mkdocs.yml

site_name: CEDAR
theme:
  name: material

markdown_extensions:
  - markdown.extensions.toc:
      permalink: true
  - pymdownx.keys
  - pymdownx.details
  - pymdownx.superfences
  - pymdownx.highlight:
      linenums: false
  - markdown.extensions.attr_list

plugins:
  - markdownextradata: { }
  - search: { }

extra:
  page:
    cedarw: "CEDAR Workbench"
    cdeb: "CDE Browser"
    fb: "caDSR Form Builder"

extra_css:
  - stylesheets/extra.css

repo_url: https://github.com/metadatacenter/cedar-mkdocs
edit_uri: edit/develop/docs/

nav:
  - Home: index.md

  - User Guide:
      - user-overview.md
      - CEDAR Basics for All Users:
          - Accounts and Logging In:
              - user-guide/basic_topics/a1_accounts_and_logging_in.md
              - user-guide/sections/a1/creating_a_cedar_account.md
              - user-guide/sections/a1/logging_in_with_cedar.md
              - user-guide/sections/a1/visibility_of_your_cedar_account.md

          - Finding Resources:
              - user-guide/basic_topics/a2_finding_resources.md
              - user-guide/sections/a2/1_simple_searching.md
              - user-guide/sections/a2/2_organizing_the_results.md
              - user-guide/sections/a2/3_constraining_the_results_by_type.md
              - user-guide/sections/a2/4_advanced_searching_search_fields.md
              - user-guide/sections/a2/5_advanced_searching_patterns.md

          - Viewing Resource Information:
              - user-guide/basic_topics/a3_viewing_resource_information.md
              - user-guide/sections/a3/1_viewing_resources_overview.md
              - user-guide/sections/a3/2_viewing_resource_content_in_cedar.md
              - user-guide/sections/a3/3_viewing_resource_content_on_the_web.md
              - user-guide/sections/a3/4_viewing_resource_as_raw_json.md
              - user-guide/sections/a3/5_viewing_resource_metadata.md

          - Desktop and Navigation:
              - user-guide/basic_topics/a4_desktop_and_navigation.md
              - user-guide/sections/a4/1_managing_cedar_resources.md
              - user-guide/sections/a4/2_navigating_within_cedar.md
              - user-guide/sections/a4/3_your_cedar_workspace.md

          - Filling Out (Creating) Metadata:
              - user-guide/basic_topics/a5_filling_out_creating_metadata.md
              - user-guide/sections/a5/1_creating_the_metadata_form_instance_for_filling.md
              - user-guide/sections/a5/2_filling_out_metadata.md
              - user-guide/sections/a5/3_saving_and_validating.md
              - user-guide/sections/a5/4_special_case_submitting_your_metadata.md

          - Sharing Your Content:
              - user-guide/basic_topics/a6_sharing_your_content.md
              - user-guide/sections/a6/1_creating_groups.md
              - user-guide/sections/a6/2_how_permissions_work.md
              - user-guide/sections/a6/3_sharing_for_reading_and_writing.md
              - user-guide/sections/a6/4_sharing_via_the_web.md

      - About CEDAR Templates:
          - Description of a Template:
              - user-guide/cedar_templates/c1_description_of_a_template.md
              - user-guide/sections/c1/1_template_overview.md
              - user-guide/sections/c1/2_template_organization.md

          - Building Basic Templates:
              - user-guide/cedar_templates/c2_building_basic_templates.md
              - user-guide/sections/c2/1_first_steps.md
              - user-guide/sections/c2/2_adding_fields.md
              - user-guide/sections/c2/3_adding_elements.md
              - user-guide/sections/c2/4_saving_and_closing.md
              - user-guide/sections/c2/field_type_reference.md

          - More FAIR Templates Using Semantics:
              - user-guide/cedar_templates/c3_more_fair_templates_using_semantics.md
              - user-guide/sections/c3/1_why_semantics_are_important.md
              - user-guide/sections/c3/2_defining_your_answers_with_term_lists.md
              - user-guide/sections/c3/3_choosing_controlled_terms.md
              - user-guide/sections/c3/4_creating_lists_in_the_metadata_entry_forms_for_users.md

          - Advanced Template Topics:
              - user-guide/cedar_templates/c4_advanced_template_topics.md
              - user-guide/sections/c4/1_extending_a_template_adding_fields.md
              - user-guide/sections/c4/2_more_semantics.md
              - user-guide/sections/c4/3_understanding_the_suggestion_system.md
              - user-guide/sections/c4/4_updating_and_versioning.md
              - user-guide/sections/c4/5_working_with_cdes.md

          - Tips for Template Creation:
              - user-guide/cedar_templates/c5_tips_for_template_creation.md
              - user-guide/sections/c5/1_about_template_compatibility.md
              - user-guide/sections/c5/2_composition.md
              - user-guide/sections/c5/3_recipes_for_filling_out_everything_titles_names_descriptions_help_text_.md
              - user-guide/sections/c5/4_term_discovery_selection.md

      - Advanced Topics for All Users:
          - CEDAR Identifiers and IRIs:
              - user-guide/advanced_topics/b1_cedar_identifiers_and_iris.md
              - user-guide/sections/b1/1_browser_address_urls_in_cedar.md
              - user-guide/sections/b1/2_building_sharable_metadata_creation_iris.md
              - user-guide/sections/b1/3_how_cedar_defines_and_accesses_identifiers.md

          - CEDAR's API:
              - user-guide/advanced_topics/b2_cedars_api.md
              - user-guide/sections/b2/1_api_about_swagger_documentation.md
              - user-guide/sections/b2/2_api_accessing_metadata_instances.md
              - user-guide/sections/b2/3_api_using_google_sheets.md

      - CEDAR for caDSR Users:
          - user-guide/pages/cedar-for-cadsr.md
          - user-guide/cadsr_users/1_building_templates.md
          - user-guide/cadsr_users/2_importing_templates.md
          - user-guide/cadsr_users/3_building_elements.md
          - user-guide/cadsr_users/4_finding_cdes.md

      - user-guide/pages/cedar-orientation.md
      - user-guide/pages/faq.md
      - user-guide/pages/glossary.md

  - Install Guides:
      - install-overview.md
      - Developer Install:
          - install-developer/intro.md
          - install-developer/system-architecture.md
          - Prerequisites:
              - install-developer/os-user.md
              - install-developer/prereq-macos.md
              - install-developer/prereq-homebrew.md
              - install-developer/prereq-homebrew-fix.md
              - install-developer/prereq-wget.md
              - install-developer/prereq-openssl.md
              - install-developer/prereq-iterm2-oh-my-zsh-powerlevel10k.md
              - install-developer/prereq-jdk.md
              - install-developer/prereq-jenv.md
              - install-developer/prereq-maven.md
              - install-developer/prereq-python.md
          - User, home directory, passwords and domain:
              - install-developer/os-home-directory.md
              - install-developer/config-usernames-and-passwords.md
              - install-developer/config-domain.md
          - CEDAR CLI:
              - install-developer/cedarcli-overview.md
              - install-developer/cedarcli-install.md
              - install-developer/cedarcli-commands.md
          - The code:
                - install-developer/code-overview.md
                - install-developer/code-git-clone.md
          - Scripts and aliases:
              - install-developer/scripts-and-aliases-install.md
              - install-developer/scripts-and-aliases-include.md
          - CEDAR CLI commands 1:
              - install-developer/commands-overview.md
              - install-developer/commands-env-list.md
              - install-developer/commands-status.md
          - Start and stop aliases:
              - install-developer/commands-startstop.md
          - SSL certificates:
              - install-developer/cert-overview.md
              - install-developer/cert-self-signed.md
              - install-developer/cert-install.md
          - Subdomains, directories:
              - install-developer/os-subdomains.md
              - install-developer/os-directories.md
          - CEDAR CLI commands 2:
              - install-developer/code-git-utils.md
          - The code:
              - install-developer/code-maven-utils.md
              - install-developer/code-build-parent-and-libraries.md
              - install-developer/code-build-project.md
              - install-developer/code-more-utils.md
          - Infrastructure services:
              - install-developer/infra-mongodb.md
              - install-developer/infra-opensearch.md
              - install-developer/infra-mysql.md
              - install-developer/infra-redis.md
              - install-developer/infra-neo4j.md
              - Keycloak:
                  - install-developer/infra-keycloak-overview.md
                  - install-developer/infra-keycloak-download.md
                  - install-developer/infra-keycloak-event-listener.md
                  - install-developer/infra-keycloak-theme.md
                  - install-developer/infra-keycloak-configure.md
                  - install-developer/infra-keycloak-realm.md
              - Nginx:
                  - install-developer/infra-nginx-overview.md
                  - install-developer/infra-nginx-install.md
                  - install-developer/infra-nginx-configure.md
                  - install-developer/infra-nginx-start.md
                  - install-developer/infra-keycloak-administrator.md
              - install-developer/infra-start.md
          - Microservices:
              - install-developer/microservices-configuration.md
              - install-developer/microservices-system-reset-1.md
              - install-developer/microservices-overview.md
              - install-developer/microservices-system-reset-2.md
          - Frontend components:
              - install-developer/frontend-overview.md
              - install-developer/frontend-node-install.md
              - install-developer/frontend-gulp-angular-cli-install.md
              - install-developer/frontend-editor.md
              - install-developer/frontend-openview.md
          - Logging in to CEDAR:
              - install-developer/frontend-logging-in.md

      - Docker Install:
          - install-docker-eval/intro.md
          - Prerequisites:
              - install-docker-eval/prereq-os.md
              - install-docker-eval/prereq-docker-install.md
              - install-docker-eval/prereq-docker-configure.md
          - User, home directory, passwords and domain:
              - install-docker-eval/os-home-directory.md
              - install-docker-eval/config-usernames-and-passwords.md
              - install-docker-eval/config-domain.md
          - Scripts and aliases:
              - install-docker-eval/cedar-cli-install.md
              - install-docker-eval/code-git-clone.md
              - install-docker-eval/scripts-and-aliases-include.md
          - CEDAR commands:
              - install-docker-eval/commands-overview.md
              - install-docker-eval/commands-cedarcli-env-list.md
              - install-docker-eval/commands-cedarcli-server-status.md
          - One-time setup:
              - install-docker-eval/one-time-setup.md
              - install-docker-eval/os-subdomains.md
              - install-docker-eval/bioportal.md
              - install-docker-eval/cert-install.md
          - Components:
              - install-docker-eval/startup-overview.md
              - install-docker-eval/startup-infra.md
              - install-docker-eval/startup-microservices.md
              - install-docker-eval/startup-frontends.md
              #              - install-docker-eval/startup-monitoring.md
              - install-docker-eval/docker-commands.md
          - Evaluate CEDAR:
              - install-docker-eval/eval-users.md
              - install-docker-eval/eval-component-urls.md

      - CEDAR Embeddable Editor:
          - cedar-embeddable-editor/intro.md
          - cedar-embeddable-editor/try-out.md

  - Developer Guide:
      - developer-overview.md
      - Guides:
          - CEDAR Repository Model: https://metadatacenter.org/tools-training/outreach/cedar-template-model
          - developer-guide/template-element-and-field-instances.md
          - developer-guide/template-element-and-fields.md
          - developer-guide/cedar-rest-apis.md

  - HOWTOs:
      - howtos/bioportal-integration-with-docker.md
      - howtos/cedar-ui-transfer-ownership-of-artifacts.md

  - Operations and Management:
      - operations-and-management.md