endoreg-db 0.8.6.1__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

endoreg_db/authz/views_auth.py

@@ -0,0 +1,66 @@
+# libs/endoreg-db/endoreg_db/authz/views_auth.py
+
+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
+
+# Map frontend page keys → (DRF route name, HTTP method)
+#
+# Route names come from your router registration, e.g.:
+#   router.register(r'patients', PatientViewSet, basename='patient')
+# => "patient-list", "patient-detail"
+PAGE_CAPS = {
+    # Vue route /patienten
+    "page.patients.view": ("patient-list", "GET"),
+    # You can extend later, e.g.:
+    # "page.reports.view": ("report-list", "GET"),
+    # "page.anonymization.view": ("anonymization-list", "GET"),
+}
+
+
+@api_view(["GET"])
+@permission_classes([IsAuthenticated])
+def auth_bootstrap(request):
+    """
+    Return auth context for the frontend:
+      - current user (username, basic info)
+      - roles (Django groups, synced from Keycloak)
+      - capabilities (what parts of UI the user may access)
+    """
+    user = request.user
+
+    # Roles = Django group names = Keycloak roles synced from Keycloak
+    roles = set(user.groups.values_list("name", flat=True))
+
+    capabilities = {}
+
+    for cap_key, (route_name, method) in PAGE_CAPS.items():
+        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 = get_needed_role(route_name, method)
+
+        if not needed:
+            # No role mapping defined → secure default: deny
+            capabilities[cap_key] = {"read": False, "write": False}
+            continue
+
+        allowed = satisfies(roles, needed)  # uses your existing rule: write ⇒ read, etc.
+
+        # For UI pages we usually only care about "read"
+        capabilities[cap_key] = {
+            "read": bool(allowed),
+            "write": False,  # or bool(allowed) if this page allows writes in UI
+        }
+
+    return Response({
+        "user": {
+            "username": user.username,
+            "roles": sorted(roles),
+        },
+        "roles": sorted(roles),
+        "capabilities": capabilities,
+    })

endoreg_db/config/env.py

@@ -5,11 +5,12 @@ This module is the single place to read environment variables and .env files.
 It avoids loading .env during pytest, and provides typed helpers.
 No Django imports here to prevent early settings configuration.
 """
+
 from __future__ import annotations
 
-from pathlib import Path
 import os
-from typing import Optional, Dict, Any
+from pathlib import Path
+from typing import Any, Dict, Optional
 
 # Detect pytest early to avoid loading .env in test runs
 IS_PYTEST = bool(os.environ.get("PYTEST_CURRENT_TEST"))
@@ -21,7 +22,8 @@ BASE_DIR = Path(__file__).resolve().parents[2]
 _DOTENV_LOADED = False
 try:
     if not IS_PYTEST:
-        import dotenv  # type: ignore
+        import dotenv
+
         dotenv.load_dotenv()
         _DOTENV_LOADED = True
 except Exception:
@@ -90,12 +92,15 @@ def snapshot() -> Dict[str, Any]:
         "SKIP_EXPENSIVE_TESTS",
     ]
     data: Dict[str, Any] = {k: os.environ.get(k) for k in keys}
-    data.update({
-        "IS_PYTEST": IS_PYTEST,
-        "DOTENV_LOADED": _DOTENV_LOADED,
-        "BASE_DIR": str(BASE_DIR),
-    })
+    data.update(
+        {
+            "IS_PYTEST": IS_PYTEST,
+            "DOTENV_LOADED": _DOTENV_LOADED,
+            "BASE_DIR": str(BASE_DIR),
+        }
+    )
     return data
 
+
 # Back-compat short aliases used by settings modules
 ENV = os.environ.get

endoreg_db/data/__init__.py

@@ -13,7 +13,7 @@ ENDOSCOPE_TYPE_DATA_DIR = DATA_DIR / "endoscope_type"
 ENDOSCOPE_DATA_DIR = DATA_DIR / "endoscope"
 ACTIVE_MODEL_DATA_DIR = DATA_DIR / "active_model"
 PROFESSION_DATA_DIR = DATA_DIR / "profession"
-PDF_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
+REPORT_TYPE_DATA_DIR = DATA_DIR / "pdf_type"
 REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
 EVENT_DATA_DIR = DATA_DIR / "event"
 GENDER_DATA_DIR = DATA_DIR / "gender"
@@ -86,15 +86,6 @@ DISTRIBUTION_MULTIPLE_CATEGORICAL_DATA_DIR = (
 )
 DISTRIBUTION_DATE_DATA_DIR = DISTRIBUTION_BASE_DIR / "date"
 
-# G-Play Stuffs
-CASE_TEMPLATE_BASE_DIR = DATA_DIR / "case_template"
-CASE_TEMPLATE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "template"
-CASE_TEMPLATE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "template_type"
-CASE_TEMPLATE_RULE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule"
-CASE_TEMPLATE_RULE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_type"
-CASE_TEMPLATE_RULE_VALUE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_value"
-CASE_TEMPLATE_RULE_VALUE_TYPE_DATA_DIR = CASE_TEMPLATE_BASE_DIR / "rule_value_type"
-
 # NETWORK
 NETWORK_DEVICE_DATA_DIR = DATA_DIR / "network_device"
 NETWORK_DEVICE_TYPE_DATA_DIR = DATA_DIR / "network_device_type"
@@ -141,4 +132,4 @@ QUALIFICATION_DATA_DIR = DATA_DIR / "qualification"
 
 TAG_DATA_DIR = DATA_DIR / "tag"
 
-EXAMINATION_REQUIREMENT_SET_DATA_DIR = DATA_DIR / "examination_requirement_set"
+EXAMINATION_REQUIREMENT_SET_DATA_DIR = DATA_DIR / "examination_requirement_set"

endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml

@@ -5,6 +5,7 @@
     version: "1"
     model: "image_multilabel_classification_colonoscopy_default"
     labelset: "multilabel_classification_colonoscopy_default"
+    labelset_version: 1
     activation: "sigmoid"
     mean: "0.485,0.456,0.406" # ImageNet defaults
     std: "0.229,0.224,0.225" # ImageNet defaults
@@ -20,8 +21,7 @@
   setup_config:
     is_primary_model: true # Mark this as the primary model for setup
     weight_filenames: # Specific weight file patterns for this model
-      - "colo_segmentation_RegNetX800MF_6.ckpt"
-      - "image_multilabel_classification_colonoscopy_default_v1_*.ckpt"
+      - "colo_segmentation_RegNetX800MF_6.safetensors"
     huggingface_fallback: # HF configuration for this model
       repo_id: "wg-lux/colo_segmentation_RegNetX800MF_base"
-      filename: "colo_segmentation_RegNetX800MF_base.ckpt"
+      filename: "colo_segmentation_RegNetX800MF_base.safetensors"

endoreg_db/data/event_classification/data.yaml

@@ -0,0 +1,4 @@
+- model: endoreg_db.event_classification
+  fields:
+    name: "stroke_origin_classification"
+    event: "stroke"

endoreg_db/data/event_classification_choice/data.yaml

@@ -0,0 +1,9 @@
+- model: endoreg_db.event_classification
+  fields:
+    name: "stroke_origin_ischemic"
+    event_classification: "stroke_origin_classification"
+
+- model: endoreg_db.event_classification
+  fields:
+    name: "stroke_origin_hemorrhagic"
+    event_classification: "stroke_origin_classification"

endoreg_db/data/examination/examinations/data.yaml

@@ -4,6 +4,45 @@
     name_de: "Koloskopie"
     name_en: "Colonoscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - colonoscopy_generic
+      - colonoscopy_screening
+      - colonoscopy_lesion_removal_small
+      - colonoscopy_lesion_removal_large
+      - colonoscopy_lesion_removal_emr
+      - colonoscopy_diagnostic_acute_symptomatic
+    findings:
+      # baseline
+      - examination_setting
+      - bowel_preparation_lc
+      - bowel_preparation_tc
+      - bowel_preparation_rc
+      - bowel_preparation_simplified
+      - colonoscopy_deepest_viewed_location
+      # observations
+      - complication_generic
+      - colon_polyp
+      - colon_post_intervention_wound
+      - colon_tumor_mass
+      - colon_inflammation
+      - colon_erosion
+      - colon_ulcer
+      - colon_scar
+      - anal_fissure
+      - anal_hemorrhoids
+      # hidden
+      - rectum_anus
+      - rectum
+      - sigmoid_colon
+      - descending_colon
+      - left_flexure
+      - transverse_colon
+      - right_flexure
+      - ascending_colon
+      - cecum
+      - appendiceal_orifice
+      - ileocecal_valve
+      - terminal_ileum
 
 - model: endoreg_db.Examination
   fields:
@@ -11,6 +50,43 @@
     name_de: "Gastroskopie"
     name_en: "Gastroscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - gastroscopy_generic
+      # - gastroscopy_diagnostic_acute_symptomatic
+      # - gastroscopy_surveillance_barretts_esophagus
+      # - gastroscopy_surveillance_gastric_atrophy
+      - gastroscopy_lesion_removal_small
+      - gastroscopy_lesion_removal_large
+      # - gastroscopy_lesion_removal_emr
+    findings:
+      # baseline
+      - sedation_endoscopy
+      - gastroscopy_esophagus_mucosa
+      - gastroscopy_gastroesophageal_junction
+      - gastroscopy_fundus_mucosa
+      - gastroscopy_corpus_mucosa
+      - gastroscopy_antrum_mucosa
+      - gastroscopy_pylorus
+      - gastroscopy_angulus_flexure_mucosa
+      - gastroscopy_duodenum_bulbus_mucosa
+      - gastroscopy_duodenum_mucosa
+      # observations
+      - gastroscopy_polyp
+      - gastroscopy_ulcer
+      - gastroscopy_erythema
+      - gastroscopy_subepithelial_tumor
+      - gastroscopy_stenosis
+      - gastroscopy_varices_esophageal
+      - gastroscopy_varices_gastric
+      - gastroscopy_varices_duodenal
+      - gastroscopy_scar
+      - gastroscopy_bleeding
+      - gastroscopy_stenosis
+      - gastroscopy_ectopic_gastric_mucosa
+      - gastroscopy_diverticulum_esophagus
+      - gastroscopy_diverticulum_duodenum
+      - gastroscopy_ectopic_pancreatic_tissue
+      - gastroscopy_obstruction_generic
 
 # endosonography_upper_gi
 - model: endoreg_db.Examination
@@ -19,6 +95,27 @@
     name_de: "Endosonographie oberer GI-Trakt"
     name_en: "Endosonography Upper GI Tract"
     examination_types: ["endoscopy"]
+    indications:
+      - gastroscopy_baseline
+      - gastroscopy_diagnostic_acute_symptomatic
+      - gastroscopy_acute_bleeding
+      - gastroscopy_percutane_enterostomy
+      - gastroscopy_varicosis_therapeutic_esophagus
+      - gastroscopy_varicosis_therapeutic_stomach
+      - gastroscopy_therapeutic_varicosis_intestine
+      - gastroscopy_lesion_removal_small
+      - gastroscopy_lesion_removal_large
+      - gastroscopy_obstruction_generic
+
+- model: endoreg_db.Examination
+  fields:
+    name: "endosonography_upper_gi"
+    name_de: "Endosonographie unterer GI-Trakt"
+    name_en: "Endosonography Lower GI Tract"
+    examination_types: ["endoscopy"]
+    indications:
+      - endosonography_upper_gi_non_invasive
+      - endosonography_upper_gi_invasive
 
 - model: endoreg_db.Examination
   fields:
@@ -26,6 +123,9 @@
     name_de: "Endosonographie unterer GI-Trakt"
     name_en: "Endosonography Lower GI Tract"
     examination_types: ["endoscopy"]
+    indications:
+      - endosonography_lower_gi_non_invasive
+      - endosonography_lower_gi_invasive
 
 # ERCP
 - model: endoreg_db.Examination
@@ -34,6 +134,12 @@
     name_de: "ERCP"
     name_en: "ERCP"
     examination_types: ["endoscopy"]
+    indications:
+      - erc
+      - erc_no_est
+      - ercp
+      - ercp_no_est
+      - ercp_therapeutic_stenosis
 
 # small bowel endoscopy
 - model: endoreg_db.Examination
@@ -42,6 +148,8 @@
     name_de: "Dünndarmendoskopie"
     name_en: "Small Bowel Endoscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - small_bowel_endoscopy_generic
 
 # capsule endoscopy
 - model: endoreg_db.Examination
@@ -50,23 +158,15 @@
     name_de: "Kapselendoskopie"
     name_en: "Capsule Endoscopy"
     examination_types: ["endoscopy"]
+    indications:
+      - capsule_endoscopy_generic
 
 - model: endoreg_db.Examination
   fields:
-    name: "percutaneous_transhepatic_biliary_drainage"
+    name: "percutaneous_transhepatic_biliary_intervention"
     name_de: "Perkutane transhepatische Gallengangdrainage"
     name_en: "Percutaneous Transhepatic Biliary Drainage"
     examination_types: ["endoscopy", "sonography", "xray"]
-
-# percutaneous_transhepatic_cholangiography
-- model: endoreg_db.Examination
-  fields:
-    name: "percutaneous_transhepatic_cholangiography"
-    name_de: "Perkutane transhepatische Cholangiographie"
-    name_en: "Percutaneous Transhepatic Cholangiography"
-    examination_types: ["endoscopy", "sonography", "xray"]
-
-- model: endoreg_db.Examination
-  fields:
-    name: "colonoscopy_austria_screening"
-    examination_types: ["endoscopy"]
+    indications:
+      - percutaneous_transhepatic_cholangiography
+      - percutaneous_transhepatic_biliary_drainage

endoreg_db/data/examination/time-type/data.yaml

@@ -3,6 +3,3 @@
     name: "colonoscopy-time"
     name_de: "Koloskopie-Zeit"
     name_en: "Colonoscopy Time"
-    examinations: [
-      "colonoscopy"
-    ]