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Re: [Gmod-tripal] Tripal & Python
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From: Stephen F. <spf...@gm...> - 2018-09-24 16:33:06
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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 |