SSJDISPATCHER

The SQS S3 Job Dispatcher is designed for centralizing all gen3 jobs in the Gen3 stack. It monitors a SQS queue receiveing CRUD messages from S3 buckets and determine an action basing on the object url pattern.

For example, an url with a pattern of s3://bucketname/user.yaml of the object uploaded to S3 will trigger an even in S3 to send a message to a configured SQS. The dispatcher service pulls the message from the queue and dispatches an job that pulls fence image and run usersync job with fence-create command. For the other url with the pattern of s3://data_upload_bucket/000ed0fb-d1f4-4b80-8d77-0d134bb4c0d6/TARGET-10-PAREBA-09A-01D_GAGTGG_L003.bam, the service will dispatch an job to compute hashes, and size and register to indexd with url.

JobConfig is an json-base string to register an job. An example might be something like this:

{
    JOBS": [
          {
            "name": "indexing",
            "pattern": "s3://bucket/[a-fA-F0-9]{8}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{4}-[a-fA-F0-9]{12}/.*",
            "deadline": 3600,
            "image": "quay.io/cdis/indexs3client:master",
            "imageConfig": {
              "url": "http://indexd-service/",
              "username": "test",
              "password": "test"
            }
          },
          {
            "name": "usersync",
            "pattern": "s3://bucket/user.yaml",
            "image": "quay.io/cdis/fence:master",
            "imageConfig" :{}
          }
}

API Documentation

OpenAPI documentation available here.

YAML file for the OpenAPI documentation is found in the openapis folder (in the root directory); see the README in that folder for more details.

Setup

ssjdispatcher is generally deployed in a Gen3 environment and makes use of AWS resources.

For instructions on how to set up ssjdispatcher and the relevant AWS resources with Gen3 cloud-automation, see here.

For a high-level view of the context in which ssjdispatcher is used with Gen3 see here.

Building From Source

Build the go code with:

go build -o bin/ssjdispatcher

Building and Running a Docker Image

Build the docker image for ssjdispatcher:

# Run from root directory
docker build -t ssjdispatcher .

Run the docker image:

docker run -p 8080:8080 ssjdispatcher --port 8080

(This command exposes ssjdispatcher on port 8080 in the docker image, and maps port 8080 from the docker image onto 8080 on the host machine.)

Development

Tests

Run all the tests:

go test ./...

Quickstart with Helm

You can now deploy individual services via Helm! Please refer to the Helm quickstart guide HERE (https://github.com/uc-cdis/ssjdispatcher/blob/master/docs/quickstart_helm.md)