Tripal Developer's Meeting 2016-04-05

Announcements / Requests

• Tripal Phylogeny module meeting in mid April.

  • http://doodle.com/poll/pugdmbhpb7cerb9h

  • Currently Wed, April 20 at 10am CST, 11am EST seems like the best time but we’ll leave the poll open a little longer.

  • Hopefully will include a demo

  • Look at the data structure and how flexible it would be to accommodate other types

  • Data Generate and input format for loading into chado

  • What features are people most interested in seeing in a generic module

  • Could be used as part of a gene annotation pipeline to determine where some annotations might be improved

  • Might be helpful to have screenshots distributed before the meeting

• Please consider adding your Tripal extension modules to our Tripal organization on GitHub

  • We will give you temporary admin access for the organization to move your project.

• Remember to add/update your module status on tripal.org

• Please help with response to the mailing list if you are able.

Report on Tripal Core Development

V2.1

• Chado v1.3 has been integrated.

• Release of Tripal v2.1 forthcoming once testing of Chado v1.3 is done.

V3

• Development is currently focused on backwards compatibility with Tripal v2.

• • Once upgraded, “nodes” from Tripal v2 sites will still work

  • Site admin can gradually switch over to use new “entities” on a per content-type basis

    • You choose to create entities for your nodes of a given type. The entities start off unpublished so admin can configure them to look as intended. When ready you just publish the entities and turn off the node content type. The URLs will be kept unless you’re using node/[nid]

    • Nodes and Entities can live side-by-side in harmony so you can switch some types (ie: features => genes, mRNAs, etc.) and leave others (ie: stock) until you’re ready

  • Templates for “nodes” will work, and we are working to try and make node templates work for entities (for those not ready to switch to tripal_panes).

• Web services is taking a bit longer to be ready for demonstration. We are expecting to have a demo meeting by mid-late April.

• Current release target date: July 1st.

Round table

Bimonthly Training

• Brought up by Lacey

• Propose to alternate between developer meetings and Tripal/Drupal training for Developers

• There would be a different topic each meeting

• Possible Topics:

  • Drupal coding standards.

  • Writing generic code for sharing.

  • Creating custom hooks.

  • How to use the d3 module.

• Seemed to be interest in these

• Like the idea of keeping our number of meetings the same but alternating between developer meetings and training-like meetings

• Some concern that due to the number of people they might not be very efficient but we’ll try them out and change the format as needed.

Views Download

• Several issues with views data export (slow, memory leaks, extremly complicated) but generic and export in several formats https://www.drupal.org/project/views_data_export

  • Main problem is currently speed which is caused by Views Data Export creating a temporary table emulating the View and then querying it repeatedly through the web interface to build the file chunk by chunk.

• Discussion about changing Views Data Export to meet our needs better.

  • If we do come up with something that extends the views data export module we should submit an issue: feature request

• Perhaps we could use live streaming instead of creating the table

• What about export through tripal jobs. This would break our tie to the web interface meaning we could simply execute the views query rather than create a temporary table.

• We Need a solution for this!

Apollo

• Who is currently using it: NAL, U of S, Meg & Nate

  • and other groups are interested in installing it in the future

• Drupal supports openAuth which works with Cyverse

  • Valentins group (CIRAD) has tested a single sign on (SSO) system including Drupal and other systems; The Breeding API Tripal extension is supposed to support OAuth (only password “protocol”)

• Concern that there are different flavours of OAuth

• Steven would prefer it as a non-core part of Tripal

• Perhaps Tripal/Drupal could use OAuth “out of the box”

• Some link: https://www.digitalocean.com/community/tutorials/an-introduction-to-oauth-2

Module Status

Valentin: Multi-Chado

• About to release the first release candidate in less than 2 weeks

• Working on an installation tutorial

  • Will be included in the module documentation

• Requires patches (for Tripal 2.0 core) at this time

Action Items

• Find a time/person (Valentin?) to demo the flag module for shopping cart functionality.

• Explore OAuth and how it could be combined with Tripal to make for easier coordination between GMOD software (ie: Apollo, maybe even Galaxy)

• Look at patches currently submitted and try to incorporate them into Tripal v2.1
• Bring up Bimonthly training calls on the mailing list for suggestion of topics, etc.