mkdocs.yml

#https://www.mkdocs.org/user-guide/configuration/#
site_name: Gen3 Documentation
site_url: https://docs.gen3.org
repo_url: https://github.com/uc-cdis/docs-gen3
nav:
  - Home: index.md
  - About Gen3: gen3-resources/about.md
  - Gen3 Community: gen3-resources/community.md
  - User Guide:
    - gen3-resources/user-guide/index.md # user guide home page, describing the contents of the user guide and linking to sections
    - Search for Data: gen3-resources/user-guide/search.md
    - Access Data Files: gen3-resources/user-guide/access-data.md
    - Analyze Data: gen3-resources/user-guide/analyze-data.md
    - Data Portal:  gen3-resources/user-guide/portal.md
    - Use the API: gen3-resources/user-guide/using-api.md
  - Operator Guide - Deploy Gen3:
    - gen3-resources/operator-guide/index.md
    # homepage for operator guide, describes contents and links to different sections
    - Prerequisites for Deploying Gen3: gen3-resources/operator-guide/prerequisites.md
    - Pre-Deployment:
      - Infrastructure as Code:
        - Infrastructure as Code - Overview: gen3-resources/operator-guide/iac-overview.md
        - Terraform: gen3-resources/operator-guide/iac-terraform.md
        - Terragrunt: gen3-resources/operator-guide/iac-terragrunt.md
        - Atlantis: gen3-resources/operator-guide/iac-atlantis.md
      - Prepare SSL Certificate: gen3-resources/operator-guide/ssl-cert.md
      - Authentication Methods: gen3-resources/operator-guide/gen3-authn-methods.md
    - Setup Gen3 (Configure and Deploy) with Helm:
      - gen3-resources/operator-guide/helm/index.md
      - Deployment Overview: gen3-resources/operator-guide/helm/helm-deploy-overview.md
      - Example - Minimal Local Deployment: gen3-resources/operator-guide/helm/helm-deploy-example.md
      - Example - Production Deployment: gen3-resources/operator-guide/helm/helm-deploy-production-example.md
      - Databases in Gen3 Helm charts: gen3-resources/operator-guide/helm/helm-deploy-databases.md
      - Configure services with Helm:
        - gen3-resources/operator-guide/helm/helm-config/index.md
        - AuthN/AuthZ: gen3-resources/operator-guide/helm/helm-config/helm-config-auth.md
        - Data-related Services: gen3-resources/operator-guide/helm/helm-config/helm-config-data-svcs.md
        - Front End: gen3-resources/operator-guide/helm/helm-config/helm-config-frontend.md
        - Workspaces: gen3-resources/operator-guide/helm/helm-config/helm-config-workspaces.md
        - Revproxy: gen3-resources/operator-guide/helm/helm-config/helm-config-revproxy.md
    - Post-Deployment:
      - Create Data Dictionary: gen3-resources/operator-guide/create-data-dictionary.md
      # contains info about creating (and maintaining?) a data dictionary
      - Submit Data:
        - Structured Data: gen3-resources/operator-guide/submit-structured-data.md
        - Unstructured Data: gen3-resources/operator-guide/submit-unstructured-data.md
        - Semi-structured data: gen3-resources/operator-guide/submit-semi-structured-data.md
        - Controlling data authorization: gen3-resources/operator-guide/authorization.md
      - Customize Gen3 Search: gen3-resources/operator-guide/customize-search.md
      # info from the current operator guide about configuring ETL and data explorer
      - Customize the Front End: gen3-resources/operator-guide/customize-frontend.md
    - Secrets and Security:
      - Secrets Manager: gen3-resources/operator-guide/tutorial_secrets-mgr.md
      - Create an AWS IAM Global User: gen3-resources/operator-guide/tutorial_global_IAM_helm_user.md
    - Observability and Monitoring:
      - Observability: gen3-resources/operator-guide/tutorial_observability.md
      - Grafana Alloy Helm Chart: gen3-resources/operator-guide/tutorial_alloy.md
      - Grafana Alloy and Faro: gen3-resources/operator-guide/tutorial_faro.md
    - Microservice Jobs and Tutorials:
      - About Jobs in Gen3: gen3-resources/operator-guide/tutorial_jobs_overview.md
      - Fence Usersync Cronjob: gen3-resources/operator-guide/tutorial_fence_usersync_job.md
  - Developer Guide - Extend Gen3:
    - gen3-resources/developer-guide/index.md
    - Gen3 Architecture:  gen3-resources/developer-guide/architecture.md
    - Gen3 Microservices:  gen3-resources/developer-guide/microservices.md
    - Contribute Code to Gen3: gen3-resources/developer-guide/contribute.md
  - Blog:
    - blog/index.md
  - Frequently Asked Questions: gen3-resources/faq.md
  - gen3-resources/glossary.md
  - Demo @ gen3.datacommons.io: https://gen3.datacommons.io/


theme:
  favicon: img/Gen3-3.ico
  logo: img/gen3_new_logo_white.svg
  name: material
  features:
    - navigation.footer
    - navigation.indexes
    - navigation.tracking
    - navigation.path
  custom_dir: overrides

  palette:
    - primary: black


   # Palette toggle for light mode
    - media: "(prefers-color-scheme: light)"
      scheme: brh_platform
      toggle:
        icon: material/eye
        name: Switch to dark mode

    # Palette toggle for dark mode
    - media: "(prefers-color-scheme: dark)"
      scheme: brh_platform_dark
      toggle:
        icon: material/eye-outline
        name: Switch to light mode
extra_css:
  - stylesheets/extra.css
extra_javascript:
  - js/dd.js
use_directory_urls: true
markdown_extensions:
  - admonition
  - attr_list
  - md_in_html
  - def_list
  - footnotes
  - toc:
      permalink: True
      toc_depth: 3
  - pymdownx.superfences
  - pymdownx.details
  - pymdownx.caret
  - pymdownx.mark
  - pymdownx.tilde
  - pymdownx.tasklist:
      custom_checkbox: true
  - pymdownx.smartsymbols
  - pymdownx.emoji:
      emoji_generator: !!python/name:pymdownx.emoji.to_svg
  - pymdownx.inlinehilite
  - pymdownx.magiclink
  - pymdownx.betterem:
      smart_enable: all
  - pymdownx.highlight:
      auto_title: true
plugins:
  - search
  - tags
  - blog:
      enabled: true
      authors: true
      authors_file: blog/authors.yml
      blog_dir: blog
      blog_toc: true
  - mkdocs-video:
      is_video: True

extra:
  social:
    - icon: fontawesome/brands/linkedin
      link: https://www.linkedin.com/company/center-for-translational-data-science/
    - icon: fontawesome/brands/x-twitter
      link: https://x.com/UChicagoCTDS
    - icon: fontawesome/brands/x-twitter
      link: https://x.com/gen3data
    - icon: fontawesome/brands/slack
      link: https://docs.google.com/forms/d/e/1FAIpQLSczyhhOXeCK9FdVtpQpelOHYnRj1EAq1rwwnm9q6cPAe5a7ug/viewform
    - icon: fontawesome/brands/youtube
      link: https://www.youtube.com/channel/UCMCwQy4EDd1BaskzZgIOsNQ/featured
    - icon: fontawesome/brands/github
      link: https://github.com/uc-cdis