Added a query for non admin users to view logs concerning elements to which they have access permissions

Moved class UserLogHandler to db.py in order to resolve issues
encountered with first logging test in patient.py

Added a handler designed to store logs in the database

Fixed an issue with the add run controller for admins that was producing
server errors

Fixed an issue with the run config links in the run index that expected a patient id
rather than a sample_set

Fixed an issue where the query for viewing a results_file's info
expected to have an entry in the patient table attached to the
results_file. This has been corrected to expect only a sample_set

Those files could quickly saturate disk space

seg['_evalue'] is rewritten by convertSeg... there's something wrong.

e-value was retrieved using getGene (which was kind of a hack), this
was broken when the seg key format evoled (see f6a2caf3).
Now e-value is tested to make sure we correctly retrieve it.

HERBERT Ryan authored Jun 17, 2016 and Mikaël Salson committed Jun 18, 2016

Reduced the group list when adding a patient or run to include only the
user's personal group and parents of the user's other groups

HERBERT Ryan authored Jun 17, 2016 and Mikaël Salson committed Jun 18, 2016

Refactored get_user_groups to returns only direct links to users.
Added method to obtain all parent groups of user

It should be more efficient to compare affects directly rather
than having an implicit conversion followed by a comparison.
However are these functions really called often?

If we have access to a patient, we can download the sequences. But we can't
modify so don't show the modification icons.

HERBERT Ryan authored Jun 16, 2016 and Mikaël Salson committed Jun 18, 2016

Apply save analysis permission to save analysis and add checkbox in
group/info.html to add permissions save to a group

Removed can_process_file to replace with has_permissions

Added owner_group to run so that it is possible to affect a run to any
group the user is a member of. Select box is currently hidden and
selects the user_group by default unless the group Lille is in the list

Added a save permission and methods to check permission to determine if
a user can save an analysis for a patient, run or sample_set

group selector is now devel-mode. user group is selected by default unless Lille is in the list. In which case Lille is selected

file.py changed access on patients list to only require read on patient or run rather than admin. upload permission is still required

Replaced accessible_query with vidjil_accessible_query and replace
strings with PermissionEnum where appropriate

Add more default permissions to admin user to ensure access is granted to admins with the new permissions

There were several places in the code where strings were still used to
determine, add or remove permissions. These have now all been replaced
with the correct Element from PermissionEnum