meta-edc 1.1.8__py3-none-any.whl → 1.1.12__py3-none-any.whl

meta_consent/models/signals.py

@@ -1,7 +1,9 @@
+import contextlib
+
 from django.core.exceptions import ValidationError
 from django.db.models.signals import post_delete, post_save
 from django.dispatch import receiver
-from edc_action_item import ActionItemDeleteError, delete_action_item
+from edc_action_item.delete_action_item import ActionItemDeleteError, delete_action_item
 from edc_appointment.utils import refresh_appointments
 from edc_constants.constants import YES
 from edc_pharmacy.exceptions import PrescriptionAlreadyExists
@@ -26,10 +28,11 @@ from .subject_consent_v1_ext import SubjectConsentV1Ext
     sender=SubjectConsentV1,
     dispatch_uid="subject_consent_on_post_save",
 )
-def subject_consent_on_post_save(sender, instance, raw, created, **kwargs):
+def subject_consent_on_post_save(sender, instance, raw, created, **kwargs):  # noqa: ARG001
     """Creates an onschedule instance for this consented subject, if
     it does not exist.
     """
+
     if not raw:
         if not created:
             _, schedule = site_visit_schedules.get_by_onschedule_model("meta_prn.onschedule")
@@ -62,7 +65,7 @@ def subject_consent_on_post_save(sender, instance, raw, created, **kwargs):
                     onschedule_datetime=instance.consent_datetime,
                 )
                 # All refills are created against this prescription
-                try:
+                with contextlib.suppress(PrescriptionAlreadyExists):
                     create_prescription(
                         subject_identifier=instance.subject_identifier,
                         report_datetime=instance.consent_datetime,
@@ -70,20 +73,16 @@ def subject_consent_on_post_save(sender, instance, raw, created, **kwargs):
                         randomizer_name=get_meta_version(),
                         site=instance.site,
                     )
-                except PrescriptionAlreadyExists:
-                    pass
 
         # create / delete action for reconsent
         if instance.completed_by_next_of_kin == YES:
             ReconsentAction(subject_identifier=instance.subject_identifier)
         else:
-            try:
+            with contextlib.suppress(ActionItemDeleteError):
                 delete_action_item(
                     action_cls=ReconsentAction,
                     subject_identifier=instance.subject_identifier,
                 )
-            except ActionItemDeleteError:
-                pass
 
 
 @receiver(
@@ -92,7 +91,7 @@ def subject_consent_on_post_save(sender, instance, raw, created, **kwargs):
     sender=SubjectConsentV1Ext,
     dispatch_uid="subject_consent_v1_ext_on_post_save",
 )
-def subject_consent_v1_ext_on_post_save(sender, instance, raw, created, **kwargs):
+def subject_consent_v1_ext_on_post_save(sender, instance, raw, created, **kwargs):  # noqa: ARG001
     if not raw:
         refresh_appointments(
             subject_identifier=instance.subject_identifier,
@@ -106,7 +105,7 @@ def subject_consent_v1_ext_on_post_save(sender, instance, raw, created, **kwargs
     weak=False,
     dispatch_uid="subject_consent_on_post_delete",
 )
-def subject_consent_on_post_delete(sender, instance, using, **kwargs):
+def subject_consent_on_post_delete(sender, instance, using, **kwargs):  # noqa: ARG001
     """Updates/Resets subject screening."""
     # don't allow if subject visits exist. This should be caught
     # in the ModelAdmin delete view

meta_consent/models/subject_consent.py

@@ -62,7 +62,7 @@ class SubjectConsent(
         max_length=15,
         help_text=_("from screening"),
         editable=False,
-        null=True,
+        default="",
     )
 
     completed_by_next_of_kin = models.CharField(

meta_consent/models/subject_reconsent.py

@@ -67,12 +67,12 @@ class SubjectReconsent(
             self.get_subject_consent(
                 screening_identifier=subject_screening.screening_identifier
             )
-        except ObjectDoesNotExist:
-            raise ValidationError("Previous consent does not exist.")
+        except ObjectDoesNotExist as e:
+            raise ValidationError("Previous consent does not exist.") from e
         super().save(*args, **kwargs)
 
     def natural_key(self):
-        return (self.subject_identifier, self.version)
+        return self.subject_identifier, self.version
 
     def get_subject_consent(self, screening_identifier=None):
         """Returns the first subject consent model instance."""

meta_dashboard/patterns.py

@@ -1 +1 @@
-screening_identifier = "[A-Z0-9]{6,8}"  # noqa
+screening_identifier = "[A-Z0-9]{6,8}"

meta_dashboard/templatetags/meta_dashboard_extras.py

@@ -64,7 +64,7 @@ def render_consent_button(context, subject_screening: SubjectScreening):
     )
 
 
-def refusal_button(context, subject_refusal):
+def refusal_button(context, subject_refusal):  # noqa: ARG001
     title = ["Capture subject's primary reason for not joining."]
 
     return dict(

meta_dashboard/view_utils/__init__.py

@@ -4,3 +4,10 @@ from .subject_screening_button import (
     SubjectScreeningPartThreeButton,
     SubjectScreeningPartTwoButton,
 )
+
+__all__ = [
+    "SubjectScreeningButton",
+    "SubjectScreeningPartOneButton",
+    "SubjectScreeningPartThreeButton",
+    "SubjectScreeningPartTwoButton",
+]

meta_dashboard/view_utils/subject_screening_button.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from dataclasses import dataclass, field
-from typing import Type
 
 from django.utils.translation import gettext as _
 from edc_constants.constants import TBD, YES
@@ -14,8 +13,8 @@ from meta_screening.models import ScreeningPartOne, ScreeningPartThree, Screenin
 
 __all__ = [
     "SubjectScreeningPartOneButton",
-    "SubjectScreeningPartTwoButton",
     "SubjectScreeningPartThreeButton",
+    "SubjectScreeningPartTwoButton",
 ]
 
 
@@ -38,17 +37,13 @@ class SubjectScreeningButton(BaseSubjectScreeningButton):
 
     @property
     def title(self) -> str:
-        if self.perms.view_only or self.model_obj.consented:
-            title = _("View")
-        else:
-            title = _("Edit")
-        return title
+        return _("View") if self.perms.view_only or self.model_obj.consented else _("Edit")
 
 
 @dataclass
 class SubjectScreeningPartOneButton(SubjectScreeningButton):
     model_obj: ScreeningPartOne = None
-    model_cls: Type[ScreeningPartOne] = field(default=ScreeningPartOne)
+    model_cls: type[ScreeningPartOne] = field(default=ScreeningPartOne)
 
     @property
     def label(self) -> str:
@@ -58,7 +53,7 @@ class SubjectScreeningPartOneButton(SubjectScreeningButton):
 @dataclass
 class SubjectScreeningPartTwoButton(SubjectScreeningButton):
     model_obj: ScreeningPartTwo = None
-    model_cls: Type[ScreeningPartTwo] = field(default=ScreeningPartTwo)
+    model_cls: type[ScreeningPartTwo] = field(default=ScreeningPartTwo)
 
     @property
     def label(self) -> str:
@@ -76,9 +71,8 @@ class SubjectScreeningPartTwoButton(SubjectScreeningButton):
             self._action = VIEW
             if self.model_obj.eligible_part_two == TBD:
                 self._action = ADD
-            elif self.model_obj:
-                if self.perms.change:
-                    self._action = CHANGE
+            elif self.model_obj and self.perms.change:
+                self._action = CHANGE
         return self._action
 
     @property
@@ -91,7 +85,7 @@ class SubjectScreeningPartTwoButton(SubjectScreeningButton):
 @dataclass
 class SubjectScreeningPartThreeButton(SubjectScreeningButton):
     model_obj: ScreeningPartThree = None
-    model_cls: Type[ScreeningPartThree] = field(default=ScreeningPartThree)
+    model_cls: type[ScreeningPartThree] = field(default=ScreeningPartThree)
 
     @property
     def label(self) -> str:
@@ -109,9 +103,8 @@ class SubjectScreeningPartThreeButton(SubjectScreeningButton):
             self._action = VIEW
             if self.model_obj.eligible_part_three == TBD:
                 self._action = ADD
-            elif self.model_obj:
-                if self.perms.change:
-                    self._action = CHANGE
+            elif self.model_obj and self.perms.change:
+                self._action = CHANGE
         return self._action
 
     @property

meta_dashboard/views/__init__.py

@@ -2,3 +2,11 @@ from .ae import AeListboardView, DeathReportListboardView
 from .screening import ListboardView as ScreeningListboardView
 from .subject import DashboardView as SubjectDashboardView
 from .subject import SubjectListboardView
+
+__all__ = [
+    "AeListboardView",
+    "DeathReportListboardView",
+    "ScreeningListboardView",
+    "SubjectDashboardView",
+    "SubjectListboardView",
+]

meta_dashboard/views/ae/__init__.py

@@ -1,2 +1,4 @@
 from .ae_listboard_view import AeListboardView
 from .death_report_listboard_view import DeathReportListboardView
+
+__all__ = ["AeListboardView", "DeathReportListboardView"]

meta_dashboard/views/ae/ae_listboard_view.py

@@ -5,7 +5,7 @@ from meta_reports.ae_report import AePdfReport
 
 
 class CustomAeReport(AePdfReport):
-    logo_data = {
+    logo_data = {  # noqa: RUF012
         "app_label": "meta_edc",
         "filename": "meta_logo.png",
         "first_page": (4.0 * cm, 0.83 * cm),

meta_dashboard/views/ae/death_report_listboard_view.py

@@ -5,7 +5,7 @@ from meta_reports.death_report import DeathPdfReport
 
 
 class CustomDeathReport(DeathPdfReport):
-    logo_data = {
+    logo_data = {  # noqa: RUF012
         "app_label": "meta_edc",
         "filename": "meta_logo.png",
         "first_page": (4.0 * cm, 0.83 * cm),

meta_dashboard/views/screening/__init__.py

@@ -1 +1,3 @@
 from .listboard_view import ListboardView
+
+__all__ = ["ListboardView"]

meta_dashboard/views/subject/__init__.py

@@ -1,2 +1,4 @@
 from .dashboard import DashboardView
 from .listboard import SubjectListboardView
+
+__all__ = ["DashboardView", "SubjectListboardView"]

meta_dashboard/views/subject/dashboard/__init__.py

@@ -1 +1,3 @@
 from .dashboard_view import DashboardView
+
+__all__ = ["DashboardView"]

meta_dashboard/views/subject/dashboard/dashboard_view.py

@@ -32,7 +32,7 @@ class DashboardView(SubjectDashboardView):
             message = format_html(
                 '{text} <A href="{url}">{verbose_name}</A>',
                 text=_("Subject has reached the protocol endpoint. See "),
-                url=mark_safe(url),  # nosec B703, B308
+                url=mark_safe(url),  # noqa: S308
                 verbose_name=GlucoseSummary._meta.verbose_name,
             )
             self.message_user(message, level=messages.WARNING)

meta_dashboard/views/subject/listboard/__init__.py

@@ -1 +1,3 @@
 from .listboard_view import SubjectListboardView
+
+__all__ = ["SubjectListboardView"]

meta_edc/__init__.py

@@ -1,14 +1,10 @@
-import os
-from importlib.metadata import PackageNotFoundError, version
+import importlib.metadata
 
 from .celery import app as celery_app
 
 try:
-    __version__ = version(os.getcwd().split(os.sep)[-1])
-except PackageNotFoundError:
-    __version__ = None
+    __version__ = importlib.metadata.version(__package__)
+except importlib.metadata.PackageNotFoundError:
+    __version__ = "unknown"
 
-
-__all__ = ["celery_app", "__version__"]
-
-os.environ.setdefault("DJANGO_SETTINGS_MODULE", "meta_edc.settings.debug")
+__all__ = ["__version__", "celery_app"]

meta_edc/celery.py

@@ -13,4 +13,4 @@ app.autodiscover_tasks()
 
 @app.task(bind=True)
 def debug_task(self):
-    print("Request: {0!r}".format(self.request))
+    print(f"Request: {self.request!r}")

meta_edc/celery_live.py

@@ -15,4 +15,4 @@ app.autodiscover_tasks()
 
 @app.task(bind=True)
 def debug_task(self):
-    print("Request: {0!r}".format(self.request))
+    print(f"Request: {self.request!r}")

meta_edc/celery_uat.py

@@ -21,4 +21,4 @@ app.autodiscover_tasks()
 
 @app.task(bind=True)
 def debug_task(self):
-    print("Request: {0!r}".format(self.request))
+    print(f"Request: {self.request!r}")

meta_edc/management/commands/update_forms_reference.py

@@ -1,36 +1,34 @@
-import os
 import sys
 
 from django.conf import settings
 from django.core.management.base import BaseCommand
 from django.core.management.color import color_style
+from edc_form_describer.forms_reference import FormsReference
 
-style = color_style()
-
+from meta_subject.admin_site import meta_subject_admin
+from meta_visit_schedule.visit_schedules import visit_schedule
 
-def update_forms_reference(sender=None, **kwargs):
-    from edc_form_describer import FormsReference
+style = color_style()
 
-    from meta_subject.admin_site import meta_subject_admin
-    from meta_visit_schedule.visit_schedules import visit_schedule
 
+def update_forms_reference(sender=None, **kwargs):  # noqa: ARG001
     sys.stdout.write(
         style.MIGRATE_HEADING("Refreshing CRF reference document for meta_subject\n")
     )
-    doc_folder = os.path.join(settings.BASE_DIR, "docs")
-    if not os.path.exists(doc_folder):
-        os.mkdir(doc_folder)
+    doc_folder = settings.BASE_DIR / "docs"
+    if not doc_folder.exists():
+        doc_folder.mkdir()
     forms = FormsReference(
         visit_schedules=[visit_schedule],
         admin_site=meta_subject_admin,
         add_per_form_timestamp=False,
     )
-    path = os.path.join(doc_folder, "forms_reference.md")
+    path = doc_folder / "forms_reference.md"
     forms.to_file(path=path, overwrite=True, pad=0)
 
 
 class Command(BaseCommand):
     help = "Update forms reference document (.md)"
 
-    def handle(self, *args, **options):
+    def handle(self, *args, **options):  # noqa: ARG002
         update_forms_reference()

meta_edc/settings/debug.py

@@ -1,15 +1,16 @@
-import os  # noqa
+import os
+import sys
 
 from multisite import SiteID
 
 from .defaults import *  # noqa
 
-print(f"Settings file {__file__}")
+sys.stdout.write(f"Settings file {__file__}\n")
 
 # TZ Sites:
 # SITE_ID = SiteID(default=20)  # Amana
-SITE_ID = SiteID(default=10)  # Hindu Mandal
-# SITE_ID = SiteID(default=40)  # Mwananyamala
+# SITE_ID = SiteID(default=10)  # Hindu Mandal
+SITE_ID = SiteID(default=40)  # Mwananyamala
 # SITE_ID = SiteID(default=50)  # Mbagala
 # SITE_ID = SiteID(default=60)  # Mnazi-Moja
 # SITE_ID = SiteID(default=30)  # Temeke

meta_edc/settings/defaults.py

@@ -32,9 +32,18 @@ env = environ.Env(
     TWILIO_ENABLED=(bool, False),
     EDC_SITES_DOMAIN_SUFFIX="meta4.clinicedc.org",
 )
+if os.getenv("DJANGO_BASE_DIR"):
+    # for deployed systems where meta-edc is pip installed.
+    # same dir as manage.py
+    BASE_DIR = Path(os.getenv("DJANGO_BASE_DIR"))
+else:
+    # when running from a repo
+    BASE_DIR = Path(__file__).resolve().parent.parent.parent
 
-BASE_DIR = Path(__file__).resolve().parent.parent.parent
-ENV_DIR = Path(__file__).resolve().parent.parent.parent
+if os.getenv("DJANGO_ENV_DIR"):
+    ENV_DIR = Path(os.getenv("DJANGO_ENV_DIR"))
+else:
+    ENV_DIR = Path(__file__).resolve().parent.parent.parent.parent
 
 # copy your .env file from .envs/ to BASE_DIR
 if "test" in sys.argv:
@@ -60,6 +69,12 @@ SECRET_KEY = env.str("DJANGO_SECRET_KEY")
 
 APP_NAME = env.str("DJANGO_APP_NAME")
 
+DJANGO_REVISION_IGNORE_WORKING_DIR = env.str("DJANGO_REVISION_IGNORE_WORKING_DIR")
+if DJANGO_REVISION_IGNORE_WORKING_DIR:
+    # get the version from the package and not a git tag
+    # this overrides django_revision
+    REVISION = version(APP_NAME)
+
 LIVE_SYSTEM = env.str("DJANGO_LIVE_SYSTEM")
 
 ETC_DIR = env.str("DJANGO_ETC_FOLDER")
@@ -471,7 +486,7 @@ if TWILIO_ENABLED:
     TWILIO_SENDER = env.str("TWILIO_SENDER")
 
 # django_revision
-GIT_DIR = BASE_DIR
+GIT_DIR = BASE_DIR.parent
 
 # django_crypto_fields
 KEY_PATH = env.str("DJANGO_KEY_FOLDER")

meta_edc/settings/live.py

@@ -1,8 +1,10 @@
+import sys
+
 from multisite import SiteID
 
 from .defaults import *  # noqa
 
-print(f"Settings file {__file__}")
+sys.stdout.write(f"Settings file {__file__}\n")
 
 SITE_ID = SiteID(default=1)
 EDC_SITES_UAT_DOMAIN = False

meta_edc/settings/logging.py

@@ -1,23 +1,28 @@
 # see http://www.simonkrueger.com/2015/05/27/logging-django-apps-to-syslog.html
-import os
+from pathlib import Path
 
 import environ
 
-__all__ = ["LOG_FOLDER", "LOGGING_FILE_LEVEL", "LOGGING_SYSLOG_LEVEL", "LOGGING"]
+__all__ = ["LOGGING", "LOGGING_FILE_LEVEL", "LOGGING_SYSLOG_LEVEL", "LOG_FOLDER"]
 
 env = environ.Env()
 env.read_env(".env")
 
-LOG_FOLDER = env.str("DJANGO_LOG_FOLDER")
+LOG_FOLDER = Path(env.str("DJANGO_LOG_FOLDER"))
 LOGGING_FILE_LEVEL = env.str("DJANGO_LOGGING_FILE_LEVEL")
 LOGGING_SYSLOG_LEVEL = env.str("DJANGO_LOGGING_SYSLOG_LEVEL")
 
+
 LOGGING = {
     "version": 1,
     "disable_existing_loggers": False,
     "filters": {
         "require_debug_false": {"()": "django.utils.log.RequireDebugFalse"},
         "require_debug_true": {"()": "django.utils.log.RequireDebugTrue"},
+        "ignore_specific_ip": {
+            "()": "edc_utils.logging_filters.IgnoreSpecificIPDisallowedHost",
+            "ip_to_ignore": "178.128.175.239",
+        },
     },
     "formatters": {
         "verbose": {
@@ -36,7 +41,7 @@ LOGGING = {
         "file": {
             "level": LOGGING_FILE_LEVEL,
             "class": "logging.FileHandler",
-            "filename": os.path.join(LOG_FOLDER, "edc.log"),
+            "filename": LOG_FOLDER / "edc.log",
             "formatter": "verbose",
         },
         "syslog": {

meta_edc/settings/minimal.py

@@ -2,21 +2,20 @@
 A settings file with the bare minimum attributes.
 """
 
-import os
 from pathlib import Path
 
 import environ
 from multisite import SiteID
 
 APP_NAME = "meta_edc"
-BASE_DIR = str(Path(os.path.dirname(os.path.abspath(__file__))).parent.parent)
-ENV_DIR = str(Path(os.path.dirname(os.path.abspath(__file__))).parent.parent)
+BASE_DIR = Path(__file__).resolve().parent.parent
+ENV_DIR = Path(__file__).resolve().parent.parent
 
 env = environ.Env()
-env.read_env(os.path.join(ENV_DIR, ".env"))
+env.read_env(ENV_DIR / ".env")
 
 EDC_SITES_MODULE_NAME = env.str("EDC_SITES_MODULE_NAME")
 ETC_DIR = env.str("DJANGO_ETC_FOLDER")
-SECRET_KEY = "blahblahblah"  # nosec B105
+SECRET_KEY = "blahblahblah"  # noqa: S105
 ALLOWED_HOSTS = ["*"]
 SITE_ID = SiteID(default=1)  # 1 is not a site

meta_edc/settings/uat.py

@@ -1,8 +1,10 @@
+import sys
+
 from multisite import SiteID
 
 from .defaults import *  # noqa
 
-print(f"Settings file {__file__}")
+sys.stdout.write(f"Settings file {__file__}\n")
 
 SITE_ID = SiteID(default=1)
 EDC_SITES_UAT_DOMAIN = True

meta_edc/views/__init__.py

@@ -1 +1,3 @@
 from .home_view import HomeView
+
+__all__ = ["HomeView"]