clinicedc 2.0.1__py3-none-any.whl → 2.0.2__py3-none-any.whl

edc_data_manager/action_items.py

@@ -72,9 +72,7 @@ class DataQueryAction(Action):
 
     def get_category(self):
         return (
-            "DM Query"
-            if self.site_response_status in [FEEDBACK, RESOLVED]
-            else "Site Query"
+            "DM Query" if self.site_response_status in [FEEDBACK, RESOLVED] else "Site Query"
         )
 
     def get_status(self):

edc_data_manager/admin/actions.py

@@ -16,9 +16,7 @@ from ..rule import update_query_rules
 DATA_MANAGER_ENABLED = getattr(settings, "DATA_MANAGER_ENABLED", True)
 
 
-@admin.action(
-    description=f"Toggle Active/Inactive {QueryRule._meta.verbose_name_plural}"
-)
+@admin.action(description=f"Toggle Active/Inactive {QueryRule._meta.verbose_name_plural}")
 def toggle_active_flag(modeladmin, request, queryset):
     for obj in queryset:
         obj.active = False if obj.active else True
@@ -37,9 +35,7 @@ def copy_query_rule_action(modeladmin, request, queryset):
     if queryset.count() == 1:
         obj = queryset[0]
         options = {
-            k: v
-            for k, v in obj.__dict__.items()
-            if not k.startswith("_") and k not in ["id"]
+            k: v for k, v in obj.__dict__.items() if not k.startswith("_") and k not in ["id"]
         }
         options["title"] = f"{options['title']} (Copy)"
         options["active"] = False
@@ -77,9 +73,7 @@ def update_query_rules_action(modeladmin, request, queryset):
         if settings.CELERY_ENABLED:
             update_query_rules.delay(pks=[o.pk for o in queryset])
             dte = get_utcnow()
-            taskresult_url = reverse(
-                "admin:django_celery_results_taskresult_changelist"
-            )
+            taskresult_url = reverse("admin:django_celery_results_taskresult_changelist")
             msg = format_html(
                 "Updating data queries in the background. "
                 "Started at {}. "

edc_data_manager/admin/data_query_admin.py

@@ -35,15 +35,11 @@ from .actions import toggle_dm_status
 
 
 @register(DataQuery, site=edc_data_manager_admin)
-class DataQueryAdmin(
-    SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin
-):
+class DataQueryAdmin(SiteModelAdminMixin, ModelAdminSubjectDashboardMixin, SimpleHistoryAdmin):
     status_column_template_name = "edc_data_manager/columns/status.html"
     query_date_column_template_name = "edc_data_manager/columns/query_date.html"
     query_text_column_template_name = "edc_data_manager/columns/query_text.html"
-    query_recipients_column_template_name = (
-        "edc_data_manager/columns/query_recipients.html"
-    )
+    query_recipients_column_template_name = "edc_data_manager/columns/query_recipients.html"
 
     rule_generated_column_template_name = "edc_data_manager/columns/rule_generated.html"
 
@@ -305,9 +301,7 @@ class DataQueryAdmin(
         return render_to_string(self.locked_column_template_name, context=context)
 
     def render_rule_generated_to_string(self, context):
-        return render_to_string(
-            self.rule_generated_column_template_name, context=context
-        )
+        return render_to_string(self.rule_generated_column_template_name, context=context)
 
     def render_query_date_to_string(self, context):
         return render_to_string(self.query_date_column_template_name, context=context)
@@ -316,9 +310,7 @@ class DataQueryAdmin(
         return render_to_string(self.query_text_column_template_name, context=context)
 
     def render_query_recipients_to_string(self, context):
-        return render_to_string(
-            self.query_recipients_column_template_name, context=context
-        )
+        return render_to_string(self.query_recipients_column_template_name, context=context)
 
     def created_details(self, obj):
         rule_generated = YES if obj.rule_generated else NO

edc_data_manager/admin/query_rule_admin.py

@@ -33,23 +33,17 @@ class QueryRuleModelAdminMixin:
 
     @staticmethod
     def form_name(obj=None):
-        data_dictionaries = [
-            dd for dd in obj.data_dictionaries.all().order_by("number")
-        ]
+        data_dictionaries = [dd for dd in obj.data_dictionaries.all().order_by("number")]
         return ", ".join(list(set([dd.model_verbose_name for dd in data_dictionaries])))
 
     @staticmethod
     def questions(obj=None):
-        numbers = [
-            str(dd.number) for dd in obj.data_dictionaries.all().order_by("number")
-        ]
+        numbers = [str(dd.number) for dd in obj.data_dictionaries.all().order_by("number")]
         return ", ".join(numbers)
 
     @staticmethod
     def field_names(obj=None):
-        fields = [
-            dd.field_name for dd in obj.data_dictionaries.all().order_by("field_name")
-        ]
+        fields = [dd.field_name for dd in obj.data_dictionaries.all().order_by("field_name")]
         return ", ".join(fields)
 
     @staticmethod
@@ -59,10 +53,7 @@ class QueryRuleModelAdminMixin:
 
     @staticmethod
     def query_timing(obj=None):
-        return (
-            f"{obj.timing} {obj.get_timing_units_display()} "
-            f"from {obj.reference_date}"
-        )
+        return f"{obj.timing} {obj.get_timing_units_display()} " f"from {obj.reference_date}"
 
     @staticmethod
     def requisition(obj=None):

edc_data_manager/auths.py

@@ -24,9 +24,7 @@ site_auths.add_custom_permissions_tuples(
 
 site_auths.add_custom_permissions_tuples(
     model="edc_data_manager.edcpermissions",
-    codename_tuples=[
-        ("edc_data_manager.special_bypassmodelform", "Can bypass modelform")
-    ],
+    codename_tuples=[("edc_data_manager.special_bypassmodelform", "Can bypass modelform")],
 )
 
 

edc_data_manager/forms/data_query.py

@@ -51,9 +51,7 @@ class DataQueryFormValidator(FormValidator):
             OPEN,
             FEEDBACK,
         ] and self.cleaned_data.get("status") in [CLOSED, CLOSED_WITH_ACTION]:
-            raise forms.ValidationError(
-                {"status": "Invalid: Site response is not resolved."}
-            )
+            raise forms.ValidationError({"status": "Invalid: Site response is not resolved."})
 
         # DM
         self.required_if(
@@ -62,9 +60,7 @@ class DataQueryFormValidator(FormValidator):
             field="status",
             field_required="resolved_datetime",
         )
-        self.required_if(
-            CLOSED, CLOSED_WITH_ACTION, field="status", field_required="dm_user"
-        )
+        self.required_if(CLOSED, CLOSED_WITH_ACTION, field="status", field_required="dm_user")
         self.required_if(
             CLOSED_WITH_ACTION,
             field="status",

edc_data_manager/forms/query_rule.py

@@ -7,9 +7,7 @@ from ..models import QueryRule
 
 class QueryRuleFormValidator(FormValidator):
     def clean(self):
-        models = list(
-            set([obj.model for obj in self.cleaned_data.get("data_dictionaries")])
-        )
+        models = list(set([obj.model for obj in self.cleaned_data.get("data_dictionaries")]))
         if len(models) > 1:
             raise forms.ValidationError(
                 {"data_dictionaries": "Invalid. Select questions from one CRF only"}

edc_data_manager/get_longitudinal_value.py

@@ -6,9 +6,7 @@ class DataDictionaryError(Exception):
     pass
 
 
-def get_longitudinal_value(
-    subject_identifier=None, reference_dt=None, model=None, field=None
-):
+def get_longitudinal_value(subject_identifier=None, reference_dt=None, model=None, field=None):
     DataDictionary = django_apps.get_model("edc_data_manager.datadictionary")
     opts = dict(field_name=field)
     if model:
@@ -22,8 +20,7 @@ def get_longitudinal_value(
         )
     except MultipleObjectsReturned:
         fields = [
-            f"{obj.model}.{obj.field_name}"
-            for obj in DataDictionary.objects.filter(**opts)
+            f"{obj.model}.{obj.field_name}" for obj in DataDictionary.objects.filter(**opts)
         ]
         raise DataDictionaryError(
             "Unable to determine longitudinal value. "

edc_data_manager/handlers/handlers.py

@@ -236,9 +236,7 @@ class QueryRuleHandler:
 
     def get_field_value(self, field_name):
         """Safely get a model instance value for this query."""
-        if not self.query_rule_obj.data_dictionaries.filter(
-            field_name=field_name
-        ).exists():
+        if not self.query_rule_obj.data_dictionaries.filter(field_name=field_name).exists():
             field_names = [
                 f"{dd.field_name} ({dd.number})"
                 for dd in self.query_rule_obj.data_dictionaries.all()
@@ -319,9 +317,7 @@ class QueryRuleHandler:
         if not self._model_obj:
             try:
                 self._model_obj = self.model_cls.objects.get(
-                    **{
-                        f"{self.model_cls.related_visit_model_attr()}": self.related_visit
-                    }
+                    **{f"{self.model_cls.related_visit_model_attr()}": self.related_visit}
                 )
             except ObjectDoesNotExist:
                 pass

edc_data_manager/migrations/0001_initial.py

@@ -12,13 +12,14 @@ import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
+import simple_history.models
+from django.conf import settings
+from django.db import migrations, models
+
 import edc_action_item.models.action_item
 import edc_registration.models.managers
 import edc_sites.models
 import edc_utils.date
-import simple_history.models
-from django.conf import settings
-from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_data_manager/migrations/0003_auto_20190806_1749.py

@@ -40,9 +40,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="dataquery",
             name="resolved_datetime",
-            field=models.DateTimeField(
-                blank=True, null=True, verbose_name="DM resolved on"
-            ),
+            field=models.DateTimeField(blank=True, null=True, verbose_name="DM resolved on"),
         ),
         migrations.AlterField(
             model_name="dataquery",
@@ -81,9 +79,7 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicaldataquery",
             name="resolved_datetime",
-            field=models.DateTimeField(
-                blank=True, null=True, verbose_name="DM resolved on"
-            ),
+            field=models.DateTimeField(blank=True, null=True, verbose_name="DM resolved on"),
         ),
         migrations.AlterField(
             model_name="historicaldataquery",

edc_data_manager/migrations/0004_auto_20190806_1750.py

@@ -9,8 +9,6 @@ class Migration(migrations.Migration):
     operations = [
         migrations.AlterUniqueTogether(
             name="dataquery",
-            unique_together={
-                ("registered_subject", "rule_reference", "visit_schedule")
-            },
+            unique_together={("registered_subject", "rule_reference", "visit_schedule")},
         )
     ]

edc_data_manager/migrations/0025_edcpermissions.py

@@ -1,12 +1,12 @@
 # Generated by Django 3.2.13 on 2022-08-25 20:09
 
 import _socket
-from django.db import migrations, models
 import django_audit_fields.fields.hostname_modification_field
 import django_audit_fields.fields.userfield
 import django_audit_fields.fields.uuid_auto_field
 import django_audit_fields.models.audit_model_mixin
 import django_revision.revision_field
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_data_manager/migrations/0027_alter_dataquery_dm_user.py

@@ -1,7 +1,7 @@
 # Generated by Django 4.1.2 on 2023-02-28 00:40
 
-from django.db import migrations, models
 import django.db.models.deletion
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):

edc_data_manager/migrations/0028_alter_dataquery_options_alter_queryrule_options_and_more.py

@@ -1,9 +1,10 @@
 # Generated by Django 4.2.1 on 2023-07-05 02:16
 
 import django.db.models.manager
-import edc_sites.models
 from django.db import migrations
 
+import edc_sites.models
+
 
 class Migration(migrations.Migration):
     dependencies = [

edc_data_manager/migrations/0029_alter_dataquery_managers.py

@@ -1,9 +1,10 @@
 # Generated by Django 4.2.1 on 2023-07-07 19:32
 
 import django.db.models.manager
-import edc_sites.models
 from django.db import migrations
 
+import edc_sites.models
+
 
 class Migration(migrations.Migration):
     dependencies = [

edc_data_manager/migrations/0030_alter_datadictionary_device_created_and_more.py

@@ -1,8 +1,8 @@
 # Generated by Django 4.2.4 on 2023-08-23 01:13
 
 import _socket
-from django.db import migrations, models
 import django_audit_fields.fields.hostname_modification_field
+from django.db import migrations, models
 
 
 class Migration(migrations.Migration):
@@ -14,16 +14,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="datadictionary",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="datadictionary",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="datadictionary",
@@ -49,16 +45,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="dataquery",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="dataquery",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="dataquery",
@@ -84,16 +76,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="edcpermissions",
@@ -119,16 +107,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicaldatadictionary",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicaldatadictionary",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicaldatadictionary",
@@ -154,16 +138,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicaldataquery",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicaldataquery",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicaldataquery",
@@ -189,16 +169,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="historicalqueryrule",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="historicalqueryrule",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="historicalqueryrule",
@@ -224,16 +200,12 @@ class Migration(migrations.Migration):
         migrations.AlterField(
             model_name="queryrule",
             name="device_created",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device created"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device created"),
         ),
         migrations.AlterField(
             model_name="queryrule",
             name="device_modified",
-            field=models.CharField(
-                blank=True, max_length=10, verbose_name="Device modified"
-            ),
+            field=models.CharField(blank=True, max_length=10, verbose_name="Device modified"),
         ),
         migrations.AlterField(
             model_name="queryrule",

edc_data_manager/models/model_mixins.py

@@ -10,9 +10,7 @@ from .user import DataManagerUser, QueryUser
 
 
 class DataQueryModelMixin(models.Model):
-    report_datetime = models.DateTimeField(
-        verbose_name="Query date", default=get_utcnow
-    )
+    report_datetime = models.DateTimeField(verbose_name="Query date", default=get_utcnow)
 
     title = models.CharField(max_length=150, null=True, blank=False)
 

edc_data_manager/populate_data_dictionary.py

@@ -102,8 +102,7 @@ def create_or_update_data_dictionary(index, model, fld):
                 data_dictionary_model_cls.objects.create(**options)
             except (OperationalError, IntegrityError) as e:
                 warn(
-                    f"Error when creating DataDictionary instance. "
-                    f"Model={model}. Got {e}"
+                    f"Error when creating DataDictionary instance. " f"Model={model}. Got {e}"
                 )
         else:
             for k, v in options.items():

edc_data_manager/post_migrate_signals.py

@@ -25,9 +25,7 @@ def update_query_rule_handlers(sender=None, **kwargs):
     from .site_data_manager import site_data_manager
 
     sys.stdout.write(
-        style.MIGRATE_HEADING(
-            "Deactivating query rules with invalid rule handler names:\n"
-        )
+        style.MIGRATE_HEADING("Deactivating query rules with invalid rule handler names:\n")
     )
     handler_names = [x for x in site_data_manager.registry.keys()]
     django_apps.get_model("edc_data_manager.queryrule").objects.exclude(

edc_data_manager/site_data_manager.py

@@ -33,9 +33,7 @@ class SiteDataManager:
     def get_rule_handler(self, name):
         name = name or "default"
         if name not in self.registry:
-            raise SiteDataManagerError(
-                f"Query rule handler is not registered. Got {name}."
-            )
+            raise SiteDataManagerError(f"Query rule handler is not registered. Got {name}.")
         return self.registry.get(name)
 
     def get_rule_handlers(self, model_name=None):

edc_document_status/model_mixins.py

@@ -26,9 +26,7 @@ class DocumentStatusModelMixin(models.Model):
         self.update_document_status_on_save(kwargs.get("update_fields"))
         super().save(*args, **kwargs)
 
-    def update_document_status_on_save(
-        self, update_fields: Optional[list] = None
-    ) -> None:
+    def update_document_status_on_save(self, update_fields: Optional[list] = None) -> None:
         """Updates `document_status` as complete unless field is listed
         in update_fields.
 

edc_egfr/__init__.py

@@ -0,0 +1 @@
+from .calculators import EgfrCkdEpi, EgfrCockcroftGault

edc_egfr/admin/__init__.py

@@ -0,0 +1 @@
+from .egfr_drop_notification_admin_mixin import EgfrDropNotificationAdminMixin

edc_egfr/admin/egfr_drop_notification_admin_mixin.py

@@ -0,0 +1,73 @@
+from typing import Dict, Optional, Tuple
+
+from django.contrib import admin
+from django_audit_fields.admin import audit_fieldset_tuple
+
+from edc_action_item.fieldsets import action_fieldset_tuple
+from edc_crf.fieldset import crf_status_fieldset
+
+
+class EgfrDropNotificationAdminMixin:
+    radio_fields = {
+        "report_status": admin.VERTICAL,
+        "creatinine_units": admin.VERTICAL,
+    }
+
+    def get_fieldsets(
+        self, request, obj=None
+    ) -> Tuple[Tuple[Optional[str], Dict[str, Tuple[str, ...]]], ...]:
+        fieldsets = [
+            (None, {"fields": ("subject_visit", "report_datetime")}),
+            (
+                "eGFR",
+                {
+                    "fields": (
+                        "egfr_percent_change",
+                        "creatinine_date",
+                        "creatinine_value",
+                        "creatinine_units",
+                    )
+                },
+            ),
+            (
+                "Narrative",
+                {"fields": ("narrative", "report_status")},
+            ),
+            crf_status_fieldset,
+        ]
+        if getattr(self.model, "action_name", None):
+            fieldsets.append(action_fieldset_tuple)
+        fieldsets.append(audit_fieldset_tuple)
+        return tuple(fieldsets)
+
+    def get_search_fields(self, request) -> Tuple[str, ...]:
+        fields = super().get_search_fields(request)
+        custom_fields = (
+            "subject_visit__subject_identifier",
+            "action_identifier",
+        )
+        return tuple(f for f in fields if f not in custom_fields) + custom_fields
+
+    def get_readonly_fields(self, request, obj=None) -> Tuple[str, ...]:
+        fields = super().get_readonly_fields(request, obj)
+        return (
+            "creatinine_date",
+            "creatinine_value",
+            "creatinine_units",
+            "egfr_percent_change",
+        ) + fields
+
+    def get_list_filter(self, request) -> Tuple[str, ...]:
+        list_filter = super().get_list_filter(request)
+        return ("report_status", "creatinine_date") + list_filter
+
+    def get_list_display(self, request) -> Tuple[str, ...]:
+        list_display = super().get_list_display(request)
+        custom_fields = (
+            "report_status",
+            "report_datetime",
+            "egfr_percent_change",
+            "creatinine_date",
+            "creatinine_value",
+        )
+        return tuple(f for f in list_display if f not in custom_fields) + custom_fields

edc_egfr/apps.py

@@ -0,0 +1,5 @@
+from django.apps import AppConfig as DjangoAppConfig
+
+
+class AppConfig(DjangoAppConfig):
+    name = "edc_egfr"

edc_egfr/calculators/__init__.py

@@ -0,0 +1,4 @@
+from .base_egrfr import EgfrCalculatorError
+from .egfr_ckd_epi import EgfrCkdEpi
+from .egfr_cockcroft_gault import EgfrCockcroftGault
+from .percent_change import egfr_percent_change