endoreg-db 0.8.9.32__py3-none-any.whl

endoreg_db/urls/examination.py

@@ -0,0 +1,63 @@
+from django.urls import path
+from endoreg_db.views import (
+    get_findings_for_examination,
+    get_classifications_for_finding,
+    get_classification_choices,
+    get_classifications_for_examination,
+    ExaminationCreateView,
+    PatientExaminationDetailView,
+    PatientExaminationListView,
+)
+
+urlpatterns = [  # URL patterns for ExaminationForm.vue API calls
+    path(
+        "examinations/<int:examination_id>/findings/",
+        get_findings_for_examination,
+        name="get_findings_for_examination",
+    ),
+    path(
+        "findings/<int:finding_id>/classifications/",
+        get_classifications_for_finding,
+        name="get_classifications_for_finding",
+    ),
+    path(
+        "classifications/<int:classification_id>/choices/",
+        get_classification_choices,
+        name="get_choices_for_classification",
+    ),
+    # NEW: Examination CRUD endpoints for SimpleExaminationForm
+    # POST /api/examinations/create/ - Create new examination
+    # GET /api/examinations/{id}/ - Get examination details
+    # PATCH /api/examinations/{id}/ - Update examination
+    # GET /api/examinations/list/ - List examinations with filtering
+    # TODO: Clearly Distinguish between Examination (the template) and PatientExamination (the instance).
+    # The views below handle PatientExamination instances, which represent a specific examination performed on a patient.
+    # The URL names are updated to reflect this, using the 'patient_examination_*' prefix for clarity.
+    # TODO: Clearly Distinguish between Examination and PatientExamination by using 'patient-examination' prefix for clarity
+    path(
+        "patient-examinations/create/",
+        ExaminationCreateView.as_view(),
+        name="patient_examination_create",
+    ),
+    path(
+        "patient-examinations/<int:pk>/",
+        PatientExaminationDetailView.as_view(),
+        name="patient_examination_detail",
+    ),
+    path(
+        "patient-examinations/list/",
+        PatientExaminationListView.as_view(),
+        name="patient_examination_list",
+    ),
+    # NEW ENDPOINTS FOR RESTRUCTURED FRONTEND
+    path(
+        "patient-examinations/<int:exam_id>/classifications/",
+        get_classifications_for_examination,
+        name="get_classifications_for_examination",
+    ),
+    path(
+        "patient-examinations/<int:examination_id>/findings/",
+        get_findings_for_examination,
+        name="get_patient_examination_findings",
+    ),
+]

endoreg_db/urls/media.py

@@ -0,0 +1,251 @@
+from django.urls import path
+
+from endoreg_db.views import VideoStreamView
+from endoreg_db.views.media import (
+                                    PdfMediaView,  # Alias to avoid conflict with legacy pdf.reportMediaView
+                                    VideoMediaView,
+                                    get_sensitive_metadata_pk,
+                                    pdf_sensitive_metadata,
+                                    pdf_sensitive_metadata_list,
+                                    pdf_sensitive_metadata_verify,
+                                    sensitive_metadata_list,
+                                    video_sensitive_metadata,
+                                    video_sensitive_metadata_verify,
+)
+from endoreg_db.views.report.reimport import ReportReimportView
+from endoreg_db.views.report.report_stream import ReportStreamView
+from endoreg_db.views.video import (
+                                    VideoReimportView,
+                                    video_segment_detail,
+                                    video_segment_validate,
+                                    video_segments_by_video,
+                                    video_segments_collection,
+                                    video_segments_stats,
+                                    video_segments_validate_bulk,
+                                    video_segments_validation_status,
+)
+from endoreg_db.views.video.ai import label_list
+from endoreg_db.views.video.correction import (
+                                    VideoApplyMaskView,
+                                    VideoCorrectionView,
+                                    VideoRemoveFramesView,
+)
+from endoreg_db.views.video.video_metadata import VideoMetadataStatsView
+
+
+# Simplified Meta and Validation Endpoints
+
+urlpatterns = [
+    path(
+        "media/sensitive-media-id/<int:pk>/<str:mediaType>/",
+        get_sensitive_metadata_pk,
+        name="sm-pk",
+    ),
+    # Video media endpoints
+    path("media/videos/", VideoMediaView.as_view(), name="video-list"),
+    path(
+        "media/videos/<int:pk>/", VideoStreamView.as_view(), name="video-detail-stream"
+    ),  # Support ?type= params
+    path(
+        "media/videos/<int:pk>/details/", VideoMediaView.as_view(), name="video-detail"
+    ),  # JSON metadata
+    path(
+        "media/videos/<int:pk>/stream/", VideoStreamView.as_view(), name="video-stream"
+    ),  # Legacy support
+    # Video Re-import API endpoint (modern media framework)
+    # POST /api/media/videos/<int:pk>/reimport/
+    # Re-imports a video file to regenerate metadata when OCR failed or data is incomplete
+    path(
+        "media/videos/<int:pk>/reimport/",
+        VideoReimportView.as_view(),
+        name="video-reimport",
+    ),
+    # ---------------------------------------------------------------------------------------
+    # VIDEO CORRECTION API ENDPOINTS (Modern Media Framework - October 14, 2025)
+    #
+    # All video correction endpoints migrated to unified /api/media/videos/<pk>/ pattern
+    # These endpoints enable video correction workflows (Phase 1.1):
+    # - Analysis: Detect sensitive frames using MiniCPM-o 2.6 or OCR+LLM
+    # - Masking: Apply device-specific masks or custom ROI masks
+    # - Frame Removal: Remove sensitive frames from videos
+    # - Reprocessing: Re-run entire anonymization pipeline
+    # - Metadata: View analysis results
+    # - History: Track all correction operations
+    # ---------------------------------------------------------------------------------------
+    # Video Correction API
+    # GET /api/media/videos/video-correction/{id}/ - Get video details for correction
+    path(
+        "media/videos/video-correction/<int:pk>",
+        VideoCorrectionView.as_view(),
+        name="video-correction",
+    ),
+    # Video Metadata API
+    # GET /api/media/videos/<int:pk>/metadata/
+    # Returns analysis results (sensitive frame count, ratio, frame IDs)
+    path(
+        "media/videos/<int:pk>/metadata/",
+        VideoMetadataStatsView.as_view(),
+        name="video-metadata",
+    ),
+    # Video Analysis API
+    # POST /api/media/videos/<int:pk>/analyze/
+    # Analyzes video for sensitive frames using MiniCPM-o 2.6 or OCR+LLM
+    # Body: { detection_method: 'minicpm'|'ocr_llm'|'hybrid', sample_interval: 30 }
+    # Video Masking API
+    # POST /api/media/videos/<int:pk>/apply-mask/
+    # Applies device mask or custom ROI mask to video
+    # Body: { mask_type: 'device'|'custom', device_name: 'olympus', roi: {...} }
+    path(
+        "media/videos/<int:pk>/apply-mask/",
+        VideoApplyMaskView.as_view(),
+        name="video-apply-mask",
+    ),
+    # Video Frame Removal API
+    # POST /api/media/videos/<int:pk>/remove-frames/
+    # Removes specified frames from video
+    # Body: { frame_list: [10,20,30] OR frame_ranges: '10-20,30' OR detection_method: 'automatic' }
+    path(
+        "media/videos/<int:pk>/remove-frames/",
+        VideoRemoveFramesView.as_view(),
+        name="video-remove-frames",
+    ),
+    path("media/videos/labels/list/", label_list, name="get_lvs_list"),
+    # ---------------------------------------------------------------------------------------
+    # VIDEO SEGMENT API ENDPOINTS (Modern Media Framework - October 14, 2025)
+    # Video Segments Collection API
+    # GET/POST /api/media/videos/segments/
+    # List all video segments across videos or create new segment
+    path(
+        "media/videos/segments/",
+        video_segments_collection,
+        name="video-segments-collection",
+    ),
+    # Video Segments Stats API
+    # GET /api/media/videos/segments/stats/
+    # Get statistics about video segments
+    path(
+        "media/videos/segments/stats/",
+        video_segments_stats,
+        name="video-segments-stats",
+    ),
+    # Video-Specific Segments API
+    # GET/POST /api/media/videos/<int:pk>/segments/
+    # List segments for specific video or create segment for video
+    path(
+        "media/videos/<int:pk>/segments/",
+        video_segments_by_video,
+        name="video-segments-by-video",
+    ),
+    # Segment Detail API
+    # GET /api/media/videos/<int:pk>/segments/<int:segment_id>/
+    # PATCH /api/media/videos/<int:pk>/segments/<int:segment_id>/
+    # DELETE /api/media/videos/<int:pk>/segments/<int:segment_id>/
+    # Manages individual segment operations
+    path(
+        "media/videos/<int:pk>/segments/<int:segment_id>/",
+        video_segment_detail,
+        name="video-segment-detail",
+    ),
+    # ---------------------------------------------------------------------------------------
+    # VIDEO SEGMENT VALIDATION API ENDPOINTS (Modern Media Framework - October 14, 2025)
+    #
+    # Unified validation endpoints replacing legacy /api/label-video-segment/*/validate/
+    # Single: POST validate individual segment
+    # Bulk: POST validate multiple segments
+    # Status: GET/POST validation status for all segments
+    # ---------------------------------------------------------------------------------------
+    # Single Segment Validation API
+    # POST /api/media/videos/<int:pk>/segments/<int:segment_id>/validate/
+    # Validates a single video segment
+    # Body: { "is_validated": true, "notes": "..." }
+    path(
+        "media/videos/<int:pk>/segments/<int:segment_id>/validate/",
+        video_segment_validate,
+        name="video-segment-validate",
+    ),
+    # Bulk Segment Validation API
+    # POST /api/media/videos/<int:pk>/segments/validate-bulk/
+    # Validates multiple segments at once
+    # Body: { "segment_ids": [1,2,3], "is_validated": true, "notes": "..." }
+    path(
+        "media/videos/<int:pk>/segments/validate-bulk/",
+        video_segments_validate_bulk,
+        name="video-segments-validate-bulk",
+    ),
+    # Segment Validation Status API
+    # GET /api/media/videos/<int:pk>/segments/validation-status/
+    # Returns validation statistics for all segments
+    # POST /api/media/videos/<int:pk>/segments/validation-status/
+    # Marks all segments (or filtered by label) as validated
+    # Body: { "label_name": "polyp", "notes": "..." }
+    path(
+        "media/videos/<int:pk>/segments/validation-status/",
+        video_segments_validation_status,
+        name="video-segments-validation-status",
+    ),
+    # ---------------------------------------------------------------------------------------
+    # SENSITIVE METADATA ENDPOINTS (Modern Media Framework)
+    # ---------------------------------------------------------------------------------------
+    # Video Sensitive Metadata (Resource-Scoped)
+    # GET/PATCH /api/media/videos/<pk>/sensitive-metadata/
+    # Get or update sensitive patient data for a video
+    path(
+        "media/videos/<int:pk>/sensitive-metadata/",
+        video_sensitive_metadata,
+        name="video-sensitive-metadata",
+    ),
+    # POST /api/media/videos/<pk>/sensitive-metadata/verify/
+    # Update verification state (dob_verified, names_verified)
+    path(
+        "media/videos/<int:pk>/sensitive-metadata/verify/",
+        video_sensitive_metadata_verify,
+        name="video-sensitive-metadata-verify",
+    ),
+    # report Sensitive Metadata (Resource-Scoped)
+    # GET/PATCH /api/media/pdfs/<pk>/sensitive-metadata/
+    # Get or update sensitive patient data for a report
+    path(
+        "media/pdfs/<int:pk>/sensitive-metadata/",
+        pdf_sensitive_metadata,
+        name="pdf-sensitive-metadata",
+    ),
+    # POST /api/media/pdfs/<pk>/sensitive-metadata/verify/
+    # Update verification state (dob_verified, names_verified)
+    path(
+        "media/pdfs/<int:pk>/sensitive-metadata/verify/",
+        pdf_sensitive_metadata_verify,
+        name="pdf-sensitive-metadata-verify",
+    ),
+    # List Endpoints (Collection-Level)
+    # GET /api/media/sensitive-metadata/
+    # List all sensitive metadata (combined reports and Videos)
+    # Supports filtering: ?content_type=pdf|video&verified=true&search=name
+    path(
+        "media/sensitive-metadata/",
+        sensitive_metadata_list,
+        name="sensitive-metadata-list",
+    ),
+    # GET /api/media/pdfs/sensitive-metadata/
+    # List sensitive metadata for reports only
+    # Replaces legacy /api/pdf/sensitivemeta/list/
+    path(
+        "media/pdfs/sensitive-metadata/",
+        pdf_sensitive_metadata_list,
+        name="pdf-sensitive-metadata-list",
+    ),
+    # report media endpoints
+    path("media/pdfs/", PdfMediaView.as_view(), name="pdf-list"),
+    path("media/pdfs/<int:pk>/", PdfMediaView.as_view(), name="pdf-detail"),
+    path(
+        "media/pdfs/<int:pk>/stream/", ReportStreamView.as_view(), name="pdf-stream"
+    ),  # Support ?type=raw|anonymized params
+    # report Re-import API endpoint (modern media framework)
+    # POST /api/media/pdfs/<int:pk>/reimport/
+    # Re-imports a report file to regenerate metadata when OCR failed or data is incomplete
+    path(
+        "media/pdfs/<int:pk>/reimport/",
+        ReportReimportView.as_view(),
+        name="report-reimport",
+    ),
+]
+# ---------------------------------------------------------------------------------------

endoreg_db/urls/patient.py

@@ -0,0 +1,23 @@
+from endoreg_db.views import (
+    GenderViewSet,
+    CenterViewSet,
+    PatientViewSet,
+    PatientFindingViewSet,
+)
+from rest_framework.routers import DefaultRouter
+from django.urls import path, include
+
+router = DefaultRouter()
+router.register(r"patients", PatientViewSet)
+router.register(r"centers", CenterViewSet)
+router.register(r"genders", GenderViewSet)
+router.register(r"patient-findings", PatientFindingViewSet)
+
+urlpatterns = [
+    path("", include(router.urls)),
+    path(
+        "check_pe_exist/<int:pk>/",
+        PatientViewSet.as_view({"get": "check_pe_exist"}),
+        name="check_pe_exist",
+    ),
+]

endoreg_db/urls/requirements.py

@@ -0,0 +1,15 @@
+from django.urls import path, include
+from rest_framework.routers import DefaultRouter
+from endoreg_db.views.requirement.lookup import LookupViewSet
+from endoreg_db.views.requirement.evaluate import evaluate_requirements
+
+
+router = DefaultRouter()
+router.register(r"lookup", LookupViewSet, basename="lookup/")
+
+urlpatterns = [
+    path("", include(router.urls)),
+    path(
+        "evaluate-requirements/", evaluate_requirements, name="evaluate-requirements/"
+    ),
+]

endoreg_db/urls/root_urls.py

@@ -0,0 +1,28 @@
+# endoreg_db/urls/root_urls.py
+from django.contrib import admin
+from django.urls import path, include
+from django.http import HttpResponse
+from django.conf import settings
+from django.conf.urls.static import static
+
+
+def public_home(_request):
+    return HttpResponse("Public home – no login required.")
+
+
+urlpatterns = [
+    # Public landing page
+    path("", public_home, name="public_home"),
+    # Django admin (optional)
+    path("admin/", admin.site.urls),
+    # Mount ALL API routes under /api/
+    # This pulls the urlpatterns exported by endoreg_db/urls/__init__.py
+    path("api/", include("endoreg_db.urls")),
+    # Keycloak OIDC (mozilla-django-oidc provides /oidc/authenticate/ and /oidc/callback/)
+    path("oidc/", include("mozilla_django_oidc.urls")),
+]
+
+# Serve static/media in DEBUG at the root (NOT under /api/)
+if settings.DEBUG:
+    urlpatterns += static(settings.MEDIA_URL, document_root=settings.MEDIA_ROOT)
+    urlpatterns += static(settings.STATIC_URL, document_root=settings.STATIC_ROOT)

endoreg_db/urls/stats.py

@@ -0,0 +1,54 @@
+from django.urls import path
+
+from endoreg_db.views import (
+    ExaminationStatsView,
+    VideoSegmentStatsView,
+    SensitiveMetaStatsView,
+    GeneralStatsView,
+)
+
+url_patterns = [
+    # ---------------------------------------------------------------------------------------
+    # STATISTICS API ENDPOINTS
+    #
+    # Diese Endpunkte stellen Dashboard-Statistiken bereit für das Frontend
+    # ---------------------------------------------------------------------------------------
+    # Examination Statistics API
+    # GET /api/examinations/stats/
+    # Liefert Statistiken über Examinations und PatientExaminations
+    path(
+        "examinations/stats/", ExaminationStatsView.as_view(), name="examination_stats"
+    ),
+    # Video Segment Statistics API
+    # GET /api/video-segment/stats/  (Note: singular 'segment' to match frontend)
+    # Liefert Statistiken über Video-Segmente und Label-Verteilung
+    path(
+        "video-segment/stats/",
+        VideoSegmentStatsView.as_view(),
+        name="video_segment_stats",
+    ),
+    # Alternative Video Segments Statistics API (plural version for compatibility)
+    # GET /api/video-segments/stats/
+    path(
+        "video-segments/stats/",
+        VideoSegmentStatsView.as_view(),
+        name="video_segments_stats",
+    ),
+    # Sensitive Meta Statistics API
+    # GET /api/video/sensitivemeta/stats/
+    # Liefert Statistiken über SensitiveMeta-Einträge und Verifikationsstatus
+    path(
+        "video/sensitivemeta/stats/",
+        SensitiveMetaStatsView.as_view(),
+        name="sensitive_meta_stats",
+    ),
+    # General Dashboard Statistics API
+    # GET /api/stats/
+    # Liefert allgemeine Übersichtsstatistiken für das Dashboard
+    path("stats/", GeneralStatsView.as_view(), name="general_stats"),
+    path(
+        "video-segments/stats/",
+        VideoSegmentStatsView.as_view(),
+        name="video_segments_stats",
+    ),
+]

endoreg_db/urls/upload.py

@@ -0,0 +1,12 @@
+from django.urls import path
+
+from endoreg_db.views import (
+    UploadFileView,
+    UploadStatusView,
+)
+
+urlpatterns = [
+    # Upload endpoints
+    path("upload/", UploadFileView.as_view(), name="video_upload"),
+    path("upload/<uuid:id>/status", UploadStatusView.as_view(), name="upload_status"),
+]

endoreg_db/urls.py

@@ -0,0 +1,9 @@
+from django.urls import include, path
+
+# Import the package-level URL patterns (defined in endoreg_db/urls/__init__.py)
+from endoreg_db.urls import urlpatterns as api_urlpatterns
+
+# Expose API under /api/
+urlpatterns = [
+    path("api/", include((api_urlpatterns, "endoreg_db"), namespace="api")),
+]

endoreg_db/utils/__init__.py

@@ -0,0 +1,97 @@
+"""Module for utility classes and functions."""
+
+# --- Imports from submodules ---
+
+# dataloader
+from endoreg_db.utils.video.ffmpeg_wrapper import (
+    assemble_video_from_frames,
+    get_stream_info,
+    transcode_video,
+    transcode_videofile_if_required,
+)
+
+from .dataloader import load_model_data_from_yaml
+
+# dates
+from .dates import ensure_aware_datetime, random_day_by_month_year, random_day_by_year
+
+# env
+from .env import DEBUG, DJANGO_SETTINGS_MODULE, get_env_var
+
+# file_operations
+from .file_operations import (
+    copy_with_progress,
+    get_content_hash_filename,
+)
+
+# hashs
+from .hashs import (
+    DJANGO_NAME_SALT,
+    get_examiner_hash,
+    get_hash_string,
+    get_patient_examination_hash,
+    get_pdf_hash,
+    get_video_hash,
+)
+
+# names
+from .names import (
+    create_mock_examiner_name,
+    create_mock_patient_name,
+    guess_name_gender,
+)
+
+# parse_and_generate_yaml
+from .parse_and_generate_yaml import collect_center_names
+
+# paths
+from .paths import data_paths
+
+# pydantic_models
+from .pydantic_models import DbConfig
+from .storage import delete_field_file, ensure_local_file, save_local_file
+from .storage import file_exists as storage_file_exists
+
+# validate_endo_roi
+from .validate_endo_roi import validate_endo_roi
+from .video import split_video
+
+# ffmpeg_wrapper
+from .video.ffmpeg_wrapper import extract_frames
+
+# --- Exports ---
+
+__all__ = [
+    "collect_center_names",
+    "copy_with_progress",
+    "create_mock_examiner_name",
+    "create_mock_patient_name",
+    "data_paths",
+    "DbConfig",
+    "DEBUG",
+    "DJANGO_NAME_SALT",
+    "DJANGO_SETTINGS_MODULE",
+    "ensure_aware_datetime",
+    "get_env_var",
+    "get_examiner_hash",
+    "get_hash_string",
+    "get_patient_examination_hash",
+    "get_pdf_hash",
+    "get_content_hash_filename",
+    "get_video_hash",
+    "guess_name_gender",
+    "load_model_data_from_yaml",
+    "random_day_by_month_year",
+    "random_day_by_year",
+    "validate_endo_roi",
+    "assemble_video_from_frames",  # Updated name
+    "get_stream_info",
+    "transcode_video",
+    "transcode_videofile_if_required",  # Added
+    "extract_frames",  # Added
+    "split_video",
+    "delete_field_file",
+    "ensure_local_file",
+    "save_local_file",
+    "storage_file_exists",
+]

endoreg_db/utils/ai/__init__.py

@@ -0,0 +1,9 @@
+from .inference_dataset import InferenceDataset
+from .multilabel_classification_net import MultiLabelClassificationNet
+from .predict import Classifier
+
+__all__ = [
+    "InferenceDataset",
+    "MultiLabelClassificationNet",
+    "Classifier",
+]