Hi all,

at InterMine we are looking to improve various aspects of our UI, and
also our interaction with Galaxy. To that end, it would be great to find
out what ways there are of depositing data in a user's account. The
ideal would be to make requests from javascript that either open in
another tab, or can be entirely backgrounded.

After some reading of the bitbucket repos I note that:

 a) I can use the current mechanism of a data_source.py tool such as
    the flymine et al. ones. This would require me to do things like
    parsing the response headers for the galaxy session though, and I
    don't see a nice way of depositing data in a user's account without
    having come originally from galaxy.
 b) The API provides mechanisms for associating data files with
    histories, provided that these files have been already uploaded.
    It is straightforward to operate on a specific account, but I didn't
    find the API controller that allows individual tools, rather than
    whole workflows to be run. This would be ok I guess if I could
    create workflows rather than just run them.

So the current situation (please correct me if I am mistaken) is a
web-app based workflow that is best originated in galaxy, and an API
workflow that lacks certain features to do what I'd like. Again, I'd
very much like to be wrong here, and have like just not connected the
dots correctly.

However, if that is an accurate summation of the situation, I would be
happy to contribute to get what I want, rather than expecting others to
provide it. If anyone is interested in pull requests and a few questions
about internals, I'd be happy to help develop the API so that:
  a) POST /workflows -> creates a new workflow (from one or more tools),
     rather than running it.
  b) GET /jobs -> lists the status of running or completed jobs.
  c) POST /jobs -> runs a job (from a workflow), returning a job id.
  d) DELETE /jobs -> cancels a job, or removes it from the history
     if completed.

All best,


Software Developer
University of Cambridge

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