GitLab

Added run task for mixcr program

Added program for MiXCR to config views

This completes 39bddf7a.

This reverts 7ed4fb29, and further adds 'germline_data =' for the second part.
germlines.data is json, ../browser/js/germline.js should be js.

A collection of sequences on all locus, gathered from other files.

This somewhat restores a test removed in 0ae4e1e6.

The type of message is determined with two variables:
* success either 'true' or 'false' determining if we had an error
* priority by default 1 if success == 'true' and 2 otherwise, can be overridden
  to be 3 (critical error: the user must see the message) or 0 (hidden message).

This is useful for the upload where we want the error message to be seen by the user.

On error show a notification corresponding to an error

Don't display the “no data file” message if we already had an error.

One upload is finished, a message is displayed.
patient_id is a Row, so display the id instead of displaying something like Row(...).
Also request.vars['id'] is the file ID which doesn't mean anything to anyone, so replace
it with the filename.

Remove the semicolon at the end (we may have nothing more after that).

We must make sure that 'upload finished' appears (and therefore find returns
something different from -1

Catch all IOError during processing of uploaded file. When filename appears
to be too long we should also probably warn the user before the upload is
finished, as soon as they submit their file.

This case cannot be tested as unit tests don't really store files on
disk when testing upload

tests/should-vdj-to-tap.py: option '-D', ignore gene/allele names for D genes in .should-vdj patterns

We should better display these measures, but at least they are here.

This should be more responsive.