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AtlasWorkers

AtlasWorkers is celery-based distributed computation module for AtlasWebService. However, it is a general computation module for other tools with standard interface by using RabbitMQ, Redis.

Recommended Usage

Install and execution

Before running, config.yml file is required to be ready with AWS credentials as well as other options. config_template.yml can be copied and furnished with required parameters.

Using docker-compose (or docker compose in recent docker versions). Exmemplary docker-compose.yml is in dockerfiles/docker-compose.yml

    $ docker-compose run <worker-service-name>

For service

    $ docker-compose up -d <worker-service-name>
API endpoint

  • [POST] /api/v1/task - Send a worker request with following arguments in JSON format

    • task : task name (e.g. gene.compute_qc)
    • queue : queue name (e.g. atxcloud_gene)
    • args : list of arguments for the task
    • kwargs : keyword arguments for the task

  • [GET] /api/v1/task/<task_id> - To get an progress or the result of the request.

List of current workers

  • gene (queue : atxcloud_gene)
    • compute_qc , this is used for the AtlasGX gene viewer
      • arguments : [filename, gene_list], e.g. ["data/D172/out/Gene/raw/spatial/genes.h5ad",["Vegfa"]]
      • example payload : 
            {
        "queue":"atxcloud_gene",
        "task":"gene.compute_qc",
        "args":["data/D172/out/Gene/raw/spatial/genes.h5ad",["Vegfa"]],
        "kwargs":{}
    }
      • example response : 
            {
        "_id": "218e2d6d-3344-4295-b318-e97c460ea59a",
        "name": "gene.compute_qc",
        "args": [
            "data/D172/out/Gene/raw/spatial/genes.h5ad",
            [
                "Vegfa"
            ]
        ],
        "kwargs": {},
        "queue": "atxcloud_gene",
        "requested_by": "admin",
        "requested_at": "2021-11-15T15:24:10.711350"
    }
  • core (queue : atxcloud_core)
    • This is test purpose worker.

Changelog

2021-11-15
  • gene_worker added with compute_qc task
2021-11-13
  • API endpoints are ready in AtlasWebService
  • RabbitMQ, Redis deployed in the server (address: api.atlasxomics.com), which are password protected
  • Celery added to the docker environment