endoreg-db 0.8.9.2__py3-none-any.whl → 0.8.9.10__py3-none-any.whl

endoreg_db/admin.py

@@ -11,6 +11,7 @@ from endoreg_db.models import (
     FindingIntervention,  #  Import Finding Interventions
     PatientFindingIntervention,
 )
+
 # from endoreg_db.forms.patient_finding_intervention_form import (
 #     PatientFindingInterventionForm,
 # )
@@ -29,7 +30,7 @@ class PatientAdmin(admin.ModelAdmin):
 @admin.register(Examination)
 class ExaminationAdmin(admin.ModelAdmin):
     list_display = ("id", "name")
-    search_fields = ("name", )
+    search_fields = ("name",)
     list_filter = ("name",)
     ordering = ("name",)
 
@@ -45,9 +46,13 @@ class PatientFindingInterventionAdmin(admin.ModelAdmin):
             "patients": Patient.objects.all(),
             "examinations": Examination.objects.all(),
             "findings": Finding.objects.all(),
-            "locations": FindingClassification.objects.filter(classification_types__name__iexact="location"),
+            "locations": FindingClassification.objects.filter(
+                classification_types__name__iexact="location"
+            ),
             "location_choices": FindingClassificationChoice.objects.none(),
-            "morphologies": FindingClassification.objects.filter(classification_types__name__iexact="morphology"),
+            "morphologies": FindingClassification.objects.filter(
+                classification_types__name__iexact="morphology"
+            ),
             "morphology_choices": FindingClassificationChoice.objects.none(),
             "finding_interventions": FindingIntervention.objects.all(),
         }
@@ -56,7 +61,7 @@ class PatientFindingInterventionAdmin(admin.ModelAdmin):
     def get_location_choices_json(self, request):
         """
         Handles AJAX requests to retrieve location classification choices as JSON.
-        
+
         Expects a "location" parameter in the GET request and returns a list of matching FindingClassificationChoice objects with their IDs and names. Returns an error message with appropriate HTTP status if the parameter is missing or an exception occurs.
         """
         location_id = request.GET.get("location")
@@ -67,7 +72,7 @@ class PatientFindingInterventionAdmin(admin.ModelAdmin):
             choices = list(
                 FindingClassificationChoice.objects.filter(
                     classifications__id=location_id,
-                    classifications__classification_types__name__iexact="location"
+                    classifications__classification_types__name__iexact="location",
                 ).values("id", "name")
             )
             if not choices:

endoreg_db/apps.py

@@ -2,17 +2,14 @@ from django.apps import AppConfig
 
 
 class EndoregDbConfig(AppConfig):
-    default_auto_field = 'django.db.models.BigAutoField'
-    name = 'endoreg_db'
-    
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "endoreg_db"
+
     def ready(self):
         """
         Performs application startup tasks when the Django app is fully loaded.
-        
+
         This method imports media-related model modules to ensure they are registered
         and ready for use when the application starts.
         """
-        import endoreg_db.models.media.video
-        import endoreg_db.models.media.frame
-        import endoreg_db.models.media.pdf
         pass

endoreg_db/authz/auth.py

@@ -8,6 +8,7 @@ from rest_framework import authentication, exceptions
 
 User = get_user_model()
 
+
 class KeycloakJWTAuthentication(authentication.BaseAuthentication):
     """
     Verifies Bearer JWTs against Keycloak JWKS.

endoreg_db/authz/backends.py

@@ -115,7 +115,7 @@ class KeycloakOIDCBackend(OIDCAuthenticationBackend):
         # Keep user profile in sync with IdP data (safe truncation to field max length)
         user.email = claims.get("email", user.email)
         user.first_name = (claims.get("given_name") or user.first_name)[:150]
-        user.last_name  = (claims.get("family_name") or user.last_name)[:150]
+        user.last_name = (claims.get("family_name") or user.last_name)[:150]
         user.save(update_fields=["email", "first_name", "last_name"])
 
         # Keep roles (groups) in sync on every login

endoreg_db/authz/management/commands/list_routes.py

@@ -1,6 +1,7 @@
 from django.core.management.base import BaseCommand
 from django.urls import get_resolver, URLPattern, URLResolver
 
+
 def iter_patterns(prefix, patterns):
     for p in patterns:
         if isinstance(p, URLPattern):
@@ -8,6 +9,7 @@ def iter_patterns(prefix, patterns):
         elif isinstance(p, URLResolver):
             yield from iter_patterns(prefix, p.url_patterns)
 
+
 class Command(BaseCommand):
     help = "List all URL names (useful to fill policy.py)"
 

endoreg_db/authz/middleware.py

@@ -20,13 +20,11 @@
 #     though using a relative path from request.get_full_path() is already safe.
 
 from django.shortcuts import redirect
-from django.conf import settings
-from urllib.parse import urlencode
 
 # Any URL path that starts with one of these prefixes is considered "protected" for browser UX.
 # You can add more prefixes if you want the same login-redirect behavior elsewhere
 # (e.g., PROTECTED_PREFIXES = ("/api/", "/reports/", "/dashboard/")).
-#PROTECTED_PREFIXES = ("/api/",)
+# PROTECTED_PREFIXES = ("/api/",)
 
 # Protect the SPA shell too (everything except static/assets/oidc)
 PROTECTED_PREFIXES = ("/",)  # catch-all; we'll skip known public paths below
@@ -36,10 +34,11 @@ PUBLIC_PREFIXES = (
     "/assets/",
     "/media/",
     "/favicon.ico",
-    "/oidc/",          # OIDC endpoints must stay public
-    "/__vite",         # if Vite dev assets ever used
+    "/oidc/",  # OIDC endpoints must stay public
+    "/__vite",  # if Vite dev assets ever used
 )
 
+
 class LoginRequiredForAPIsMiddleware:
     """
     For browser traffic:
@@ -51,7 +50,8 @@ class LoginRequiredForAPIsMiddleware:
 
     """
 
-    def __init__(self, get_response): self.get_response = get_response
+    def __init__(self, get_response):
+        self.get_response = get_response
 
     def __call__(self, request):
         # request.path is the URL path without scheme/host/query (e.g., "/api/patients/").
@@ -76,8 +76,9 @@ class LoginRequiredForAPIsMiddleware:
         if not request.user.is_authenticated:
             from django.conf import settings
             from urllib.parse import urlencode
+
             params = urlencode({"next": request.get_full_path()})
             return redirect(f"{settings.LOGIN_URL}?{params}")
 
         # 4) Authenticated → pass through
-        return self.get_response(request)
+        return self.get_response(request)

endoreg_db/authz/permissions.py

@@ -29,11 +29,12 @@ from rest_framework.permissions import BasePermission
 from django.contrib.auth.models import AnonymousUser
 from django.utils.functional import cached_property
 from endoreg_db.utils.permissions import is_debug_mode
-from .policy import REQUIRED_ROLES, DEFAULT_ROLE_BY_METHOD, satisfies, get_needed_role
+from .policy import REQUIRED_ROLES, satisfies, get_needed_role
 import logging
 
 logger = logging.getLogger(__name__)
 
+
 def _normalized_route_name(request, view) -> str:
     """
     Return a stable, de-namespaced route name, e.g. 'patient-list'.
@@ -51,6 +52,7 @@ def _normalized_route_name(request, view) -> str:
             return url_name
     return view.__class__.__name__
 
+
 def _route_name(request, view):
     """
     Resolve a stable name for the current endpoint.
@@ -95,8 +97,12 @@ class PolicyPermission(BasePermission):
 
         # 1) DEBUG bypass
         if is_debug_mode():
-            logger.info("RBAC BYPASS (DEBUG): route=%s method=%s user=%s",
-                        route, method, getattr(getattr(request, "user", None), "username", "anon"))
+            logger.info(
+                "RBAC BYPASS (DEBUG): route=%s method=%s user=%s",
+                route,
+                method,
+                getattr(getattr(request, "user", None), "username", "anon"),
+            )
             return True
 
         # 2) Must be authenticated
@@ -108,11 +114,12 @@ class PolicyPermission(BasePermission):
         # 3) Determine needed role
         needed = get_needed_role(route, method)
         if not needed:
-          logger.info(
-            "RBAC DENY (NO ROLE): route=%s method=%s reason=no mapping",
-            route, method
-          )
-          return False
+            logger.info(
+                "RBAC DENY (NO ROLE): route=%s method=%s reason=no mapping",
+                route,
+                method,
+            )
+            return False
 
         # 4) Collect roles and decide
         user_roles = set(user.groups.values_list("name", flat=True))
@@ -120,8 +127,12 @@ class PolicyPermission(BasePermission):
 
         logger.info(
             "RBAC DECISION: route=%s method=%s need=%s user=%s roles=%s => %s",
-            route, method, needed, getattr(user, "username", "anon"),
-            sorted(user_roles), "ALLOW" if allowed else "DENY"
+            route,
+            method,
+            needed,
+            getattr(user, "username", "anon"),
+            sorted(user_roles),
+            "ALLOW" if allowed else "DENY",
         )
 
         return allowed

endoreg_db/authz/policy.py

@@ -52,7 +52,7 @@ RESOURCE_ROLES = {
         "read": "video:read",
         "write": "video:write",
     },
-    #anonymization resource
+    # anonymization resource
     "anonymization": {
         "read": "anonymization:read",
         "write": "anonymization:write",
@@ -75,20 +75,15 @@ RESOURCE_ROLES = {
 #       exactly that "name"
 ROUTE_RESOURCE = {
     # Patients
-    "patient-list":   "patient",   # /api/patients/
-    "patient-detail": "patient",   # /api/patients/{id}/
-
+    "patient-list": "patient",  # /api/patients/
+    "patient-detail": "patient",  # /api/patients/{id}/
     # Custom patient helper
     "check_pe_exist": "patient",
-
     # Example for videos (if you have these ViewSets registered)
-    "videos-list":   "video",
+    "videos-list": "video",
     "videos-detail": "video",
-
     "anonymization_items_overview": "anonymization",
     # Add more mappings as your API grows
-
-    
 }
 
 # ------------------------------------------------------------
@@ -108,7 +103,6 @@ REQUIRED_ROLES: RouteRoles = {
     # "patient-detail": {
     #     "DELETE": "admin",  # admin role in Keycloak
     # },
-
     # Example: a special helper route that you always want read-only patients role:
     # "check_pe_exist": "patient:read",
 }
@@ -125,21 +119,21 @@ REQUIRED_ROLES: RouteRoles = {
 # If you move fully to resource-based roles, you can leave this as None
 # or a generic "data:read"/"data:write" depending on your preference.
 DEFAULT_ROLE_BY_METHOD = {
-    "GET":     "data:read",
-    "HEAD":    "data:read",
+    "GET": "data:read",
+    "HEAD": "data:read",
     "OPTIONS": "data:read",
-    "POST":    "data:write",
-    "PUT":     "data:write",
-    "PATCH":   "data:write",
-    "DELETE":  "data:write",
+    "POST": "data:write",
+    "PUT": "data:write",
+    "PATCH": "data:write",
+    "DELETE": "data:write",
 }
 
 
-
 # ------------------------------------------------------------
 # Role satisfaction rule
 # ------------------------------------------------------------
 
+
 def satisfies(user_roles: set[str], needed: str) -> bool:
     """
     Return True if user_roles satisfy the needed role.
@@ -160,8 +154,8 @@ def satisfies(user_roles: set[str], needed: str) -> bool:
     """
     if not needed:
         return False
-    
-     #  Global override: any user with role "endoregdb_user" passes all checks
+
+    #  Global override: any user with role "endoregdb_user" passes all checks
     if "endoregdb_user" in user_roles:
         return True
 
@@ -182,6 +176,7 @@ def satisfies(user_roles: set[str], needed: str) -> bool:
 # Helper: compute which role is needed for a given route + method
 # ------------------------------------------------------------
 
+
 def get_needed_role(route_name: str, method: str) -> str | None:
     """
     Compute the required role for a given route + HTTP method.

endoreg_db/authz/views_auth.py

@@ -4,7 +4,7 @@ from rest_framework.decorators import api_view, permission_classes
 from rest_framework.permissions import IsAuthenticated
 from rest_framework.response import Response
 
-from .policy import REQUIRED_ROLES, DEFAULT_ROLE_BY_METHOD, satisfies, get_needed_role
+from .policy import satisfies, get_needed_role
 
 # Map frontend page keys → (DRF route name, HTTP method)
 #
@@ -40,7 +40,7 @@ def auth_bootstrap(request):
         method = method.upper()
 
         # Look up which role is needed for this route/method
-        #needed = REQUIRED_ROLES.get(route_name) or DEFAULT_ROLE_BY_METHOD.get(method)
+        # needed = REQUIRED_ROLES.get(route_name) or DEFAULT_ROLE_BY_METHOD.get(method)
         needed = get_needed_role(route_name, method)
 
         if not needed:
@@ -48,7 +48,9 @@ def auth_bootstrap(request):
             capabilities[cap_key] = {"read": False, "write": False}
             continue
 
-        allowed = satisfies(roles, needed)  # uses your existing rule: write ⇒ read, etc.
+        allowed = satisfies(
+            roles, needed
+        )  # uses your existing rule: write ⇒ read, etc.
 
         # For UI pages we usually only care about "read"
         capabilities[cap_key] = {
@@ -56,11 +58,13 @@ def auth_bootstrap(request):
             "write": False,  # or bool(allowed) if this page allows writes in UI
         }
 
-    return Response({
-        "user": {
-            "username": user.username,
+    return Response(
+        {
+            "user": {
+                "username": user.username,
+                "roles": sorted(roles),
+            },
             "roles": sorted(roles),
-        },
-        "roles": sorted(roles),
-        "capabilities": capabilities,
-    })
+            "capabilities": capabilities,
+        }
+    )

endoreg_db/codemods/rename_datetime_fields.py

@@ -1,7 +1,9 @@
 # endoreg_db/codemods/rename_datetime_fields.py
 from bowler import Query
 from pathlib import Path
-import argparse, yaml, sys
+import argparse
+import yaml
+import sys
 
 # Paths
 BASE = Path(__file__).resolve().parents[1]  # .../endoreg_db
@@ -9,6 +11,7 @@ RENAMES_YML = BASE / "renames.yml"
 DEFAULT_TARGETS = ["endoreg_db/models"]  # safer default
 EXCLUDE_DIR_NAMES = {"migrations", "__pycache__"}
 
+
 def load_renames():
     if not RENAMES_YML.exists():
         print(f"ERROR: renames.yml not found at {RENAMES_YML}", file=sys.stderr)
@@ -19,6 +22,7 @@ def load_renames():
         sys.exit(2)
     return data
 
+
 def iter_python_targets(paths):
     """Yield *.py files under given paths, excluding migrations and caches."""
     for p in map(Path, paths):
@@ -31,10 +35,12 @@ def iter_python_targets(paths):
                     continue
                 yield str(f)
 
+
 def build_query(files):
     # Bowler can take a list of files; we’ve already filtered them
     return Query(list(files))
 
+
 def main(argv=None):
     parser = argparse.ArgumentParser(
         description="Rename legacy datetime fields to standardized names."
@@ -88,5 +94,6 @@ def main(argv=None):
         )
     return 0
 
+
 if __name__ == "__main__":
     raise SystemExit(main())

endoreg_db/exceptions.py

@@ -1,21 +1,24 @@
 import logging
+
 logger = logging.getLogger(__name__)
 
 
 class InsufficientStorageError(Exception):
     """Raised when there's not enough disk space for an operation."""
-    
+
     def __init__(self, message, required_space=None, available_space=None):
         super().__init__(message)
         self.required_space = required_space
         self.available_space = available_space
-        
+
 
 class TranscodingError(Exception):
     """Raised when video transcoding fails."""
+
     pass
 
 
 class VideoProcessingError(Exception):
     """Base class for video processing errors."""
+
     pass

endoreg_db/forms/__init__.py

@@ -2,4 +2,3 @@ from .unit import Unit
 from .settings import ActiveModelForm
 from .questionnaires import *
 from .patient_form import PatientForm
-

endoreg_db/forms/examination_form.py

@@ -1,11 +1,12 @@
 from django import forms
 from endoreg_db.models.medical import Examination
 
+
 class ExaminationForm(forms.ModelForm):
     class Meta:
         model = Examination
-        fields = '__all__'
+        fields = "__all__"
         widgets = {
-            'date': forms.DateInput(attrs={'type': 'date', 'class': 'form-control'}),
-            'time': forms.TimeInput(attrs={'type': 'time', 'class': 'form-control'}),
+            "date": forms.DateInput(attrs={"type": "date", "class": "form-control"}),
+            "time": forms.TimeInput(attrs={"type": "time", "class": "form-control"}),
         }

endoreg_db/forms/patient_finding_intervention_form.py

@@ -1,18 +1,40 @@
 from django import forms
 from endoreg_db.models import (
-    Patient, PatientExamination, Finding, 
-    FindingClassification, FindingClassificationChoice,
-    FindingIntervention, PatientFindingIntervention
+    Patient,
+    PatientExamination,
+    Finding,
+    FindingClassification,
+    FindingClassificationChoice,
+    FindingIntervention,
+    PatientFindingIntervention,
 )
 
+
 class PatientFindingInterventionForm(forms.ModelForm):
     patient = forms.ModelChoiceField(queryset=Patient.objects.all(), required=True)
-    examination = forms.ModelChoiceField(queryset=PatientExamination.objects.none(), required=True)
+    examination = forms.ModelChoiceField(
+        queryset=PatientExamination.objects.none(), required=True
+    )
     finding = forms.ModelChoiceField(queryset=Finding.objects.none(), required=True)
-    classification = forms.ModelChoiceField(queryset=FindingClassification.objects.none(), required=True)
-    classification_choice = forms.ModelChoiceField(queryset=FindingClassificationChoice.objects.none(), required=True)
-    interventions = forms.ModelMultipleChoiceField(queryset=FindingIntervention.objects.none(), widget=forms.CheckboxSelectMultiple, required=True)
+    classification = forms.ModelChoiceField(
+        queryset=FindingClassification.objects.none(), required=True
+    )
+    classification_choice = forms.ModelChoiceField(
+        queryset=FindingClassificationChoice.objects.none(), required=True
+    )
+    interventions = forms.ModelMultipleChoiceField(
+        queryset=FindingIntervention.objects.none(),
+        widget=forms.CheckboxSelectMultiple,
+        required=True,
+    )
 
     class Meta:
         model = PatientFindingIntervention
-        fields = ["patient", "examination", "finding", "classification", "classification_choice", "interventions"]
+        fields = [
+            "patient",
+            "examination",
+            "finding",
+            "classification",
+            "classification_choice",
+            "interventions",
+        ]

endoreg_db/forms/patient_form.py

@@ -1,27 +1,23 @@
 from django import forms
 from django.forms import ModelForm, Select
-from endoreg_db.models import (
-    Patient,
-    Gender,
-    Center
-)
+from endoreg_db.models import Patient, Gender, Center
 
 
 class PatientForm(ModelForm):
     gender = forms.ModelChoiceField(
-        queryset=Gender.objects.all(),  
-        empty_label="Select Gender",  
-        widget=Select(attrs={'class': 'form-control'})
+        queryset=Gender.objects.all(),
+        empty_label="Select Gender",
+        widget=Select(attrs={"class": "form-control"}),
     )
     center = forms.ModelChoiceField(
-        queryset=Center.objects.all(),  
-        empty_label="Select Center",  
-        widget=Select(attrs={'class': 'form-control'})
+        queryset=Center.objects.all(),
+        empty_label="Select Center",
+        widget=Select(attrs={"class": "form-control"}),
     )
 
     class Meta:
         model = Patient
-        fields = '__all__'
+        fields = "__all__"
         widgets = {
-            'dob': forms.DateInput(attrs={'type': 'date', 'class': 'form-control'}),
+            "dob": forms.DateInput(attrs={"type": "date", "class": "form-control"}),
         }

endoreg_db/forms/questionnaires/__init__.py

@@ -1 +1 @@
-# from .tto_questionnaire import TtoQuestionnaireForm, TtoQuestionnaireCreate
+# from .tto_questionnaire import TtoQuestionnaireForm, TtoQuestionnaireCreate

endoreg_db/forms/settings/__init__.py

@@ -2,7 +2,10 @@
 from django import forms
 from endoreg_db.models import ActiveModel
 
+
 class ActiveModelForm(forms.ModelForm):
     class Meta:
         model = ActiveModel
-        fields = ["model_meta"]  # Or list the specific fields you want to include in the form.
+        fields = [
+            "model_meta"
+        ]  # Or list the specific fields you want to include in the form.

endoreg_db/forms/unit.py

@@ -1,6 +1,7 @@
 from django import forms
 from ..models import Unit
 
+
 class UnitForm(forms.Form):
     class Meta:
-        model = Unit
+        model = Unit

endoreg_db/helpers/count_db.py

@@ -1,29 +1,30 @@
-# endoreg_db/helpers/count_db.py  
+# endoreg_db/helpers/count_db.py
 from endoreg_db.models.state.audit_ledger import AuditLedger
 
+
 def _distinct(object_type: str, action: str):
     """
     Returns the count of distinct primary keys for records in AuditLedger filtered by object type and action.
-    
+
     Args:
         object_type: The type of object to filter by.
         action: The action to filter by.
-    
+
     Returns:
         The number of unique object primary keys matching the specified type and action.
     """
     return (
-        AuditLedger.objects
-        .filter(object_type=object_type, action=action)
-        .values('object_pk')
+        AuditLedger.objects.filter(object_type=object_type, action=action)
+        .values("object_pk")
         .distinct()
         .count()
     )
 
+
 def collect_counters():
     """
     Returns a dictionary with statistical counts for cases, videos, annotations, anonymizations, images, and video statuses.
-    
+
     The returned dictionary includes:
     - "totalCases": Count of distinct created video files.
     - "totalVideos": Count of distinct created video files.
@@ -34,12 +35,14 @@ def collect_counters():
     - "videosAnonym": Count of distinct video files that have been anonymized.
     """
     return {
-        #TODO @maxhild can we remove the totalCases key?
+        # TODO @maxhild can we remove the totalCases key?
         # "totalCases":           _distinct("VideoFile", "created"),
-        "totalVideos":          _distinct("VideoFile", "created"),
-        "totalAnnotations":     AuditLedger.objects.filter(action="annotation_added").count(),
-        "totalAnonymizations":  _distinct("VideoFile", "anonymized"),
-        "totalImages":          _distinct("Image",     "created"),
-        "videosCompleted":      _distinct("VideoFile", "validated"),
-        "videosAnonym":         _distinct("VideoFile", "anonymized"),
+        "totalVideos": _distinct("VideoFile", "created"),
+        "totalAnnotations": AuditLedger.objects.filter(
+            action="annotation_added"
+        ).count(),
+        "totalAnonymizations": _distinct("VideoFile", "anonymized"),
+        "totalImages": _distinct("Image", "created"),
+        "videosCompleted": _distinct("VideoFile", "validated"),
+        "videosAnonym": _distinct("VideoFile", "anonymized"),
     }

endoreg_db/helpers/default_objects.py

@@ -8,7 +8,7 @@ from typing import Optional
 from django.conf import settings  # Import settings
 from django.core.files.storage import default_storage  # Import default storage
 from django.db.models.fields.files import FieldFile
-
+from endoreg_db.utils.file_operations import sha256_file
 from endoreg_db.models import (
     AiModel,
     Center,
@@ -408,6 +408,7 @@ def get_default_video_file():
         center_name=DEFAULT_CENTER_NAME,  # Pass center name as expected by _create_from_file
         delete_source=False,  # Keep the original asset for other tests
         processor_name=DEFAULT_ENDOSCOPY_PROCESSOR_NAME,
+        video_hash=sha256_file(video_path),
     )
 
     return video_file