diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json new file mode 100644 index 000000000..4c8b712e6 --- /dev/null +++ b/.devcontainer/devcontainer.json @@ -0,0 +1,43 @@ +// For format details, see https://aka.ms/devcontainer.json. For config options, see the +// README at: https://github.com/devcontainers/templates/tree/main/src/python +{ + "name": "Python 3", + // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile + "image": "mcr.microsoft.com/devcontainers/python:3.13-bookworm", + "features": { + "ghcr.io/devcontainers/features/docker-outside-of-docker:1": {}, + "ghcr.io/devcontainers/features/git-lfs:1": {}, + "ghcr.io/va-h/devcontainers-features/uv:1": { + "shellautocompletion": true + } + }, + + // Features to add to the dev container. More info: https://containers.dev/features. + // "features": {}, + + // Use 'forwardPorts' to make a list of ports inside the container available locally. + // "forwardPorts": [], + + // Use 'postCreateCommand' to run commands after the container is created. + // "postCreateCommand": "pip3 install --user -r requirements.txt", + + // Configure tool-specific properties. + // "customizations": {}, + + // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root. + // "remoteUser": "root" + "workspaceFolder": "${localWorkspaceFolder}", + "workspaceMount": "source=${localWorkspaceFolder},target=${localWorkspaceFolder},type=bind", + "mounts": [ + "source=${localEnv:HOME}/.cache/pip,target=/home/vscode/.cache/pip,type=bind", + "source=${localEnv:HOME}/.cache/uv,target=/home/vscode/.cache/uv,type=bind", + "source=${localEnv:HOME}/.cache/huggingface,target=/home/vscode/.cache/huggingface,type=bind", + ], + "customizations": { + "vscode": { + "extensions": [ + "charliermarsh.ruff" + ] + } + } +} \ No newline at end of file diff --git a/.gitattributes b/.gitattributes index 8e5c1acf0..c7b30618e 100644 --- a/.gitattributes +++ b/.gitattributes @@ -41,9 +41,9 @@ *.br -text diff *.gz -text diff *.tar -text diff -*.zip -text diff *.tgz -text diff *.tbz2 -text diff +*.zip binary # Win Executable *.exe binary @@ -72,4 +72,3 @@ #docs/_static/img filter=lfs diff=lfs merge=lfs -text #services/cogstack-cohort/cui_pt2ch.json filter=lfs diff=lfs merge=lfs -text #services/cogstack-cohort/snomed_terms.json filter=lfs diff=lfs merge=lfs -text -*.zip !text !filter !merge !diff diff --git a/.github/workflows/doc_build.yml b/.github/workflows/doc_build.yml index 42d5b95eb..45023b2fa 100644 --- a/.github/workflows/doc_build.yml +++ b/.github/workflows/doc_build.yml @@ -21,22 +21,22 @@ jobs: steps: - uses: actions/checkout@v7 - - name: Set up Python - uses: actions/setup-python@v7 + - name: Install uv + uses: astral-sh/setup-uv@v5 with: - python-version: "3.11" - cache: "pip" - cache-dependency-path: docs/requirements.txt + python-version: "3.12" + enable-cache: true + cache-dependency-glob: "docs/uv.lock" - name: Run docs QA checks run: | python3 scripts/tests/lint_markdown.py python3 scripts/tests/check_docs_links.py + - name: Install docs dependencies + working-directory: docs + run: uv sync --frozen + - name: Build docs - run: | - cd docs - python3 -m pip install --upgrade pip - python3 -m pip install -r requirements.txt - make clean - make html + working-directory: docs + run: uv run mkdocs build -f ../mkdocs.yml diff --git a/.gitignore b/.gitignore index bae75c1c9..c781ab916 100644 --- a/.gitignore +++ b/.gitignore @@ -44,6 +44,7 @@ security/templates/** # docs docs/build/* +site/ # Ignore all .env files at any level .env diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 877ff3f23..ce6bbae71 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -5,13 +5,19 @@ version: 2 build: - os: ubuntu-24.04 + os: "ubuntu-24.04" tools: - python: "3.11" + python: "3.13" + jobs: + pre_create_environment: + - cd docs + - asdf plugin add uv + - asdf install uv latest + - asdf global uv latest + create_environment: + - uv venv "${READTHEDOCS_VIRTUALENV_PATH}" + install: + - cd docs && UV_PROJECT_ENVIRONMENT="${READTHEDOCS_VIRTUALENV_PATH}" uv sync --frozen -sphinx: - configuration: docs/conf.py - -python: - install: - - requirements: docs/requirements.txt +mkdocs: + configuration: mkdocs.yml \ No newline at end of file diff --git a/docs/.markdownlint.yaml b/docs/.markdownlint.yaml deleted file mode 100644 index a890a148f..000000000 --- a/docs/.markdownlint.yaml +++ /dev/null @@ -1,15 +0,0 @@ -# Disable rules that conflict with Sphinx/MyST conventions -default: true - -MD013: false # Line length — Sphinx often has long code blocks / directives -MD033: false # Inline HTML — needed for raw HTML and directives -MD041: false # First line should be a heading — breaks for included partials -MD024: false # Multiple headings with same content — Sphinx pages can reuse titles -MD034: false # Bare URL — Sphinx cross-refs handle this -MD043: false # Required heading structure — not needed for Sphinx TOC - -# Optional fine-tuning -MD007: - indent: 2 # Consistent list indentation -MD004: - style: dash # Consistent unordered list marker (-) diff --git a/docs/Makefile b/docs/Makefile deleted file mode 100644 index ed8809902..000000000 --- a/docs/Makefile +++ /dev/null @@ -1,20 +0,0 @@ -# Minimal makefile for Sphinx documentation -# - -# You can set these variables from the command line, and also -# from the environment for the first two. -SPHINXOPTS ?= -SPHINXBUILD ?= sphinx-build -SOURCEDIR = . -BUILDDIR = build - -# Put it first so that "make" without argument is like "make help". -help: - @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) - -.PHONY: help Makefile - -# Catch-all target: route all unknown targets to Sphinx using the new -# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). -%: Makefile - @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) diff --git a/docs/README.md b/docs/README.md new file mode 100644 index 000000000..c450d8522 --- /dev/null +++ b/docs/README.md @@ -0,0 +1,40 @@ +# CogStack NiFi Documentation + +The central documentation for cogstack, hosted on docs.cogstack.org + +## Setup + +### Prerequisites + +- Python 3.10 or higher +- [uv](https://github.com/astral-sh/uv) package manager + +### Installation + +```bash +uv venv --python 3.12 --allow-existing +source .venv/bin/activate +uv sync --dev +``` + +## Usage + +### Serve documentation locally (Development) + +To preview the documentation locally with live reload: + +```bash +uv run mkdocs serve +``` + +The documentation will be available at `http://127.0.0.1:8000` + +### Build documentation + +To build the static site: + +```bash +uv run mkdocs build +``` + +The built site will be in the `site/` directory. diff --git a/docs/_static/cogstack-logo.png b/docs/_static/cogstack-logo.png new file mode 100644 index 000000000..0b6048318 Binary files /dev/null and b/docs/_static/cogstack-logo.png differ diff --git a/docs/conf.py b/docs/conf.py deleted file mode 100644 index 0556b1b8b..000000000 --- a/docs/conf.py +++ /dev/null @@ -1,79 +0,0 @@ -# Configuration file for the Sphinx documentation builder. -# -# This file only contains a selection of the most common options. For a full -# list see the documentation: -# https://www.sphinx-doc.org/en/master/usage/configuration.html - -# -- Path setup -------------------------------------------------------------- - -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -# -import datetime -import os -import sys - -current_time = datetime.datetime.now() -sys.path.insert(0, os.path.abspath('.')) - - -# -- Project information ----------------------------------------------------- - -project = 'CogStack-Nifi' -copyright = str(current_time.year) + ', CogStack Org' -author = 'CogStack Org' - -# The full version, including alpha/beta/rc tags -release = 'latest' - - -# -- General configuration --------------------------------------------------- - -# Add any Sphinx extension module names here, as strings. They can be -# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom -# ones. -extensions = [ - 'sphinx_rtd_theme', - 'sphinx.ext.autodoc', - 'myst_parser', - 'sphinx.ext.inheritance_diagram', -] - -# Add any paths that contain templates here, relative to this directory. -templates_path = ['_templates'] - -# List of patterns, relative to source directory, that match files and -# directories to ignore when looking for source files. -# This pattern also affects html_static_path and html_extra_path. -exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', "requirements.txt"] - -source_suffix = { - '.rst': 'restructuredtext', - - '.md': 'markdown', -} - -# -- Options for HTML output ------------------------------------------------- - -# The theme to use for HTML and HTML Help pages. See the documentation for -# a list of builtin themes. -# -html_theme = 'sphinx_rtd_theme' - -# Add any paths that contain custom static files (such as style sheets) here, -# relative to this directory. They are copied after the builtin static files, -# so a file named "default.css" will overwrite the builtin "default.css". -html_static_path = ['_static'] - -html_css_files = [ - 'css/overrides.css' -] - -html_theme_options = { - 'display_version': True, -} - -myst_heading_anchors = 4 - -myst_enable_extensions = ["colon_fence"] diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 000000000..e596b37fa --- /dev/null +++ b/docs/index.md @@ -0,0 +1,93 @@ +# CogStack-NiFi + +[![nifi](https://github.com/CogStack/CogStack-NiFi/actions/workflows/docker_nifi.yml/badge.svg?branch=main)](https://github.com/CogStack/CogStack-NiFi/actions/workflows/docker_nifi.yml) +[![doc-build](https://github.com/CogStack/CogStack-NiFi/actions/workflows/doc_build.yml/badge.svg?branch=main)](https://github.com/CogStack/CogStack-NiFi/actions/workflows/doc_build.yml) +[![elasticsearch-stack](https://github.com/CogStack/CogStack-NiFi/actions/workflows/docker_elasticsearch_stack.yml/badge.svg?branch=main)](https://github.com/CogStack/CogStack-NiFi/actions/workflows/docker_elasticsearch_stack.yml) + +## 💡 Introduction + +This repository proposes a possible next step in the evolution of free-text data processing originally implemented in [CogStack-Pipeline](https://github.com/CogStack/CogStack-Pipeline), moving towards a more modular, Platform-as-a-Service (PaaS) approach. + +**CogStack-NiFi** demonstrates how to use [Apache NiFi](https://nifi.apache.org/) as the central data workflow engine for clinical document processing, integrating services such as text extraction and natural language processing (NLP). Each component runs as a standalone service, with NiFi handling data routing between components and data sources/sinks. + +All NLP/ML/data services are expected to implement a uniform RESTful API, allowing seamless integration into existing pipelines and making it easy to incorporate any NLP application into the stack. + +--- + +## ⚠️ Important Notice + +This project is under active development. New features or services may impact existing deployments. Please review the [release notes](https://cogstack-nifi.readthedocs.io/en/latest/news.html) and [documentation](https://cogstack-nifi.readthedocs.io) before upgrading. + +--- + +## 💬 Asking Questions + +Need help? Feel free to: + +- Open an issue on the [GitHub Issue Tracker](https://github.com/CogStack/CogStack-NiFi/issues) +- Start a discussion on our [Discourse forum](https://discourse.cogstack.org) (actively monitored by the dev team) + +--- + +## 🗂️ Project + +This table describes repository layout. For setup and operations, use the deployment and NiFi docs linked below. + +| Folder | Description | +|----------------|-------------| +| [`nifi`](https://github.com/CogStack/CogStack-NiFi/tree/main/nifi) | Custom Apache NiFi Docker image with workflows, configs, drivers, and user resources. | +| [`security`](https://github.com/CogStack/CogStack-NiFi/tree/main/security) | Scripts for generating SSL certificates and other security-related tools. | +| [`services`](https://github.com/CogStack/CogStack-NiFi/tree/main/services) | NLP and auxiliary services, each with its own configs and resources. | +| [`deploy`](https://github.com/CogStack/CogStack-NiFi/tree/main/deploy) | Example deployment setup, combining NiFi and related services. | +| [`scripts`](https://github.com/CogStack/CogStack-NiFi/tree/main/scripts) | Helper scripts (e.g., setup tools, sample DB ingestion, Elasticsearch ingestion). | +| [`data`](https://github.com/CogStack/CogStack-NiFi/tree/main/data) | Place any test or data to be ingested here. | +| [`typings`](https://github.com/CogStack/CogStack-NiFi/tree/main/typings) | Stubs for code linting/type-hint, etc. | + +--- + +## 📚 Documentation & Getting Started + +### Quick Start (5 minutes) + +```bash +# from repository root +git lfs pull +make -C deploy git-update-submodules +make -C deploy help +make -C deploy start-data-infra +``` + +After services start: + +- NiFi: `https://localhost:8443` +- Elasticsearch: `http://localhost:9200` +- Kibana/OpenSearch Dashboards: `https://localhost:5601` + +Stop the core stack with: + +```bash +make -C deploy stop-data-infra +``` + +**Prerequisites**: + +- Docker + Docker Compose (mandatory) +- `make` +- `git` + `git-lfs` +- `python3.11` +- Basic Linux/UNIX shell familiarity + +📖 Official documentation: [cogstack-nifi.readthedocs.io](https://cogstack-nifi.readthedocs.io/en/latest/) + +🚀 New to the project? Start with the [deployment guide](https://cogstack-nifi.readthedocs.io/en/latest/deploy/main.html) for example setups and workflows. + +🐞 For troubleshooting or bug reports, consult the [known issues section](https://cogstack-nifi.readthedocs.io/en/latest/deploy/troubleshooting.html) before opening a ticket. + +--- + +## 🛑 Important Updates + +Check the [release notes](https://cogstack-nifi.readthedocs.io/en/latest/news.html) section regularly for: + +- Major changes to project structure or configuration +- Security advisories or vulnerabilities affecting deployments diff --git a/docs/index.rst b/docs/index.rst deleted file mode 100644 index 7afc6cc34..000000000 --- a/docs/index.rst +++ /dev/null @@ -1,29 +0,0 @@ -.. CogStack-Nifi documentation master file, created by - sphinx-quickstart on Thu Feb 17 15:01:20 2022. - You can adapt this file completely to your liking, but it should at least - contain the root `toctree` directive. - -Welcome to CogStack-Nifi's documentation! -========================================= - -.. toctree:: - :maxdepth: 2 - :caption: Contents: - - main.md - news.md - deploy/main.md - deploy/deployment.md - deploy/services.md - deploy/troubleshooting.md - deploy/workflows.md - deploy/workflows_legacy.md - nifi/main.md - security/main.md - -Indices and tables -================== - -* :ref:`genindex` -* :ref:`modindex` -* :ref:`search` diff --git a/docs/main.md b/docs/main.md deleted file mode 100644 index 451bedaec..000000000 --- a/docs/main.md +++ /dev/null @@ -1,2 +0,0 @@ -```{include} ../README.md -``` diff --git a/docs/make.bat b/docs/make.bat deleted file mode 100644 index 061f32f91..000000000 --- a/docs/make.bat +++ /dev/null @@ -1,35 +0,0 @@ -@ECHO OFF - -pushd %~dp0 - -REM Command file for Sphinx documentation - -if "%SPHINXBUILD%" == "" ( - set SPHINXBUILD=sphinx-build -) -set SOURCEDIR=source -set BUILDDIR=build - -if "%1" == "" goto help - -%SPHINXBUILD% >NUL 2>NUL -if errorlevel 9009 ( - echo. - echo.The 'sphinx-build' command was not found. Make sure you have Sphinx - echo.installed, then set the SPHINXBUILD environment variable to point - echo.to the full path of the 'sphinx-build' executable. Alternatively you - echo.may add the Sphinx directory to PATH. - echo. - echo.If you don't have Sphinx installed, grab it from - echo.https://www.sphinx-doc.org/ - exit /b 1 -) - -%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% -goto end - -:help -%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O% - -:end -popd diff --git a/docs/nifi/main.md b/docs/nifi/main.md index 5454db781..e25306184 100644 --- a/docs/nifi/main.md +++ b/docs/nifi/main.md @@ -37,16 +37,6 @@ For user script organization and usage guidelines, see [user scripts](user_scrip For Python extension processors, see [Python extensions](user_python_extensions.md). For end-to-end scripting patterns (including `ExecuteStreamCommand` stdin/stdout and args), see [processor scripting guide](processor_scripting.md). -```{toctree} -:maxdepth: 1 - -development_guide.md -processors_catalog.md -processor_scripting.md -user_scripts.md -user_python_extensions.md -``` - ## Custom Docker image For any deployment it is recommended to build and use the custom Docker image of Apache NiFi that will contain all the necessary configuration, drivers, custom user scripts and workflows. diff --git a/docs/overrides/partials/integrations/analytics/custom.html b/docs/overrides/partials/integrations/analytics/custom.html new file mode 100644 index 000000000..6d4896cd1 --- /dev/null +++ b/docs/overrides/partials/integrations/analytics/custom.html @@ -0,0 +1,21 @@ +{#- + PostHog analytics integration (custom provider). + Loads on every page; works with instant navigation via location$. + -#} + + \ No newline at end of file diff --git a/docs/pyproject.toml b/docs/pyproject.toml new file mode 100644 index 000000000..c1b827c10 --- /dev/null +++ b/docs/pyproject.toml @@ -0,0 +1,18 @@ +[project] +name = "cogstack-nifi-documentation" +version = "0.1.0" +description = "CogStack Nifi Documentation" +readme = "README.md" +requires-python = ">=3.10" +dependencies = [ + "mkdocs-material>=9.7.0", +] + +[project.optional-dependencies] +dev = [ + "ruff>=0.12.11", +] + +[tool.ruff] +line-length = 120 + diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 94bf3cc6f..000000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,3 +0,0 @@ -Sphinx==8.2.3 -sphinx-rtd-theme==3.0.2 -myst-parser==4.0.1 \ No newline at end of file diff --git a/docs/security/main.md b/docs/security/main.md index 17abb4109..13faa51ca 100644 --- a/docs/security/main.md +++ b/docs/security/main.md @@ -68,15 +68,3 @@ security/ └── templates/ # OpenSSL / X.509 configuration templates └── ssl-extensions-x509.cnf # SAN extensions used across 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deploy/services.md + - 📛 Troubleshooting: deploy/troubleshooting.md + - Workflows: deploy/workflows.md + - 🔀 Workflows: deploy/workflows_legacy.md + - 💧 NiFi: + - nifi/main.md + - Development Guide: nifi/development_guide.md + - Processors Catalog: nifi/processors_catalog.md + - Processor Scripting: nifi/processor_scripting.md + - User Scripts: nifi/user_scripts.md + - Python Extensions: nifi/user_python_extensions.md + - Configuration: deploy/configuration.md + - 🛡️ Security: + - security/main.md + - 🏛️ Certificates and Root CA: security/certificates.md + - 🗄️ Security for CogStack provided other services: security/services.md + - 🔐 NiFi TLS & Admin Access Setup (with NGINX): security/nifi.md + - 🌐 Elasticsearch / OpenSearch Security: security/elasticsearch_opensearch.md + +plugins: + + - search + + +extra: + analytics: + provider: custom + + +markdown_extensions: + - md_in_html + - admonition + - attr_list + - pymdownx.details + - pymdownx.superfences + - pymdownx.tabbed: + 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