Aurélien Béliard authored Jan 10, 2017 and Mathieu Giraud committed Jan 10, 2017

Closes #1765

Aurélien Béliard authored Jan 10, 2017 and Mathieu Giraud committed Jan 10, 2017

See #1765

Aurélien Béliard authored Jan 10, 2017 and Mathieu Giraud committed Jan 10, 2017

See #1765

Fixed by parent commit

Completes 0333bf01 and fixes #2091.

Armand Bour authored Jan 06, 2017 and Mathieu Giraud committed Jan 09, 2017

Closes #2064.

The browser is quite large and can sometimes take some time to download
and start up.
Therfore the "patients" menu entry could sometimes take a long time to
be displayed if at all.
Adding this indicator will let the user know when everything has
finished loading and whether or not a server is configured with the
browser more clearly.

There was already an indicator that tracked uploads, so having the ajax
spinner on during uploads was redundant.

Once germline.js is loaded we can load the remainder. Otherwise
germline_builder.js could be loaded before germline.js finished loading which
caused germline_builder to complain because it didn't know the variable
germline_data

This commit just moved lines and reindented them.

make browser (for instance) could not have been launched because the directory
browser existed.

Added an error message when editing a file if the user doesn't specify a
patient, run or sample set to associate the file to.

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