Part of the GA4GH Starter Kit. Open source reference implementation of the GA4GH Data Repository Service (DRS) specification
The current Starter Kit DRS has some experimental features added to it. It does not match any published DRS Specification. We refer to this version as 1.3.0experimental in the starter kit documentation.
This starter Kit will be re-visited and updated once the new DRS specification is released.
We recommend running the DRS service as a docker container for most contexts. Images can be downloaded from docker hub. To download the image and run a container:
Pull the image:
docker pull ga4gh/ga4gh-starter-kit-drs:latest
Run container with default settings:
docker run -p 4500:4500 ga4gh/ga4gh-starter-kit-drs:latest
OR, run container with config file overriding defaults
docker run -p 4500:4500 ga4gh/ga4gh-starter-kit-drs:latest java -jar ga4gh-starter-kit-drs.jar -c path/to/config.yml
Postgres will be run on a separate container and simultaneously ran with Starter Kit DRS via docker compose.
Postgres container is running on port 5432, while DRS is run on port 4500 (4501 for admin):
Clone this repo:
git clone https://github.com/ga4gh/ga4gh-starter-kit-drs.git
Navigate into the repo's root folder
docker compose -f docker-compose-postgres.yml up -d
To ensure that both Starter-Kit DRS and Postgres containers are running:
docker ps
This command should list both containers with names drs and postgres
From the DRS config file > databaseProps attribute, we map DRS to the PostgreSQL database using its jdbc URL as well as Postgres credentials (username/password)
config-drs-postgres.yml:
databaseProps:
url: jdbc:postgresql://host.docker.internal:5432/starter_kit_db
username: postgres
password: postgres
To shut down the services, enter the following command:
docker-compose -f docker-compose-postgres.yml down
The service can also be installed locally in cases where docker deployments are not possible, or for development of the codebase. Native installations require:
- Java 11+
- Gradle 7.3.2+
- SQLite (for creating the dev database)
First, clone the repository from Github:
git clone https://github.com/ga4gh/ga4gh-starter-kit-drs.git
cd ga4gh-starter-kit-drs
The service can be run in development mode directly via gradle:
Run with all defaults
./gradlew bootRun
Run with config file
./gradlew bootRun --args="--config path/to/config.yml"
Alternatively, the service can be built as a jar and/or war and run:
Build jar:
./gradlew bootJar
Run with all defaults
java -jar build/libs/ga4gh-starter-kit-drs-${VERSION}.jar
Run with config file
java -jar build/libs/ga4gh-starter-kit-drs-${VERSION}.jar --config path/to/config.yml
Build war:
./gradlew bootWar
Run with all defaults
java -jar build/libs/ga4gh-starter-kit-drs-${VERSION}.war
Run with config file
java -jar build/libs/ga4gh-starter-kit-drs-${VERSION}.war --config path/to/config.yml
Whether running via docker or natively on a local machine, confirm the DRS API is up running by visiting its service-info endpoint, you should receive a valid ServiceInfo response.
GET http://localhost:4500/ga4gh/drs/v1/service-info
Response:
{
"id": "org.ga4gh.starterkit.drs",
"name": "GA4GH Starter Kit DRS Service",
"description": "An open source, community-driven implementation of the GA4GH Data Repository Service (DRS)API specification.",
"contactUrl": "mailto:[email protected]",
"documentationUrl": "https://github.com/ga4gh/ga4gh-starter-kit-drs",
"createdAt": "2020-01-15T12:00:00",
"updatedAt": "2020-01-15T12:00:00",
"environment": "test",
"version": "0.1.0",
"type": {
"group": "org.ga4gh",
"artifact": "drs",
"version": "1.3.0experimental"
},
"organization": {
"name": "Global Alliance for Genomics and Health",
"url": "https://ga4gh.org"
}
}
Additional setup steps to run the DRS server in a local environment for development and testing.
A local SQLite database must be set up before running the DRS service in a development context. If make and sqlite3 are already installed on the system PATH, this database can be created and populated with a dev dataset by simply running:
make sqlite-db-refresh
This will create a SQLite database named ga4gh-starter-kit.dev.db in the current directory.
If make and/or sqlite are not installed, this file contains SQLite commands for creating the database schema, and this file contains SQLite commands for populating it with the dev dataset.
Confirm the DRS service can connect to the dev database by submitting a DRS id to the /objects/{object_id} endpoint. For example, a DRS id of b8cd0667-2c33-4c9f-967b-161b905932c9 represents a root DRS bundle for a phenopacket test dataset:
GET http://localhost:4500/ga4gh/drs/v1/objects/b8cd0667-2c33-4c9f-967b-161b905932c9
Response:
{
"id": "b8cd0667-2c33-4c9f-967b-161b905932c9",
"description": "Open dataset of 384 phenopackets",
"created_time": "2021-03-12T20:00:00Z",
"name": "phenopackets.test.dataset",
"size": 143601,
"updated_time": "2021-03-13T12:30:45Z",
"version": "1.0.0",
"self_uri": "drs://localhost:4500/b8cd0667-2c33-4c9f-967b-161b905932c9",
"contents": [
{
"name": "phenopackets.mundhofir.family",
"drs_uri": [
"drs://localhost:4500/1af5cdcf-898c-4dbc-944e-1ac95e82c0ea"
],
"id": "1af5cdcf-898c-4dbc-944e-1ac95e82c0ea"
},
{
"name": "phenopackets.zhang.family",
"drs_uri": [
"drs://localhost:4500/355a74bd-6571-4d4a-8602-a9989936717f"
],
"id": "355a74bd-6571-4d4a-8602-a9989936717f"
},
{
"name": "phenopackets.cao.family",
"drs_uri": [
"drs://localhost:4500/a1dd4ae2-8d26-43b0-a199-342b64c7dff6"
],
"id": "a1dd4ae2-8d26-43b0-a199-342b64c7dff6"
},
{
"name": "phenopackets.lalani.family",
"drs_uri": [
"drs://localhost:4500/c69a3d6c-4a28-4b7c-b215-0782f8d62429"
],
"id": "c69a3d6c-4a28-4b7c-b215-0782f8d62429"
}
]
}
NOTE: If running via docker, the dev database is already bundled within the container.
NOTE: The unit and end-to-end test suite is predicated on a preconfigured database. The SQLite dev database must be present for tests to pass.
The endpoints that are made available at the admin port are beyond the DRS specification. These endpoints provide the users of the Starter Kit (the data provider) with the functionalities of creating, updating and deleting DRS Objects from the DRS Starter Kit server.
Please see the Configuration page for instructions on how to configure the DRS service with custom properties.
Multiple datasets are currently contained in this repo for development and testing. Raw bytes are located in src/test/resources and the SQLite dev database is preconfigured with DrsObjects for each of these files. The following datasets are included:
-
Test data from the htsjdk
- see the datasets page for a list of
DRS IDsforDrsObjectsin the htsjdk dataset
- see the datasets page for a list of
-
Open dataset of 384 Phenopackets: Paper, Dataset homepage
- see the datasets page for a list of
DRS IDsforDrsObjectsin the Phenopackets dataset
- see the datasets page for a list of
- Update the DRS specification version from
1.1.0to1.3.0experimentalin the service-info response and in the documentation.
- Fixed a bug where admin requests to create a controlled access DRS object (i.e. with visas) did not complete successfully
- DRS object batch requests
- Passport support - Passport mediated auth to DRS objects (using Starter Kit implementation of Passports)
- Auth info - Discover Passport broker(s) and visa(s) for requested controlled access DRS Objects (single object and bulk request)
- patched log4j dependencies to v2.16.0 to avoid Log4j Vulnerability
- GA4GH Tech Team [email protected]