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CEDAR

Overview

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CEDAR

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User Guide
User Guide
- Introduction
- CEDAR Basics for All Users
  CEDAR Basics for All Users
  - Accounts and Logging In
    Accounts and Logging In
    
    Intro: Accounts and Logging In
    
    Creating a CEDAR Account
    
    Logging in with CEDAR
    
    Visibility of your CEDAR Account
  - Finding Resources
    Finding Resources
    
    Intro: Finding Resources
    
    Simple Searching
    
    Organizing the Results
    
    Constraining the Results by Type
    
    Advanced Searching - Search Fields
    
    Advanced Searching - Patterns
  - Viewing Resource Information
    Viewing Resource Information
    
    Intro: Viewing Resource Information
    
    Viewing Resources Overview
    
    Viewing Resource Content in CEDAR
    
    Viewing Resource Content on the Web
    
    Viewing Resource as Raw JSON
    
    Viewing Resource Metadata
  - Desktop and Navigation
    Desktop and Navigation
    
    Intro: Desktop and Navigation
    
    Managing CEDAR Resources
    
    Navigating Within CEDAR
    
    Your CEDAR Workspace
  - Filling Out (Creating) Metadata
    Filling Out (Creating) Metadata
    
    Intro: Filling Out (Creating) Metadata
    
    Creating the Metadata Form (Instance) for Filling
    
    Filling Out Metadata
    
    Saving and Validating
    
    Special Case—Submitting Your Metadata
  - Sharing Your Content
    Sharing Your Content
    
    Intro: Sharing Your Content
    
    Creating Groups
    
    How Permissions Work
    
    Sharing for Reading and Writing
    
    Sharing Via the Web
- About CEDAR Templates
  About CEDAR Templates
  - Description of a Template
    Description of a Template
    
    Intro: Description of a Template
    
    Template Overview
    
    Template Organization
  - Building Basic Templates
    Building Basic Templates
    
    Intro: Building Basic Templates
    
    First Steps
    
    Adding Fields
    
    Adding Elements
    
    Saving and Closing
    
    Field Type Reference
  - More FAIR Templates Using Semantics [Partial]
    More FAIR Templates Using Semantics [Partial]
    
    Intro: More FAIR Templates Using Semantics
    
    Why Semantics Are Important
    
    Defining Your Answers with Term Lists
    
    Choosing Controlled Terms
    
    Creating lists in the metadata entry forms for users
  - Advanced Template Topics [Partial]
    Advanced Template Topics [Partial]
    
    Intro: Advanced Template Topics
    
    Extending a Template (adding fields)
    
    More Semantics
    
    Understanding the Suggestion System
    
    Updating and Versioning
    
    Working with CDEs
  - Tips for Template Creation [Pending]
    Tips for Template Creation [Pending]
    
    Intro: Tips for Template Creation
    
    About Template Compatibility
    
    Composition
    
    Recipes for Filling Out Everything (Titles, Field Names, Descriptions, Help Text)
    
    Term Discovery/Selection
- Advanced Topics for All Users
  Advanced Topics for All Users
  - CEDAR Identifiers and IRIs
    CEDAR Identifiers and IRIs
    
    Intro: CEDAR Identifiers and IRIs
    
    Browser Address URLs in CEDAR
    
    Building Shareable Metadata Creation IRIs
    
    How CEDAR Defines and Applies IRIs (URIs, URLs)
  - CEDAR's API
    CEDAR's API
    
    Intro: CEDAR's API
    
    API—About Swagger Documentation
    
    API—Finding and Accessing Metadata Instances
    
    API—Using Google Sheets
- CEDAR for caDSR Users
  CEDAR for caDSR Users
- CEDAR Workbench Orientation
- Frequently Asked Questions
- Glossary
Install Guides
Install Guides
- Overview
- Developer Install
  Developer Install
  - Introduction
  - System Architecture
  - Prerequisites
    Prerequisites
    
    CEDAR User
    
    macOS
    
    Homebrew
    
    Fix Homebrew
    
    Wget
    
    OpenSSL
    
    iTerm2, oh-my-zsh, powerlevel10k
    
    JDK
    
    Jenv
    
    Maven
    
    Python
  - User, home directory, passwords and domain
    User, home directory, passwords and domain
    
    CEDAR Home Directory
    
    Usernames and Passwords
    
    CEDAR Domain
  - CEDAR CLI
    CEDAR CLI
    
    Overview
    
    cedar-cli
    
    cedar-cli commands
  - The code
    The code
    
    Overview
    
    Clone the project repos
  - Scripts and aliases
    Scripts and aliases
    
    Install the scripts
    
    Source shell scripts
  - CEDAR CLI commands 1
    CEDAR CLI commands 1
    
    Overview
    
    env list
    
    status
  - Start and stop aliases
    Start and stop aliases
    
    Startup and stop scripts
  - SSL certificates
    SSL certificates
    
    Overview
    
    Copy self-signed certificates
    
    Install the self-signed root certificates
  - Subdomains, directories
    Subdomains, directories
    
    Subdomains
    
    Directories
  - CEDAR CLI commands 2
    CEDAR CLI commands 2
    
    cedarcli git commands
  - The code
    The code
    
    CEDAR Maven utils
    
    Build CEDAR parent and libraries
    
    Build CEDAR project
    
    More CEDAR utils
  - Infrastructure services
    Infrastructure services
    
    MongoDB
    
    OpenSearch
    
    MySql
    
    Redis
    
    Neo4j
    
    Keycloak
    Keycloak
    
    Overview
    
    Download Keycloak
    
    Install Keycloak event listener
    
    Install CEDAR Keycloak theme
    
    Configure Keycloak
    
    Set up CEDAR realm
    
    Nginx
    Nginx
    
    Overview
    
    Install Nginx
    
    Configure nginx
    
    Start nginx
    
    Set up CEDAR Keycloak administrator
    
    Starting the infrastructure services
  - Microservices
    Microservices
    
    Configuring the CEDAR microservices
    
    Initializing the backend data stores
    
    Starting the CEDAR microservices
    
    Performing a system reset
  - Frontend components
    Frontend components
    
    Overview
    
    Install Node.js
    
    Install Gulp and Angular CLI
    
    Launch main frontend
    
    Launch OpenView frontend
  - Logging in to CEDAR
    Logging in to CEDAR
    
    Logging in to CEDAR
- Docker Install
  Docker Install
  - Introduction
  - Prerequisites
    Prerequisites
    
    Operating System
    
    Install Docker
    
    Configure Docker
  - User, home directory, passwords and domain
    User, home directory, passwords and domain
    
    CEDAR Docker Home Directory
    
    Usernames and Passwords
    
    CEDAR Docker Domain
  - Scripts and aliases
    Scripts and aliases
    
    Install CEDAR CLI
    
    Clone the Docker repos
    
    Source shell scripts
  - CEDAR commands
    CEDAR commands
    
    Overview
    
    cedarcli env list
    
    cedarcli server status
  - One-time setup
    One-time setup
    
    One-time setup
    
    Subdomains
    
    BioPortal integration
    
    Install the self-signed root certificates
  - Components
    Components
    
    Overview
    
    Infrastructure services
    
    Microservices
    
    Frontends
    
    Docker commands
  - Evaluate CEDAR
    Evaluate CEDAR
    
    Users
    
    Components, URLs
- CEDAR Embeddable Editor
  CEDAR Embeddable Editor
  - Introduction
  - Try CEDAR Embeddable Editor
Developer Guide
Developer Guide
- Overview
- Guides
  Guides
HOWTOs
HOWTOs
- BioPortal integration with Docker
- Transfer the ownership of several CEDAR artifacts
Operations and Management
Operations and Management
- Operations and Management

Overview¶

During the installation and maintenance of CEDAR you can take advantage of the numerous commands available in cedarcli.

Previous Source shell scripts

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