CEDAR technical documentation

Quick Start Developer Guides

• CEDAR Repository Model This document describes the CEDAR repository model, which defines the representation of all CEDAR metadata artifacts, such as templates, elements, fields and the metadata instances themselves. More formally we have written a paper describing this model.
• CEDAR Metadata Instances Description of the format of metadata instances in the CEDAR repository.
• Getting Started with CEDAR REST APIs Instructions for interacting with CEDAR REST services
• Processing CEDAR Metadata Instances Examples of how JSON Schema-based code generation tools can be used to read and write CEDAR metadata instances.

Other Documentation

• CEDAR Install Guide Instructions for installing a CEDAR server from scratch
• BioPortal API documentation CEDAR uses BioPortal for all terminology services
• CEDAR Project Proposal
• CEDAR architecture diagram

Tools

General-purpose links to the tools that we use for developing our system.

Team collaboration tools

(Links are to our the general site. See the Team page for links to our accounts.)

• Waffle Used for tracking all CEDAR development tasks.
• GitHub Developer Wiki Developer-centric CEDAR wiki.
• Box Used for discussions, meeting minutes and document exchange
• Google Drive Used for document authoring; completed documents are transferred to Box, public documents are made visible to all via Google Drive.
• Slack. Used for development discussions
• Basecamp. Used for communication with external collaborators.

Development Stack

IDEs

• IntelliJ

Programming Languages & Development Frameworks

Front-End

• Javascript, HTML, CSS
• AngularJS

Back-End

• Java
• Dropwizard

Databases and NoSQL Datastores

• MongoDB
• Neo4j
• MySQL
• Redis

Search Engine

• Elasticsearch

HTTP Server

• Nginx

Identity and Access Management

• Keycloak

Other tools

• OmniGraffle

Git: Documentation, Code, Models, Issues

Documentation

Publicly available documentation about the project.

• Metadatacenter Developer Documentation Main GitHub entry point for developer documentation
• CEDAR Git Workflow The CEDAR development team uses the Git-Flow model

Code

• GitHub repositories (note more repositories are available than listed here)
• cedar-docs: Configuration and development-related documents.
• cedar-template-editor: A Web application for creating and filling in Metadata Templates
• cedar-template-server: CEDAR server to manage Metadata Templates, Metadata Template Elements, and Metadata Template Instances

Issues

CEDAR issues are tracked in each of the above repositories. To get an overview, you'd want to look at our Agile display of those issues, using the highly recommended Waffle.io.

• Agile task board, Waffle, synced with GitHub issues

Information Specifications and Related Resources

More information about the information model specifications we've applied.

JSON Schema and JSON-LD

JSON Schema and JSON-LD are used extensively in CEDAR.

• Understanding JSON Schema (book)
• JSON-LD Playground
• Validators
• JSON validator (online): http://jsonlint.com
• JSON validator (Python, command line): http://deron.meranda.us/python/demjson/
• JSON Schema validator (online): http://jsonschemalint.com/draft4
• JSON Schema validator (Python, command line): http://python-jsonschema.readthedocs.org/en/latest/validate
• Viewers
• Online JSON viewer: http://jsonviewer.stack.hu

RDF

Interoperation with RDF and Linked Open Data is a core CEDAR goal.

• EasyRDF Online Converter
• RDF to graph representation

Collaborating and Related Websites

• CEDAR
• BioPortal
• Immport
• ISA Tools
• Stanford University Libraries