934fb10c answers the question in daec6797. Therefore the try/except construction
is not useful anymore (even as a memory).

When VDJ positions cannot be determined because of a lack of information in the
original file, the function just returns a None.

Fix #2089

The configs added by the init_db function were missing some values, and
could therefore not be used 'out of the box'.
This should resolve the issue and move us closer to a 'plug and play'
situation with our chosen installation methods

In the debian packages all git revision information has been removed.
Therefore, for the time being we will simply display 'not versioned' if
git res-parse HEAD causes an exception

Streamlines things before thinking seriously to #1471.

Master is our stable branch.

Fixes 2f117f42

See 2f117f42

This follows a suggestion by @magiraud in #2085 about
the usefulness of hasSeg.
Now hasSeg is used to reduce the code written, enhance the
readability and minimize my cognitive dissonance (see c97705f9).

Closes #2085.

At the moment I don't see a good reason for ignoring exceptions.
As this is not explained, I prefer removing this behaviour.
If it appears necessary to put it back, that should be clearly explained.

Lack of this argument created a problem when accessing it.

According to our format, sequence is not in the seg field.

js/model_loader.js show sample information

modify model loader to show sample information when a local file is download, by @aurelBZH 

@magiraud @RyanHerb

See merge request !2

modify model loader to show sample information when a local file is download

Most of the time, it is now the most important group and the place
to check or update the permissions.

Fix #2077.

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

A somewhat large part of this section dated back from more than two years ago.

Fix “db is undefined” lorsque la base de données n'est pas utilisée

Dans le cas où l’utilisation de la base de données est désactivée dans le fichier de configuration, une exception lancée dans `segmenter.js` est remontée dans la console JavaScript, ce qui facilite le développement. Ce commit implémente ce comportement (qui était donc absent) dans les fichiers :
* `builder.js` ;
* `graph.js` ;
* `list.js` ;
* `scatterPlot.js`.

Il permet également d’éviter une erreur JavaScript `this.db is undefined` si une erreur survient dans ces fichiers.

See merge request !1

Armand Bour authored Dec 15, 2016 and Mathieu Giraud committed Dec 18, 2016

The scatterplot, builder, graph, and list classes were not checking if
the database reference was defined, causing a JavaScript error when an
exception was thrown in the functions. This could only occur when not
using any database. This commit implements the behaviour seen in
segmenter.js: the exception is thrown if no database reference is defined
so that the exception can be seen in the JavaScript console, using a
function added to tools.js.

In d67262 the DIR_PEAR variable was applied incorrectly.
Instead, we now pass the pear directory to the pear.py script

closes #2051

Currently PEAR must be installed in a specific directory in order to be
executed during pre-processes.
Therefore adding a DIR_PEAR to the defs.py file will allow users to
reference existing PEAR installations without the need for adding
symbolic links to the vidjil installation.