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From: bradford c. <bra...@gm...> - 2018-12-04 16:01:30
|
Hi all, I think Stephen copied the wrong link for the Chado meeting. This is the correct link: https://utia.zoom.us/j/811848876 <https://utia.zoom.us/j/811848876> Apologies Bradford > On Dec 3, 2018, at 11:52 AM, Stephen Ficklin <ste...@ws...> wrote: > > Hi All, > > Tomorrow the normal Tripal User's Meeting is being moved to plan for the Tripal/Chado Codefest just before PAG in San Diego. To help ensure our Codefest in January is as productive as possible we will have three separate meetings for each of the 3 primary topics for the Codefest. If you will be attending the Codefest and if you can attend the online meeting tomorrow please join one of the of the following meetings below: > > 1. Tripal v3 Python Proof of Concept. > Group Lead: Stephen Ficklin > Connect via Zoom: https://zoom.us/j/455940438 > > 2. Tripal v3 Breeders API (BrAPI) Implementation: > Group Lead: Valentin Guignon > Connect via GoToMeeting https://global.gotomeeting.com/join/173361157 > > 3. Chado Updates (open to non-Tripal developers). > Group Lead: Scott Cain > Connect via Zoom: https://zoom.us/u/acrqoPpqZ6 > > The meetings all begin at 5pm European Central, 12pm US Eastern, 10am Regina, 8am US Pacific. You find the time in your area via this link: > > https://www.timeanddate.com/worldclock/fixedtime.html?iso=20181204T1600 > > If you are considering attending but have not yet signed up please add your name to our registration document: > https://docs.google.com/spreadsheets/d/1agEK8S4yxphTOC7cojvsVjTxsPH5PenvtHDBDz5XotE/edit#gid=0 > > Chat soon! > Stephen > > -- > Stephen Ficklin, PhD > Assistant Professor > Bioinformatics and Systems Genetics > Department of Horticulture > Washington State University > 153 Johnson Hall > Pullman, WA 99164-6414 > Office: (509) 335-4295 > > http://ficklinlab.cahnrs.wsu.edu/ > > > > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
From: Stephen F. <ste...@ws...> - 2018-12-03 17:25:39
|
Hi All, Tomorrow the normal Tripal User's Meeting is being moved to plan for the Tripal/Chado Codefest just before PAG in San Diego. To help ensure our Codefest in January is as productive as possible we will have three separate meetings for each of the 3 primary topics for the Codefest. If you will be attending the Codefest and if you can attend the online meeting tomorrow please join one of the of the following meetings below: 1. Tripal v3 Python Proof of Concept. Group Lead: Stephen Ficklin Connect via Zoom: https://zoom.us/j/455940438 2. Tripal v3 Breeders API (BrAPI) Implementation: Group Lead: Valentin Guignon Connect via GoToMeeting https://global.gotomeeting.com/join/173361157 3. Chado Updates (open to non-Tripal developers). Group Lead: Scott Cain Connect via Zoom: https://zoom.us/u/acrqoPpqZ6 The meetings all begin at 5pm European Central, 12pm US Eastern, 10am Regina, 8am US Pacific. You find the time in your area via this link: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20181204T1600 If you are considering attending but have not yet signed up please add your name to our registration document: https://docs.google.com/spreadsheets/d/1agEK8S4yxphTOC7cojvsVjTxsPH5PenvtHDBDz5XotE/edit#gid=0 Chat soon! Stephen -- Stephen Ficklin, PhD Assistant Professor Bioinformatics and Systems Genetics Department of Horticulture Washington State University 153 Johnson Hall Pullman, WA 99164-6414 Office: (509) 335-4295 http://ficklinlab.cahnrs.wsu.edu/ |
From: Stephen F. <spf...@gm...> - 2018-11-16 19:44:00
|
Dear Chado Community, Last year a GMOD Hackathon was held prior to PAG with some work done on Chado. Also, the last few years we have held a Tripal Hackathon (now Codefest) on the Thursday and Friday before PAG in San Diego. This year we will combine the Chado with our Tripal Hackathons into a Tripal/Chado Codefest, held Jan 10th-11th in San Diego. This Codefest will have several topics one of which is dedicated to Chado. If you use Chado, regardless if you use Tripal or not, we invite you to attend the Chado session of the Codefest. Scott Cain, GMOD Project Lead, will direct the session. If you are interested in attending please let us know by adding your name to the Chado section of our signup sheet: https://docs.google.com/spreadsheets/d/1agEK8S4yxphTOC7cojvsVjTxsPH5PenvtHDBDz5XotE/edit#gid=0 If you have specific issues you want to address please let either myself or Scott Cain know. We may schedule an online meeting Tuesday Dec 4th to discuss priorities if discussion is needed. Hope to see you then! Stephen |
From: Stephen F. <spf...@gm...> - 2018-11-13 01:20:11
|
Hi All, If you are planning to attend our Tripal User's Meeting or the Tripal v4 Proof of Concept meeting (immediately following the User's Meeting) below are the links to the agenda documents for each meeting: User's Meeting: https://docs.google.com/document/d/11bJj5GFY1_ZCkd9xwJrsWtVyhQOQ8bw_5aaZdCkZVto/edit# PoC Meeting: https://docs.google.com/document/d/1qRBxkfG_zh6neDx5JCvwkH_e1Q8WryDvxiEZCpDWjUs/edit# As a reminder, the meeting will be held Nov 13th at 8am US Pacific, 10am Regina Canada, 12 US Eastern, 5pm European Central. You can find the meeting time in other areas at this link: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20181113T1600. (But with changes in daylight savings time please verify I have not incorrectly listed your time) Best, Stephen *Join from PC, Mac, Linux, iOS or Android:* https://zoom.us/j/455940438 Or iPhone one-tap : US: +14086380968,,455940438# or +16468769923,,455940438# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 408 638 0968 or +1 646 876 9923 or +1 669 900 6833 Meeting ID: 455 940 438 International numbers available: https://zoom.us/u/cXre9E3v8 |
From: Stephen F. <spf...@gm...> - 2018-11-07 23:29:20
|
Calling all Tripal developers for our annual Tripal Codefest at PAG 2019! This year’s activities include a coding marathon with a user meeting at the end. *Meeting Details* San Diego, CA. Room TBA. Thursday January 10th, 9:00am - 5:00pm: Codefest Friday, January 11th, 9:00am-2:30pm: Codefest continued Friday, January 11th, 3:00pm-5:00pm Monthly Tripal User's Meeting *Codefest Topics* To encourage coding over discussion during the Codefest, we have selected a few sessions topics, each with a predefined leader that will help prioritize tasks to work on as a group. If you would like to participate, please sign up for a group. Or, you can propose your own topic so long as you agree to lead it! Please sign up by adding your name to the session you are interested in (or would like to propose) at this document: https://docs.google.com/document/d/1yS8983SS62QhbROizIYmssnZpYa9S9FTJ9U7kvxHg00/edit?usp=sharing On December 4th during our normal online Tripal User's Meetings we will meet by groups (in different Zoom meetings) to plan our tasks for the Hackathon to help encourage more coding. We hope to see you there! Stephen |
From: Stephen F. <spf...@gm...> - 2018-11-05 17:07:29
|
Dear Tripal Community, Due to some scheduling issues we were not able to schedule our regular Tripal User's Meeting for tomorrow Nov 6th. As per our last User's Meeting and previous email it was our intention to move our monthly meeting to Tuesdays from Fridays to allow for more involvement from our European colleagues. So, we would like to have our meeting next Tuesday instead rather than skip the month of November. I apologize for the inconvenience of moving the meeting. I hope we can still have good participation. The meeting will be held Nov 13th at 8am US Pacific, 10am Regina Canada, 12 US Eastern, 5pm European Central. You can find the meeting time in other areas at this link: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20181113T1600. (But with changes in daylight savings time please verify I have not incorrectly listed your time) The Tripal User's meeting will last 45-60 minutes followed by a second meeting related to Tripal v4 and our Python pilot project. All are invited to attend both meetings. Meeting connection details follow below: See you then, Stephen *Join from PC, Mac, Linux, iOS or Android:* https://zoom.us/j/455940438 Or iPhone one-tap : US: +14086380968,,455940438# or +16468769923,,455940438# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 408 638 0968 or +1 646 876 9923 or +1 669 900 6833 Meeting ID: 455 940 438 International numbers available: https://zoom.us/u/cXre9E3v8 |
From: bradford c. <bra...@gm...> - 2018-10-29 15:30:37
|
Hello all, We have decided to extend the Tripal talk abstract deadline to coincide with the PAG poster submission deadline, which was extended to November 2nd. Please send talk abstracts to myself and/or Valentin (v.g...@cg... <mailto:v.g...@cg...>). You can find the PAG website here: http://www.intlpag.org/2019/ <http://www.intlpag.org/2019/> Please let us know if you have any questions. Bradford |
From: Guignon, V. (Bioversity-France) <v.g...@cg...> - 2018-10-26 15:42:34
|
By the way, if you are planning to come to PAG and make travel and hotel reservations, please note the Tripal Codefest and User Meeting prior to PAG will be held on *Thursday & Friday, Jan 10&11*, 2019 (and not 11 and 12 as written on a previous mail). See you there! Valentin -----Original Message----- From: bradford condon [mailto:bra...@gm...] Sent: jeudi 25 octobre 2018 15:05 To: gmo...@li... Subject: [Gmod-tripal] PAG Tripal Abstracts due this week Hi everyone, This is a friendly reminder to please email myself and Valentin (v.g...@cg...) with abstracts for PAG Tripal talks. We highly encourage submissions on any Tripal topic of any length. The deadline is tomorrow. Thank you Bradford _______________________________________________ Gmod-tripal mailing list Gmo...@li... https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
From: bradford c. <bra...@gm...> - 2018-10-25 13:04:44
|
Hi everyone, This is a friendly reminder to please email myself and Valentin (v.g...@cg...) with abstracts for PAG Tripal talks. We highly encourage submissions on any Tripal topic of any length. The deadline is tomorrow. Thank you Bradford |
From: Nathan D. <nat...@lb...> - 2018-10-16 14:37:41
|
I’m passing this along to the Apollo list as well as I’m sure we have (or should have) a few Tripal there as well. Nathan > On Oct 15, 2018, at 1:56 PM, Bradford Condon <bra...@gm...> wrote: > > I’m developing an Apollo user management framework in cooperation with Chris Childers/ Monica Poelchau /Meg Staton. The basic goal of this module is to use Apollo API calls to manage users permissions and chado content in an apollo instance. > > I’m wondering if any tripal sites use, or want to use, Apollo, and if they would be interested in such a module. If so please get in touch with me, I’d love to make this module inclusive of your use case. > > The work in progress code is here: > > https://github.com/NAL-i5K/tripal_apollo <https://github.com/NAL-i5K/tripal_apollo> > > > Cheers > > Bradford > > > Bradford Condon > Postdoctoral Scholar, University of Tennessee Knoxville > www.bradfordcondon.com <http://www.bradfordcondon.com/> > > > > > _______________________________________________ > Gmod-tripal mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-tripal |
From: Bradford C. <bra...@gm...> - 2018-10-15 20:56:58
|
I’m developing an Apollo user management framework in cooperation with Chris Childers/ Monica Poelchau /Meg Staton. The basic goal of this module is to use Apollo API calls to manage users permissions and chado content in an apollo instance. I’m wondering if any tripal sites use, or want to use, Apollo, and if they would be interested in such a module. If so please get in touch with me, I’d love to make this module inclusive of your use case. The work in progress code is here: https://github.com/NAL-i5K/tripal_apollo <https://github.com/NAL-i5K/tripal_apollo> Cheers Bradford Bradford Condon Postdoctoral Scholar, University of Tennessee Knoxville www.bradfordcondon.com |
From: Stephen F. <spf...@gm...> - 2018-10-02 17:55:40
|
Dear Tripal Developers and Users, We will have our monthly Tripal Developer and User meeting this Friday, Oct 5th. The meeting is open for everyone. If you have not previously attended, please consider attending especially if you are considering development of custom extensions. The goal of the meeting is to share news about Tripal, provide an opportunity to share ideas, ask questions, provide training, and to advertise what you are doing. The meeting begins at 3pm UTC. You can find your local start time at this link: https://www.timeanddate.com/worldclock/fixedtime.html?iso=20181005T1500 Starting in November, we propose to hold the meeting on the first Tuesday of the month to allow our European colleagues a better opportunity to join. The time will remain the same. If there is a major objection to this change please let me know. Below is connection details for the meeting. Stephen Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/455940438 Or iPhone one-tap : US: +14086380968,,455940438# or +16468769923,,455940438# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 408 638 0968 or +1 646 876 9923 or +1 669 900 6833 Meeting ID: 455 940 438 International numbers available: https://zoom.us/u/cXre9E3v8 |
From: Stephen F. <ste...@ws...> - 2018-10-02 09:00:09
|
A few more details I should include.... *To Upgrade from an existing pre-release 3.x version:* Simply use Drupal or Drush to retrieve the most recent version of Tripal v3 and update the database. For example, to update using Drush: drush updatedb *To Upgrade from Tripal v2* Please see the Upgrade Instructions in the User's Guide: https://tripal.readthedocs.io/en/latest/user_guide/install_tripal/upgrade_from_tripal2.html *Getting Help* If you encounter any issues please use the Tripal GitHub queue to post a description of the problem and someone will respond in short order. On 10/2/2018 1:39 AM, Stephen Ficklin wrote: > > Dear Tripal Community, > > On behalf of the The Tripal Program Management Committee (PMC) I am > happy to announce the stable release of Tripal v3. > > This release represents the first stable release for Tripal v3.0 and > succeeds all previous release candidates. Because Tripal v3 is a major > overhaul, there may still be bugs. However, this release is currently > in use by several production sites and provides good performance with > no major problems. The following improvements have been made: > > * Tripal v3.0 represents a major overhaul from Tripal v2.0. > Specifically, all content is now organized via controlled vocabularies > * Content types are more tightly integrated with Drupal Entities and > Fields. > * Tripal v3.0 requires no editing of PHP templates to alter the > placement and order of content on the page > * More of Chado is supported than in previous versions. > * RESTful web services are provided to allow for programmatic access > to data on the site, > * New data collections are available to allow site visitors to place > content found via searching into collections for download or use > by other tools. > > In addition, several more changes have been made leading up to this > release: > > * The User's Guide and Developer's Handbook have been converted to > restructuredText and is now part of the Tripal source code > allowing for more easy updates by anyone. Both Guides have been > moved to ReadTheDocs. > * Tripal now includes unit testing to help speed new releases and to > maintain quality. > > What you should see in the near future > > * We are still working on documentation. You will see updates to > the functional annotation for an example site in the User's Guide > as well as more tutorials in the Developer's Guide. > * We hope to offer more frequent minor releases as bugs are > discovered and addressed. > * There are quite a few extension modules that are already > compatible with Tripal v3. We are currently working to get the > BLAST, InterPro and KEGG modules fully supported. > > You can help improve the quality of Tripal in the future by being > engaged! Please submit issues you find, consider submitting code > fixes or reach out for help getting your site setup if you need it. > > Thank you to everyone who contributed to this release! > > -- > Stephen Ficklin, PhD > Assistant Professor > Bioinformatics and Systems Genetics > Department of Horticulture > Washington State University > 153 Johnson Hall > Pullman, WA 99164-6414 > Office: (509) 335-4295 > > http://ficklinlab.cahnrs.wsu.edu/ -- Stephen Ficklin, PhD Assistant Professor Bioinformatics and Systems Genetics Department of Horticulture Washington State University 153 Johnson Hall Pullman, WA 99164-6414 Office: (509) 335-4295 http://ficklinlab.cahnrs.wsu.edu/ |
From: Stephen F. <ste...@ws...> - 2018-10-02 08:40:01
|
Dear Tripal Community, On behalf of the The Tripal Program Management Committee (PMC) I am happy to announce the stable release of Tripal v3. This release represents the first stable release for Tripal v3.0 and succeeds all previous release candidates. Because Tripal v3 is a major overhaul, there may still be bugs. However, this release is currently in use by several production sites and provides good performance with no major problems. The following improvements have been made: * Tripal v3.0 represents a major overhaul from Tripal v2.0. Specifically, all content is now organized via controlled vocabularies * Content types are more tightly integrated with Drupal Entities and Fields. * Tripal v3.0 requires no editing of PHP templates to alter the placement and order of content on the page * More of Chado is supported than in previous versions. * RESTful web services are provided to allow for programmatic access to data on the site, * New data collections are available to allow site visitors to place content found via searching into collections for download or use by other tools. In addition, several more changes have been made leading up to this release: * The User's Guide and Developer's Handbook have been converted to restructuredText and is now part of the Tripal source code allowing for more easy updates by anyone. Both Guides have been moved to ReadTheDocs. * Tripal now includes unit testing to help speed new releases and to maintain quality. What you should see in the near future * We are still working on documentation. You will see updates to the functional annotation for an example site in the User's Guide as well as more tutorials in the Developer's Guide. * We hope to offer more frequent minor releases as bugs are discovered and addressed. * There are quite a few extension modules that are already compatible with Tripal v3. We are currently working to get the BLAST, InterPro and KEGG modules fully supported. You can help improve the quality of Tripal in the future by being engaged! Please submit issues you find, consider submitting code fixes or reach out for help getting your site setup if you need it. Thank you to everyone who contributed to this release! -- Stephen Ficklin, PhD Assistant Professor Bioinformatics and Systems Genetics Department of Horticulture Washington State University 153 Johnson Hall Pullman, WA 99164-6414 Office: (509) 335-4295 http://ficklinlab.cahnrs.wsu.edu/ |
From: Bradford C. <bra...@gm...> - 2018-10-01 17:02:44
|
Hi Everyone, Every year Digital Ocean/GitHub hosts hacktober fest. you can get a free t-shirt for making 5 PRs to open source repositories. But more importantly, it’s a celebration of open-source. Interested in getting involved? One way to help is to look at the Tripal Documentation at https://tripal.readthedocs.io/en/latest/ <https://tripal.readthedocs.io/en/latest/> . Questions/typos/stuff missing? You can click the “Edit on Github” link to create a PR to fix it! This means everyone, including non-coders, can contribute to Tripal on the GitHub repo. Please let me know if you need help contributing. Bradford Bradford Condon Postdoctoral Scholar, University of Tennessee Knoxville www.bradfordcondon.com > Begin forwarded message: > > From: DigitalOcean <hac...@ne...> > Subject: Hacktoberfest is back! > Date: October 1, 2018 at 12:54:48 PM EDT > To: bra...@gm... > Reply-To: hac...@di... > > > > > <http://pages.news.digitalocean.com/SI0D3V0I62h0XEG0b00buE7> > > > It’s that time of year again! Hacktoberfest is back. If you’ve been meaning to give back to your favorite open source projects then set aside time this October to start hacking, and you can earn this year’s brand new, limited-edition Hacktoberfest T-shirt! > > Read the blog post <http://pages.news.digitalocean.com/lbIuF0006bIG0D3Vh0X082E>for all the details and share on your favorite social media networks with #Hacktoberfest <http://pages.news.digitalocean.com/GbI0Db30IGh9E0V60200GXu>! > > > GET STARTED > <http://pages.news.digitalocean.com/n/SI0D3V0I62h0XEG0b00buE7> > > > > > Happy Hacking, > Team DigitalOcean > > > > <http://pages.news.digitalocean.com/n/o03aX00Hb00bGE0hIDIVu62> <http://pages.news.digitalocean.com/n/c0h03uGE06XI2bVDI0Ibb00> <http://pages.news.digitalocean.com/n/ZIXhG0bJV0002u0Ic306DEb> <http://pages.news.digitalocean.com/n/wIIDXhVE60000GbK20u3d0b> <http://pages.news.digitalocean.com/n/Bb00LE3DX000h2bI0Ie6GuV> > Refer a Friend <http://pages.news.digitalocean.com/n/FbII600fM0E2G3bu000DVXh> > Trouble seeing this email? View it as a web page. <https://go.digitalocean.com/index.php/email/emailWebview?mkt_tok=eyJpIjoiTnpJNU1Ea3hOek5tT0RVMCIsInQiOiJ5VHFXRzRMSHVWazhDalJkSDQ5UHJrMC8rTWc1amRnTEUyMTJPUWo1MmpTT3hKRzV4TXdRVjVJdXp6MTExNnJaS3R1WUp0WVQ1Qzg1Z0hiaFV0TDVHZGJ2MDg0QnZzSGttWDZJYkdnSFY3RXlPdEt3S2pKRjRYdEwrb2hPQlB3NiJ9> > > > > Copyright © 2018 DigitalOcean > Floor 10, 101 Avenue of the Americas, New York, NY, 10013 > All rights reserved. > > > <http://pages.news.digitalocean.com/TNXEb0G0b000IIg326huVD0>This email was sent to bra...@gm... <mailto:bra...@gm...>. You can update your email subscription preferences <http://pages.news.digitalocean.com/u/Ab2R0hEI30XVbGu0060k0ID> at any time. |
From: Bradford C. <bra...@gm...> - 2018-09-26 19:58:08
|
Like previous years, Tripal community will meet at PAG XXVII 2019 in San Diego! Currently planned events are: 1. PAG Tripal Session (Sunday, Jan 13, 2019, 4:00pm-6:00) - Abstract submissions due Oct 26th 2. Codefest and User Meeting prior to PAG (Thursday & Friday, Jan 11&12, 2019) 1. PAG Tripal Session (Sunday, Jan 13, 2019, 4:00pm-6:00, California Room) The Tripal session at PAG (http://www.intlpag.org/ <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.intlpag.org_&d=DwMF-g&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=j-ywhwnhi_AAeuA49VAKD_6OCxW3YH40WVtBDjy9t6c&m=hiIfQocCyuZ3BxLjG1BG6ladvkdrjBqEbp9gwM88YyI&s=lq8UX1sRn6BlTWvJDfYleYvp4yC2oF0_C7AFufMAzc8&e=>) will be the same time and place this year . We are now requesting abstracts for oral presentations, due October 26th. Anyone who is attending the conference is welcome to submit an abstract, and we are particularly encouraging groups that are new to Tripal or haven’t presented in this session in previous years to submit. However, be aware that a new policy has been set by the PAG committee: workshop speakers cannot present in the same workshop more than 2 years in a row. A variety of topics are welcome: new databases, custom extensions, integration with other tools, or any other Tripal related projects. Abstracts should be limited to 250 words, and can be submitted by email in MS Word or PDF. Please send to both Bradford Condon at bra...@gm... <mailto:bra...@gm...> and Valentin Guignon at v.g...@cg... <mailto:v.g...@cg...>. As we would like to optimize speakers time, we ask you to tell us how long you would like to talk, between 5 min (flash talk) and 25 minutes. Depending on the number and types of submissions, we will do our best to allocate time for the selected talks. We look forward to hearing from you! (Poster abstracts for the PAG conference are handled separately and due the same day, please see https://pag.confex.com/pag/xxvi/cfp.cgi <https://urldefense.proofpoint.com/v2/url?u=https-3A__pag.confex.com_pag_xxvi_cfp.cgi&d=DwMF-g&c=C3yme8gMkxg_ihJNXS06ZyWk4EJm8LdrrvxQb-Je7sw&r=j-ywhwnhi_AAeuA49VAKD_6OCxW3YH40WVtBDjy9t6c&m=hiIfQocCyuZ3BxLjG1BG6ladvkdrjBqEbp9gwM88YyI&s=ZRsGQr0OcG3wFlz5wUG6tUCpS5PNhTbpHXCRJNm-2Hk&e=>) 2. Codefest and User Meeting (Thursday & Friday, Jan 11&12, 2019, rm tbd) We will also be continuing the Codefest/User Meeting to be held in the 2 days prior to the start of PAG. This year we are planning to implement some ideas for Tripal 4, so come prepared to write code. If you have specific requests for the codefest or user meeting, please contact the organizers below*. Please look for further announcements from the Codefest organizers! More information on room location and times will be forthcoming shortly. Bradford (bra...@gm... <mailto:bra...@gm...>), Val (v.g...@cg... <mailto:v.g...@cg...>), and Meg Bradford Condon www.bradfordcondon.com |
From: Stephen F. <spf...@gm...> - 2018-09-26 19:20:02
|
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 |
From: Stephen F. <spf...@gm...> - 2018-09-24 16:33:06
|
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 |
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; 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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> |
From: Guignon, V. (Bioversity-France) <v.g...@cg...> - 2018-09-21 16:35:59
|
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 |
From: Stephen F. <spf...@gm...> - 2018-09-21 15:56:52
|
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... >>>> 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 |
From: Anthony B. <ant...@in...> - 2018-09-19 16:07:56
|
<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> </head> <body bgcolor="#FFFFFF" text="#000000"> <p>Hi,</p> <p>Thanks for the clarification, no problem to make a demo whenever you like!<br> </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.</p> <p>So I think what you'd like to do for Tripal 4 is closer to python-chado?</p> <p>What is not clear yet for me is :</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 class="moz-txt-link-freetext" href="https://tripal.readthedocs.io/en/latest/dev_guide/custom_field/manual_field_creation.html">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:<br> </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...</p> <p>I think example of codes that you would like to move to python would help me understand better the whole idea.<br> </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.</p> <p>(Let me know if you prefer to continue discussing in the github issue)<br> </p> <p>Anthony</p> <div class="moz-cite-prefix">Le 18/09/2018 à 19:00, Lacey Sanderson a écrit :<br> </div> <blockquote type="cite" cite="mid:CAL...@ma..."> <meta http-equiv="content-type" content="text/html; charset=UTF-8"> <style>body{font-family:Helvetica,Arial;font-size:13px}</style> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Hi Anthony,</div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br> </div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Thank you for reaching out! </div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">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. </div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br> </div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">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> </div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br> </div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">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.</div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br> </div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">So to summarize, there are many reasons we are considering python for the core Tripal library:</div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">- Abstract customizing a Tripal/Drupal site from the Drupal logic to protect our users from the Drupal release cycle</div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">- To facilitate interaction with Tripal to/from python programs (your modules already cover this)</div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">- Allow python developers to extend a Tripal/Drupal site without needing to learn PHP/Drupal</div> <div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">- Allow Tripal to be used without Drupal, either as a library for interacting with Chado or to feed a different CMS</div> <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. <div><br> </div> <div>~Lacey<br> <p class="airmail_on">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:</p> <blockquote type="cite" class="clean_bq"><span> <div bgcolor="#FFFFFF" text="#000000"> <div> <title></title> <p>Hi,</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:</p> <ul> <li>python-tripal (<a class="moz-txt-link-freetext" 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</li> <li>python-chado (<a class="moz-txt-link-freetext" 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).</li> <li>chado-schema-builder (<a class="moz-txt-link-freetext" 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.</li> </ul> <p>So I think building on these bases would be much easier than starting something from scratch and reinventing the wheel...</p> <p>Of course contributions and feature requests are warmly welcome for all these projects.<br> </p> <p>I'd be happy to discuss it in a meeting if there's interest (french timezone).<br> </p> <p>Cheers<br> </p> <p>Anthony Bretaudeau</p> <p>BIPAA/GenOuest, Rennes, France<br> </p> <p><br> </p> <div class="moz-cite-prefix">Le 17/09/2018 à 18:00, Stephen Ficklin a écrit :<br> </div> <blockquote type="cite" cite="mid:b96...@gm...">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 class="moz-txt-link-abbreviated" href="mailto:Gmo...@li..." moz-do-not-send="true">Gmo...@li...</a><br> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/gmod-tripal" moz-do-not-send="true">https://lists.sourceforge.net/lists/listinfo/gmod-tripal</a><br> </blockquote> _______________________________________________ <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> <br> </div> </div> </span></blockquote> </div> </blockquote> </body> </html> |
From: Lacey S. <lac...@gm...> - 2018-09-18 17:00:26
|
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 _______________________________________________ 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 |
From: Anthony B. <ant...@in...> - 2018-09-18 09:48:39
|
<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> </head> <body bgcolor="#FFFFFF" text="#000000"> <p>Hi,</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:</p> <ul> <li>python-tripal (<a class="moz-txt-link-freetext" 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</li> <li>python-chado (<a class="moz-txt-link-freetext" 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).</li> <li>chado-schema-builder (<a class="moz-txt-link-freetext" 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.</li> </ul> <p>So I think building on these bases would be much easier than starting something from scratch and reinventing the wheel...</p> <p>Of course contributions and feature requests are warmly welcome for all these projects.<br> </p> <p>I'd be happy to discuss it in a meeting if there's interest (french timezone).<br> </p> <p>Cheers<br> </p> <p>Anthony Bretaudeau</p> <p>BIPAA/GenOuest, Rennes, France<br> </p> <p><br> </p> <div class="moz-cite-prefix">Le 17/09/2018 à 18:00, Stephen Ficklin a écrit :<br> </div> <blockquote type="cite" cite="mid:b96...@gm...">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 class="moz-txt-link-abbreviated" href="mailto:Gmo...@li..." moz-do-not-send="true">Gmo...@li...</a> <br> <a class="moz-txt-link-freetext" href="https://lists.sourceforge.net/lists/listinfo/gmod-tripal" moz-do-not-send="true">https://lists.sourceforge.net/lists/listinfo/gmod-tripal</a> <br> </blockquote> </body> </html> |
From: Stephen F. <spf...@gm...> - 2018-09-17 16:00:30
|
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 |