DynamoDB

The Disease Normalizer can store and retrieve disease records from a local DynamoDB database instance.

Note

See the DynamoDB handler API reference for information on programmatic access.

Local setup

See the instructions for deploying and running DynamoDB local in the AWS docs for server setup instructions.

By default, the Disease Normalizer expects to find a DynamoDB instance running at http://localhost:8000. The DISEASE_NORM_DB_URL environment variable can be used to designate an alternate location:

export DISEASE_NORM_DB_URL=http://localhost:8001

Warning

By default, DynamoDB Local serves to port 8000, which is also the port at which Uvicorn serves by default. This means that when running Disease Normalizer REST service with DynamoDB, you may have to use a different port for one of those processes. To do so with DynamoDB, use the -port option:

java -Djava.library.path=./DynamoDBLocal_lib -jar DynamoDBLocal.jar -sharedDb -port 8001
# then, in the Disease Normalizer's environment:
export DISEASE_NORM_DB_URL=http://localhost:8001

Configuration

By default, the DynamoDB interface uses a table named disease_normalizer for all DB items (source records, aliases, etc, as well as metadata like source data version, licensing, etc). The environment variable DISEASE_DYNAMO_TABLE can be used to define a different table name.

Managing persistent DynamoDB data

DynamoDB Local will store all data in a file named shared-local-instance.db when called with the sharedDb flag. This file persists after the database process ends and can be shared with other users. An alternate directory can be provided with the dbPath option if the DB file is stored in a different directory, e.g.:

java -Djava.library.path=./DynamoDBLocal_lib -jar DynamoDBLocal.jar -sharedDb -dbPath ../other_directory/

If the sharedDb flag is not provided, then data will not persist after the DynamoDB process ends.