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  1. Apache Taverna
  2. TAVERNA-941

Use Docker microservices from workflow

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    • Story
    • Status: To Do
    • Major
    • Resolution: Unresolved
    • None
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    • Taverna Engine
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    Description

      While TAVERNA-901 suggests a way to run Docker command line tools from Taverna, a more interesting aspect could be to run microservices from Taverna - with bindings to the dynamic ports of Docker.

      This would allow usage of existing WSDL and REST services in a Taverna workflow, but with an alternative Profile to use local Docker microservices.
      This could then use server-based web UI tools like OpenRefine and Jupyter - but also pure servers like RServe, ElasticSearch and Jena Fuseki SPARQL endpoints.

      Taken to the extreme this could be to start up a local Open PHACTS stack (multiple Docker images combined with docker-compose). (As this requires 32 GB of RAM and 0.5 TB of disk space that would not be a microservice though!)

      This is more architecturally challenging than the activity of TAVERNA-901 - as it would mean preprocessing steps like

      • Workflow Bundle lists required docker images
      • Fetch Docker images
        • Optional: load images stored in workflow bundle
      • Start Docker containers - possibly listening on dynamic ports
      • Optional: Using docker-compose for combining many containers
      • Check that containers are "ready" (unsolved problem in Docker world)
      • Modify/generate workflow profile to use the assigned localhost/port bindings for the docker microservices
      • Run the rest of the workflow
      • Shut down containers
      • Remove containers (optional)
      • Store provenance about Docker containers into Docker Bundle (optional)
        • Snapshot docker images used into Data Bundle

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              Unassigned Unassigned
              stain Stian Soiland-Reyes

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