GitLab

Removed a permission check on patient logging which was not only
redundant but also introduced a bug

When the seg[key] is not an object, we convert it to an object such as seg[key] = {'val': value}.
e-values were stored that way (without object).

As Clone can be built independently it is important that convertSeg
is called directly in the Clone constructor and not afterwards in the model.

As code is duplicated between the edit form and the add form, this
is the same code as efc4589

Who said watir tests are useless? Two unexpected bugs have been caught by making this test
(see the two previous commits).

There definitely should be a watir test on the monitor report.

For instance in offline mode (with old files?). Make sure
the code will still work

By generating a scatterplot for each locus, the  last locus
may not be the current one. Therefore, at the end, we explicitly
the current locus to the former one.

A typo (a misplaced ]) gave an undefined value which JS didn't complain about.
Therefore for N2, the sequence was retrieved until the end (thus including the J).

It will allow to watir-test it more easily

Added patient and run names as well as usernames in log views

Moved software and parameters to the end of the sample log

There was an inconsistency in the specification: "stop" was used several times, and "end" once.

We should follow format-analysis.org specification: "Positions on the sequence start at 1."
Note that these tests were introduced in 745b47db (Feb 2016), but, at this time, we did not check these positions.

Resolved an issue where samples would not be displayed in the global
compare view if the sequence file involved was present in multiple
sample_sets (patient + run)

Resolved an issue where attempting to remove a file from a patient or
run which was attached to a patient or run that was previously deleted
could cause a server error when checking permissions

Resolved some issues with the new queries which would systematically
cause a server error

This allows to know where we come from and therefore where we must redirect to.

It was not provided to the file/edit.html view which needs them to display
help on each pre-process.

This two views (file/add.html and file/edit.html) should definitely be
merged. The form has been renamed as for file/add.html.

Fix 6d28e261

Added button to compare sample_set view in run list

Fixed an issue where runs did not appear in the compare sample view and
one could not compare samples of a run

On some browser (at least Chrome 42) this may totally fail the filter()
function which breaks the autocomplete feature.

This is some documentation on how groups and users work inside the
permissions system. It also includes a procedure to follow when creating
an organisation with multiple roles

Fixed an issue with the calculation of associated_id when deleting
sequence files.

Added some packaging documentation.
It contains instructions to create a debian standards compliant package
of a vidjil release version (so only the algorithm part)