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bcgsc / pori_graphkb_api

REST API for the GraphKB project
https://bcgsc.github.io/pori
GNU General Public License v3.0
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genomics graphdb knowledge-base personalized-medicine pori

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GraphKB API

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This repository is part of the platform for oncogenomic reporting and interpretation.

The GraphKB database is implemented using orientDB and orientjs. It is a graph database which is used to store variants, ontologies, and the relevance of this terms and variants. The KB uses strict controlled vocabulary to provide a parsable and machine-readable interface for other applications to build on. The API is a REST API built on node/express.

About

Database Schema

The schema is defined in a separate NPM package. In general it consists of four major types of data: ontology terms, variants, evidence, and statements.

OpenAPI Specification

All KB API routes are documented with OpenAPI specification. The specification is hosted with the api under /api/spec

Authentication

Authentication in the KB uses tokens. KB API tokens can be generated using the token route defined in the API specification. The first layer of authentication happens when KB uses keycloak to authenticate users against the LDAP. A request is sent to keycloak with the users credentials and a token is returned if the user exists and has access to KB.

The next step happens when KB looks up the username in the KB database. Each user in KB belongs to one or more UserGroups. Each of these UserGroups contains table-level permission schemas.

KB Authentication Process

In summary, KB Client will send user credentials and receive a token which will be used in the header of all subsequent requests.

Quick Start

Most of the time you will want the deployment instructions rather than the ones below. For these please see the contributing guide.

Requirements

Clone the repository

git clone https://github.com/bcgsc/pori_graphkb_api.git
cd pori_graphkb_api
git checkout develop

Install the dependencies

npm install

To actually use the API, the orientDB instance must already be running. To configure where the tests will point to the user can either modify config/config.js or set the environment variables which override this config (default values are shown below, this will change depending on how you db server is configured).

GKB_DBS_PASS=root
GKB_DBS_USER=root
GKB_DB_HOST='HOST NAME'
GKB_DB_PORT=2424
GKB_KEY_FILE='id_rsa'  # used in generating the tokens

Create the keyfile (pick the current directory)

yes | ssh-keygen -t rsa -b 4096 -f id_rsa -N ''

After these options are configured, the server can be started

npm start