clinicedc 2.0.6__py3-none-any.whl → 2.0.8__py3-none-any.whl

edc_export/model_exporter/model_exporter.py

@@ -1,11 +1,10 @@
 import csv
-import os
 import uuid
+from pathlib import Path
 
 from django.apps import apps as django_apps
 from django.core.exceptions import ValidationError
-
-from edc_utils import get_utcnow
+from django.utils import timezone
 
 from ..utils import get_export_folder
 from .file_history_updater import FileHistoryUpdater
@@ -17,11 +16,11 @@ class ModelExporterError(Exception):
     pass
 
 
-class ModelExporterInvalidLookup(Exception):
+class ModelExporterInvalidLookup(Exception):  # noqa: N818
     pass
 
 
-class ModelExporterUnknownField(ValidationError):
+class ModelExporterUnknownField(ValidationError):  # noqa: N818
     pass
 
 
@@ -40,14 +39,14 @@ class ModelExporter:
     value_getter_cls = ValueGetter
     additional_values_cls = AdditionalValues
 
-    export_fields = [
+    export_fields = (
         "export_uuid",
         "timestamp",
         "export_datetime",
         "export_change_type",
-    ]
-    required_fields = ["subject_identifier", "report_datetime"]
-    audit_fields = [
+    )
+    required_fields = ("subject_identifier", "report_datetime")
+    audit_fields = (
         "hostname_created",
         "hostname_modified",
         "created",
@@ -55,7 +54,7 @@ class ModelExporter:
         "user_created",
         "user_modified",
         "revision",
-    ]
+    )
 
     def __init__(
         self,
@@ -103,7 +102,10 @@ class ModelExporter:
             if f in self.export_fields or f in self.audit_fields or f in self.required_fields:
                 self._field_names.pop(self._field_names.index(f))
         self._field_names = (
-            self.export_fields + self.required_fields + self.field_names + self.audit_fields
+            *self.export_fields,
+            *self.required_fields,
+            *self.field_names,
+            *self.audit_fields,
         )
 
     @property
@@ -117,13 +119,13 @@ class ModelExporter:
                 self._model_cls = self.queryset.model
         return self._model_cls
 
-    def export(self, queryset=None):
+    def export(self, queryset=None) -> Path:
         """Writes the export file and returns the file name."""
         self.queryset = queryset or self.queryset
-        exported_datetime = get_utcnow()
+        exported_datetime = timezone.now()
         filename = self.get_filename(exported_datetime)
-        path = os.path.join(get_export_folder(), filename)
-        with open(path, "w") as f:
+        path = get_export_folder() / filename
+        with path.open("w") as f:
             csv_writer = csv.DictWriter(
                 f, fieldnames=self.field_names, delimiter=self.delimiter
             )

edc_export/model_exporter/object_history_helpers.py

@@ -1,9 +1,9 @@
 from django.apps import apps as django_apps
 from django.core import serializers
 from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
+from django.utils import timezone
 
 from edc_constants.constants import NEW
-from edc_utils import get_utcnow
 
 from ..constants import EXPORTED, INSERT, UPDATE
 
@@ -24,7 +24,7 @@ class ObjectHistoryCreator(Base):
     def create(self, model_obj=None, change_type=None, using=None):
         if not change_type:
             change_type = self.get_change_type(model_obj=model_obj)
-        export_datetime = get_utcnow()
+        export_datetime = timezone.now()
         if model_obj._meta.proxy_for_model:  # if proxy model, get main model
             model_obj = model_obj._meta.proxy_for_model.objects.get(id=model_obj.id)
         obj = self.model_cls.objects.using(using).create(

edc_export/models/data_request_history.py

@@ -1,10 +1,10 @@
 from django.db import models
 from django.db.models import Index
 from django.db.models.deletion import PROTECT
+from django.utils import timezone
 
 from edc_model.models import BaseUuidModel
 from edc_sites.model_mixins import SiteModelMixin
-from edc_utils import get_utcnow
 
 from .data_request import DataRequest
 
@@ -12,15 +12,15 @@ from .data_request import DataRequest
 class DataRequestHistory(SiteModelMixin, BaseUuidModel):
     data_request = models.ForeignKey(DataRequest, on_delete=PROTECT)
 
-    archive_filename = models.CharField(max_length=200, null=True)
+    archive_filename = models.CharField(max_length=200, default="")
 
-    emailed_to = models.EmailField(null=True)
+    emailed_to = models.EmailField(default="")
 
     emailed_datetime = models.DateTimeField(null=True)
 
     summary = models.TextField(default="")
 
-    exported_datetime = models.DateTimeField(default=get_utcnow)
+    exported_datetime = models.DateTimeField(default=timezone.now)
 
     class Meta:
         verbose_name = "Data Request History"

edc_export/utils.py

@@ -1,10 +1,11 @@
 from __future__ import annotations
 
-import os
 import re
 from collections.abc import Iterable
+from pathlib import Path
 
 from django import forms
+from django.conf import settings
 from django.utils.html import format_html
 
 from edc_protocol.research_protocol_config import ResearchProtocolConfig
@@ -13,15 +14,13 @@ from .constants import EXPORT_PII
 from .exceptions import ExporterExportFolder
 
 
-def get_export_folder() -> str:
-    from django.conf import settings
-
+def get_export_folder() -> Path:
     if path := getattr(settings, "EDC_EXPORT_EXPORT_FOLDER", None):
-        return os.path.expanduser(path)
-    return os.path.join(settings.MEDIA_ROOT, "data_folder", "export")
+        return Path(path).expanduser()
+    return Path(settings.MEDIA_ROOT) / "data_folder" / "export"
 
 
-def get_base_dir() -> str:
+def get_base_dir() -> Path:
     """Returns the base_dir used by, for example,
     shutil.make_archive.
 
@@ -37,20 +36,16 @@ def get_base_dir() -> str:
             "Invalid base_dir, invalid characters. Using `protocol_lower_name`. "
             f"Got `{base_dir}`."
         )
-    return base_dir
-
+    return Path(base_dir)
 
-def get_upload_folder() -> str:
-    from django.conf import settings
 
+def get_upload_folder() -> Path:
     if path := getattr(settings, "EDC_EXPORT_UPLOAD_FOLDER", None):
-        return os.path.expanduser(path)
-    return os.path.join(settings.MEDIA_ROOT, "data_folder", "upload")
+        return Path(path).expanduser()
+    return Path(settings.MEDIA_ROOT) / "data_folder" / "upload"
 
 
 def get_export_pii_users() -> list[str]:
-    from django.conf import settings
-
     return getattr(settings, "EDC_EXPORT_EXPORT_PII_USERS", [])
 
 

edc_facility/auths.py

@@ -2,6 +2,11 @@ from edc_auth.site_auths import site_auths
 
 from .auth_objects import EDC_FACILITY, EDC_FACILITY_SUPER, EDC_FACILITY_VIEW, codenames
 
-site_auths.add_group(*codenames, name=EDC_FACILITY_VIEW, view_only=True)
-site_auths.add_group(*codenames, name=EDC_FACILITY, no_delete=True)
-site_auths.add_group(*codenames, name=EDC_FACILITY_SUPER)
+
+def update_site_auths():
+    site_auths.add_group(*codenames, name=EDC_FACILITY_VIEW, view_only=True)
+    site_auths.add_group(*codenames, name=EDC_FACILITY, no_delete=True)
+    site_auths.add_group(*codenames, name=EDC_FACILITY_SUPER)
+
+
+update_site_auths()

edc_facility/facility.py

@@ -7,17 +7,17 @@ from zoneinfo import ZoneInfo
 
 import arrow
 from arrow import Arrow
-from dateutil._common import weekday
-from dateutil.relativedelta import relativedelta
+from dateutil.relativedelta import relativedelta, weekday
 from django.conf import settings
+from django.utils import timezone
 
-from edc_utils import convert_php_dateformat, get_utcnow, to_utc
+from edc_utils import convert_php_dateformat, to_utc
 
 from .exceptions import FacilityError
 from .holidays import Holidays
 
 if TYPE_CHECKING:
-    from django.contrib.sites.models import Site
+    pass
 
 
 class Facility:
@@ -34,24 +34,19 @@ class Facility:
 
     def __init__(
         self,
-        name: str = None,
-        days: list = None,
-        slots: list[int] = None,
+        name: str | None = None,
+        days: list[weekday] | None = None,
+        slots: list[int] | None = None,
         best_effort_available_datetime: datetime | None = None,
     ):
-        self.days = []
+        self.days = days
         self.name = name
         if not name:
             raise FacilityError(f"Name cannot be None. See {self!r}")
         self.best_effort_available_datetime = (
             True if best_effort_available_datetime is None else best_effort_available_datetime
         )
-        for day in days:
-            try:
-                day.weekday
-            except AttributeError:
-                day = weekday(day)
-            self.days.append(day)
+        self.weekdays = [d.weekday for d in self.days]
         self.slots = slots or [99999 for _ in self.days]
         self.config = dict(zip([str(d) for d in self.days], self.slots, strict=False))
         self.holidays = self.holiday_cls()
@@ -72,9 +67,9 @@ class Facility:
             slots_per_day = 0
         return slots_per_day
 
-    @property
-    def weekdays(self) -> list[int]:
-        return [d.weekday for d in self.days]
+    # @property
+    # def weekdays(self) -> list[int]:
+    #     return [d.weekday for d in self.days]
 
     @staticmethod
     def open_slot_on(arr) -> Arrow:
@@ -112,7 +107,7 @@ class Facility:
         span_gt = [arw for arw in span if arw.date() > suggested_arr.date()]
         arr_span = []
         max_len = max(len(span_lt), len(span_gt))
-        for i in range(0, max_len):
+        for _ in range(0, max_len):
             try:
                 item = span_lt.pop()
             except IndexError:
@@ -135,7 +130,7 @@ class Facility:
         reverse_delta=None,
         taken_datetimes=None,
         schedule_on_holidays=None,
-        site: Site = None,
+        **kwargs,  # noqa: ARG002
     ):
         """Returns an arrow object for a datetime equal to or
         close to the suggested datetime.
@@ -153,7 +148,7 @@ class Facility:
         if suggested_datetime:
             suggested_arr = arrow.Arrow.fromdatetime(suggested_datetime)
         else:
-            suggested_arr = arrow.Arrow.fromdatetime(get_utcnow())
+            suggested_arr = arrow.Arrow.fromdatetime(timezone.now())
         arr_span_range, min_arr, max_arr = self.get_arr_span(
             suggested_arr,
             forward_delta,
@@ -185,7 +180,6 @@ class Facility:
                     f"{forward_delta.days} days of {formatted_date}. "
                     f"Facility is {self!r}."
                 )
-        available_arr = arrow.Arrow.fromdatetime(
+        return arrow.Arrow.fromdatetime(
             datetime.combine(available_arr.date(), suggested_arr.time())
         )
-        return available_arr

edc_facility/import_holidays.py

@@ -9,10 +9,10 @@ from typing import TYPE_CHECKING
 from django.conf import settings
 from django.core.exceptions import ObjectDoesNotExist
 from django.db import transaction
+from django.utils import timezone
 from tqdm import tqdm
 
 from edc_sites.site import sites
-from edc_utils import get_utcnow
 
 from .exceptions import HolidayFileNotFoundError, HolidayImportError
 from .utils import get_holiday_model_cls
@@ -30,14 +30,14 @@ def import_holidays(verbose: bool | None = None, test: bool | None = None) -> No
     if test:
         import_for_tests(model_cls)
     else:
-        path = settings.HOLIDAY_FILE
+        path = Path(settings.HOLIDAY_FILE)
         try:
             if not Path(path).exists():
                 raise HolidayFileNotFoundError(path)
-        except TypeError:
+        except TypeError as e:
             raise HolidayImportError(
                 f"Invalid path importing holiday file. See settings.HOLIDAY_FILE. Got {path}."
-            )
+            ) from e
         if verbose:
             sys.stdout.write(
                 f"\nImporting holidays from '{path}' into {model_cls._meta.label_lower}\n"
@@ -52,9 +52,9 @@ def import_holidays(verbose: bool | None = None, test: bool | None = None) -> No
             sys.stdout.write("Done.\n")
 
 
-def check_for_duplicates_in_file(path) -> list:
+def check_for_duplicates_in_file(path: Path) -> list:
     """Returns a list of records."""
-    with open(path) as f:
+    with path.open("r") as f:
         reader = csv.DictReader(f, fieldnames=["local_date", "label", "country"])
         recs = [(row["local_date"], row["country"]) for row in reader]
     if len(recs) != len(list(set(recs))):
@@ -62,18 +62,18 @@ def check_for_duplicates_in_file(path) -> list:
     return recs
 
 
-def import_file(path: str, recs: list, model_cls: Holiday):
-    with open(path) as f:
+def import_file(path: Path, recs: list, model_cls: Holiday):
+    with path.open("r") as f:
         reader = csv.DictReader(f, fieldnames=["local_date", "label", "country"])
         for index, row in tqdm(enumerate(reader), total=len(recs)):
             if index == 0:
                 continue
             try:
-                local_date = datetime.strptime(row["local_date"], "%Y-%m-%d").date()
+                local_date = datetime.strptime(row["local_date"], "%Y-%m-%d").date()  # noqa: DTZ007
             except ValueError as e:
                 raise HolidayImportError(
                     f"Invalid format when importing from {path}. Got '{e}'"
-                )
+                ) from e
             else:
                 try:
                     obj = model_cls.objects.get(country=row["country"], local_date=local_date)
@@ -87,7 +87,7 @@ def import_file(path: str, recs: list, model_cls: Holiday):
 
 
 def import_for_tests(model_cls: type[Holiday]):
-    year = get_utcnow().year
+    year = timezone.now().year
     country = sites.get_current_country()
     if not country:
         raise HolidayImportError(
@@ -112,11 +112,11 @@ def import_for_tests(model_cls: type[Holiday]):
         if index == 0:
             continue
         try:
-            local_date = datetime.strptime(row[LOCAL_DATE], "%Y-%m-%d").date()
+            local_date = datetime.strptime(row[LOCAL_DATE], "%Y-%m-%d").date()  # noqa: DTZ007
         except ValueError as e:
             raise HolidayImportError(
                 f"Invalid format when importing holidays (test). Got '{e}'"
-            )
+            ) from e
         else:
             objs.append(
                 model_cls(country=row[COUNTRY], local_date=local_date, name=row[LABEL])

edc_facility/migrations/0005_healthfacility_healthfacilitytypes_and_more.py

@@ -17,7 +17,8 @@ from django.db import migrations, models
 import edc_facility.model_mixins
 import edc_model_fields.fields.other_charfield
 import edc_sites.models
-import edc_utils.date
+import django.utils.timezone
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -46,14 +47,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
@@ -105,7 +106,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "report_datetime",
-                    models.DateTimeField(default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(default=django.utils.timezone.now),
                 ),
                 ("name", models.CharField(max_length=25, unique=True)),
                 (
@@ -265,14 +266,14 @@ class Migration(migrations.Migration):
                     "created",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
                     "modified",
                     models.DateTimeField(
                         blank=True,
-                        default=django_audit_fields.models.audit_model_mixin.utcnow,
+                        default=django.utils.timezone.now,
                     ),
                 ),
                 (
@@ -323,7 +324,7 @@ class Migration(migrations.Migration):
                 ),
                 (
                     "report_datetime",
-                    models.DateTimeField(default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(default=django.utils.timezone.now),
                 ),
                 ("name", models.CharField(db_index=True, max_length=25)),
                 (

edc_facility/migrations/0016_alter_healthfacility_device_created_and_more.py

@@ -0,0 +1,139 @@
+# Generated by Django 5.2.6 on 2025-09-17 16:53
+
+import edc_model_fields.fields.other_charfield
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_facility", "0015_alter_healthfacility_revision_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="health_facility_type_other",
+            field=edc_model_fields.fields.other_charfield.OtherCharField(
+                blank=True,
+                default="",
+                max_length=35,
+                verbose_name="If other, please specify ...",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="locale_created",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale created",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="notes",
+            field=models.TextField(blank=True, default=""),
+        ),
+        migrations.AlterField(
+            model_name="healthfacilitytypes",
+            name="extra_value",
+            field=models.CharField(default="", max_length=250),
+        ),
+        migrations.AlterField(
+            model_name="healthfacilitytypes",
+            name="field_name",
+            field=models.CharField(
+                blank=True,
+                default="",
+                editable=False,
+                help_text="Not required",
+                max_length=25,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthfacilitytypes",
+            name="plural_name",
+            field=models.CharField(
+                default="", max_length=250, verbose_name="Plural name"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="health_facility_type_other",
+            field=edc_model_fields.fields.other_charfield.OtherCharField(
+                blank=True,
+                default="",
+                max_length=35,
+                verbose_name="If other, please specify ...",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="locale_created",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale created",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="locale_modified",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="Auto-updated by Modeladmin",
+                max_length=10,
+                verbose_name="Locale modified",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="notes",
+            field=models.TextField(blank=True, default=""),
+        ),
+    ]

edc_facility/migrations/0017_alter_healthfacility_gps_and_more.py

@@ -0,0 +1,54 @@
+# Generated by Django 5.2.6 on 2025-09-18 00:24
+
+import django.utils.timezone
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("edc_facility", "0016_alter_healthfacility_device_created_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="gps",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="copy and paste directly from google maps",
+                max_length=50,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="report_datetime",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.AlterField(
+            model_name="healthfacility",
+            name="title",
+            field=models.CharField(blank=True, default="", max_length=150),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="gps",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="copy and paste directly from google maps",
+                max_length=50,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="report_datetime",
+            field=models.DateTimeField(default=django.utils.timezone.now),
+        ),
+        migrations.AlterField(
+            model_name="historicalhealthfacility",
+            name="title",
+            field=models.CharField(blank=True, default="", max_length=150),
+        ),
+    ]