This implementation has been superceded by https://github.com/DNAstack/data-connect-trino. The standard as implemented here is obsolete.
An implementation of the GA4GH Discovery Search API, on top of PrestoSQL. This software enables users to enumerate and query data surfaced by an instance of PrestoSQL in a manner compliant with the GA4GH Discovery Search specification, and receive responses compliant with the Table specification.
Any structural changes to this README should be checked against the README_TEMPLATE available in dnastack-development-tools, with that document updated as necessary.
Get started in 30s.
- Java 11+
- A presto server you can access anonymously over HTTP(S).
mvn clean package
Set these two environment variables.
PRESTO_DATASOURCE_URL=https://<your-presto-server>
SPRING_PROFILES_ACTIVE=no-auth
The search adapter requires a Postgres database. To start the app locally quickly with the default settings, you can spin up the database with this docker command:
docker run -d -p 5432:5432 --name ga4ghsearchadapterpresto -e POSTGRES_USER=ga4ghsearchadapterpresto -e POSTGRES_PASSWORD=ga4ghsearchadapterpresto postgres
mvn clean spring-boot:run
The app can be deployed using one of 3 different spring profiles which configure the authentication expectations. The default profile will be used if no other profile is activated.
Each profile also enables the following set of spring configuration variables:
APP_AUTH_AUTHORIZATIONTYPE="bearer" or "basic" or "none"
APP_AUTH_ACCESSEVALUATOR="scope" or "wallet" # only applies when AUTHORIZATIONTYPE=bearer
APP_AUTH_GLOBALMETHODSECURITY_ENABLED=true or false # enables security annotations on REST endpoints To set a profile simply set the SPRING_PROFILES_ACTIVE environment variable
to one of the three profiles outlined below:
The default profile requires every inbound request to include a JWT, validated by the settings configured below. The configuration is described by the AuthConfig class. This is the profile used if no profile is set.
Set the environment variables below, replacing the values below with values appropriate to your context.
# (Required) The STS which issued this token.
APP_AUTH_TOKENISSUERS_0_ISSUERURI="https://your.expected.issuer.com"
# (Required) The Json Web Key Set URI (where to find token validation keys)
APP_AUTH_TOKENISSUERS_0_JWKSETURI="https://your.expected.issuer/oauth/jwks"
# (Optional) Set audience if you want your token's audience to be validated.
APP_AUTH_TOKENISSUERS_0_AUDIENCES_0_="ga4gh-search-adapter-presto"
# (Optional) Set scopes if you want your token's scopes to be validated. Set multiple with _SCOPES_1_, SCOPES_2_...
APP_AUTH_TOKENISSUERS_0_SCOPES_0_="read:*"One may alternatively set the token validation key directly by setting the environment variable APP_AUTH_TOKENISSUERS_1_RSAPUBLICKEY to the desired key,
and omitting the JWKSETURI variable.
The wallet-auth profile requires every inbound request to include a JWT, validated by the settings configured below. The configuration is described by the AuthConfig class. This is the profile used if no profile is set.
The wallet-auth profile also sets up JWT-based authentication, and is configured with the same environment variables as the above, but also enables evaluation of Wallet-based access policies at endpoints.
DO NOT USE IN PRODUCTION
This profile will publicly expose all routes and does not require any authentication. Best left in your dev environment.
This profile will protect API routes with basic authentication. Additionally, when a user makes a request, if they have
not logged in they will be redirected to a login screen. The default username is user, and the default password is set in
the application.yaml.
To configure the username and password, set the following environment variables:
SPRING_SECURITY_USER_NAME={some-user-name}
SPRING_SECURITY_USER_PASSWORD={some-password}
The search adapter uses presto to save queries, so that it can reparse them during pagination to re-evaluate functions that need to be processed prior to submitting queries to presto.
The following is a quick start for local development:
docker pull postgres:latest
docker run -p 5432:5432 --rm --name ga4ghsearchadapterpresto -e POSTGRES_USER=ga4ghsearchadapterpresto -e POSTGRES_DB=ga4ghsearchadapterpresto -e POSTGRES_PASSWORD=ga4ghsearchadapterpresto postgres
There are a number of required configuration properties that need to be set in order to communicate with a presto deployment.
Point the service to a presto server by setting the following environment variable:
PRESTO_DATASOURCE_URL
If your presto instance is also protected, this adapter supports performing OAuth 2.0 Client Credential grants in order to retrieve access tokens for its configured Presto instance.
Configuration of the presto auth setup is quite easy and can be done directly through the following environment variables.
APP_AUTH_PRESTOOAUTHCLIENT_TOKENURI="https://your.sts/oauth/token"
APP_AUTH_PRESTOOAUTHCLIENT_CLIENTID="your-client-id"
APP_AUTH_PRESTOOAUTHCLIENT_CLIENTSECRET="your-client-secret"
APP_AUTH_PRESTOOAUTHCLIENT_AUDIENCE="your-requested-audience"
APP_AUTH_PRESTOOAUTHCLIENT_SCOPES="your space delimited requested scopes"