Initialise the repo with a current snapshot of Bunny

.dockerignore

@@ -0,0 +1,24 @@
+**/.dockerignore
+**/.env
+**/.venv
+**/.git
+**/.gitignore
+**/.project
+**/.settings
+**/.toolstarget
+**/.vs
+**/.vscode
+**/.idea
+**/*.*proj.user
+**/*.dbmdl
+**/*.jfm
+**/azds.yaml
+**/bin
+**/charts
+**/docker-compose*
+**/Dockerfile*
+**/node_modules
+**/npm-debug.log
+**/obj
+**/secrets.dev.yaml
+**/values.dev.yaml

.editorconfig

@@ -0,0 +1,16 @@
+# EditorConfig is awesome: https://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines with a newline ending every file
+[*]
+end_of_line = lf
+insert_final_newline = true
+charset = utf-8
+indent_style = space
+indent_size = 2
+
+[*.py]
+indent_size = 4 # pep8
+profile = black

.gitattributes

@@ -0,0 +1 @@
+* text=auto eol=lf

.gitignore

@@ -0,0 +1,171 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# 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
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.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/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# 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/
+
+# PyPI configuration file
+.pypirc

.python-version

@@ -0,0 +1 @@
+3.13

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+  "python.testing.pytestArgs": [
+    "test"
+  ],
+  "python.testing.unittestEnabled": false,
+  "python.testing.pytestEnabled": true
+}

Dockerfile

@@ -0,0 +1,8 @@
+FROM ghcr.io/astral-sh/uv:bookworm-slim
+
+COPY . /app
+WORKDIR /app
+
+RUN uv sync --frozen
+
+ENTRYPOINT ["uv", "run", "bunny-daemon"]

README.md

@@ -1 +1,23 @@
-# hutch-bunny
+[![Hutch][hutch-logo]][hutch-repo]
+
+# 🐇 Hutch Bunny ![MIT License][license-badge]
+
+| | | |
+|-|-|-|
+| ![Python][python-badge] | [![Bunny Docker Images][docker-badge]][bunny-containers] | [![Bunny Docs][docs-badge]][bunny-docs] |
+
+An HDR UK Cohort Discovery Task Resolver.
+
+Fetches and resolves Availability and Distribution Queries against an OMOP-CDM database.
+
+[hutch-logo]: https://raw.githubusercontent.com/HDRUK/hutch/main/assets/Hutch%20splash%20bg.svg
+[hutch-repo]: https://github.com/health-informatics-uon/hutch
+
+[bunny-docs]: https://health-informatics-uon.github.io/hutch/bunny
+[bunny-containers]: https://github.com/Health-Informatics-UoN/hutch-cohort-discovery/pkgs/container/hutch%2Fbunny
+
+[license-badge]: https://img.shields.io/github/license/health-informatics-uon/hutch-cohort-discovery.svg
+[python-badge]: https://img.shields.io/badge/Python-3776AB?style=for-the-badge&logo=python&logoColor=white
+[docker-badge]: https://img.shields.io/badge/docker-%230db7ed.svg?style=for-the-badge&logo=docker&logoColor=white
+[docs-badge]: https://img.shields.io/badge/docs-black?style=for-the-badge&labelColor=%23222
+[readme-badge]: https://img.shields.io/badge/readme-lightgrey?style=for-the-badge&labelColor=%23222

dev.compose.yml

@@ -0,0 +1,76 @@
+name: hutch-bunny-dev
+
+services:
+  db:
+    image: postgres:16
+    restart: always
+    ports:
+      - 5432:5432
+    environment:
+      POSTGRES_PASSWORD: postgres
+
+  adminer:
+    image: wodby/adminer
+    depends_on:
+      - db
+    restart: always
+    ports:
+      - 9000:9000
+    environment:
+      ADMINER_DEFAULT_DB_DRIVER: pgsql
+      ADMINER_DEFAULT_DB_HOST: db
+      ADMINER_DESIGN: pepa-linha
+
+  rabbitmq:
+    image: rabbitmq:3-management
+    ports:
+      - 5672:5672
+      - 15672:15672
+    environment:
+      RABBITMQ_DEFAULT_USER: user
+      RABBITMQ_DEFAULT_PASS: password
+
+  relay:
+    image: ghcr.io/health-informatics-uon/hutch/relay:dev-latest
+    depends_on:
+      - rabbitmq
+      - db
+    restart: always
+    ports:
+      - 8080:8080
+      - 8081:8081
+    environment:
+      DOTNET_Environment: Development
+      ConnectionStrings__Default: Server=db;Port=5432;Database=hutch-relay;User Id=postgres;Password=postgres
+      RelayTaskQueue__ConnectionString: amqp://user:password@rabbitmq:5672
+      Obfuscation__LowNumberSuppressionThreshold: 0
+      Obfuscation__RoundingTarget: 0
+      UpstreamTaskApi__BaseUrl: https://<task_api_host>
+      UpstreamTaskApi__CollectionId: collection_id
+      UpstreamTaskApi__Username: username
+      UpstreamTaskApi__Password: password
+      Database__ApplyMigrationsOnStartup: true
+
+  bunny:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    depends_on:
+      - db
+      - relay
+    restart: always
+    environment:
+      DATASOURCE_DB_USERNAME: postgres
+      DATASOURCE_DB_PASSWORD: postgres
+      DATASOURCE_DB_DATABASE: hutch-omop
+      DATASOURCE_DB_DRIVERNAME: postgresql
+      DATASOURCE_DB_SCHEMA: public
+      DATASOURCE_DB_PORT: 5432
+      DATASOURCE_DB_HOST: db
+      TASK_API_BASE_URL: http://relay:8080/
+      TASK_API_USERNAME: username
+      TASK_API_PASSWORD: password
+      LOW_NUMBER_SUPPRESSION_THRESHOLD:
+      ROUNDING_TARGET:
+      POLLING_INTERVAL: 5
+      COLLECTION_ID: collection_id

dev.standalone.compose.yml

@@ -0,0 +1,22 @@
+name: hutch-bunny-standalone-dev
+
+services:
+  bunny:
+    build:
+      context: .
+      dockerfile: Dockerfile
+    environment:
+      DATASOURCE_DB_USERNAME: postgres
+      DATASOURCE_DB_PASSWORD: postgres
+      DATASOURCE_DB_DATABASE: hutch-omop
+      DATASOURCE_DB_SCHEMA: public
+      DATASOURCE_DB_PORT: 5432
+      DATASOURCE_DB_HOST: host.docker.internal
+      TASK_API_BASE_URL: https://<task_api_host>/link_connector_api
+      TASK_API_USERNAME: username
+      TASK_API_PASSWORD: password
+      COLLECTION_ID: collection_id
+      TASK_API_TYPE: a
+      LOW_NUMBER_SUPPRESSION_THRESHOLD:
+      ROUNDING_TARGET:
+      POLLING_INTERVAL: 5