Tripal Developer's Meeting 2015-10-06

Major Tripal Fixes/Updates

• Ontology Loader:  

  • Support new Relationship Ontology (RO).

  • Support new link for Sequence Ontology (SO).

  • Latest OBO spec is 1.4, which permits terms that lack names (found in the ENVO ontology).

  • Would be nice to have prefix URLs too, to be used to build PURLs. BioPortal?   How to deal with RO as some terms have different namespaces.

  • TODO: have loader fixed by November Monthly

• Chado v1.3 Support

  • Need Testing -- Valentin (custom views check)

• Chado installation has a substitution that has converted the word ‘public’ as ‘chado’... take a look at this.

• CVterm synoyms has some sort of related issues (Andrew F. will send more information).

GitHub Tripal community page

Chado/Drupal Stress Testing

• Chris Childer (i5K) -- create and shared loading script.

• Andrew Farmer (NCGR) -- working with iPlant. Atmosphere system (analgous to Amazon web services for creating a VM spun up on demand).  Created an instance with a vanilla install of Drupal.

  • Been thinking of frameworks for regression testing (Jenkins).  

  • Atmosphere can be linked up to the iPlant data store.  

  • Chris: may need to request a VM with more resources for testing.

  • Nathan: TravisCI?

  • Stephen:  

    • TODO: will try to look into Jenkins/Travis CI

    • TODO: look into atmosphere on iPlant.

    • TODO: coordinate by email the stress testing a plan for genomic testing (will communicate on gmod-tripal-devel mailing list.

  • Agree on where the base installation stops and what setup we need for test operations.  (i.e. which Tripal modules are needed, based on which tests we want to do).

    • Base Install:

      • Drupal installed

      • Tripal modules:  tripal_core, tripal_organism, tripal_analysis, tripal_cv, tripal_db, tripal_feature, tripal_stock (ND module??).

      • Chado Installed v1.2

      • CV’s loaded: sequence, (need to perhaps settle on an community ontology for what we’re storing).  What other ontologies do we need?

        • TODO:  determine which ontologies are needed.

  • Use Cases:  Phase #1: start on genomic data for stress testing (using sequence ontology, GO).

Site-Wide Indexing

• Valentin recommendations: http://sourceforge.net/p/gmod/mailman/message/34426451/

• Suggests creating a new module that separates the keyword identification from the search engine module.  This way we can all use the same admin interface but use our search engine of choice on the back-end.

• Look at integrating this suggestion with Entities for Tripal v3.

  • Still need the ability to pre-process and convert data for indexing.

• Codefest Idea:  come up with a more unified approach (perhaps code merging?) for site-wide indexing.

PAG (Lacey Sanderson & Meg Staton Co-chairs; Stephen assisting).

• Oral Presentation Abstracts (Due next Friday Oct 16th). please email to mestato@gmail.com

• Poster Presentation Abstracts (Due October 30th)

• Codefest (Jan 8th Friday.  9-5pm).  

Revisit downloading via views_data_export (currently being tested for LIS)

• TODO:  might be recommended on Tripal documentation. If so need to take off.

• TODO:  design for Tripal v3.0… explore export options for entity with ability to filter which properties are included.

• Perhaps ask Lacey? (past comments… didn’t clean up itself).

Tripal feature: GFF Downloader.   

• TODO:  look at the status of this and report where it left off.

Developer Best Practices & Tips

• Handling (or avoiding) inter-module dependencies

• Tips for debugging Drupal and Tripal modules

  • Use devel module https://www.drupal.org/project/devel.  Use ‘dpm’ function call to expose variables.

  • Use drupal_debug() calls when dpm not useful.

  • Eclipse for PHP very useful for coding and maintaining coding standards.

  • Never tried, but can use Eclipse + Xdebug + Drupal.  Tutorial here: http://programmingbulls.com/debugging-drupal-php--xdebug-eclipse

• Review techniques for customization (to keep customizations out of core Tripal code)

• Handling (or avoiding) inter-module dependencies

  • Suggestion:  to create a custom in-house only module for customizations specific for your site.