-
Notifications
You must be signed in to change notification settings - Fork 2
ClinGen Submission and Access
This page is intended to provide a useful guide for submitting and accessing MaveDB data via ClinGen APIs.
CLIN_GEN_SUBMISSION_ENABLED: boolean. Whether or not ClinGen submission is enabled for worker processes.
GENBOREE_ACCOUNT_NAME: string. The account name of the submission account.
GENBOREE_ACCOUNT_PASSWORD: string. The password for the submission account.
CLIN_GEN_TENANT: string. The tenant to which submissions are sent. This can be either dev-clingen or stg-clingen.
LDH_ACCESS_ENDPOINT: string. The base URL at which access to submitted data can be found. See the table below for information about environments and endpoints.
| LDH env | Role | Submission Endpoint | Access Endpoint |
|---|---|---|---|
| local dev/stg | development | https://genboree.org/mq/brdg/pulsar/dev-clingen/ldh/submissions/maveDb | https://genboree.org/ldh-stg/srvc |
| Local prod | staging | https://genboree.org/mq/brdg/pulsar/stg-clingen/ldh/submissions/maveDb | https://genboree.org/ldh/srvc |
| test | staging | https://genboree.org/mq/brdg/pulsar/stg-clingen/ldh/submissions/maveDb | https://ldh.test.genome.network/ldh/srvc |
| prod | production | not exposed | https://ldh.genome.network/ldh/srvc |
To submit data to the LDH:
GENBOREE_ACCOUNT_NAME=<account> GENBOREE_ACCOUNT_PASSWORD=<password> CLIN_GEN_TENANT=<tenant> DB_PORT=5434 DB_DATABASE_NAME=mavedb_staging DB_USERNAME=postgres DB_PASSWORD=<db_password> poetry run python3 src/mavedb/scripts/clingen_ldh_submission.py <urn_1> <urn_2> ...
To link records to LDH data:
GENBOREE_ACCOUNT_NAME=<account> GENBOREE_ACCOUNT_PASSWORD=<password> CLIN_GEN_TENANT=<tenant> LDH_ACCESS_ENDPOINT=<access_endpoint> DB_PORT=5434 DB_DATABASE_NAME=mavedb_staging DB_USERNAME=postgres DB_PASSWORD=<db_password> poetry run python3 src/mavedb/scripts/link_clingen_variants.py <score-set-urn_1> ... --score-sets --commit
If the environment variable CLIN_GEN_SUBMISSION_ENABLED is set to true, any score set where variants are mapped will have its variation submitted to ClinGen. After submission, attempts will be made to link the submitted data back to the records. Due to possible delays in the ingestion of data to the LDH, this linkage is backed off exponentially over a period of a few days to give the message queue time to process each submission.