Grant Task 4a: Linking to the Physiome Model Repository

[jonc125]

The authoritative source for curated models of cardiac electrophysiology is the Auckland Bioengineering Institute PMR. At present the Web Lab contains copies of CellML files that are annotated with our new metadata, but we do not wish to maintain a second ‘version’ of these models. Instead, definitive versions will be stored in PMR and used directly by our system, and we will provide new annotations in PMR, which will in turn add value to their curation process. Planned additions to PMR will link to our Web Lab to provide users with insights into model behaviours and comparisons to experimental data.

[MichaelClerx]

Andre & Tommy are happy to help

[mirams]

Keen to do this sooner rather than later, as we've already got a bit of drift in the Chaste/cellml repo from the main one...

[jonc125]

Hi Jonathan,

Just to echo Tommy’s comment that this sounds fantastic and something we’d really love to see, so if you need any help just shout out and we’ll try to help as much as possible.

Not sure if you have met Dave Brooks (of BiosignalML fame), but he is the one who mostly implemented the PMR integration into OpenCOR along with Alan Garny, and he is “fluent” in python and C++ so likely to be another useful point of contact. He only works a few days a week for the ABI working on OpenCOR, along with some other consulting work he does, so if you were ever looking for some extra temporary development/implementation help he might be interested (just in case that ever comes up and I forget to mention it again).

Cheers,
Andre.

-----Original Message-----
From: Tommy Yu [email protected]
Date: Wednesday, 24 May 2017 at 00:19
To: Jonathan Cooper [email protected], David Nickerson [email protected]
Cc: Michael Clerx [email protected]
Subject: Re: Linking the Web Lab to PMR

    Hi Jonathan,
    
    That is some exciting development, glad to see more collaborations like this.
    
    If your intended workflow is to give users on your Web Lab platform the ability to list their repositories (workspaces) that they have stored on PMR, retrieve whatever they select into Web Lab via Git (either from that list or a direct URL), modify that within the Web Lab platform, and then push all that back up to where it came from, it can be done already since we have OAuth enabled for this.  For a demo, a simple client in Python that uses the legacy JSON protocol is provided at https://github.com/PMR2/pmr2.client.
    
    A more current documentation for the current protocol is available at https://aucklandphysiomerepository.readthedocs.io/en/latest/webservice.html.
    
    For pushing (or pulling a private git workspace), it is a bit tricky because it requires the generation of a temporary password for the given workspace, but again that is a simple POST request to a specific end point under the workspace with the OAuth credentials.  It does require one extra scope (which is specified in the example script https://github.com/PMR2/pmr2.client/blob/master/src/pmr2/client/script.py), so that POSTing to the specific endpoint ($workspace_url/request_temporary_password) will provide a one use, quick to expire temporary password for the client (Web Lab) to push back to the workspace on behalf of the resource owner.  OpenCOR has implemented Git push/pull integration with PMR via this mechanism.
    
    In the future if PMR ever gets OAuth 2.0 support, the temporary password method will probably not be needed for git due to how the token doesn't require computing the signature for the body.
    
    Oh yeah, the key associated for the demo client only support the out of band method and so for actual web services a client key/secret will need to be added and be associated with a real domain name, which I can do for you once you have that ready.
    
    Any more questions please feel free to ask me.
    
    Cheers,
    Tommy.
    
    
    On 23/05/17 23:49, Cooper, Jonathan wrote:
    > Hi Andre & Tommy,
    >
    >
    >
    > We’re getting our new Web Lab project off the ground, and having a
    > kick-off meeting on the 12^th June to discuss a revised architecture
    > for the system. One of the things I’d like to make sure of with this
    > is that we don’t make our lives difficult when we want to develop
    > closer links with PMR later in the project!
    >
    >
    >
    > We are considering using git repositories for models & protocols in
    > the Web Lab, cloning repositories hosted elsewhere where possible.
    > Since you also have models as git repositories, I’m hoping it’ll be
    > very easy for users to add their (or others’) models to Web Lab –
    > simply give the PMR URL, and authenticate with OAuth if it’s a
    > private repo. Are there any technicalities we should be aware of?
    > Would there be any difficulties if we wanted to push changes back to
    > PMR, e.g. adding annotations to a model?