Second Sprint has set some essential groundwork

This week we finished Sprint #2, the primary aim of which was to lay some essential groundwork so that users of the BPA Data Portal can invoke the Galaxy-Australia API so that analysis jobs will be able to be submitted on their behalf.

To put this in context from a use-case perspective, this graphic highlights where the work in Sprint #2 sits (the base image is from our 'First set of User Stories prioritised' post):

Great news is that we achieved what we set out to produce in this sprint (on our development/staging instances):

• We upgraded Galaxy-Australia to the latest Galaxy version (i.e. 18.1) which was required since it includes the latest version of the API (#1 on the graphic above)
• We then developed functionality so that a user, once logged into the BPA Data Portal, can hit a 'Send to Galaxy' button which: 
• invokes the Galaxy-Australia API (#2 on the Graphic)
• determines if that person has an existing account on Galaxy-Australia
• and sends a job to Galaxy-Australia (in this case we just used a simple tool to produce a 'Hello world' message) 
• If no user of that email address exists in Galaxy-Australia, an account is made on their behalf

We know it works because when we visit Galaxy-Australia, we can see that the API has been invoked by the BPA Data Portal because a user account has been made in Galaxy-Australia with the same email address as is used by that person when they use the BPA Data Portal.


Also undertaken in this sprint was some other necessary preliminary work to "wrap" (i.e. to make them suitable for the GUI-based Galaxy-Australia interface) some python scripts from Andrew Bissett that can be used to undertake basic NMDS ordination. This is shown as #3 in the graphic above. Currently this is sitting on a test instance of Galaxy, but here's a movie showing the outputs:

All in all, a great sprint with lots of groundwork set for the next steps!