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Mikaël Salson authored Oct 25, 2016 and Vidjil Team committed Oct 25, 2016

Since we just use the ID in the request, just retrieve it.
This is about a 2-fold increase in time.

Mikaël Salson authored Oct 25, 2016 and Vidjil Team committed Oct 25, 2016

Instead of filtering on patiend IDs after the request, filter directly
in the request using the belong operator.

For users with few patients, this makes a huge difference.

This is important as the alignment is computed with the first sequence as
the reference. The order must thus be perserved.

On the contrary, m.getSelected() doesn't ensure to preserve order.

Added email notifications to admins when disk space passes below the
allowed threshhold

This reverts commit 75e01801.

Due to an issue with self-signed certificates in the python ssl library,
https has been put off for the custom fuse.

Mikaël Salson authored Oct 21, 2016 and Vidjil Team committed Oct 21, 2016

Fix e3bdc9fc.
The field must still appear in the form for the value
to be sent to the server. Now the field is just hidden.

Thanks to @RyanHerb for pointing out that issue.

I'm glad when I succeed to spot typos coming from English people ;)

For users having only one group (the huge majority), there
is no need to add fields they won't be able to modify

mail variable from db model not available here. Temporarily disable
notification email.

check for available disk space test was wrong and returning the opposite
of the desired result

fix keyword error

This function can be called when one needs to check disk space. If the
disk space is below a specified percentage threshhold, the function
notifies the system administrators.
A boolean is returned to indicate the disk space situation.

Fused files with many samples are large.
By default, we limit the number of samples taken into account.

In case of success we can remove the file in the temporary directory as it is
stored elsewhere through Web2py mechanism. Storing it twice was space
consuming.

We modifie the log message correspondingly so that it can display the real
stored file.

If a file from the germlines.data doesn't exist in the current directory,
complain about it but provide a possible solution.

Reraising an exception was done following martineau's advices (see
http://stackoverflow.com/a/6062799).

Code was not working without providing the output filename.
Just make it mandatory.

The file will provide us with the list of germline files
that will be used by the browser (eg. IGHV.fa, TRAJ.fa...).

The need to provide them was error prone as we had to indicate
those files in several places (in germlines.data, in the
Makefile, ...)

PDF output has been replaced by HTML output since more than 18 months.

We don't expect make data to install a webserver.
Moreover we have other ways to do so, more reliably.

Use the -m option of tar so that the dates of the
germline files are the extraction date.
This will prevent re-extracting files if they are not newer

Standardize'' the Makefile with all rule and add a .PHONY to avoid ambiguities.

It recovers the files from the *saved* germlines, it does not retrieve the new ones.
This rule has no reason to create the germline.js. That file is created by the
corresponding rule.

It relies on other rules to do so.