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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.

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.

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.

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.

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

As the pre-process name can be quite long, we first show the status
otherwise it could be hidden.

We must show that we can click on the preprocess to have further informations.

editing permissions or deleting a patient was broken due to the wrong id
being passed to the controller.

The downloaded files are now the same are the ones served by the server to the client.
Before that the served files were the ones stored on disk but get_data and
get_analysis do some work to slightly modify the files.

See #2102

Regular support is currently done by @flothoni (fr), @mikael-s and @magiraud (en).

There was a reference to the type variable in the view, although the
type variable had been replaced a few commits ago.

Added missing parameter to request when sorting the sample_set list

passing the helper to the view instead of the type in order to call some
helper functions from the view. Notably to fix the add button which only
worked for generic.

In order to be able to indicate whether another page is available, we
query one more item than we would like to display. Therefore we need to
filter out this last element.

Previously patient and run lists has filtering. Generic sample_sets now
have filtering too.

With the recent changes, going back to a multi-table system, it was
necessary to add a table to contain some extra information to generic
sample sets

Due to the amount of data being applied there was a considerable amount
of overhead involved in creating an object for each row in the query.

In order to attempt to preserve some of the generic code, the models
have been converted to helper classes.

Making things as generic as possible. The view now relies on a set of
methods provided by the model in order to generate each row in the table