extensions

Here are the scheduled Tripal Help Desk meetings for tomorrow, Friday, April 20, 2018.

Subject: Integrating Tripal Collections with the Drupal Search API
Time: 11 am PST, 12 pm Mountain Time, 2 pm EST
Link: https://zoom.us/j/471551977

Subject: Tripal Galaxy API and blend4php
Time: 12:00pm PST | 1:00pm MDT | 3:00pm EST
Link: https://zoom.us/j/266997126

1. Fixed various spelling errors, improved inline code documentation and fixed many bugs in core code and templates.
2. The “Search Data” views present in Tripal 1.1 are now available in Tripal 2.0
3. The directory structure for template files has been simplified.
4. Core code and templates files now use the new API functions.
5. Sequences on feature pages now appear on a single page.
6. Bulk Loader template creation workflow has changed slightly.  Site developers now add template name prior to template construction.
7. Join handlers are now supported in the Views Integration.
8. Legacy MViews can no longer be created. Although legacy views will still work. The Schema API format must be used for new MViews.
9. Site admins can now customize the titles and URLs for all content types.
10. Tripal now manages default vocabularies for all Chado tables with a foreign key relationship to the cvterm table. Site admins can use the web interface to set which vocabularies are used by default.
11. Organism images no longer disappear.
12. The display of administrative messages can now be hidden by setting the proper Drupal permissions.
13. The sidebar Table of Contents (TOC) that appears on each page is now customizable. Site admins can rename, reorder or hide items on the TOC on a per node basis or per content type.
14. Tripal 1.1 supported use of CCK fields (now called content fields in Drupal 7) for adding custom entries to the content sidebar (called the TOC in Tripal 2.0).  These fields are now supported in Tripal 2.0
15. Improved error reporting and logging. Error messages now appear in web server logs.
16. Drupal blocks are no longer supported. They will be redesigned and re-added at a future date.
17. FASTA loader no longer over runs the memory for large sequences.
18. The OBO loader now supports use of relative paths for defining location of OBO files.
19. Development of naming and argument standards for Drush commands.  Major Drush commands have been converted to the new names.  But older commands still work.
20. Minor changes to some API functions to ensure naming and argument standards.

Release Note:

Tripal MegaSearch v1.4.0 contains bug fixes and new features, including:

1. Extra fields/filters on static forms

   - Updated static forms with extra fields/filters for Marker/Map/QTL/Pub/Gene Search

2. New search

   - Added Ortholog/Paralog Search

3. Subset download

   - Allowed downloading subset of results by selecting row(s) from the table. Can be turned on/off with the 'checkbox_filter' setting in the MView definition conf file.

4. MView stats

   - Displayed MView statistics and dates on MegaSearch landing page (See screenshot in the README)

5. Sequence retrieval tool

   - Added Sequence Retrieval Tool for inclusion of flanking sequences in the Download for Gene/Marker Search. (Enabled from the Admin interface, screenshot in the README)

6. Direct URL for search

   - Added direct URL link for individual search. For example, path '/tripal_megasearch?datatype=tripal_megasearch_gene' leads directly to the MegaSearch Gene Search

7. Short static forms

   - Through Chado Search settings (under the User Interface section, i.e. /admin/mainlab/chado_search/settings), configure fieldsets to open/close like an accordion which make the static forms shorter and more succinct

8. Performance optimization

   - drush commands for managing MView indexes and partitioning tables (See the 'Performance' section in the README)

9. UI refresh for Ajax calls

   - Updated UI theme when AJAX calls are made

10. Maintenance message   - For long maintenance operations such as populating a big MView, allowed displaying a maintenance message if 'maintenance' = TRUE is set in the MView definition conf file.

This will be where new code changes are pushed.   Here are a few important links:

Tripal Organization:  https://github.com/tripal
Tripal source Code:  https://github.com/tripal/tripal

GitHub offers better tools to allow those of you who want or need to suggest code changes to the Tripal core packages to fork, and issue pull requests.   We will still keep a copy of the Tripal code on the Drupal.org site, as this is needed for Drupal to automatically package Tripal releases for us.   We will also maintain our issue and bug tracking queues on the Drupal.org site as well. 

The Tripal organization on GitHub will allow us to keep all Tripal code, whether it's the core package or extension modules in a single place.  If you have extension modules we encourage you to use GitHub and create a repository for your extension code in the Tripal organization.  You will still have complete control over your repositories, but your Tripal-based projects can be grouped together with others.  

If you would like to become a member of the Tripal organization on GitHub so that you can add a new repository please subscribe to the tripal-devel mailing list and let us know.

Major Issues  #1

Tripal Annotation Extensions

Ready:

• Tripal Analysis Blast

• Tripal Analysis InterproScan

  • Minor issues, minor fixes?  Stil ready for release (BC’s opinion)

  • Coordinate issue: clarify in instructions.

• Need updated README.

Not Ready:

• Tripal Analysis KEGG

  • Possible solution: Chado DBs can be linked.  See EDAM problem.

    • OBO loader would need to be updated for the db-linker.

  • No README.md

Should we deprecate?

• Tripal Analysis GO

  • Just an importer.   Could easily be a bulk loader instead?

  • No display field, for example.

  • Do we bother releasing as 3.0?

• Tripal Analysis Unigene

  • Obviously deprecated

Major #2  New Tripal v3 Release

Current bugs are preventing creation of content.

Extensions

1. Add the Tripal Docker, Python Tripal

2. Gold/Silver/Bronze

   1. Purpose: The Tripal Community recognizes these qualities as making good code.  They are ideals to strive for…..

   2. “Terms and conditions apply” we can change the list and you need to do something to qualify for silver again.

   3.  What is the list of extension criteria?

      1. Bronze:

         1. Has a public release that follows Drupal release naming rules.

         2. Should install on any Tripal site

            1. defines any custom tables or mviews

            2. adds any needed controlled vocabulary terms

         3. Installation and admin instructions README.md (or RTD)

         4. Need a license (distributed with module)

      2. Silver:

         1. Follows Drupal code standards (how to measure this?)

         2. USING TripalField class to add data to pages.

         3. Use tripal API functions

            1. Queries Chado using chado_generate_var, chado_expand_var, the ChadoRecord class or chado_xxx_record functions (except for complicated queries).

         4. Provides an admin interface to allow for customization

      3. Gold:

         1. Imports data via Tripal's importer class

         2. Tripal 3 fields are fully compatible with web services

            1. The elementInfo function is fully implemented.

            2. Field as query and queryOrder functions fully implemented.

         3. Web Services uses Tripal's Web Service Classes.

         4. PHPUnit testing

         5. CI testing

         6. Project should have a public development branch (following Drupal naming rules) to encourage collaboration and pull requests.

         7. Extensive documentation for the module (similar to Tripal User's Guide).

Cross-compatibility?

Requirements function in the install file so that it wont install without tripal 3 or 2.  

See: Tripal Galaxy install

• Tripal microservices proof of concept discussion.

  • Stephen will contact EC

Tripal 3.1 release

• https://github.com/tripal/tripal/projects/4

• Test the tripal_install module.

• Don’t wait for blast, interpro releases.

• Don’t wait for tripal.info site d8 registration (put in 3.2 release instead)

• Module rating system in RTD.

Tripal 3.2 goals

• https://github.com/tripal/tripal/projects/5

• Tripal registration form and Tripal.info D8 site needs to be in production.

• We need to tag open issues that should be on the 3.2 release.

• Open pull requests merge on this version.

Module rating system

• https://github.com/tripal/tripal/issues/774

• How “Drupal” should requirements for styling, branches, releases, pushing to Drupal, be?  Vs recommendations.

• Action item: Lacey to clean this up and make a PR for review.

Bronze

• Any Tripal version

  • Has a public release that follows Drupal release naming rules.

  • Should install on a Tripal site appropriate for the versions it supports.

  • Defines any custom tables or mviews in the install file (if applicable).

  • Provides Installation and admin instructions README.md (or RTD)

  • Has a license (distributed with module)

• Tripal v3 specific

  • Adds any needed controlled vocabulary terms in the install file  (if applicable)

Silver

• Any Tripal version

  • Follows Drupal code standards (how to measure this?)

  • Use tripal API functions (is this too generic)?

    • Uses the Chado API: Queries Chado using chado_generate_var, chado_expand_var, the ChadoRecord class or chado_xxx_record functions (except for complicated queries).

  • Provides an admin interface to allow for customization

  • Latest releases should follow drupal best practices.

    • e.g. first release for Drupal 7 should be: 7.x-1.x

• Tripal v3 specific:

  • Uses the TripalField class to add data to pages (if applicable).

Gold:

• Any Tripal version

  • Required:

    • Extensive documentation for the module (similar to Tripal User's Guide).

    • Unit testing is implemented using PHPUnit with the TripalTestSuite or something similar.

    • Continuous integration is setup (e.g. such as with TravisCI).

  • Optional (but encouraged):  

    • code sniffing and testing coverage reports.

    • Drupal.org vetted release.

  •  

• Tripal v3 specific:  

  • Imports data via Tripal's importer class

  • Tripal 3 fields are    

    • Fully compatible with web services

    • The elementInfo function is fully implemented.

    • query and queryOrder functions fully implemented.

    • Web Services uses Tripal's Web Service Classes.

Open items

• Tripal 4/D8?

• Chado 1.4 and governance?

• PMC voting tags: https://github.com/tripal/tripal/issues?q=is%3Aissue+is%3Aopen+label%3A%22PMC+voting%22

• Redo PR template possibly?

  • People are submitting!  But i’d love it if they provided more details on how ot test their PRs and/or adding tests...

1. Tripal v3.2 release

   1. Open Issues:

      1. We moved all of the documentation and enhancement issues to the v3.3 task

   2. Pull requests

      1. Lacey will review the chado_Select and registration PRs.

      2. Stephen will fix the issue with the other one.

   3. May 31st release.

      1. Finish out all of the issues in the "In Progress" column for the release to happen.

2. Issues from the meeting

   1. Performance of fields

   2. Can someone leapfrog over Tripal v3 to go to Tripal v4.

      1. No, the migration code may not be present in the Tv4 code.

3. At the next User's Meeting

   1. Should we change the format of the meetings?

   2. Are they still valuable?

   3. Meeting format change:

      1. PMC:  5-10 minutes of updates,

      2. TAC:  5-10 minutes from the President (when something to discuss).

      3. Presentation by a Tripal community member.

   4. Send out an email about the meetings to get feedback.