Update every analysis stored in Song to have meta data matching the latest schema model.
npm ci- Copy .env.schema file to a new file named
.env. Populate all fields. See description of env variables in the Configuration section. npm run onceto run the script.
Currently there is only one run profile, which will attempt to update all analyses from all studies in Song.
Before running the script, several variables require configuration in order to connect the script to Song and provide authorization. These values can be added to the file .env. See details in the following table.
Read from .env file and provided to the script through the src/config.ts file
| Variable Name | Required | Default | Description |
|---|---|---|---|
| EGO_HOST | Required | - | Base URL for requests to Ego. Needed to fetch application JWT for Song Update Authorization. |
| EGO_CLIENT_ID | Required | - | Ego Application client ID, for Song Update Authorization. |
| EGO_CLIENT_SECRET | Required | - | Ego Application client secret, for Song Update Authorization |
| SONG_HOST | Required | - | Base URL for requests to Song. |
| SONG_ENV | Optional | - | Optional descriptor for log file to indicate which song instance is being used. |
| SONG_CONCURRENT_REQUESTS | Optional | 5 |
Maximum number of requests that can be initiated to song. Higher values should complete the update requests faster, but ensure that there is enough capacity on the song service to handle the requests. Too many concurrent requests typically result in frequent timeouts (and possible script crashes) due to limited pool of JDBC connections from Song to its database. |
| SONG_PAGE_SIZE | Optional | 100 |
Total number of analyses returned per paged request for analyses. 100 seems to be a fine value. Increasing this has a negligable effect on script completion time. This will limit the number of concurrent update requests, so make sure this is larger than the SONG_CONCURRENT_REQUESTS value. |
| MIGRATION_CHAIN | Optional | dev |
dev or prod. The migration chains in each environment are slightly different, so make sure in Production this is set to prod or there will be errors |
| VAULT_ENABLED | Optional | false |
If set to true then secrets will be read from vault. The service will crash if the secrets cannot be retrieved. This will replace the env variables for Ego Client ID and Secret. |
| VAULT_SECRETS_PATH | Required if VAULT_ENABLED is true |
- | Path to vault secrets for this job. |
| VAULT_URL | Required if VAULT_ENABLED is true |
- | URL to reach vault. |
| VAULT_ROLE | Required if VAULT_ENABLED is true |
- | Role defined in vault that this service can use to read the secrets at the provided path. |
| VAULT_TOKEN | Optional | - | Vault Token that can be used to authorize reading from vault. Used in place of system provided token. |