GSCF and Molgenis Hackathon project

From BioAssist
Jump to: navigation, search

Background

Both the Generic Study Capturing Framework (GSCF) and several MOLGENIS-based applications, such as AnimalDB, can be used to capture and share data related to studies in man and animals. Each have their strong points: GSCF with its advanced templating mechanism and well-developed user interface, and MOLGENIS with its generator to make applications at will and the flexible PhenoOM datamodel.

It would be nice to integrate the two systems and so achieve "the best of both worlds". Technically, this should be feasible, both applications are programmed in Java (MOLGENIS) or Java-based (GSCF: built in Grails which runs on Groovy) which is a language that compiles to the JVM) and have API's (MOLGENIS Database API, SOAP API and GSCF REST API). Also, most of the GSCF wizards and template mechanism have recently been refactored into a Grails plugin.

Participants

  • Erik Roos (MOLGENIS, UMCG - GCC, confirmed)
  • Joris Lops (MOLGENIS, UMCG - GCC, confirmed)
  • Joeri van der Velde (MOLGENIS, RUG - GCC, confirmed)
  • Kees van Bochove (GSCF, confirmed)
  • Tjeerd Abma (GSCF, UMC Utrecht, confirmed)
  • Jeroen Wesbeek (GSCF, TNO Zeist, confirmed)
  • Siemen Sikkema (GSCF, UvA, confirmed)

RESULTS

The result of the 2 day hackathon can be viewed at http://hackathon.nmcdsp.org

User Stories

See: File:Use-case MOLGENIS-GSCF AnimalDB.doc

As an AnimalDB user, I want to use a GSCF-style Study Wizard so I can easily and intuitively make a new Study, add protocols and animals, etc.

Acceptance Criteria:

  • I can add a new Study from the UI.
  • When making a new Study, I can drag animals, protocols etc. into it.
  • I can also make new animals, protocols etc. on the fly and drag them into my Study.

How to demo:

  • Let someone who is new to the system create a new Study containing both existing and new animals, protocol etc.

Importance:

Story Points:

As an AnimalDB user, I want to apply a protocol to multiple animals in my Study at once, directly from the UI

Acceptance Criteria:

  • I want to edit my data in an intuitive way, directly from the matrix.
  • There are two ways of editing to be discerned here:
    • Edit/correct an existing value (for values that are only measured once, like Species)
    • Edit/add a new value (for values that can be measured multiple times, like Weight)
  • However, if you make a mistake, it should also be possible to use the edit/correct option for singular measurements.

How to demo:

  • In the AnimalDB app, go to the Matrix view, select an animal, apply the Weight protocol (edit/add option) and check if the new value shows up, with the previous one(s) still present.
  • In the AnimalDB app, go to the Matrix view, select an animal, apply the Weight protocol (edit/correct option) and check if the new value shows up, with the previous one no longer present.
  • In the AnimalDB app, go to the Matrix view, select an animal, apply the Sex protocol and check if the new value (e.g. Male instead of Female) shows up, with the previous one no longer present.

Importance:

Story Points: