Re: [Gmod-tripal] Tripal & Python

[Lacey S. <lac...@gm...>]

Hi Anthony,

Thank you for reaching out!
The modules you linked to are actually part of the motivation of this
proposition and we definitely want to build on the lessons learned during
their development.

The python library proposed is a “pilot” project to re-write the non-Drupal
components of Tripal into a standalone Tripal library that would be
released as Tripal 4. This would be a re-write, not a plug-in of the
current Tripal 3. What remains after removing all the non-Drupal-specific
code would be a much slimmed down "Tripal Drupal" module. Stephen has made
an awesome schematic showing the difference between Tripal 3 and the
proposed Tripal4 here:
https://github.com/tripal/tripal/issues/636#issuecomment-422463648

In my mind the benifits of switching to python for the core Tripal library
is that it would allow your modules to interact with Tripal directly rather
then through web services. It would also make it easier for yourself and
other python developers to customize a Drupal/Tripal site without needing
to learn PHP or deal with the steep learning curve of Drupal. The intent is
to use a python class-based approach to make extending the implementation
of an entity (e.g. gene) and/or field (e.g. unique identifier) a simple
matter of extending the correct class. The same goes for chado data
loaders, installers, etc.

So to summarize, there are many reasons we are considering python for the
core Tripal library:
- Abstract customizing a Tripal/Drupal site from the Drupal logic to
protect our users from the Drupal release cycle
- To facilitate interaction with Tripal to/from python programs (your
modules already cover this)
- Allow python developers to extend a Tripal/Drupal site without needing to
learn PHP/Drupal
- Allow Tripal to be used without Drupal, either as a library for
interacting with Chado or to feed a different CMS

We would greatly appretiate the participation of your group in this
feasibility study! I think a great second meeting of the group would be a
demo of your modules so we can see all the capability that already exists
-if you are willing and have time of course. Regardless, we have already
started to look closely at these modules.

~Lacey

On September 18, 2018 at 3:48:44 AM, Anthony Bretaudeau (
ant...@in...) wrote:

Hi,

I'm a little confused, from what I understand, it looks a lot like what we
(Helena Rasche, me and now Matéo Boudet) have been working on during the
last years:

   - python-tripal (
   https://github.com/galaxy-genome-annotation/python-tripal/) to
   load/query data to/from a Tripal instance
   - python-chado (https://github.com/galaxy-genome-annotation/python-chado/)
   to load/query data to/from a Chado database (Tripal or not).
   - chado-schema-builder (https://github.com/erasche/chado-schema-builder/)
   to prepare pre-loaded, ready-to-use Chado SQL dumps.

So I think building on these bases would be much easier than starting
something from scratch and reinventing the wheel...

Of course contributions and feature requests are warmly welcome for all
these projects.

I'd be happy to discuss it in a meeting if there's interest (french
timezone).

Cheers

Anthony Bretaudeau

BIPAA/GenOuest, Rennes, France


Le 17/09/2018 à 18:00, Stephen Ficklin a écrit :

Hi All,

In our recent Tripal User's meeting we spoke about several issues related
to longevity and flexibility of Tripal.  One of the decisions from this
meeting was to work towards separation of components of Tripal that are not
specific to Drupal so that others who would prefer to not use Drupal can
take advantage of the infrastructure that Tripal provides.   These
non-Drupal components (such as Chado installers, data loaders, entities and
fields) will form a new Tripal library which can be used by the Tripal
Drupal module or by others who decide not to use Drupal.

One suggestion that was put forth was to perform a feasibility study to see
if a Python implementation of this new Tripal library could work.  Python
was selected because if of its broad use in informatics and data
analytics.  To be clear, this does not mean that Tripal will be abandoning
Drupal or PHP.  If the feasibility study demonstrates difficulty
integrating with Drupal or not-enough interest from our community then we
will explore a PHP-based Tripal core library instead.

We are reaching out to the community to solicit volunteers to help with
this initial feasibility project.  We'd like to have a kick off meeting for
the Python implementation in the next few weeks. If you are interested in
participating can you please send me an email as well as your time zone so
we can coordinate a meeting time.

Thanks!
Stephen




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