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Although the jquery plugin autocomplete.js was providing the basic
functionnality we needed, it was not natively able to display the list
of suggestions in the desired position for our textareas.

At.js is capable through the use of Caret.js of displaying a suggestion
box under the caret in a textarea.

This javascript code is heavily inspired by the code present in the
gitlab-ce project and allows us to have a nicely cached data-set to
limit database queries.

The group_id had previously been committed as a hard-coded value, thus
locking the completion to a single group. Obviously we want completion
to work for everyone, so this will achieve our goal.

autocomplete.js contains a binding function to bind the autocomplete
library to a DOM element.

The views then call this function when they are focused

there were a couple issues with calls to in non-existant helper
instance, so now we have an instance to work with

See #2519.

If the config has results_files associated, gisable the delete button

Add an indication of which file has been selected in the jstree module.

add a database field to indicate whether a sequence file is from the
network. As well as an indication in the sample set file list to inform
the user.

See #2523

Fixes #2512.

Follows e13ff56e.

Previously only groups that contained at least one member were
displayed. Leading to an issue where if the last member of a group were
to be removed, it was no longer possible to interact with said group fro
the interface. Therefore requiring database-level intervention.

the controller was developed without the corresponding view and hence
was never debugged.

See #2381

See #2141.

The permissions controller was not refactored into the new sample_set
system and therefore prevented giving access to sample_sets to new
users.

when editing files, pre_processes can be run again, so we want to fetch
the most recent one.

This code was used once when migrating the database to sample sets. See 11d4c64f and #2284.
This is now dangerous, nobody should click on that link.

Thanks @flothoni for the suggestion.
Fixes #2278.

Following the previous commit, we encode a new method to display 'set' for SET_TYPE_GENERIC.
See #2282.

The confirm page was not making proper use of the helper classes
implemented for the generic sample_set system.

Only the sequence_file is needed since the entry already contains the
correct pre_process_id

The controller expects two parameters: the sequence file id and the pre
process id and returns a reload redirect message.

when loading the sample_set index page a permission check was performed
on the default config entry (empty select box) which is not a valid
config reference. This was breaking the new existance checks in the
permissions.

The controller does not manage the form anymore. The controller is
now restricted to its minimum: returning a JSON with the results.

The sequences are sent by the request.

moving the page navigation buttons and redesigning it a litte to match
the rest of the style and make it a little more visible