Pedigree (Sequence Lineage updating script)

The purpose of this script is to syncronize data from a Cloud Object Storage (as a .tsv format) to VirusSeq data repository.

Getting started

This script has been tested using NodeJS v^16.

Local configuration

1. npm ci
2. Copy .env.schema file to a new file named .env. Populate all fields. See description of env variables in the Environment variables section.
3. npm run dev or npm run dev:[profile] See description of profiles in the Profiles section

Environment variables

VARIABLE	TYPE	DESCRIPTION
NODE_ENV	String	Optional. Defines the environment
DEBUG	Boolean	Default true. true enables debug logs; false disables debug logs
GS_BUCKET_NAME	String	Google Storage bucket name
GS_FOLDER	String	Google Storage folder path
SONG_ENDPOINT	String	Song endpoint
EGO_CLIENT_ID	String	Ego Client ID
EGO_CLIENT_SECRET	String	Ego Client Secret
EGO_URL	String	Ego URL API
JWT_KEY	String	Public key. This variable is optional if JWT_KEY_URL is set
JWT_KEY_URL	String	URL to fetch the public key. This variable is optional if JWT_KEY is set
REDIS_HOST	String	Default localhost
REDIS_PORT	Number	Default 6379
REDIS_PASSWORD	String	Redis password
ANALYSIS_TYPE_VERSION	Number	Default 1. Process only the Analysis within this schema version.
API_RETRIES	Number	Default 3. Retries when API call fails
API_TIMEOUT	Number	Default 10000. (Milliseconds) Response timeout on API calls.
NOTIFICATIONS_SLACK_URL	String	Webhook URL defines to which channel post notifications
TIMEZONE	String	Default America/Toronto. Use a zoneId format {area}/{city} to handle daylight savings.

Profiles

Profile	DESCRIPTION
updateCache	This profile will only update Pedigree cache DB
updateAnalysis	Synchronize VirusSeq data using the already existing Pedigree cache DB
	Not specifying a profile will do updateCache and then do updateAnalaysis (Recommended)