lx-annotate 0.0.1__tar.gz

lx_annotate-0.0.1/.gitignore

@@ -0,0 +1,173 @@
+conf/db.yaml
+conf/db_pwd.example
+conf/db_pwd
+.devenv-vars.json
+.devenv/
+django-settings.json
+#frozen_east_text_detection.pb
+# Byte-compiled / optimized / DLL files
+.direnv/
+.venv/
+__pycache__/
+*.py[cod]
+*$py.class
+*.kate-swp
+db.sqlite3
+conf/
+.direnv/
+logs/
+.env
+result
+result/
+result/*
+data/
+endoreg-db/
+lx-annotate/endoreg-db/
+# ignore any file that ends with .env anywhere
+**/*.env
+.devenv/
+.direnv/
+.devenv.flake.nix
+devenv.lock
+.devenv.nix
+.env
+flake.json
+.make-cache/
+storage/
+.staticfiles/
+staticfiles
+./frontend/public/video.mp4
+libs/
+# C extensions
+*.so
+results/
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+EAST/
+.venv/
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# -------------------------------
+# Python / Django files
+# -------------------------------
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# Django SQLite database (if you use SQLite in development)
+db.sqlite3
+
+# Django static files generated by collectstatic (do not version generated assets)
+staticfiles/
+# (Also ignore media files if they are generated)
+media/
+
+# Log files and directories
+logs/
+*.log
+
+# -------------------------------
+# Environment & Local Configurations
+# -------------------------------
+# If you don’t want to version your local development environment files, you can ignore these:
+devenv.lock
+# (Uncomment if you decide not to version these development configs)
+# devenv.yaml
+# devenv.nix
+
+# Django settings symlink generated by Nix (points to a system store, may vary between machines)
+django-settings.json
+# Also ignore the result symlink
+result
+
+# -------------------------------
+# Python virtual environments
+# (Usually these are created outside the project, but if you accidentally include one, ignore it)
+venv/
+.env/
+
+# -------------------------------
+# Node / NPM related (for the root and frontend)
+# -------------------------------
+node_modules/
+frontend/node_modules/
+static/img/frames_demo/*
+
+# -------------------------------
+# Frontend build and Vite-related files
+# -------------------------------
+# Although your Vite config outputs to ../static (which is versioned in STATICFILES_DIRS),
+# you don’t want to commit any other generated files.
+# (If you ever have a build folder inside the frontend directory, ignore it)
+frontend/dist/
+
+# -------------------------------
+# OS-specific files
+# -------------------------------
+.DS_Store
+Thumbs.db
+
+# -------------------------------
+# Editor and IDE settings
+# -------------------------------
+.vscode/
+.idea/
+*.sublime-workspace
+*.sublime-project
+
+# -------------------------------
+# Temporary files
+# -------------------------------
+*.tmp
+*.swp
+.env
+.env
+
+*./conf
+
+secret.key
+
+./lx-terminology-editor
+./lx-report-generator
+study_data/*.csv

lx_annotate-0.0.1/LICENSE

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+MIT License
+
+Copyright (c) 2024 AG-Lux
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

lx_annotate-0.0.1/PKG-INFO

@@ -0,0 +1,236 @@
+Metadata-Version: 2.4
+Name: lx-annotate
+Version: 0.0.1
+Summary: This webapp provides a frontend interface for annotating AI generated output.
+Author: Hamza Zahid
+Author-email: Max Hild <maxhild10@gmail.com>, "Thomas J. Lux" <lux_t1@ukw.de>
+Maintainer: Hamza Zahid, Peter Kowalczyk
+Maintainer-email: Max Hild <maxhild10@gmail.com>, "Thomas J. Lux" <lux_t1@ukw.de>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: <3.13,>=3.12.0
+Requires-Dist: black>=25.12.0
+Requires-Dist: celery>=5.5.3
+Requires-Dist: daphne>=4.2.1
+Requires-Dist: de-core-news-lg
+Requires-Dist: django-cors-headers>=4.0.0
+Requires-Dist: django-environ>=0.12.0
+Requires-Dist: django-extensions>=3.2.3
+Requires-Dist: django-modeltranslation>=0.19.16
+Requires-Dist: django-ninja==1.5.3
+Requires-Dist: django-rest-framework>=0.1.0
+Requires-Dist: django-stubs>=5.2.8
+Requires-Dist: django-vite>=3.0.6
+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==0.9.2.3
+Requires-Dist: gunicorn>=23.0.0
+Requires-Dist: lx-anonymizer==0.9.0.5
+Requires-Dist: lx-dtypes
+Requires-Dist: mozilla-django-oidc>=4.0.1
+Requires-Dist: mypy>=1.18.2
+Requires-Dist: numpy>=1.21.0
+Requires-Dist: pillow>=9.0.0
+Requires-Dist: pre-commit>=4.5.0
+Requires-Dist: psycopg[binary,pool]>=3.2.12
+Requires-Dist: pydantic-settings>=2.12.0
+Requires-Dist: pydantic>=2.12.5
+Requires-Dist: pytest-cov>=7.0.0
+Requires-Dist: pytest-django>=4.11.1
+Requires-Dist: pytest>=8.3.5
+Requires-Dist: python-dotenv>=1.0.1
+Requires-Dist: python-environ>=0.4.54
+Requires-Dist: requests>=2.32.3
+Requires-Dist: sops>=1.18
+Requires-Dist: torch>=2.0.0
+Requires-Dist: torchvision>=0.15.0
+Requires-Dist: transformers<4.45.0,>=4.44.0
+Requires-Dist: types-requests>=2.32.4.20250913
+Requires-Dist: watchdog>=3.0.0
+Requires-Dist: whitenoise>=6.8.2
+Provides-Extra: dev
+Requires-Dist: build>=1.3.0; extra == 'dev'
+Requires-Dist: flake8>=7.3.0; extra == 'dev'
+Requires-Dist: furo>=2025.9.25; extra == 'dev'
+Requires-Dist: linkify-it-py>=2.0.3; extra == 'dev'
+Requires-Dist: mypy>=1.16.0; extra == 'dev'
+Requires-Dist: myst-parser>=4.0.1; extra == 'dev'
+Requires-Dist: pip>=25.2; extra == 'dev'
+Requires-Dist: pre-commit>=4.5.0; extra == 'dev'
+Requires-Dist: pytest-cov>=6.1.1; extra == 'dev'
+Requires-Dist: pytest-env>=1.1.5; extra == 'dev'
+Requires-Dist: pytest-mypy-plugins>=3.2.0; extra == 'dev'
+Requires-Dist: pytest-xdist>=3.8.0; extra == 'dev'
+Requires-Dist: pytest>=9.0.2; extra == 'dev'
+Requires-Dist: ruff>=0.14.8; extra == 'dev'
+Requires-Dist: sphinx-autodoc-typehints>=3.5.2; extra == 'dev'
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == 'dev'
+Requires-Dist: sphinx<9.0,>=8.2.3; extra == 'dev'
+Requires-Dist: twine>=6.2.0; extra == 'dev'
+Provides-Extra: docs
+Requires-Dist: furo>=2025.9.25; extra == 'docs'
+Requires-Dist: linkify-it-py>=2.0.3; extra == 'docs'
+Requires-Dist: myst-parser>=4.0.1; extra == 'docs'
+Requires-Dist: sphinx-autodoc-typehints>=3.5.2; extra == 'docs'
+Requires-Dist: sphinx-copybutton>=0.5.2; extra == 'docs'
+Requires-Dist: sphinx<9.0,>=8.2.3; extra == 'docs'
+Description-Content-Type: text/markdown
+
+# LX-Annotate
+
+LX-Annotate is a Django + Vue application for annotating AI-generated outputs,
+with a media ingestion pipeline for videos and PDFs. This project was created by a team at Universitätsklinikum Würzburg, Bavaria.  
+
+## Highlights
+
+- Django backend with REST APIs and optional OIDC authentication
+- Vue 3 SPA frontend integrated with Django via `django-vite`
+- File watcher for automated video and PDF processing
+- Reproducible environments via `devenv`/Nix and Docker
+
+## Repository Layout
+
+- `lx_annotate/` Django app and settings
+- `frontend/` Vue 3 application
+- `scripts/` operational tooling and file watcher scripts
+- `data/` runtime data (raw videos, PDFs, model cache)
+- `conf_template/` sample configuration templates
+- `container/` Dockerfiles and container docs
+
+## Requirements
+
+- Python 3.12
+- Node.js 18+ (frontend)
+- PostgreSQL (main app)
+- Optional: `uv`, `direnv`, `devenv`, Nix, Docker
+
+## Quick Start (Development)
+
+1. `direnv allow` (if you use `devenv`)
+2. `uv sync` (or install dependencies with `pip`)
+3. `cp conf_template/default.env .env` and update values
+4. `export DJANGO_SETTINGS_MODULE=lx_annotate.settings.settings_dev`
+5. `python manage.py load_base_db_data`
+6. `python manage.py runserver`
+
+Open `http://127.0.0.1:8000/`.
+
+## Environment Variables and Secrets
+
+Production secrets are typically injected by the host system.
+For local development, use either `secretspec.toml` defaults or a local `.env` file.
+
+Do not commit secrets. `secretspec.toml` is tracked in git.
+
+Example:
+
+```bash
+direnv allow
+secretspec --provider dotenv --profile development python manage.py runserver
+```
+
+See <https://secretspec.dev/> for details.
+
+## Frontend
+
+```bash
+cd frontend
+npm install
+npm run build
+```
+
+Hot-reload development:
+
+```bash
+cd frontend
+npm run dev
+```
+
+In another terminal:
+
+```bash
+export DJANGO_SETTINGS_MODULE=lx_annotate.settings.settings_dev
+python manage.py runserver
+```
+
+## File Watcher
+
+The file watcher ingests media placed in:
+
+- `data/import/video_import/`
+- `data/import/report_import/`
+
+```bash
+./scripts/start_filewatcher.sh dev
+# or
+python scripts/file_watcher.py
+```
+
+## Configuration
+
+- Development `.env` is read from the repository root or `~/.local/share/lx-annotate/.env`.
+- Settings are driven by environment variables (see `secretspec.toml` defaults).
+- Sample configs live in `conf_template/`.
+
+## Nix Builds
+
+Nix build targets are available, but deployment paths may still need project-specific adjustments.
+
+```bash
+nix build .#prod-server
+./result/bin/run-prod-server
+```
+
+```bash
+nix build .#file-watcher
+./result/bin/run-file-watcher
+```
+
+## Wheel Deployment
+
+The CI pipeline can now build a production wheel with frontend staticfiles
+included via `hatchling`. Production runtime no longer needs Node.js or the
+full `devenv` shell.
+
+Deployment assets live in `deploy/`:
+
+- `deploy/bootstrap-host.sh`
+- `deploy/deploy.sh`
+- `deploy/lx-annotate.service`
+- `deploy/.env.systemd.example`
+
+See `docs/guides/wheel-deployment.md` for the full host bootstrap and `systemd`
+flow.
+
+## Containers
+
+Docker images now install Python packages into `/app/.devenv/state/venv` so the
+container path matches the repository's preferred virtualenv layout.
+
+This does **not** mean Docker runs the full Nix/`devenv` shell. Inside the
+container, `uv` creates and manages the environment at that path, and the image
+`PATH` is configured to use `/app/.devenv/state/venv/bin`.
+
+See `container/README.md` for development and production Docker usage.
+
+## Tests
+
+```bash
+pytest
+```
+
+```bash
+cd frontend
+npm run test:unit
+```
+
+## License
+
+MIT. See `LICENSE`.

lx_annotate-0.0.1/README.md

@@ -0,0 +1,151 @@
+# LX-Annotate
+
+LX-Annotate is a Django + Vue application for annotating AI-generated outputs,
+with a media ingestion pipeline for videos and PDFs. This project was created by a team at Universitätsklinikum Würzburg, Bavaria.  
+
+## Highlights
+
+- Django backend with REST APIs and optional OIDC authentication
+- Vue 3 SPA frontend integrated with Django via `django-vite`
+- File watcher for automated video and PDF processing
+- Reproducible environments via `devenv`/Nix and Docker
+
+## Repository Layout
+
+- `lx_annotate/` Django app and settings
+- `frontend/` Vue 3 application
+- `scripts/` operational tooling and file watcher scripts
+- `data/` runtime data (raw videos, PDFs, model cache)
+- `conf_template/` sample configuration templates
+- `container/` Dockerfiles and container docs
+
+## Requirements
+
+- Python 3.12
+- Node.js 18+ (frontend)
+- PostgreSQL (main app)
+- Optional: `uv`, `direnv`, `devenv`, Nix, Docker
+
+## Quick Start (Development)
+
+1. `direnv allow` (if you use `devenv`)
+2. `uv sync` (or install dependencies with `pip`)
+3. `cp conf_template/default.env .env` and update values
+4. `export DJANGO_SETTINGS_MODULE=lx_annotate.settings.settings_dev`
+5. `python manage.py load_base_db_data`
+6. `python manage.py runserver`
+
+Open `http://127.0.0.1:8000/`.
+
+## Environment Variables and Secrets
+
+Production secrets are typically injected by the host system.
+For local development, use either `secretspec.toml` defaults or a local `.env` file.
+
+Do not commit secrets. `secretspec.toml` is tracked in git.
+
+Example:
+
+```bash
+direnv allow
+secretspec --provider dotenv --profile development python manage.py runserver
+```
+
+See <https://secretspec.dev/> for details.
+
+## Frontend
+
+```bash
+cd frontend
+npm install
+npm run build
+```
+
+Hot-reload development:
+
+```bash
+cd frontend
+npm run dev
+```
+
+In another terminal:
+
+```bash
+export DJANGO_SETTINGS_MODULE=lx_annotate.settings.settings_dev
+python manage.py runserver
+```
+
+## File Watcher
+
+The file watcher ingests media placed in:
+
+- `data/import/video_import/`
+- `data/import/report_import/`
+
+```bash
+./scripts/start_filewatcher.sh dev
+# or
+python scripts/file_watcher.py
+```
+
+## Configuration
+
+- Development `.env` is read from the repository root or `~/.local/share/lx-annotate/.env`.
+- Settings are driven by environment variables (see `secretspec.toml` defaults).
+- Sample configs live in `conf_template/`.
+
+## Nix Builds
+
+Nix build targets are available, but deployment paths may still need project-specific adjustments.
+
+```bash
+nix build .#prod-server
+./result/bin/run-prod-server
+```
+
+```bash
+nix build .#file-watcher
+./result/bin/run-file-watcher
+```
+
+## Wheel Deployment
+
+The CI pipeline can now build a production wheel with frontend staticfiles
+included via `hatchling`. Production runtime no longer needs Node.js or the
+full `devenv` shell.
+
+Deployment assets live in `deploy/`:
+
+- `deploy/bootstrap-host.sh`
+- `deploy/deploy.sh`
+- `deploy/lx-annotate.service`
+- `deploy/.env.systemd.example`
+
+See `docs/guides/wheel-deployment.md` for the full host bootstrap and `systemd`
+flow.
+
+## Containers
+
+Docker images now install Python packages into `/app/.devenv/state/venv` so the
+container path matches the repository's preferred virtualenv layout.
+
+This does **not** mean Docker runs the full Nix/`devenv` shell. Inside the
+container, `uv` creates and manages the environment at that path, and the image
+`PATH` is configured to use `/app/.devenv/state/venv/bin`.
+
+See `container/README.md` for development and production Docker usage.
+
+## Tests
+
+```bash
+pytest
+```
+
+```bash
+cd frontend
+npm run test:unit
+```
+
+## License
+
+MIT. See `LICENSE`.

lx_annotate-0.0.1/lx_annotate/admin.py

@@ -0,0 +1 @@
+# Register your models here.

lx_annotate-0.0.1/lx_annotate/apps.py

@@ -0,0 +1,42 @@
+from django.apps import AppConfig
+import os
+import sys
+import threading
+
+
+class LxAnnotateConfig(AppConfig):
+    default_auto_field = "django.db.models.BigAutoField"
+    name = "lx_annotate"
+
+    # This is running in development server only. On luxnix, filewatcher is started via systemd service.
+    def ready(self):
+        # Only for runserver
+        if "runserver" not in sys.argv:
+            return
+
+        # Only in autoreload child, not in the parent
+        if os.environ.get("RUN_MAIN") != "true":
+            return
+
+        self.start_file_watcher()
+
+    def start_file_watcher(self) -> bool:
+        def run_watcher():
+            try:
+                from django.core.management import call_command
+
+                print("📁 Starting file watcher service...")
+                call_command("start_filewatcher", log_level="INFO")
+            except Exception as e:
+                print(f"⚠️ Failed to start file watcher: {e}")
+                return False
+
+        watcher_thread = threading.Thread(target=run_watcher, daemon=True)
+        watcher_thread.start()
+        print("✅ File watcher service started in background")
+        return True
+
+
+# class lxAnonymizerConfig(AppConfig):
+#    default_auto_field = 'django.db.models.BigAutoField'
+#    name = 'lx-anonymizer'

lx_annotate-0.0.1/lx_annotate/asgi.py

@@ -0,0 +1,40 @@
+"""
+ASGI config for lx-annotate project.
+
+It exposes the ASGI callable as a module-level variable named ``application``.
+
+For more information on this file, see
+https://docs.djangoproject.com/en/4.2/howto/deployment/asgi/
+"""
+
+import os
+
+os.environ["DJANGO_SETTINGS_MODULE"] = "lx_annotate.settings.settings_prod"
+from django.core.asgi import get_asgi_application
+from django.core.wsgi import get_wsgi_application
+
+from asgiref.wsgi import WsgiToAsgi
+from whitenoise import WhiteNoise
+
+import importlib
+import traceback
+import sys
+
+print("DJANGO_SETTINGS_MODULE =", os.getenv("DJANGO_SETTINGS_MODULE"))
+print("sys.path[:10] =", sys.path[:10])
+
+m = os.getenv("DJANGO_SETTINGS_MODULE", "lx_annotate.settings.settings_prod")
+staticfiles_dir = os.getenv(
+    "DJANGO_STATIC_ROOT", os.path.join(os.path.dirname(__file__), "static")
+)
+try:
+    importlib.import_module(m)
+    print("Imported settings module OK:", m)
+except Exception:
+    traceback.print_exc()
+os.environ.setdefault("DJANGO_SETTINGS_MODULE", "lx_annotate.settings.settings_prod")
+
+wsgi_application = get_wsgi_application()
+application = get_asgi_application()
+whitenoise_application = WhiteNoise(wsgi_application, root=staticfiles_dir)
+wsgi_asgi_application = WsgiToAsgi(wsgi_application)