The purpose of this script is to syncronize data from a Cloud Object Storage (as a .tsv format) to VirusSeq data repository.
This script has been tested using NodeJS v^16.
npm ci.env. Populate all fields. See description of env variables in the Environment variables section.npm run dev or npm run dev:[profile] See description of profiles in the Profiles section| 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. |
| 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) |