lx-annotate 0.2.2__tar.gz → 0.2.4__tar.gz

{lx_annotate-0.2.2 → lx_annotate-0.2.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: lx-annotate
-Version: 0.2.2
+Version: 0.2.4
 Summary: This webapp provides a frontend interface for pseudonymizing and annotating data and applying AI predictions.
 Author-email: Max Hild <maxhild10@gmail.com>, "Thomas J. Lux" <lux_t1@ukw.de>
 Maintainer: Hamza Zahid, Peter Kowalczyk
@@ -31,9 +31,8 @@ Requires-Dist: django-webpack-loader>=0.7.0
 Requires-Dist: django==6.0.3
 Requires-Dist: djangorestframework>=3.12.4
 Requires-Dist: drf-spectacular>=0.28.0
-Requires-Dist: endoreg-db==0.9.4.6
+Requires-Dist: endoreg-db==0.9.5.2
 Requires-Dist: gunicorn>=23.0.0
-Requires-Dist: lx-anonymizer==0.9.0.9
 Requires-Dist: lx-dtypes==0.1.4
 Requires-Dist: mozilla-django-oidc>=4.0.1
 Requires-Dist: mypy>=1.18.2
@@ -222,7 +221,7 @@ deployment requirements for LuxNix and host environments:
   `central_hub`, `site_node`, `standalone`
 - for `central_hub`, require authenticated API uploads with declared
   `center_key`; do not rely on default-center fallback for API ingest
-- keep `STORAGE_DIR` and `IO_DIR` inside
+- keep `STORAGE_DIR` inside
   `LX_ANNOTATE_ENCRYPTED_DATA_DIR`
 - run package migrations during upgrade so upload-job and content-hash lifecycle
   changes are active
@@ -322,7 +321,7 @@ Current runtime path roles:
 - `LX_ANNOTATE_DATA_DIR`: compatibility alias for the same root
 - `DATA_DIR`: legacy compatibility alias for the same root
 - `STORAGE_DIR`: managed storage subtree, usually `${LX_ANNOTATE_ENCRYPTED_DATA_DIR}/storage`
-- `IO_DIR`: import/export/workflow subtree root, currently still inside the protected root
+
 
 New deployment code should anchor path derivation on
 `LX_ANNOTATE_ENCRYPTED_DATA_DIR` and treat the other variables as derived paths

{lx_annotate-0.2.2 → lx_annotate-0.2.4}/README.md

@@ -136,7 +136,7 @@ deployment requirements for LuxNix and host environments:
   `central_hub`, `site_node`, `standalone`
 - for `central_hub`, require authenticated API uploads with declared
   `center_key`; do not rely on default-center fallback for API ingest
-- keep `STORAGE_DIR` and `IO_DIR` inside
+- keep `STORAGE_DIR` inside
   `LX_ANNOTATE_ENCRYPTED_DATA_DIR`
 - run package migrations during upgrade so upload-job and content-hash lifecycle
   changes are active
@@ -236,7 +236,7 @@ Current runtime path roles:
 - `LX_ANNOTATE_DATA_DIR`: compatibility alias for the same root
 - `DATA_DIR`: legacy compatibility alias for the same root
 - `STORAGE_DIR`: managed storage subtree, usually `${LX_ANNOTATE_ENCRYPTED_DATA_DIR}/storage`
-- `IO_DIR`: import/export/workflow subtree root, currently still inside the protected root
+
 
 New deployment code should anchor path derivation on
 `LX_ANNOTATE_ENCRYPTED_DATA_DIR` and treat the other variables as derived paths

{lx_annotate-0.2.2 → lx_annotate-0.2.4}/lx_annotate/file_watcher.py

@@ -16,41 +16,42 @@ from pathlib import Path
 from typing import Iterator, Set
 
 import requests
-from watchdog.events import FileCreatedEvent, FileMovedEvent, FileSystemEventHandler
+from watchdog.events import (
+    DirCreatedEvent,
+    FileCreatedEvent,
+    FileMovedEvent,
+    FileSystemEventHandler,
+    DirMovedEvent,
+)
 from watchdog.observers import Observer
-
+from django.db.models.fields.files import FieldFile
 from endoreg_db.models import Center, EndoscopyProcessor, VideoFile
 from endoreg_db.services.environment_readiness import assert_environment_readiness
 from endoreg_db.services.hub.ingest import (
     process_preanonymized_watcher_file,
     process_watcher_file,
+    UploadProvenance,
 )
-from endoreg_db.utils.paths import (
-    data_paths,
-    WATCHER_VIDEO_DROP_DIR,
-    WATCHER_REPORT_DROP_DIR,
-)
+import endoreg_db.utils.paths as path_utils
 from endoreg_db.utils.storage import ensure_local_file
-
-try:
-    from endoreg_db.utils import data_paths as root_data_paths
-
-    project_root = root_data_paths["project_root"]
-except (ImportError, ModuleNotFoundError, KeyError):
-    project_root = Path(__file__).resolve().parent.parent
-
-PROJECT_ROOT = Path(project_root)
-RUNTIME_DATA_DIR = Path(
-    os.getenv(
-        "LX_ANNOTATE_ENCRYPTED_DATA_DIR",
-        os.getenv(
-            "LX_ANNOTATE_DATA_DIR",
-            os.getenv("DATA_DIR", "/var/lib/lx-annotate/data"),
-        ),
-    )
+from endoreg_db.exceptions import InsufficientStorageError
+from endoreg_db.models.media.video.create_from_file import (
+    check_storage_capacity,
 )
-LOG_DIR = RUNTIME_DATA_DIR / "logs"
+
+
+LOG_DIR = path_utils.LOG_DIR
 LOG_DIR.mkdir(parents=True, exist_ok=True)
+MANAGED_VAULT_ROOT = path_utils.STORAGE_DIR.resolve()
+
+INTAKE_VIDEO_DIR = path_utils.WATCHER_VIDEO_DROP_DIR
+INTAKE_REPORT_DIR = path_utils.WATCHER_REPORT_DROP_DIR
+INTAKE_PREANONYMIZED_DIR = path_utils.WATCHER_PREANONYMIZED_DROP_DIR
+
+
+storage_root_global = path_utils.STORAGE_DIR
+storage_root_report_sensitive = path_utils.SENSITIVE_REPORT_DIR
+storage_root_video_sensitive = path_utils.SENSITIVE_VIDEO_DIR
 
 
 def _setup_ffmpeg() -> None:
@@ -93,21 +94,6 @@ logging.getLogger("watchdog.observers.inotify_buffer").setLevel(logging.WARNING)
 logger = logging.getLogger(__name__)
 
 
-def _resolve_intake_dir(env_name: str, data_paths_key: str) -> Path:
-    configured = os.getenv(env_name, "").strip()
-    if configured:
-        return Path(configured).expanduser().resolve()
-    return data_paths[data_paths_key].resolve()
-
-
-INTAKE_VIDEO_DIR = WATCHER_VIDEO_DROP_DIR
-INTAKE_REPORT_DIR = WATCHER_REPORT_DROP_DIR
-INTAKE_PREANONYMIZED_DIR = _resolve_intake_dir(
-    "WATCHER_PREANONYMIZED_DIR", "import_preanonymized"
-)
-MANAGED_VAULT_ROOT = RUNTIME_DATA_DIR.resolve()
-
-
 def _is_relative_to(path: Path, root: Path) -> bool:
     try:
         path.resolve().relative_to(root.resolve())
@@ -136,7 +122,7 @@ def is_managed_vault_path(path: str | Path) -> bool:
 
 
 def iter_storage_chunks(
-    field_file, *, chunk_size: int = 1024 * 1024
+    field_file: FieldFile, *, chunk_size: int = 1024 * 1024
 ) -> Iterator[bytes]:
     """
     Yield managed-media bytes through Django's storage API.
@@ -153,7 +139,9 @@ def iter_storage_chunks(
 
 
 @contextmanager
-def managed_media_temp_path(field_file, *, suffix: str | None = None) -> Iterator[Path]:
+def managed_media_temp_path(
+    field_file: FieldFile, *, suffix: str | None = None
+) -> Iterator[Path]:
     """
     Materialize managed media into a short-lived plaintext temp file.
 
@@ -361,11 +349,11 @@ class AutoProcessingHandler(FileSystemEventHandler):
 
         super().dispatch(event)
 
-    def on_created(self, event):
+    def on_created(self, event: DirCreatedEvent | FileCreatedEvent):
         if isinstance(event, FileCreatedEvent) and not event.is_directory:
             self._submit_file(str(event.src_path))
 
-    def on_moved(self, event) -> None:
+    def on_moved(self, event: DirMovedEvent | FileMovedEvent) -> None:
         if isinstance(event, FileMovedEvent) and not event.is_directory:
             self._submit_file(str(event.dest_path))
 
@@ -419,8 +407,7 @@ class AutoProcessingHandler(FileSystemEventHandler):
             logger.debug("Parent: %s", parent_dir)
 
             if (
-                parent_dir == data_paths["import_video"].resolve()
-                and parent_dir == INTAKE_VIDEO_DIR
+                parent_dir == INTAKE_VIDEO_DIR
                 and file_extension in self.video_extensions
             ):
                 logger.info("New video detected: %s", path)
@@ -481,15 +468,7 @@ class AutoProcessingHandler(FileSystemEventHandler):
                 )
 
             try:
-                from endoreg_db.exceptions import InsufficientStorageError
-                from endoreg_db.models.media.video.create_from_file import (
-                    check_storage_capacity,
-                )
-
-                storage_root = os.getenv(
-                    "DJANGO_DATA_DIR", str(RUNTIME_DATA_DIR / "videos")
-                )
-                check_storage_capacity(video_path, Path(storage_root))
+                check_storage_capacity(video_path, Path(storage_root_global))
             except InsufficientStorageError as storage_error:
                 logger.error(
                     "Insufficient storage space for %s: %s",
@@ -514,7 +493,7 @@ class AutoProcessingHandler(FileSystemEventHandler):
                 )
                 video_hash = str(getattr(upload_job, "content_hash", "") or "").strip()
                 if not video_hash:
-                    provenance = (
+                    provenance: UploadProvenance = (
                         getattr(upload_job, "processing_provenance", None) or {}
                     )
                     video_hash = str(provenance.get("content_hash", "")).strip()
@@ -623,14 +602,7 @@ class AutoProcessingHandler(FileSystemEventHandler):
                 )
 
             try:
-                from endoreg_db.exceptions import InsufficientStorageError
-
-                storage_root = os.getenv(
-                    "report_STORAGE_ROOT", str(RUNTIME_DATA_DIR / "reports")
-                )
-                storage_root_path = Path(storage_root)
-                if not storage_root_path.is_absolute():
-                    storage_root_path = PROJECT_ROOT / storage_root_path
+                storage_root_path = storage_root_report_sensitive
                 storage_root_path.mkdir(parents=True, exist_ok=True)
                 if not storage_root_path.exists():
                     raise InsufficientStorageError(
@@ -644,7 +616,7 @@ class AutoProcessingHandler(FileSystemEventHandler):
                     center=source_center,
                     source_system="watcher",
                 )
-                if upload_job.is_successful:
+                if upload_job.is_complete:
                     logger.info(
                         "Report imported through shared hub ingest: %s",
                         upload_job.id,
@@ -845,7 +817,7 @@ class FileWatcherService:
             self.observer.start()
 
         try:
-            storage_root = RUNTIME_DATA_DIR / "storage" / "videos"
+            storage_root = storage_root_global
             if storage_root.exists():
                 total, used, free = shutil.disk_usage(storage_root)
                 free_gb = free / (1024**3)
@@ -867,6 +839,5 @@ class FileWatcherService:
 
 def run_file_watcher() -> None:
     logger.info("Starting File Watcher Service")
-    logger.info("Project root: %s", PROJECT_ROOT)
     logger.info("Django settings: %s", os.environ.get("DJANGO_SETTINGS_MODULE"))
     FileWatcherService().start()

lx_annotate-0.2.4/lx_annotate/migration_overrides/endoreg_db/0016_rename_streamable_relative_path_videofile_raw_streamable_relative_path_and_more.py

@@ -0,0 +1,213 @@
+# Generated by Django 6.0.3 on 2026-04-21 13:24
+
+from django.conf import settings
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("endoreg_db", "0015_uploadjob_content_hash_and_more"),
+        migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+    ]
+
+    operations = [
+        migrations.RenameField(
+            model_name="videofile",
+            old_name="streamable_relative_path",
+            new_name="raw_streamable_relative_path",
+        ),
+        migrations.AddField(
+            model_name="aidataset",
+            name="video_annotations",
+            field=models.ManyToManyField(
+                blank=True,
+                help_text="Video-segment annotations collected from the video examination annotation workflow.",
+                related_name="video_ai_datasets",
+                to="endoreg_db.labelvideosegment",
+            ),
+        ),
+        migrations.AddField(
+            model_name="applicationsettings",
+            name="ai_dataset_name",
+            field=models.CharField(blank=True, default="", max_length=255),
+        ),
+        migrations.AddField(
+            model_name="applicationsettings",
+            name="ai_dataset_type",
+            field=models.CharField(
+                blank=True,
+                choices=[("", "Unset"), ("image", "Image"), ("video", "Video")],
+                default="",
+                max_length=32,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="aidataset",
+            name="ai_model_type",
+            field=models.CharField(
+                default="image_multilabel_classification",
+                help_text='AI model family this dataset is for, e.g. "image_multilabel_classification".',
+                max_length=255,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="aidataset",
+            name="dataset_type",
+            field=models.CharField(
+                choices=[("image", "Image"), ("video", "Video")],
+                default="image",
+                help_text="Primary annotation modality used for training. Export helpers may still include both frame and video annotations attached to the dataset.",
+                max_length=32,
+            ),
+        ),
+        migrations.AlterField(
+            model_name="aidataset",
+            name="image_annotations",
+            field=models.ManyToManyField(
+                blank=True,
+                help_text="Frame-level annotations collected from the frame annotation workflow.",
+                related_name="image_ai_datasets",
+                to="endoreg_db.imageclassificationannotation",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="endoscope_image_height",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="endoscope_image_width",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="endoscope_image_x",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="endoscope_image_y",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="examination_date_height",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="examination_date_width",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="examination_date_x",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="examination_date_y",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="image_height",
+            field=models.IntegerField(default=1),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="image_width",
+            field=models.IntegerField(default=1),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_dob_height",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_dob_width",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_dob_x",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_dob_y",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_first_name_height",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_first_name_width",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_first_name_x",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_first_name_y",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_last_name_height",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_last_name_width",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_last_name_x",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AlterField(
+            model_name="endoscopyprocessor",
+            name="patient_last_name_y",
+            field=models.IntegerField(default=0),
+        ),
+        migrations.AddConstraint(
+            model_name="uploadjob",
+            constraint=models.UniqueConstraint(
+                condition=models.Q(
+                    models.Q(("content_hash", ""), _negated=True),
+                    models.Q(("status__in", ["error", "lost"]), _negated=True),
+                ),
+                fields=("source_center", "content_type", "content_hash"),
+                name="uniq_uploadjob_content_hash_active",
+            ),
+        ),
+        migrations.AddConstraint(
+            model_name="uploadjob",
+            constraint=models.UniqueConstraint(
+                condition=models.Q(
+                    models.Q(("idempotency_key", ""), _negated=True),
+                    models.Q(("status__in", ["error", "lost"]), _negated=True),
+                ),
+                fields=(
+                    "source_center",
+                    "source_system",
+                    "ingest_mode",
+                    "storage_class",
+                    "storage_tier",
+                    "idempotency_key",
+                ),
+                name="uniq_uploadjob_idempotency_scope_active",
+            ),
+        ),
+    ]

{lx_annotate-0.2.2 → lx_annotate-0.2.4}/lx_annotate/settings/settings_base.py

@@ -38,7 +38,6 @@ XDG_DATA_HOME = Path(os.getenv("XDG_DATA_HOME", Path.home() / ".local" / "share"
 APP_DATA_DIR = _resolve_runtime_data_dir()
 APP_DATA_DIR.mkdir(parents=True, exist_ok=True)
 APP_STORAGE_DIR = APP_DATA_DIR / "storage"
-APP_IO_DIR = APP_DATA_DIR
 APP_STORAGE_DIR.mkdir(parents=True, exist_ok=True)
 
 PROTECTED_MEDIA_URL = (
@@ -104,7 +103,6 @@ os.environ.setdefault("LX_ANNOTATE_DATA_DIR", str(APP_DATA_DIR))
 os.environ.setdefault("DATA_DIR", str(APP_DATA_DIR))
 os.environ.setdefault("LX_ANNOTATE_ENCRYPTED_DATA_DIR", str(APP_DATA_DIR))
 os.environ.setdefault("STORAGE_DIR", str(APP_STORAGE_DIR))
-os.environ.setdefault("IO_DIR", str(APP_IO_DIR))
 os.environ.setdefault("NGINX_PROTECTED_MEDIA_URL", PROTECTED_MEDIA_URL)
 os.environ["PROTECTED_MEDIA_ROOT"] = str(PROTECTED_MEDIA_ROOT)
 os.environ.setdefault("LX_ANNOTATE_STREAMABLE_VIDEO_ROOT", str(STREAMABLE_VIDEO_ROOT))

{lx_annotate-0.2.2 → lx_annotate-0.2.4}/manage.py

@@ -61,12 +61,10 @@ default_data_dir = os.environ.get(
 if not default_data_dir:
     default_data_dir = str(Path(BASE_DIR) / "data")
 default_storage_dir = os.environ.get("STORAGE_DIR", str(Path(default_data_dir) / "storage"))
-default_io_dir = os.environ.get("IO_DIR", default_data_dir)
 os.environ.setdefault("LX_ANNOTATE_ENCRYPTED_DATA_DIR", default_data_dir)
 os.environ.setdefault("LX_ANNOTATE_DATA_DIR", default_data_dir)
 os.environ.setdefault("DATA_DIR", default_data_dir)
 os.environ.setdefault("STORAGE_DIR", default_storage_dir)
-os.environ.setdefault("IO_DIR", default_io_dir)
 
 
 def main():

{lx_annotate-0.2.2 → lx_annotate-0.2.4}/pyproject.toml

@@ -5,7 +5,7 @@ build-backend = "hatchling.build"
 [project]
 name = "lx-annotate"
 
-version = "0.2.2"
+version = "0.2.4"
 description = "This webapp provides a frontend interface for pseudonymizing and annotating data and applying AI predictions."
 authors = [
     { name = "Max Hild", email = "maxhild10@gmail.com"},
@@ -61,7 +61,7 @@ dependencies = [
     "types-requests>=2.32.4.20250913",
     "black>=25.12.0",
     "mypy>=1.18.2",
-    "endoreg-db==0.9.4.6",
+    "endoreg-db==0.9.5.2",
     "pydantic-settings>=2.12.0",
     "pydantic>=2.12.5",
     "sops>=1.18",
@@ -71,7 +71,6 @@ dependencies = [
     "django-linear-migrations>=2.19.0",
     "build>=1.4.2",
     "lx-dtypes==0.1.4",
-    "lx-anonymizer==0.9.0.9",
 ]
 
 [tool.pytest.ini_options]

{lx_annotate-0.2.2 → lx_annotate-0.2.4}/staticfiles/.vite/manifest.json

@@ -130,7 +130,8 @@
     "file": "videoStore.js",
     "name": "videoStore",
     "imports": [
-      "src/main.ts"
+      "src/main.ts",
+      "_mediaUrls.js"
     ]
   },
   "node_modules/pdf-lib/es/index.js": {
@@ -189,7 +190,8 @@
     "isDynamicEntry": true,
     "imports": [
       "src/main.ts",
-      "_mediaTypeStore.js"
+      "_mediaTypeStore.js",
+      "_mediaUrls.js"
     ],
     "dynamicImports": [
       "node_modules/pdfjs-dist/legacy/build/pdf.mjs",
@@ -290,7 +292,8 @@
     "imports": [
       "src/main.ts",
       "_videoStore.js",
-      "_mediaTypeStore.js"
+      "_mediaTypeStore.js",
+      "_mediaUrls.js"
     ],
     "css": [
       "AnonymizationOverview.css"
@@ -339,7 +342,8 @@
     "imports": [
       "src/main.ts",
       "_videoStore.js",
-      "_timeHelpers.js"
+      "_timeHelpers.js",
+      "_mediaUrls.js"
     ],
     "css": [
       "Export.css"
@@ -466,7 +470,8 @@
     "src": "src/views/reporting/FinalizedResultPage.vue",
     "isDynamicEntry": true,
     "imports": [
-      "src/main.ts"
+      "src/main.ts",
+      "_mediaUrls.js"
     ]
   },
   "src/views/reporting/FindingsCapturePage.vue": {

lx_annotate-0.2.4/staticfiles/AnonymizationCorrectionComponent.css

@@ -0,0 +1 @@
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