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Methods to check whether a user can create or modify pre-processes

method for checking whether a group exists and a user can view said
group

method for checking whether a user can create a new config

$(DATA) was not working anymore, and was too human-specific.

New .tar.gz with the new germline/directory structure.

IMGT changes:
 - removal of IGLJ4*01, IGLJ5*01, IGLJ7*01
 - removal of IGHV3-23D*02
 - changes in all fasta headers (no more ‘rev-compl’)

Fixes #1766.

See https://www.ncbi.nlm.nih.gov/news/09-17-2014-simple-FASTA-headers-genomes-FTP/
Fixes #2173.

See #2173.

Having such a high value for uwsgi_read_timeout does not make sense for
most requests. Therefore it makes sense to create a new route for
uploading which has its own value for that parameter.

Placing the configuration in the separate file helps prevent
duplication.

adding a test on get_default_user_group to ensure the correct behaviour
is maintained.

By default section IDs in org-mode export are based on section numbers
which may change when adding or reorganizing sections.
We should rely as much as possible on custom IDs.

Opens #2168.

Our servers tend to have little space on the filesystem, but mount large
partitions to /mnt for file storage. This was hindering our upload
capabilities due to the creation of temporary files by nginx and uwsgi.
Redirecting these files to /mnt/data/tmp means this problem would only
occur when our main storage becomes limited in available space.

Fixes #2149

Sequence file downloads were limited to 1GB in size. Increasing this
parameter allows nginx to serve large files.

Fixes #1464

When uploading large files, users would sometimes encounter a gateway
timeout due to the fact that nginx was dropping the connection to the
backend after a set amount of time and indicating that the upload may
have failed, although the backend would continue to process the file and
ultimately -- in most cases -- correctly finish the upload.
Increasing the value should reduce the amount of confusion incurred for
users.

This makes the code more regular, and fixes #1006.

These tests were previously launched without '-i', on purpose.

See #2153.

New features with -g.
-g is the recommended way, -V/-D/-J/-G are more advanced.

This failing test is linked to #2003.

Now we mark as 'ignored' the failing tests (see #2158),
but set a milestone for issues that 'should be resolved before next release' (here %1).

It's curious that this test was not failing before: The fasta file was wrong.
Anyway, the test does not work.
Opens #2157.

This implies a change in the -m value.
See #1673.

They are not happy with -g, as they use specific parameters.
See #2156.

The recommended option is now '-g germline/homo-sapiens.g'.

Defers to core/germline.cpp the possible failure in opening the file.
Completes the previous commit to fix #2134.

We now recognize only exact matches. See #2134.

See #1233

Germlines are now on the www for consistency.

When using custome germlines the
this.m.germlineList.list[system]['recombinations'] was not defined and generated an error that prevented the loading of the germlines.

Fix vidjil/vdj#334