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workflow-api

This service exposes a WES compliant REST API and an ARGO Graphql API for getting, starting and canceling runs. Data fetching for both APIs is backed by elasticsearch (filter, paging, & sorting).

Tech Stack

  • Java 11
  • SpringBoot
  • Spring Security
  • Springfox Swagger
  • Elasticsearch
  • Graphql-java
  • Apollo Federation
  • Reactor Rabbitmq Streams

REST API Endpoints

  • List the workflow runs:

    GET /runs

  • Get detailed info about a workflow run:

    GET /runs/{run_id}

  • Get quick status info about a workflow run:

    GET /runs/{run_id}/status

  • Get information about workflow execution service:

    GET /service-info

  • Send request to start new runs:

    POST /runs

  • Post request to cancel existing run:

    POST /runs/{run_id}/cancel

If using secure profile, include token in authorization header: { Authorization: Bearer $JWT }

Graphql

  • Graphql Endpoint:

    POST /graphql

  • full schema can be found here: ./src/main/resources/schema.graphql

If using secure profile, include token in authorization header: { Authorization: Bearer $JWT }

Apollo Federation support:

This service has support for Apollo Federation which extends certain gql types found in song-search.

With a service like rdpc-gateway the schemas from these two services can be federated into a larger schema that joins the entities.

Configuration

Configuration is setup in ./src/main/resources/application.yaml

Elasticsearch:

This service requires two elastic search index, workflowIndex and taskIndex.

The mappings for these indices can be found from workflow-relay's mappings:

workflow - https://github.com/icgc-argo/workflow-relay/blob/develop/src/main/resources/run_log_mapping.json

task - https://github.com/icgc-argo/workflow-relay/blob/develop/src/main/resources/task_log_mapping.json

Configure other es properties as required.

Secure profile:

The secure profile enables Oauth2 scope based authorization on requests.

Configure jwtPublicKeyUrl (or jwtPublicKeyStr for dev setup) in conjunction with the JWT issuer. Also configure the expected scopes as needed.

Test

mvn clean test

Build

With maven:

mvn clean package

With docker:

docker build . -t icgcargo/workflow-api:test

Run

Maven with app default and secure profile:

mvn spring-boot:run
mvn -Dspring-boot.run.profiles=secure spring-boot:run

Docker with app default and secure profile:

docker run icgcargo/workflow-api:test
docker run -e "SPRING_PROFILES_ACTIVE=secure" icgcargo/workflow-api:test