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

edc_offstudy/migrations/0023_alter_historicalsubjectoffstudy_action_identifier_and_more.py

@@ -0,0 +1,188 @@
+# 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_offstudy", "0022_alter_historicalsubjectoffstudy_revision_and_more"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="action_identifier",
+            field=models.CharField(
+                blank=True, db_index=True, default="", max_length=50
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="action_item_reason",
+            field=models.TextField(default="", editable=False),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="comment",
+            field=models.TextField(
+                blank=True,
+                default="",
+                max_length=500,
+                verbose_name="Please provide further details if possible",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            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="historicalsubjectoffstudy",
+            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="historicalsubjectoffstudy",
+            name="other_offstudy_reason",
+            field=edc_model_fields.fields.other_charfield.OtherCharField(
+                blank=True,
+                default="",
+                max_length=35,
+                verbose_name="If other, please specify ...",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="parent_action_identifier",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="action identifier that links to parent reference model instance.",
+                max_length=30,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="related_action_identifier",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="action identifier that links to related reference model instance.",
+                max_length=30,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="action_identifier",
+            field=models.CharField(blank=True, default="", max_length=50, unique=True),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="action_item_reason",
+            field=models.TextField(default="", editable=False),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="comment",
+            field=models.TextField(
+                blank=True,
+                default="",
+                max_length=500,
+                verbose_name="Please provide further details if possible",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="device_created",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device created"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="device_modified",
+            field=models.CharField(
+                blank=True, default="", max_length=10, verbose_name="Device modified"
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            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="subjectoffstudy",
+            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="subjectoffstudy",
+            name="other_offstudy_reason",
+            field=edc_model_fields.fields.other_charfield.OtherCharField(
+                blank=True,
+                default="",
+                max_length=35,
+                verbose_name="If other, please specify ...",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="parent_action_identifier",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="action identifier that links to parent reference model instance.",
+                max_length=30,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="related_action_identifier",
+            field=models.CharField(
+                blank=True,
+                default="",
+                help_text="action identifier that links to related reference model instance.",
+                max_length=30,
+            ),
+        ),
+    ]

edc_offstudy/migrations/0024_alter_historicalsubjectoffstudy_offstudy_datetime_and_more.py

@@ -0,0 +1,43 @@
+# Generated by Django 5.2.6 on 2025-09-18 00:24
+
+import django.utils.timezone
+import edc_model.validators.date
+import edc_protocol.validators
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        (
+            "edc_offstudy",
+            "0023_alter_historicalsubjectoffstudy_action_identifier_and_more",
+        ),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="historicalsubjectoffstudy",
+            name="offstudy_datetime",
+            field=models.DateTimeField(
+                default=django.utils.timezone.now,
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Off-study date and time",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="subjectoffstudy",
+            name="offstudy_datetime",
+            field=models.DateTimeField(
+                default=django.utils.timezone.now,
+                validators=[
+                    edc_protocol.validators.datetime_not_before_study_start,
+                    edc_model.validators.date.datetime_not_future,
+                ],
+                verbose_name="Off-study date and time",
+            ),
+        ),
+    ]

edc_offstudy/model_mixins/offstudy_model_mixin.py

@@ -3,12 +3,13 @@ from zoneinfo import ZoneInfo
 from django.conf import settings
 from django.core.exceptions import ValidationError
 from django.db import models
+from django.utils import timezone
 
 from edc_identifier.model_mixins import UniqueSubjectIdentifierFieldMixin
 from edc_model.validators import datetime_not_future
 from edc_model_fields.fields import OtherCharField
 from edc_protocol.validators import datetime_not_before_study_start
-from edc_utils import convert_php_dateformat, get_utcnow
+from edc_utils import convert_php_dateformat
 from edc_visit_schedule.utils import (
     off_all_schedules_or_raise,
     offstudy_datetime_after_all_offschedule_datetimes,
@@ -39,7 +40,7 @@ class OffstudyModelMixin(UniqueSubjectIdentifierFieldMixin, models.Model):
     offstudy_datetime = models.DateTimeField(
         verbose_name="Off-study date and time",
         validators=[datetime_not_before_study_start, datetime_not_future],
-        default=get_utcnow,
+        default=timezone.now,
     )
 
     report_datetime = models.DateTimeField(null=True, editable=False)

edc_pdutils/df_exporters/csv_exporter.py

@@ -1,13 +1,15 @@
 from __future__ import annotations
 
-import os
+import contextlib
 import sys
+from pathlib import Path
 
 import pandas as pd
 from django.apps import apps as django_apps
 from django.conf import settings
 from django.core.management.color import color_style
 from django.db.models import QuerySet
+from django.utils import timezone
 
 from edc_export.exceptions import (
     ExporterExportFolder,
@@ -15,7 +17,6 @@ from edc_export.exceptions import (
     ExporterInvalidExportFormat,
 )
 from edc_export.utils import get_base_dir
-from edc_utils import get_utcnow
 
 from ..site_values_mappings import site_values_mappings
 from ..utils import get_export_folder, get_model_from_table_name
@@ -24,9 +25,7 @@ style = color_style()
 
 
 class Exported:
-    def __init__(
-        self, path: str = None, model_name: str = None, record_count: int | None = None
-    ):
+    def __init__(self, path: Path, model_name: str, record_count: int):
         self.path = path
         self.model_name = model_name
         self.record_count = record_count
@@ -53,7 +52,7 @@ class CsvExporter:
         data_label: str | None = None,
         app_label: str | None = None,
         sort_by: list | tuple | str | None = None,
-        export_folder: str = None,
+        export_folder: Path | None = None,
         delimiter: str | None = None,
         date_format: str | None = None,
         index: bool | None = None,
@@ -75,13 +74,11 @@ class CsvExporter:
         self.verbose = verbose
         if not self.export_folder:
             raise ExporterExportFolder("Invalid export folder. Got None")
-        if not os.path.exists(self.export_folder):
+        if not self.export_folder.exists():
             raise ExporterExportFolder(f"Invalid export folder. Got {self.export_folder}")
         if self.model_name:
-            try:
+            with contextlib.suppress(LookupError, AttributeError):
                 self.model_cls = django_apps.get_model(self.model_name)
-            except (LookupError, AttributeError):
-                pass
         elif self.table_name:
             self.model_cls = get_model_from_table_name(table_name)
             if self.model_cls:
@@ -89,7 +86,7 @@ class CsvExporter:
         self.data_label = data_label or model_name or table_name
 
     def to_format(
-        self, export_format, dataframe=None, export_folder=None, **kwargs
+        self, export_format: str, dataframe: pd.DataFrame, export_folder: Path, **kwargs
     ) -> Exported:
         """Returns the full path of the written CSV file if the
         dataframe is exported otherwise None.
@@ -109,18 +106,18 @@ class CsvExporter:
         if not dataframe.empty:
             path = self.get_path()
             if self.sort_by:
-                dataframe.sort_values(by=self.sort_by, inplace=True)
+                dataframe = dataframe.sort_values(by=self.sort_by)
             if self.verbose:
                 sys.stdout.write(f"( ) {self.model_name} ...     \r")
             if export_format == "csv":
-                path = ".".join([path, "csv"])
+                path = path.with_suffix(".csv")
                 dataframe.to_csv(path_or_buf=path, **self.csv_options)
             elif export_format == "stata":
-                path = ".".join([path, "dta"])
+                path = path.with_suffix(".dta")
                 dta_version: str | None = kwargs.pop("dta_version", None)
                 dta_version = int(dta_version) if dta_version else None
                 dataframe.to_stata(
-                    path=path, **self.stata_options, version=dta_version, **kwargs
+                    path=str(path), **self.stata_options, version=dta_version, **kwargs
                 )
             else:
                 raise ExporterInvalidExportFormat(
@@ -135,7 +132,7 @@ class CsvExporter:
             sys.stdout.write(f"(?) {self.model_name} empty  \n")
         return Exported(path, self.model_name, record_count)
 
-    def to_csv(self, dataframe: pd.DataFrame = None, export_folder: str = None) -> Exported:
+    def to_csv(self, dataframe: pd.DataFrame, export_folder: Path) -> Exported:
         """Returns the full path of the written CSV file if the
         dataframe is exported otherwise None.
 
@@ -149,9 +146,9 @@ class CsvExporter:
 
     def to_stata(
         self,
-        dataframe: pd.DataFrame = None,
-        export_folder: str = None,
-        dta_version: str = None,
+        dataframe: pd.DataFrame,
+        export_folder: Path,
+        dta_version: str | None = None,
     ) -> Exported:
         """Returns the full path of the written STATA file if the
         dataframe is exported otherwise None.
@@ -184,16 +181,16 @@ class CsvExporter:
         """Returns default options for dataframe.to_stata()."""
         return dict(data_label=f"{self.data_label}.dta")
 
-    def get_path(self) -> str:
+    def get_path(self) -> Path:
         """Returns a full path with filename."""
         root_dir = self.export_folder
-        if not os.path.exists(root_dir):
+        if not root_dir.exists():
             raise ExporterExportFolder(f"Base folder does not exist. Got {root_dir}.")
-        base_dir: str = get_base_dir()
-        if not os.path.exists(os.path.join(root_dir, base_dir)):
-            os.makedirs(os.path.join(root_dir, base_dir))
-        path = os.path.join(root_dir, base_dir, self.filename)
-        if os.path.exists(path) and not self.file_exists_ok:
+        base_dir = get_base_dir()
+        if not (root_dir / base_dir).exists():
+            (root_dir / base_dir).mkdir(parents=True, exist_ok=False)
+        path = root_dir / base_dir / self.filename
+        if path.exists() and not self.file_exists_ok:
             raise ExporterFileExists(
                 f"File '{path}' exists! Not exporting {self.model_name}.\n"
             )
@@ -212,7 +209,7 @@ class CsvExporter:
             if not timestamp_format:
                 suffix = ""
             else:
-                suffix = f"_{get_utcnow().strftime(timestamp_format)}"
+                suffix = f"_{timezone.now().strftime(timestamp_format)}"
             prefix = (self.model_name or self.data_label).replace("-", "_").replace(".", "_")
             filename = f"{prefix}{suffix}"
         return filename
@@ -229,15 +226,14 @@ class CsvExporter:
         choices = {}
         if self.model_cls:
             for field_cls in self.model_cls._meta.get_fields():
-                if field_cls.get_internal_type() == "CharField":
-                    if field_cls.choices:
-                        responses = []
-                        for tpl in field_cls.choices:
-                            if mapped_choice := site_values_mappings.get_by_choices(tpl):
-                                responses.append([mapped_choice[0], mapped_choice[1]])
-                            else:
-                                responses.append([tpl[0], tpl[1]])
-                        choices.update({field_cls.name: responses})
+                if field_cls.get_internal_type() == "CharField" and field_cls.choices:
+                    responses = []
+                    for tpl in field_cls.choices:
+                        if mapped_choice := site_values_mappings.get_by_choices(tpl):
+                            responses.append([mapped_choice[0], mapped_choice[1]])
+                        else:
+                            responses.append([tpl[0], tpl[1]])
+                    choices.update({field_cls.name: responses})
             for fname, responses in choices.items():
                 labels = []
                 if fname in list(dataframe.columns):
@@ -248,7 +244,7 @@ class CsvExporter:
                     commands.append(f"ren {fname} {fname}_edc")
                     commands.append(f"ren {fname}_encoded {fname}")
                     commands.append("")
-            with open(f"{self.get_path()}.do", "w") as f:
+            with (self.get_path() / ".do").open("w") as f:
                 f.writelines(f"{command}\n" for command in commands)
         return commands
 

edc_pdutils/df_exporters/csv_model_exporter.py

@@ -1,5 +1,6 @@
 from __future__ import annotations
 
+from pathlib import Path
 from typing import TYPE_CHECKING
 
 from django.core.management.color import color_style
@@ -24,11 +25,12 @@ class CsvModelExporter:
         queryset: QuerySet | None = None,
         decrypt: bool | None = None,
         sort_by: list | tuple | str | None = None,
-        export_folder: str | None = None,
+        export_folder: Path | None = None,
         site_ids: list[int] | None = None,
         **kwargs,
     ):
         self.model = model or queryset.model._meta.label_lower
+        self.export_folder = export_folder
         self.df_maker = self.df_maker_cls(
             model=model,
             queryset=queryset,
@@ -45,8 +47,10 @@ class CsvModelExporter:
 
     def to_csv(self):
         dataframe = self.df_maker.dataframe
-        return self.csv_exporter.to_csv(dataframe=dataframe)
+        return self.csv_exporter.to_csv(dataframe=dataframe, export_folder=self.export_folder)
 
     def to_stata(self):
         dataframe = self.df_maker.dataframe
-        return self.csv_exporter.to_stata(dataframe=dataframe)
+        return self.csv_exporter.to_stata(
+            dataframe=dataframe, export_folder=self.export_folder
+        )

edc_pdutils/migrations/0001_initial.py

@@ -10,7 +10,7 @@ from django.db import migrations, models
 
 import edc_model_fields.fields.hostname_modification_field
 import edc_model_fields.fields.userfield
-import edc_utils
+import django.utils.timezone
 
 
 class Migration(migrations.Migration):
@@ -24,11 +24,11 @@ class Migration(migrations.Migration):
             fields=[
                 (
                     "created",
-                    models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",
@@ -109,11 +109,11 @@ class Migration(migrations.Migration):
             fields=[
                 (
                     "created",
-                    models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",
@@ -179,7 +179,7 @@ class Migration(migrations.Migration):
                 ("summary", models.TextField(null=True)),
                 (
                     "exported_datetime",
-                    models.DateTimeField(default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(default=django.utils.timezone.now),
                 ),
                 (
                     "data_request",
@@ -196,11 +196,11 @@ class Migration(migrations.Migration):
             fields=[
                 (
                     "created",
-                    models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "modified",
-                    models.DateTimeField(blank=True, default=edc_utils.date.get_utcnow),
+                    models.DateTimeField(blank=True, default=django.utils.timezone.now),
                 ),
                 (
                     "user_created",

edc_pharmacy/admin/prescription/rx_refill_admin.py

@@ -2,12 +2,13 @@ from django.conf import settings
 from django.contrib import admin
 from django.template.loader import render_to_string
 from django.urls import reverse
+from django.utils import timezone
 from django.utils.html import format_html
 from django.utils.safestring import mark_safe
 from django_audit_fields.admin import audit_fieldset_tuple
 
 from edc_appointment.models import Appointment
-from edc_utils import convert_php_dateformat, formatted_age, get_utcnow
+from edc_utils import convert_php_dateformat, formatted_age
 
 from ...admin_site import edc_pharmacy_admin
 from ...forms import RxRefillForm
@@ -21,7 +22,7 @@ class RxRefillAdmin(ModelAdminMixin, admin.ModelAdmin):
 
     ordering: tuple[str, ...] = ("refill_start_datetime",)
 
-    autocomplete_fields = ["dosage_guideline", "formulation"]
+    autocomplete_fields = ("dosage_guideline", "formulation")
 
     form = RxRefillForm
 
@@ -140,7 +141,7 @@ class RxRefillAdmin(ModelAdminMixin, admin.ModelAdmin):
             "initials": obj.rx.registered_subject.initials,
             "gender": obj.rx.registered_subject.gender,
             "age_in_years": formatted_age(
-                born=obj.rx.registered_subject.dob, reference_dt=get_utcnow()
+                born=obj.rx.registered_subject.dob, reference_dt=timezone.now()
             ),
             "number_of_days": obj.number_of_days,
             "remaining": obj.remaining,

edc_pharmacy/admin/reports/stock_availability_admin.py

@@ -1,6 +1,7 @@
 from django.contrib import admin
 from django.db.models import QuerySet
 from django.urls import reverse
+from django.utils import timezone
 from django.utils.html import format_html
 from rangefilter.filters import DateRangeFilterBuilder, NumericRangeFilterBuilder
 
@@ -8,7 +9,6 @@ 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_utils import get_utcnow
 
 from ...admin_site import edc_pharmacy_admin
 from ...analytics.dataframes.no_stock_for_subjects_df import stock_for_subjects_df
@@ -21,7 +21,8 @@ def wrap_html(s, url):
 
 
 def update_report(modeladmin, request):
-    now = get_utcnow()
+    now = timezone.now()
+    created = 0
     modeladmin.model.objects.all().delete()
 
     df = stock_for_subjects_df()
@@ -50,9 +51,8 @@ def update_report(modeladmin, request):
             )
             for _, row in df.iterrows()
         ]
-        created = len(modeladmin.model.objects.bulk_create(data))
-        # messages.success(request, "{} records were successfully created.".format(created))
-        return created
+        return len(modeladmin.model.objects.bulk_create(data))
+    return created
 
 
 @admin.register(StockAvailability, site=edc_pharmacy_admin)
@@ -63,7 +63,6 @@ class StockAvailabilityModelAdmin(
     TemplatesModelAdminMixin,
     admin.ModelAdmin,
 ):
-
     queryset_filter: dict | None = None
     qa_report_list_display_insert_pos = 3
     include_note_column = False

edc_pharmacy/auths.py

@@ -18,21 +18,25 @@ from .auth_objects import (
     prescriber_codenames,
 )
 
-site_auths.add_post_update_func(
-    "edc_pharmacy", remove_default_model_permissions_from_edc_permissions
-)
-site_auths.add_custom_permissions_tuples(
-    model="edc_pharmacy.edcpermissions", codename_tuples=navbar_tuples
-)
 
-site_auths.add_group(*pharmacy_codenames, name=PHARMACY_VIEW, view_only=True)
-site_auths.add_group(*prescriber_codenames, name=PHARMACY_PRESCRIBER, no_delete=True)
-site_auths.add_group(*pharmacy_site_codenames, name=PHARMACY_SITE, no_delete=False)
-site_auths.add_group(*pharmacy_codenames, name=PHARMACY, no_delete=False)
+def update_site_auths() -> None:
+    site_auths.add_post_update_func(
+        "edc_pharmacy", remove_default_model_permissions_from_edc_permissions
+    )
+    site_auths.add_custom_permissions_tuples(
+        model="edc_pharmacy.edcpermissions", codename_tuples=navbar_tuples
+    )
+
+    site_auths.add_group(*pharmacy_codenames, name=PHARMACY_VIEW, view_only=True)
+    site_auths.add_group(*prescriber_codenames, name=PHARMACY_PRESCRIBER, no_delete=True)
+    site_auths.add_group(*pharmacy_site_codenames, name=PHARMACY_SITE, no_delete=False)
+    site_auths.add_group(*pharmacy_codenames, name=PHARMACY, no_delete=False)
+
+    site_auths.add_role(PHARMACY_VIEW, name=PHARMACY_AUDITOR_ROLE)
+    site_auths.add_role(PHARMACY_PRESCRIBER, name=PHARMACY_PRESCRIBER_ROLE)
+    site_auths.add_role(PHARMACY_SITE, PYLABELS, name=SITE_PHARMACIST_ROLE)
+    site_auths.add_role(PHARMACY, PYLABELS, name=PHARMACIST_ROLE)
+    site_auths.add_role(PHARMACY, name=PHARMACY_SUPER_ROLE)
 
 
-site_auths.add_role(PHARMACY_VIEW, name=PHARMACY_AUDITOR_ROLE)
-site_auths.add_role(PHARMACY_PRESCRIBER, name=PHARMACY_PRESCRIBER_ROLE)
-site_auths.add_role(PHARMACY_SITE, PYLABELS, name=SITE_PHARMACIST_ROLE)
-site_auths.add_role(PHARMACY, PYLABELS, name=PHARMACIST_ROLE)
-site_auths.add_role(PHARMACY, name=PHARMACY_SUPER_ROLE)
+update_site_auths()