = Celery("meta_edc", include=["meta_reports"])
+app.config_from_object("django.conf:settings", namespace="CELERY")
+app.autodiscover_tasks()
+
+
+@app.task(bind=True)
+def debug_task(self):
+    print("Request: {0!r}".format(self.request))

meta_edc-0.3.22/meta_edc/celery/uat.py

@@ -0,0 +1,17 @@
+import os
+
+from celery import Celery
+
+# load settings
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "meta_edc.settings.uat")
+
+# config celery
+# remember to include additional apps with tasks
+app = Celery("meta_edc", include=["meta_reports"])
+app.config_from_object("django.conf:settings", namespace="CELERY")
+app.autodiscover_tasks()
+
+
+@app.task(bind=True)
+def debug_task(self):
+    print("Request: {0!r}".format(self.request))

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_edc/settings/defaults.py

@@ -2,6 +2,7 @@ import os
 import sys
 from importlib.metadata import version
 from pathlib import Path
+from urllib.parse import quote
 
 import django
 import environ
@@ -91,6 +92,8 @@ INSTALLED_APPS = [
     "django.contrib.sites",
     "multisite.apps.AppConfig",
     "defender",
+    # "django_celery_beat",
+    # "django_celery_results",
     "django_db_views",
     "fontawesomefree",
     "django_crypto_fields.apps.AppConfig",
@@ -521,36 +524,16 @@ else:
     STATIC_ROOT = env.str("DJANGO_STATIC_ROOT")
 
 # CELERY
-# see docs on setting up the broker
 CELERY_ENABLED = env("CELERY_ENABLED")
 if CELERY_ENABLED:
-    CELERY_BROKER_USER = env.str("CELERY_BROKER_USER")
-    CELERY_BROKER_PASSWORD = env.str("CELERY_BROKER_PASSWORD")
-    CELERY_BROKER_HOST = env.str("CELERY_BROKER_HOST")
-    CELERY_BROKER_PORT = env.str("CELERY_BROKER_PORT")
-    if DEBUG:
-        CELERY_BROKER_VHOST = f"{APP_NAME}_debug"
-    elif LIVE_SYSTEM:
-        CELERY_BROKER_VHOST = f"{APP_NAME}_production"
-    else:
-        CELERY_BROKER_VHOST = f"{APP_NAME}_uat"
+    CELERY_CACHE_BACKEND = "default"
+    if env.str("DJANGO_REDIS_PASSWORD"):
         CELERY_BROKER_URL = (
-            f"amqp://{CELERY_BROKER_USER}:{CELERY_BROKER_PASSWORD}@"
-            f"{CELERY_BROKER_HOST}:{CELERY_BROKER_PORT}/{CELERY_BROKER_VHOST}"
+            f"redis://:{quote(env.str('DJANGO_REDIS_PASSWORD'), safe='')}@127.0.0.1:6379/0"
         )
-        DJANGO_CELERY_RESULTS_TASK_ID_MAX_LENGTH = 191
-        CELERY_RESULT_BACKEND = "django-db"
-        #     CELERY_QUEUES = (
-        #         Queue('high', Exchange('high'), routing_key='high'),
-        #         Queue('normal', Exchange('normal'), routing_key='normal'),
-        #         Queue('low', Exchange('low'), routing_key='low'),
-        #     )
-        #     CELERY_DEFAULT_QUEUE = 'normal'
-        #     CELERY_DEFAULT_EXCHANGE = 'normal'
-        #     CELERY_DEFAULT_ROUTING_KEY = 'normal'
-        #     CELERY_ROUTES = {
-        #         'edc_data_manager.tasks.*': {'queue': 'normal'},
-        #     }
+    else:
+        CELERY_BROKER_URL = "redis://127.0.0.1:6379/0"
+    # CELERY_BEAT_SCHEDULER = "django_celery_beat.schedulers.DatabaseScheduler"
 
 
 if "test" in sys.argv:

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_edc.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: meta-edc
-Version: 0.3.20
+Version: 0.3.22
 Summary: META Trial EDC (http://www.isrctn.com/ISRCTN76157257)
 Home-page: https://github.com/meta-trial/meta-edc
 Author: Erik van Widenfelt
@@ -19,10 +19,11 @@ Requires-Python: >=3.12
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS
-Requires-Dist: edc==0.5.60
+Requires-Dist: edc==0.6.1
 Requires-Dist: edc-microscopy
 Requires-Dist: beautifulsoup4
 Requires-Dist: edc-analytics
+Requires-Dist: celery[redis]
 Requires-Dist: Django==5.1
 
 |pypi| |actions| |codecov| |downloads|
@@ -35,7 +36,7 @@ Metformin treatment in Africa- META
 
 https://www.lstmed.ac.uk/research/departments/international-public-health/respond-africa/meta
 
-py 3.11 / DJ 4.2.7 / edc 0.5.37 (META3)
+py 3.12 / DJ 5.1 / edc 0.6.0 (META3)
 
 This codebase is used for two randomized clinical trials:
 

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_edc.egg-info/SOURCES.txt

@@ -17,6 +17,8 @@ releases
 runtests.py
 setup.cfg
 .github/workflows/build.yml
+bin/celery/celery.live.conf
+bin/celery/celery.uat.conf
 bin/nginx/meta2/conf/live.conf
 bin/nginx/meta2/conf/live_sites.conf
 bin/nginx/meta2/conf/meta.clinicedc.org.conf
@@ -49,10 +51,6 @@ bin/nginx/meta4/www/html/uat.meta3.clinicedc.org/tz/index.html
 bin/scripts/list_db_files.sh
 bin/scripts/restore_db_file.sh
 bin/scripts/update_edc.sh
-bin/systemd/celery-uat.service
-bin/systemd/celery.service
-bin/systemd/celerybeat-uat.service
-bin/systemd/celerybeat.service
 bin/systemd/meta3/gunicorn-live.service
 bin/systemd/meta3/gunicorn-live.socket
 bin/systemd/meta3/gunicorn-uat.service
@@ -289,7 +287,6 @@ meta_edc/__init__.py
 meta_edc/admin.py
 meta_edc/apps.py
 meta_edc/asgi.py
-meta_edc/celery.py
 meta_edc/meta_version.py
 meta_edc/model_callers.py
 meta_edc/models.py
@@ -305,6 +302,10 @@ meta_edc.egg-info/dependency_links.txt
 meta_edc.egg-info/not-zip-safe
 meta_edc.egg-info/requires.txt
 meta_edc.egg-info/top_level.txt
+meta_edc/celery/__init__.py
+meta_edc/celery/debug.py
+meta_edc/celery/live.py
+meta_edc/celery/uat.py
 meta_edc/management/__init__.py
 meta_edc/management/commands/__init__.py
 meta_edc/management/commands/update_forms_reference.py
@@ -508,10 +509,12 @@ meta_reports/ae_report.py
 meta_reports/apps.py
 meta_reports/death_report.py
 meta_reports/pdf_report.py
+meta_reports/tasks.py
 meta_reports/urls.py
 meta_reports/admin/__init__.py
 meta_reports/admin/endpoints_admin.py
 meta_reports/admin/unmanaged/__init__.py
+meta_reports/admin/unmanaged/missing_screening_ogtt_admin.py
 meta_reports/admin/unmanaged/patient_history_missing_baseline_cd4_admin.py
 meta_reports/admin/unmanaged/unattended_three_in_row2_admin.py
 meta_reports/admin/unmanaged/unattended_three_in_row_admin.py
@@ -534,11 +537,22 @@ meta_reports/migrations/0012_auto_20240813_1516.py
 meta_reports/migrations/0013_auto_20240813_1516.py
 meta_reports/migrations/0014_auto_20240813_1517.py
 meta_reports/migrations/0015_alter_endpoints_site.py
+meta_reports/migrations/0016_missingscreeningogtt.py
+meta_reports/migrations/0017_auto_20240819_1711.py
+meta_reports/migrations/0018_auto_20240819_1713.py
+meta_reports/migrations/0019_auto_20240819_1721.py
+meta_reports/migrations/0020_auto_20240819_1811.py
+meta_reports/migrations/0021_auto_20240819_1817.py
+meta_reports/migrations/0022_auto_20240819_1832.py
+meta_reports/migrations/0023_endpoints_meta_report_subject_a56b22_idx.py
 meta_reports/migrations/__init__.py
 meta_reports/models/__init__.py
 meta_reports/models/endpoints.py
 meta_reports/models/dbviews/README
 meta_reports/models/dbviews/__init__.py
+meta_reports/models/dbviews/missing_screening_ogtt/__init__.py
+meta_reports/models/dbviews/missing_screening_ogtt/unmanaged_model.py
+meta_reports/models/dbviews/missing_screening_ogtt/view_definition.py
 meta_reports/models/dbviews/patient_history_missing_baseline_cd4/__init__.py
 meta_reports/models/dbviews/patient_history_missing_baseline_cd4/unmanaged_model.py
 meta_reports/models/dbviews/patient_history_missing_baseline_cd4/view_definition.py
@@ -561,6 +575,7 @@ meta_reports/models/unmanaged/unattended_three_in_row2.py
 meta_reports/models/unmanaged/unattended_three_in_row2.sql
 meta_reports/models/unmanaged/unattended_two_in_row.py
 meta_reports/models/unmanaged/unattended_two_in_row.sql
+meta_reports/templates/meta_reports/endpoints_changelist_note.html
 meta_reports/tests/__init__.py
 meta_reports/tests/test_reports.py
 meta_reports/tests/urls.py

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_edc.egg-info/requires.txt

@@ -1,5 +1,6 @@
-edc==0.5.60
+edc==0.6.1
 edc-microscopy
 beautifulsoup4
 edc-analytics
+celery[redis]
 Django==5.1

meta_edc-0.3.22/meta_reports/__init__.py

@@ -0,0 +1 @@
+from .tasks import update_unmanaged_table

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_reports/admin/__init__.py

@@ -1,5 +1,6 @@
 from .endpoints_admin import EndpointAdmin
 from .unmanaged import (
+    MissingScreeningOgttAdmin,
     PatientHistoryMissingBaselineCd4Admin,
     UnattendedThreeInRow2Admin,
     UnattendedThreeInRowAdmin,

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_reports/admin/endpoints_admin.py

@@ -1,27 +1,35 @@
 from typing import Type
 
+from django.conf import settings
 from django.contrib import admin
 from django.contrib.admin import SimpleListFilter
+from django.db.models import QuerySet
+from django.template.loader import render_to_string
 from edc_model_admin.dashboard import ModelAdminDashboardMixin
-from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_model_admin.mixins import (
+    ModelAdminFormInstructionsMixin,
+    TemplatesModelAdminMixin,
+)
 from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
 from edc_sites.admin import SiteModelAdminMixin
 from edc_sites.admin.list_filters import SiteListFilter
 from edc_visit_schedule.admin import ScheduleStatusListFilter
 
-from meta_analytics.dataframes import GlucoseEndpointsByDate
-
 from ..admin_site import meta_reports_admin
 from ..models import Endpoints
+from ..tasks import update_unmanaged_table
 
 
-def generate_table(modeladmin, request, queryset):
-    cls = GlucoseEndpointsByDate()
-    cls.run()
-    cls.to_model()
+def update_unmanaged_table_action(modeladmin, request, queryset):
+    subject_identifiers = []
+    if queryset.count() != modeladmin.model.objects.count():
+        subject_identifiers = [o.subject_identifier for o in queryset]
+    if settings.CELERY_ENABLED:
+        return update_unmanaged_table.delay(subject_identifiers)
+    return update_unmanaged_table(subject_identifiers)
 
 
-generate_table.short_description = "Regenerate report data"
+update_unmanaged_table_action.short_description = "Regenerate report for selected subjects"
 
 
 @admin.register(Endpoints, site=meta_reports_admin)
@@ -29,10 +37,13 @@ class EndpointAdmin(
     QaReportModelAdminMixin,
     SiteModelAdminMixin,
     ModelAdminDashboardMixin,
+    ModelAdminFormInstructionsMixin,
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-    actions = [generate_table]
+
+    change_list_note = render_to_string("meta_reports/endpoints_changelist_note.html")
+    actions = [update_unmanaged_table_action]
     qa_report_list_display_insert_pos = 2
     ordering = ["-fbg_datetime"]
     list_display = [
@@ -57,6 +68,11 @@ class EndpointAdmin(
 
     search_fields = ["subject_identifier"]
 
+    def get_queryset(self, request) -> QuerySet:
+        qs = super().get_queryset(request)
+        qs = qs.filter(offstudy_datetime__isnull=True)
+        return qs
+
     def get_list_filter(self, request) -> tuple[str | Type[SimpleListFilter], ...]:
         list_filter = super().get_list_filter(request)
         list_filter = list_filter + (SiteListFilter,)

{meta_edc-0.3.20 → meta_edc-0.3.22}/meta_reports/admin/unmanaged/__init__.py

@@ -1,3 +1,4 @@
+from .missing_screening_ogtt_admin import MissingScreeningOgttAdmin
 from .patient_history_missing_baseline_cd4_admin import (
     PatientHistoryMissingBaselineCd4Admin,
 )

meta_edc-0.3.22/meta_reports/admin/unmanaged/missing_screening_ogtt_admin.py

@@ -0,0 +1,59 @@
+from django.contrib import admin
+from django.template.loader import render_to_string
+from django.urls import reverse
+from django.utils.translation import gettext as _
+from edc_model_admin.dashboard import ModelAdminDashboardMixin
+from edc_model_admin.mixins import TemplatesModelAdminMixin
+from edc_qareports.modeladmin_mixins import QaReportModelAdminMixin
+from edc_sites.admin import SiteModelAdminMixin
+from edc_visit_schedule.admin import ScheduleStatusListFilter
+
+from ...admin_site import meta_reports_admin
+from ...models import MissingScreeningOgtt
+
+
+@admin.register(MissingScreeningOgtt, site=meta_reports_admin)
+class MissingScreeningOgttAdmin(
+    QaReportModelAdminMixin,
+    SiteModelAdminMixin,
+    ModelAdminDashboardMixin,
+    TemplatesModelAdminMixin,
+    admin.ModelAdmin,
+):
+    ordering = ["site", "screening_identifier"]
+    list_display = [
+        "dashboard",
+        "screening_identifier",
+        "site",
+        "screening_datetime",
+        "fbg_datetime",
+        "fbg_value",
+        "ogtt_value",
+        "repeated",
+        "p3_ltfu",
+        "fbg2_value",
+        "ogtt2_value",
+        "fbg2_datetime",
+        "ogtt2_datetime",
+        "consented",
+    ]
+
+    list_filter = [
+        ScheduleStatusListFilter,
+        "screening_datetime",
+        "fbg_datetime",
+        "repeated",
+        "p3_ltfu",
+    ]
+
+    search_fields = ["screening_identifier"]
+
+    def dashboard(self, obj=None, label=None) -> str:
+        url = self.get_subject_dashboard_url(obj=obj)
+        if not url:
+            url = reverse(
+                "meta_screening_admin:meta_screening_subjectscreening_change",
+                args=(obj.original_id,),
+            )
+        context = dict(title=_("Go to subject screening"), url=url, label=label)
+        return render_to_string("dashboard_button.html", context=context)

meta_edc-0.3.22/meta_reports/migrations/0016_missingscreeningogtt.py

@@ -0,0 +1,47 @@
+# Generated by Django 5.1 on 2024-08-19 14:01
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("meta_reports", "0015_alter_endpoints_site"),
+    ]
+
+    operations = [
+        migrations.CreateModel(
+            name="MissingScreeningOgtt",
+            fields=[
+                (
+                    "id",
+                    models.BigAutoField(
+                        auto_created=True, primary_key=True, serialize=False, verbose_name="ID"
+                    ),
+                ),
+                ("report_model", models.CharField(max_length=50)),
+                ("subject_identifier", models.CharField(max_length=25)),
+                ("created", models.DateTimeField()),
+                ("screening_identifier", models.CharField(max_length=25)),
+                ("screening_datetime", models.DateTimeField(null=True)),
+                ("fbg_datetime", models.DateTimeField(null=True)),
+                ("fbg_value", models.DecimalField(decimal_places=2, max_digits=8, null=True)),
+                ("ogtt_value", models.DecimalField(decimal_places=2, max_digits=8, null=True)),
+                ("fbg2_value", models.DecimalField(decimal_places=2, max_digits=8, null=True)),
+                (
+                    "ogtt2_value",
+                    models.DecimalField(decimal_places=2, max_digits=8, null=True),
+                ),
+                ("fbg2_datetime", models.DateTimeField(null=True)),
+                ("ogtt2_datetime", models.DateTimeField(null=True)),
+                ("consented", models.BooleanField(null=True)),
+            ],
+            options={
+                "verbose_name": "Screening: Missing OGTT",
+                "verbose_name_plural": "Screening: Missing OGTT",
+                "db_table": "missing_screening_ogtt_view",
+                "managed": False,
+                "default_permissions": ("view", "export", "viewallsites"),
+            },
+        ),
+    ]