extensions

Change in this version

1. Performance improvements to the Cross References, Relationships, and References.
2. A rewritten GFF3 loader that is extremely fast, even with a fully populated Tripal site.
3. A new Sequences fields that combines reference-dervied sequences with primary sequences, and CDS/proteins for mRNA features and sequences now have more informative definition lines for FASTA sequences.
4. Updates to the online documentation
5. Bug fixes in web services
6. Bug fixes in the OBO loader for ontologies that won't import.

Specifically, this release contains the following changes

• Bug Fixes
  • PHP 7.0 compatibility fix for web services.
  • Multiple bug fixes to the bulk loader.
  • Bug fixes for the relationship field.
• New Functionality
  • An improved transcript field supports customization of gene pages to include as much or as little information about transcripts as possible. Edit the field in Structure > Tripal Content Types > manage fields (in the gene column) > transript. Set and order the transcript fields that should be displayed on the gene page.
  • Site admins can now mark files as permanent. These files will not expire and will note be deleted.

The following changes are present in this release:

1. Fixed a security bug that allowed authenticated privilege's users to access other privileged users accounts. This was only an issue for users that had permission to edit Tripal content types.
2. Bug fixes for the Chado bulk loader
3. Bug fixes for the field listing publications and references
4. Adds back in the missing synonyms field
5. Fixes access denied bug when in legacy mode.
6. Updates to the user's documentation.

Changes in this release.

1. Addition of a new API functions for fully writing out infraspecific ranks of species.
2. Various typos corrected.
3. Fixes for PHP 7.4 compatibility.
4. Fixes for improved web accessibility compliance.
5. Fixes to the relationship field verb parsing.
6. Fix for PubMed dates when importing publications.
7. Fixes to the EBI Ontology Lookup in the OBO loader.

Special thanks to Doug Senalik and Sofia Robb for contributions!

The following changes have been made:

1. Bug fixes in the Organism API functions.
2. Bug fixes in some fields: sbo__database_cross_reference, sep__protocol, .
3. Bug fixes when selecting terms for content types and fields.
4. Bug fix to correct missing definitions in controlled vocabulary terms.
5. Improvements to species nomenclature text.
6. Some Fixes for PHP 8 compatibility.
7. Fixes for functional testing.
8. Bug fix in web services

Special thanks to Doug Senalik for many of the fixes in this release!

Tripal v3 represents a major redesign over Tripal v2 with a more Drupal compatible design, RESTful web services, greater control of layouts with less programming, the ability to create data mash-ups between Tripal sites, and support storage of data other than Chado. See the Tripal v3.x User's Guide for installation and setup instructions. This version is beta and is expected to have bugs and some functionality is still under construction.   The Developer's Handbook and API documentation are coming this Spring!

Tripal v3.x

For those following along with Tripal v4 Development you can now find badges for Drupal and PHP compatibility with the current development code (see https://github.com/tripal/t4d8)

This version is still alpha, and despite that we have more functional testing than ever before, there may be bugs or unexpected behavior. Please let the Tripal core development team know if you encounter any problems so we can prioritize fixes.