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Re: [Gmod-tripal] Tripal & Python
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From: Stephen F. <spf...@gm...> - 2018-09-26 19:20:02
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It looks like Oct 2nd works for everyone who filled out the Doodle Poll. The meeting time is 5pm European Central, 11am US Eastern, 10am US Central, 9 am Regina Canada and 8am US Pacific. Here are meeting connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/374095820 Or iPhone one-tap : US: +16468769923,,374095820# or +16699006833,,374095820# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 646 876 9923 or +1 669 900 6833 or +1 408 638 0968 Meeting ID: 374 095 820 International numbers available: https://zoom.us/u/aoufZDBQB See you then! Stephen On 9/24/2018 9:32 AM, Stephen Ficklin wrote: > > Okay, sounds like a plan. I have created a Doodle poll for the next > two week to see if there is a time we can meet at 5pm European Central > / 8am US Pacific (excluding Fridays). Here's the link > > https://doodle.com/poll/eptshzfzyiz2n8t6 > > This meeting is open to anyone who wants to participate in the Tripal > v4 Python Proof of Concept. > > Thanks, > Stephen > > > On 9/24/2018 8:11 AM, Anthony Bretaudeau wrote: >> >> Hi, >> >> 4 or 5pm France time is usually fine for me, but not on friday :) >> >> Anthony >> >> Le 21/09/2018 à 18:01, Guignon, Valentin (Bioversity-France) a écrit : >>> >>> In my case 5pm (France time) is ok. >>> >>> Val >>> >>> *From:*Stephen Ficklin [mailto:spf...@gm...] >>> *Sent:* vendredi 21 septembre 2018 17:57 >>> *To:* gmo...@li... >>> *Subject:* Re: [Gmod-tripal] Tripal & Python >>> >>> Hi Anthony, >>> >>> 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. >>> >>> 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? >>> >>> Stephen >>> >>> On 9/19/2018 9:07 AM, Anthony Bretaudeau wrote: >>> >>> Hi, >>> >>> Thanks for the clarification, no problem to make a demo whenever >>> you like! >>> >>> 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. >>> >>> So I think what you'd like to do for Tripal 4 is closer to >>> python-chado? >>> >>> What is not clear yet for me is : >>> >>> - 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 >>> https://tripal.readthedocs.io/en/latest/dev_guide/custom_field/manual_field_creation.html) >>> or entities probably too? This is linked to the second point: >>> >>> - 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... >>> >>> I think example of codes that you would like to move to python >>> would help me understand better the whole idea. >>> >>> Maybe these are stupid questions as I'm not very up to date on >>> the latest Tripal 4 plans and Drupal 8 features. >>> >>> (Let me know if you prefer to continue discussing in the github >>> issue) >>> >>> Anthony >>> >>> Le 18/09/2018 à 19:00, Lacey Sanderson a écrit : >>> >>> 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... >>> <mailto: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 >>> >>> >>> >>> >>> _______________________________________________ >>> Gmod-tripal mailing list >>> Gmo...@li... >>> <mailto:Gmo...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal >>> >>> _______________________________________________ >>> Gmod-tripal mailing list >>> Gmo...@li... >>> <mailto:Gmo...@li...> >>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal >>> >>> >>> >>> >>> >>> >>> _______________________________________________ >>> >>> Gmod-tripal mailing list >>> >>> Gmo...@li... >>> <mailto:Gmo...@li...> >>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal >>> >>> >>> >>> _______________________________________________ >>> Gmod-tripal mailing list >>> Gmo...@li... >>> https://lists.sourceforge.net/lists/listinfo/gmod-tripal >> >> >> >> >> _______________________________________________ >> Gmod-tripal mailing list >> Gmo...@li... >> https://lists.sourceforge.net/lists/listinfo/gmod-tripal |