Getting Started

The easiest way to understand Arranger, is to simply use it!

Below is a description of how to get Arranger quickly up and running, as well as a description of how Arranger works and some important terms.

Quick Start

The goal of this quick start is to get a working application quickly up and running.

Using Docker:

1. Download the latest version of Arranger.
2. From the Arranger root directory, run docker-compose:

$ docker-compose up -d

Arranger should now be deployed locally.

Alternatively, see the Installation instructions.

How Arranger Works

1. Starting with some Elasticsearch (ES) indices with mappings.

• Arranger makes no assumption about your data model.
• Model your index mappings and index them.
• For demo convenience, you can follow a tutorial bellow to index some test data from our Kids First project.

See also

The Overture software suite also provides Maestro for indexing genomic data to ES

2. Create an API version for your project from Arranger Admin.

• From your browser, navigate to http://localhost:8080
• Click “Add Project”
• Input your project id in snake_case
• Click “Add Index” for each index you want to expose from ES, with the following fields:
  • “Name”: any name for your index, in camelCase
  • “ES Index”: the index that you want to expose
  • “ES Type”: the type that you want to expose
• Click “Add” once finalized.
• Navigate into your newly registered project’s configuration and ensure that “Has Mapping” is “yes” for all indices registered.
• Configure your project from the API and click “Save” to save as a new project.

3. View your data in a portal.

• From a UI:
  • Go to http://localhost:8081/?selectedKind=Portal.
  • Select your project and index from the dropdown.
  • Note: a production-ready white-label portal using UI components provided by Arranger is in our roadmap for Arranger.
• From the GraphQL API:
  • Each Arranger project created through the Admin system in step 2 creates a new Graphql endpoint.
  • Start a GraphQL IDE (such as GraphiQL or GraphQL Playground
  • Point your IDE to http://localhost:5050/<project_id>/graphql to explore the API schema (where <project_id> is the project id you have input in step 2).
  • For documentation regarding this API, check out the Arranger for Application Developers guide

Architecture

Indexing Demo Data

• From your browser, visit the locally running Kibana at http://localhost:5601 and go to Dev Tools
• Creating a file_centric index:
  • Run these commands to create a file_centric index and add a mapping then these commands to index some demo documents into the index
  • Run these commands to create a participant_centric index and add a mapping then these commands to index some demo documents into the index
• You can run GET file_centric/_mapping and GET participant_centric/_mapping to confirm that the mapping has been created successfully