Menu
▾
▴
Re: [Gmod-tripal] Tripal & Python
|
From: Anthony B. <ant...@in...> - 2018-09-24 15:11:28
|
<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<p>Hi,</p>
<p>4 or 5pm France time is usually fine for me, but not on friday :)</p>
<p>Anthony<br>
</p>
<div class="moz-cite-prefix">Le 21/09/2018 à 18:01, Guignon,
Valentin (Bioversity-France) a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:DB7PR03MB3579675BF4D49280EF487E5AFB120@DB7PR03MB3579.eurprd03.prod.outlook.com">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Wingdings;
panose-1:5 0 0 0 0 0 0 0 0 0;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman",serif;
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;
color:black;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
p.airmailon, li.airmailon, div.airmailon
{mso-style-name:airmail_on;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;
color:black;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;
color:black;}
span.EmailStyle21
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
/* List Definitions */
@list l0
{mso-list-id:578712956;
mso-list-template-ids:-1161904034;}
@list l0:level1
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Symbol;}
@list l0:level2
{mso-level-number-format:bullet;
mso-level-text:o;
mso-level-tab-stop:72.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:"Courier New";
mso-bidi-font-family:"Times New Roman";}
@list l0:level3
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:108.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level4
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:144.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level5
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:180.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level6
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:216.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level7
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:252.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level8
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:288.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
@list l0:level9
{mso-level-number-format:bullet;
mso-level-text:;
mso-level-tab-stop:324.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
mso-ansi-font-size:10.0pt;
font-family:Wingdings;}
ol
{margin-bottom:0cm;}
ul
{margin-bottom:0cm;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">In
my case 5pm (France time) is ok.<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">
Val<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"
moz-do-not-send="true"><o:p> </o:p></a></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">From:</span></b><span
style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:windowtext">
Stephen Ficklin [<a class="moz-txt-link-freetext" href="mailto:spf...@gm...">mailto:spf...@gm...</a>]
<br>
<b>Sent:</b> vendredi 21 septembre 2018 17:57<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:gmo...@li...">gmo...@li...</a><br>
<b>Subject:</b> Re: [Gmod-tripal] Tripal & Python<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p>Hi Anthony,<o:p></o:p></p>
<p>I think the answers to your questions would best be addressed
in a meeting with multiple participants because some of those
questions don't yet have answers. The biggest item is that we
do not want to lose the entity/field design of Tripal v3 which
allows for cross-site querying. Also, just by way of
information, the Tripal loaders are slow but can be improved.
For example, loading the Gene Ontology using Tripal's OBO
loader used to take 6-8 hours. In the most recent development
version it only takes 30-45 minutes to load GO (10 minutes to
actually load GO and 20-30 for populating the cvtermpath
table). Also, the loader can load some of the newer ontologies
that have borrowed terms from other vocabularies, so it's much
more robust now. I'm sure we can improve performance of other
loaders as well, especially as we move towards a middle-layer
Tripal library.
<o:p></o:p></p>
<p>Unfortunately time zones don't help with getting everyone
together for a meeting. Our current Tripal User's Meeting is
at 8am US Pacific time and 5pm Central European time. But
typically those in Europe are not attending because I suspect
of the late time of the day in Europe and our meeting
typically occurs on a Friday. If we shift it one direction or
the other it makes it difficult for folks to be there on
either continent. We'd like to have you included in the
discussions. I'm wondering, and this question is for everyone
interested in participating. If we have a meeting regarding
Tripal and Python at 5pm Central European/8am US Pacific Time
can those in Europe make the call? Could folks do a 4pm
Central European/7am US Pacific Meeting? I think if we go to
6am US Pacific that will be too early and 6pm Central European
will be to late. I think folks in-between are probably okay
either way. Thoughts?<o:p></o:p></p>
<p>Stephen<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 9/19/2018 9:07 AM, Anthony Bretaudeau
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p>Hi,<o:p></o:p></p>
<p>Thanks for the clarification, no problem to make a demo
whenever you like!<o:p></o:p></p>
<p>At the moment, the main features of both python-chado and
python-tripal are to load data
(fasta/gff/blast/interproscan/blast2go/orthology/expression).
Python-tripal calls Tripal webservices to do it,
Python-chado do it directly by making SQL queries on the
chado db.<o:p></o:p></p>
<p>So I think what you'd like to do for Tripal 4 is closer to
python-chado?<o:p></o:p></p>
<p>What is not clear yet for me is :<o:p></o:p></p>
<p>- what exactly would you like to be implemented in this
tripal4-python library? Doing the data loading outside of
tripal is easy (well), but I guess templates for example
would need to remain in the php code? Field definitions
(like
<a
href="https://tripal.readthedocs.io/en/latest/dev_guide/custom_field/manual_field_creation.html"
moz-do-not-send="true">
https://tripal.readthedocs.io/en/latest/dev_guide/custom_field/manual_field_creation.html</a>)
or entities probably too? This is linked to the second
point:<o:p></o:p></p>
<p>- how you would make the tripal 4 php code communicate with
this tripal-python library? For data loading, it's just
writing one time the db with python, then reading the db
from php anytime. I have no idea if calling python code is
possible/advicable if field or entity definition is coded in
python for example...<o:p></o:p></p>
<p>I think example of codes that you would like to move to
python would help me understand better the whole idea.<o:p></o:p></p>
<p>Maybe these are stupid questions as I'm not very up to date
on the latest Tripal 4 plans and Drupal 8 features.<o:p></o:p></p>
<p>(Let me know if you prefer to continue discussing in the
github issue)<o:p></o:p></p>
<p>Anthony<o:p></o:p></p>
<div>
<p class="MsoNormal">Le 18/09/2018 à 19:00, Lacey Sanderson
a écrit :<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">Hi
Anthony,<o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">Thank
you for reaching out! <o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">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. <o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">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: <a
href="https://github.com/tripal/tripal/issues/636#issuecomment-422463648"
moz-do-not-send="true">https://github.com/tripal/tripal/issues/636#issuecomment-422463648</a> <o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">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.<o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif"><o:p> </o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">So
to summarize, there are many reasons we are
considering python for the core Tripal library:<o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">-
Abstract customizing a Tripal/Drupal site from the
Drupal logic to protect our users from the Drupal
release cycle<o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">-
To facilitate interaction with Tripal to/from python
programs (your modules already cover this)<o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">-
Allow python developers to extend a Tripal/Drupal site
without needing to learn PHP/Drupal<o:p></o:p></span></p>
</div>
<div id="bloop_customfont">
<p class="MsoNormal"><span
style="font-size:10.0pt;font-family:"Helvetica",sans-serif">-
Allow Tripal to be used without Drupal, either as a
library for interacting with Chado or to feed a
different CMS<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><br>
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. <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">~Lacey<o:p></o:p></p>
<p class="airmailon">On September 18, 2018 at 3:48:44 AM,
Anthony Bretaudeau (<a
href="mailto:ant...@in..."
moz-do-not-send="true">ant...@in...</a>)
wrote:<o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p>Hi,<o:p></o:p></p>
<p>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:<o:p></o:p></p>
<ul type="disc">
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">
python-tripal (<a
href="https://github.com/galaxy-genome-annotation/python-tripal/"
moz-do-not-send="true">https://github.com/galaxy-genome-annotation/python-tripal/</a>)
to load/query data to/from a Tripal instance<o:p></o:p></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">
python-chado (<a
href="https://github.com/galaxy-genome-annotation/python-chado/"
moz-do-not-send="true">https://github.com/galaxy-genome-annotation/python-chado/</a>)
to load/query data to/from a Chado database
(Tripal or not).<o:p></o:p></li>
<li class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l0
level1 lfo1">
chado-schema-builder (<a
href="https://github.com/erasche/chado-schema-builder/"
moz-do-not-send="true">https://github.com/erasche/chado-schema-builder/</a>)
to prepare pre-loaded, ready-to-use Chado SQL
dumps.<o:p></o:p></li>
</ul>
<p>So I think building on these bases would be much
easier than starting something from scratch and
reinventing the wheel...<o:p></o:p></p>
<p>Of course contributions and feature requests are
warmly welcome for all these projects.<o:p></o:p></p>
<p>I'd be happy to discuss it in a meeting if
there's interest (french timezone).<o:p></o:p></p>
<p>Cheers<o:p></o:p></p>
<p>Anthony Bretaudeau<o:p></o:p></p>
<p>BIPAA/GenOuest, Rennes, France<o:p></o:p></p>
<p><o:p> </o:p></p>
<div>
<p class="MsoNormal">Le 17/09/2018 à 18:00,
Stephen Ficklin a écrit :<o:p></o:p></p>
</div>
<blockquote
style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi All,<br>
<br>
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.<br>
<br>
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.<br>
<br>
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.<br>
<br>
Thanks!<br>
Stephen<br>
<br>
<br>
<br>
<br>
_______________________________________________<br>
Gmod-tripal mailing list<br>
<a
href="mailto:Gmo...@li..."
moz-do-not-send="true">Gmo...@li...</a><br>
<a
href="https://lists.sourceforge.net/lists/listinfo/gmod-tripal"
moz-do-not-send="true">https://lists.sourceforge.net/lists/listinfo/gmod-tripal</a><o:p></o:p></p>
</blockquote>
<p class="MsoNormal">_______________________________________________
<br>
Gmod-tripal mailing list <br>
<a href="mailto:Gmo...@li..."
moz-do-not-send="true">Gmo...@li...</a>
<br>
<a
href="https://lists.sourceforge.net/lists/listinfo/gmod-tripal"
moz-do-not-send="true">https://lists.sourceforge.net/lists/listinfo/gmod-tripal</a>
<o:p></o:p></p>
</div>
</div>
</blockquote>
</div>
</blockquote>
<p class="MsoNormal"><br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Gmod-tripal mailing list<o:p></o:p></pre>
<pre><a href="mailto:Gmo...@li..." moz-do-not-send="true">Gmo...@li...</a><o:p></o:p></pre>
<pre><a href="https://lists.sourceforge.net/lists/listinfo/gmod-tripal" moz-do-not-send="true">https://lists.sourceforge.net/lists/listinfo/gmod-tripal</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Gmod-tripal mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Gmo...@li...">Gmo...@li...</a>
<a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/gmod-tripal">https://lists.sourceforge.net/lists/listinfo/gmod-tripal</a>
</pre>
</blockquote>
</body>
</html>
|