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titleDeployment (K8S refactoring)

Major tasks:

  • Fragalysis stack → kubernetes

    Status
    colourYellowGreen
    titleIn progress(ish)
    Status
    titleFragalysis questions coming

    • Plus JupyterHub(?)

    prototype

    • Backend neo4j

    • Deploy JupyterHub (ORN version)

    • Switch to postgres

    • Fragalysis backend to Fragment Network by API

  • Fragment network → kubernetes

    Status
    colourGreen
    titleDONE

  • Squonk → kubernetes

    Status
    colourGreen
    titleDONE

  • Galaxy → kubernetes

    Status
    colourRed
    titleplanning

  • Migrating Verne to K8s

    Status
    colourRed
    titlePlanning

  • Fragalysis stack CI/CD

    Status
    colourYellow
    titleHOLDPENDING

  • Fragment network CI/CD

    Status
    colourYellow
    titleHOLDPENDING

  • Openshift K8s

    Status
    titleHOLD

Notes:

  • Early March for K8S

  • Don’t need CI/CD for demo on kubernetes – should we hold off for 2/3 months? (Travis vs. Jenkins)

  • Testing of documentation (Janssen)

  • Process for AWS exists, but openstack doesn’t (for DLS) – 1 week after start (as long as networking, accessibility etc. work)

  • Need to discuss Galaxy:

    • use helm charts instead of playbooks?

  • Fragalysis questions: Mechanisms for running the data loaders?

  • Janssen: Scott will have a better idea of wether it will be applicable outside of the Fragalysis scope/use (still investigate)

  • Pin down date for starting deployment

  • Long TC for deployment on AWS

  • M2M/Janssen can deploy - can run playbook, entering version that deploys stack to cluster

Actions:

  •  Follow-up on technology stack questions with Janssen (TD)
  •  Second technology stack meeting - arrange (RS) [week after next]
  •  Send containers to Janssen so they can run through tests (TD) - keep sending
  •  Link Janssen up with Björn for Galaxy deployment
  •  Documentation Repo (for deployment) (RS)
  •  Dates for STFC for deployment (openstack) (TD/AC)

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titleFragment Network

Major tasks:

  1. Improve fragmentation algorithm

    Status
    colourYellow
    titlein progress

  2. Define data-building workflow

    Status
    colourYellow
    titlein progress

  3. Implement API

    Status
    titleHOLD

  4. Add compounds into network via. API

    Status
    colourPurpleYellow
    titleDiscoverIN progress

Notes:

  • Relational database - being used to index molecules (all datasets that are processed) – it’s where the molecules are stored before the graph network is created

  • Upper limit (guess) of adding molecules directly into network is ~10,000

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