endoreg-db 0.6.4__tar.gz → 0.8.1__tar.gz

endoreg_db-0.8.1/.devenv-vars.json

@@ -0,0 +1,8 @@
+{
+  "DJANGO_MODULE": "endoreg_db",
+  "HOST": "localhost",
+  "PORT": "8188",
+  "CONF_DIR": "./conf",
+  "HOME_DIR": "/home/admin",
+  "WORKING_DIR": "/home/admin/endoreg-db"
+}

endoreg_db-0.8.1/.env.example

@@ -0,0 +1,89 @@
+# EndoReg-DB .env.example
+# Copy to .env for local development: cp .env.example .env
+DJANGO_SETTINGS_MODULE=config.settings.test
+# -------------------------------------------------------------------
+# Core
+# -------------------------------------------------------------------
+# DJANGO_SETTINGS_MODULE=config.settings.dev
+TIME_ZONE=Europe/Berlin
+
+# -------------------------------------------------------------------
+# Paths (relative to repo root unless absolute)
+# -------------------------------------------------------------------
+STORAGE_DIR=storage
+ASSET_DIR=tests/assets
+STATIC_URL=/static/
+MEDIA_URL=/media/
+
+# -------------------------------------------------------------------
+# Feature flags
+# -------------------------------------------------------------------
+RUN_VIDEO_TESTS=false
+SKIP_EXPENSIVE_TESTS=true
+
+# -------------------------------------------------------------------
+# Django REST Framework throttles
+# -------------------------------------------------------------------
+DRF_THROTTLE_USER=1000/hour
+DRF_THROTTLE_ANON=1000/hour
+
+# -------------------------------------------------------------------
+# Development database (SQLite by default)
+# For non-SQLite, set ENGINE and provide NAME/USER/PASSWORD/HOST/PORT
+# -------------------------------------------------------------------
+DEV_DB_ENGINE=django.db.backends.sqlite3
+DEV_DB_NAME=dev_db.sqlite3
+# DEV_DB_USER=
+# DEV_DB_PASSWORD=
+# DEV_DB_HOST=
+# DEV_DB_PORT=
+
+# -------------------------------------------------------------------
+# Testing database (persistent SQLite by default)
+# pytest uses config.settings.test; first run: pytest --reuse-db --create-db
+# -------------------------------------------------------------------
+TEST_DB_ENGINE=django.db.backends.sqlite3
+TEST_DB_NAME=data/tests/db/test_db.sqlite3
+TEST_DISABLE_MIGRATIONS=false
+
+# -------------------------------------------------------------------
+# Production (override these in your deployment environment)
+# -------------------------------------------------------------------
+# DJANGO_SECRET_KEY=<generate-strong-random-value>  # REQUIRED in production; generate securely (e.g., python -c 'import secrets; print(secrets.token_urlsafe(64))'); never commit real secrets
+# DJANGO_DEBUG=false  # Use false in production; set true only for local debugging
+# DJANGO_ALLOWED_HOSTS=example.com,api.example.com  # Set to your domains; required in production
+# DB_ENGINE=django.db.backends.postgresql  # Example: use Postgres in production
+# DB_NAME=endoreg_db  # Production database name
+# DB_USER=postgres  # Database user
+# DB_PASSWORD=  # Database password; never commit real secrets
+# DB_HOST=localhost  # Database host
+# DB_PORT=5432  # Database port
+# SECURE_SSL_REDIRECT=true  # Redirect HTTP->HTTPS in production; set false only locally
+# SESSION_COOKIE_SECURE=true  # Secure cookies in production; set false only for local/dev
+# CSRF_COOKIE_SECURE=true  # Secure CSRF cookie in production; set false only for local/dev
+# SECURE_HSTS_SECONDS=31536000  # 1 year HSTS; enable only after confirming HTTPS everywhere
+# SECURE_HSTS_INCLUDE_SUBDOMAINS=true  # Include subdomains for HSTS when appropriate
+# SECURE_HSTS_PRELOAD=false  # Enable only if you intend to submit to preload list
+
+# -------------------------------------------------------------------
+# Optional: Keycloak token validator (used by manage.py runserver)
+# -------------------------------------------------------------------
+# KEYCLOAK_REALM=master
+# KEYCLOAK_SERVER_URL=https://keycloak.endo-reg.net
+# KEYCLOAK_CLIENT_ID=lx-frontend
+# KEYCLOAK_CLIENT_SECRET=
+# TOKEN_VALIDATOR_PORT=3001
+
+# -------------------------------------------------------------------
+# Overrides when embedding this app into another Django project
+# -------------------------------------------------------------------
+# STATIC_ROOT=/abs/path/to/staticfiles
+# STORAGE_DIR=/abs/path/to/storage
+
+
+TEST_RUN=False
+TEST_RUN_FRAME_NUMBER=1000
+RUST_BACKTRACE=1
+DJANGO_FFMPEG_EXTRACT_FRAME_BATCHSIZE=500
+VIDEO_ALLOW_FPS_FALLBACK=True
+VIDEO_DEFAULT_FPS=50

endoreg_db-0.8.1/.envrc

@@ -0,0 +1,20 @@
+# Source ENV_PATH if explicitly set and file exists
+if [ -n "${ENV_PATH:-}" ] && [ -f "${ENV_PATH}" ]; then
+  log_status "Sourcing environment from ENV_PATH: ${ENV_PATH}"
+  source_env "${ENV_PATH}"
+else
+  # DEFAULT SHOULD BE THE CURRENT DIRECTORY AS WE INTRODUCE UNEXPECTED BEHAVIOR
+  # OTHERWISE. IF YOU WANT TO SOURCE FROM SOMEWHERE ELSE, SET ENV_PATH
+  if [ -f ".env" ]; then # .env in the current directory (endoreg-db/.env)
+    log_status "Sourcing environment from current: ./.env"
+    source_env .env # This will override/add to what was sourced from ../.env
+  fi
+fi
+
+# e.g.:
+
+#  direnv fetchurl "https://raw.githubusercontent.com/cachix/devenv/v1.6.1/devenv/direnvrc" 
+
+# Original devenv direnvrc sourcing
+source_url "https://raw.githubusercontent.com/cachix/devenv/v1.6.1/devenv/direnvrc" "sha256-LzXLAtBt0TZW0vgIZnHwOuKzQ74cwVMVYLpfi5FmVT8="
+use devenv

endoreg_db-0.8.1/.github/ISSUE_TEMPLATE/label-request.yml

@@ -0,0 +1,68 @@
+name: Label Request
+description: Suggest a new label for this project
+title: "[Label Request] "
+labels: ["label-request"]
+assignees: []
+
+body:
+  - type: markdown
+    attributes:
+      value: |
+        **Main label changelog**:
+        [Current and previous labels](https://github.com/wg-lux/endoreg-db/issues/102)
+
+        Please fill out the fields below to request a new label.
+
+  - type: input
+    id: label_name
+    attributes:
+      label: Label Name
+      description: What should the new label be called?
+      placeholder: e.g. polyp
+    validations:
+      required: true
+
+  - type: textarea
+    id: description
+    attributes:
+      label: Description
+      description: What does this label mean? What is its purpose?
+      placeholder: Describe what this label should represent
+    validations:
+      required: true
+
+  - type: textarea
+    id: importance
+    attributes:
+      label: Why is this label important?
+      description: Why do you think we need this label?
+      placeholder: Explain its value and how it helps the project
+    validations:
+      required: true
+
+  - type: textarea
+    id: interactions
+    attributes:
+      label: Redundancy or Interactions
+      description: Does it conflict with or duplicate any existing labels?
+      placeholder: Mention overlaps with labels.
+    validations:
+      required: true
+
+  - type: input
+    id: labelsets
+    attributes:
+      label: Labelsets
+      description: Which labelsets should include this label?
+      placeholder: e.g. Instrument
+    validations:
+      required: true
+
+  - type: textarea
+    id: related_label
+    attributes:
+      label: Related to an existing label?
+      description: Is this improving or modifying an existing label?
+      placeholder: Name the label it's related to or replacing
+    validations:
+      required: true

endoreg_db-0.8.1/.gitignore

@@ -0,0 +1,184 @@
+result
+result/
+*result
+.ruff_cache/
+.devenv
+untracked_notes.md
+tests/sensitive/
+erc_data/
+/data/
+test_reports/*
+staticfiles/
+.ansible/
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+_build
+.direnv
+
+*.sqlite3
+
+.devenv.flake.nix
+
+###### Do not Remove ###### # Deprecated?
+# Protects temporary files from being comitted
+endoreg_client_manager/data/* 
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+storage/*

endoreg_db-0.8.1/.gitmodules

@@ -0,0 +1,4 @@
+# [submodule "lx-anonymizer"]
+# 	path = lx-anonymizer
+# 	url = https://github.com/wg-lux/lx-anonymizer.git
+# 	branch = prototype

endoreg_db-0.8.1/.pylintrc

@@ -0,0 +1,22 @@
+[MESSAGES CONTROL]
+disable=
+    E1101,
+    W0611,
+    W0621, ; Redefining name from outer scope
+    W0718, ; too broad exception
+    W0212, ; accessing protected member
+    W0404, ; reimported
+    W1203, ; logging-fstring-interpolation
+    C0201, ; Consider iterating dictionary
+    C0206, ; consider using dict items
+    C0114, ; Missing module docstring
+    C0115, ; Missing class docstring
+    C0116, ; Missing function or method docstring
+    C0301, ; Line too long
+    C0303, ; Trailing whitespace
+    C0411,
+    C0412,
+    C0413, 
+    C0415, ; Import outside toplevel
+    W0613, ; Unused argument
+    W0719, ; Broad exception raised

endoreg_db-0.8.1/.python-version

@@ -0,0 +1 @@
+3.12

endoreg_db-0.8.1/.vscode/settings.json

@@ -0,0 +1,17 @@
+{
+  "python.linting.pylintArgs": ["--rcfile", "${workspaceFolder}/.pylintrc"],
+  "python.linting.enabled": true,
+  "python.linting.pylintEnabled": true,
+  "python.analysis.extraPaths": [ "./endoreg_db/tests/" ],
+  "python.testing.pytestArgs": [
+    "tests"
+  ],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true,
+
+  // Ensure VS Code uses the project virtualenv
+  "python.defaultInterpreterPath": "${workspaceFolder}/.devenv/state/venv/bin/python",
+  "python.pythonPath": "${workspaceFolder}/.devenv/state/venv/bin/python",
+  "python.testing.pytestPath": "${workspaceFolder}/.devenv/state/venv/bin/pytest",
+  "python.envFile": "${workspaceFolder}/.env"
+}

endoreg_db-0.8.1/CONFIGURATION_GUIDE.md

@@ -0,0 +1,82 @@
+# EndoReg-DB Configuration and Environment Guide
+
+This repository is a reusable Django app. It ships a small, robust settings package for local development and CI, while encouraging host projects to provide their own settings.
+
+## Settings modules
+
+- config/settings/base.py: shared defaults; driven by environment variables.
+- config/settings/dev.py: local development; SQLite by default.
+- config/settings/test.py: tests; persistent SQLite test DB by default.
+- config/settings/prod.py: production defaults; fully env-driven.
+
+Legacy settings (prod_settings.py, dev/dev_settings.py, tests/test_settings.py) are thin wrappers and can be removed after consumers update.
+
+## Centralized environment handling
+
+- Use helpers in `endoreg_db/config/env.py` (env_str, env_bool, env_int, env_path).
+- .env is not loaded during pytest to prevent test runs from picking up dev settings.
+- Under pytest, `DJANGO_SETTINGS_MODULE` is forced to `config.settings.test`.
+
+## Key environment variables
+
+General
+- DJANGO_SETTINGS_MODULE: choose settings module (defaults used in manage.py/wsgi.py/pytest.ini).
+- STORAGE_DIR: absolute path to media storage (defaults to storage/ in repo).
+- STATIC_URL, STATIC_ROOT, MEDIA_URL: override static/media paths if embedding.
+- TIME_ZONE: defaults to Europe/Berlin.
+
+Development (config.settings.dev)
+- DEV_DB_ENGINE: default django.db.backends.sqlite3
+- DEV_DB_NAME: default BASE_DIR/dev_db.sqlite3
+- DEV_DB_USER, DEV_DB_PASSWORD, DEV_DB_HOST, DEV_DB_PORT: used for non-SQLite engines.
+
+Testing (config.settings.test)
+- TEST_DB_ENGINE: default django.db.backends.sqlite3
+- TEST_DB_NAME: default data/tests/db/test_db.sqlite3
+- TEST_DB_FILE: alternative way to set SQLite DB path
+- TEST_DISABLE_MIGRATIONS: true|false (default false)
+
+Production (config.settings.prod)
+- DJANGO_SECRET_KEY: required (must be a strong random value; never commit real secrets)
+- DJANGO_DEBUG: true|false (use false in production)
+- DJANGO_ALLOWED_HOSTS: comma-separated
+- DB_ENGINE, DB_NAME, DB_USER, DB_PASSWORD, DB_HOST, DB_PORT
+- SECURE_SSL_REDIRECT, SESSION_COOKIE_SECURE, CSRF_COOKIE_SECURE
+- SECURE_HSTS_SECONDS, SECURE_HSTS_INCLUDE_SUBDOMAINS, SECURE_HSTS_PRELOAD
+
+## Typical usage patterns
+
+As an embedded app in a host project:
+- Add 'endoreg_db' to INSTALLED_APPS in the host settings.
+- Define STORAGE_DIR in the host environment.
+- Run migrations in the host project (this app contributes its migrations).
+
+This repo standalone (local):
+- Development server: DJANGO_SETTINGS_MODULE=config.settings.dev python manage.py runserver
+- Tests (persistent test DB): pytest --reuse-db --create-db
+- Clean test DB: rm -f data/tests/db/test_db.sqlite3
+
+CI tips
+- Use DJANGO_SETTINGS_MODULE=config.settings.test
+- First run use --create-db to run migrations once; subsequent runs can cache the database file.
+- Override TEST_DB_NAME to a workspace cache path if needed.
+
+## Direnv/Devenv
+- Ensure devenv.nix and direnv don’t mutate repo files. Editor should inherit direnv env if used.
+
+## Removing legacy settings
+- Replace imports of prod_settings, dev/dev_settings.py, tests/test_settings.py with config.settings.prod/dev/test.
+- Update scripts: scripts/django_setup.py, check_video_files.py, etc., to default to config.settings.dev/test.
+
+## Troubleshooting
+- If numpy/opencv import errors appear in VS Code discovery, ensure the editor inherits direnv env (Direnv extension) or use a pytest wrapper.
+- If tests fail with missing tables, recreate test DB with: pytest --reuse-db --create-db.
+- Run migrations and seed base data for tests when needed:
+  - DJANGO_SETTINGS_MODULE=config.settings.test python manage.py migrate
+  - DJANGO_SETTINGS_MODULE=config.settings.test python manage.py load_base_db_data
+
+## Production checklist
+- Set DJANGO_SECRET_KEY to a strong random value (never commit). 
+- Set DJANGO_ALLOWED_HOSTS to your domains.
+- Enforce HTTPS: SECURE_SSL_REDIRECT=true, cookie secure flags true.
+- Consider HSTS: set SECURE_HSTS_SECONDS (e.g., 31536000) only when ready; include subdomains/preload as appropriate.