This release represents a major update to Tripal v4. Site developers can now fully publish all content types. This release should allow all Tripal v3 sites managers to begin exploration for how to upgrade their Tripal v3 sites to v4 in anticipation of Drupal's end of life for Drupal 7 at the end of the year.

This version is still alpha, and despite that we have more functinal 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.

Changes in this release:

• Addition of new autocomplete API functions for analyses, assays, biomaterials, featuremaps, projects, studies and contacts
• Better support for infraspecific naming and linking for organisms including updates to:
  • Fixes to the Newick phylogenetic tree loader
  • Fixes to the Taxonomy Importer
  • Fixes to the FASTA Importer
  • Fixes to the GFF3 Importer
  • Fixes to the phylogenetic tree API
  • Updates to Chado API functions
• Tooltips on the phylogenetic tree viewer
• Bug fix in the Tripal OBO importer related to specifying local files
• Bug fix in the Tripal GFF importer related to finding landmarks
• Bug fix in progress report when publishing
• PHP 8 warnings/errors fixes
• Documentation updates
• Fixes/updates to functional/unit testing
• Bug fix to the relationship field widget
• Bug fix to the publication field widget
• Bug fix to the contact field widget and formatter
• Bug fix to the location on map field
• Bug fix to the location on seqeunce record field
• Bug fix for Tripal Job tracking
• Bug fix in the analysis data source field related to text lenght limits
• Minor update to Bulk Loader sorting

Tripal4-alpha1 Release Notes

This is the very first release of Tripal 4. It is NOT FOR USE ON PRODUCTION sites at this time.

That said, it is a well-tested version with a lot of functionality which is listed below. This version is meant to be used to start updating all extension modules and to explore the new functionality. We recommend using the Development Tripal Docker for this purpose rather then installing directly at this point.

Documentation

You can access the documentation for Tripal 4 here: https://tripaldoc.readthedocs.io/en/latest/

• Tripal Docker usage
• Developer Guide
• Short Snippets of code useful when upgrading an extension module

Features

The following functionality has been implemented in this first alpha version of Tripal 4:

• Development Tripal Docker
• Full Tripal Administrative menu
• Full Chado Support through Tripal DBX including Querying using the Drupal query builder, installation, upgrade, clone, etc. Multiple schema support.
• Prepare functionality (automatic creation of content types, attaching fields, importing ontology, creating custom tables + mviews)
• Tripal Content Types including auto-creation of the same types in Tripal 3.
• Tripal Content, Chado Storage API + Tripal field support (Basic data type fields, Organism field, Chado Property field, Chado Cvterm/Type field).
• Tripal Vocab, ID Space + Term API including integration into content types + fields.
• Importer API, OBO Importer, GFF3 Importer, HTML5 file upload form element
• Automated testing through GitHub workflows on PHP 8.0 + 8.1, PostgreSQL 13, Drupal 9.2.x, 9.3.x, 9.4.x, 9.5.x and 10.0.x
• Tripal + Chado Automated testing API including support for test chado instances and creation of Tripal Content, Tripal Content Types, Tripal Terms, an organism Tripal Content Type specifically, retrieving cvterms, etc.
• Tripal Job Management
• Tripal Custom Table + Chado MViews API
• Admin Dashboard + Blocks: Powered By Tripal, Notifications, and Content Type Bar Chart.
• Initial port of the registration form (not complete)
• Administrative + User interfaces for the File API

Important Notes:

• We will be separating all data-type specific content types and fields into community extension modules (e.g. genomic-related components into a future tripal_genome module). Therefore, alpha sites will most likely not be upgradable to the next version without a fresh install
• Creation of content types and addition of fields will be managed in the future via a YML configuration. This alpha release expects these are created programmatically. If you create a custom module with this alpha release be prepared to refactor code you design to create new content types and fields to se the future YML configuration.
• Only Chado 1.3 is supported at this time. All existing Tripal sites should prepare now to upgrade to Chado 1.3. That way when functionality to upgrade a site from Drupal 7, Tripal 3 to Drupal 9, Tripal 4 is available, you will be ready.

Changes in this Release:

This release consists mostly of minor bug fixes and compatibility improvements. 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!

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 @dsenalik and Sofia Robb @srobb1 for contributions!

This release contains the following changes:

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.

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.

Changes 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.

This release contains the following changes

1. An updated, and now working, USDA Agricultural Library publication importer. Thank you @dsenalik!
2. Updates to the Tripal documentation. Thank you @laceysanderson and @pgrimaud .
3. Improvements to the Phylogenetic tree viewer. Thank you @noahcaldwell7 and @almasaeed2010
4. Fixes to the Taxonomy Importer that avoids errors with NCBI timeouts. Thank you @par12005
5. Updates to the Chado installation to fix problems with upgrades. Thank you @Ferrisx4
6. Fix to the protein sequence field for finding finding proteins associated via the 'part_of' or 'derives_from' relationship. Thanks @Ferrisx4
7. Lots of typo corretions. Thanks @dsenalik

This release is primary bug fixes such as:

1. User's Guide documentation.
2. Fix to data collection creation from search results.
3. Fix to the publication importer.
4. Various fixes for web services.
5. Fixes for date ranges in TripalFields.
6. Fixes to delete databases on the edit form.
7. Fixed bug when creating new content type.
8. Fixes to the SIO vocabulary widget
9. Fixes to the registration form.
10. Fixes to the SO genotype field.
11. Fixes to the search forms to support case-insensitive queries.
12. Fixed bug with all importers.

New functionality

1. The ability to find and delete orphaned Tripal content (pages whose Chado content was removed).
2. Improvements to the error messages from the FASTA loader.
3. Additional functional testing for web services.

Thanks to all those who contributed issues and code fixes!!!

This release includes mostly bug fixes and updates to documentation. There is however, a new registration page that allows site owners/developers to register their site. This is optional and the information collected will help the Tripal advisory and project management committee stay better engaged with the Tripal community and help provide usage statistics for anyone seeking funding for Tripal-related projects.

Change Log

1. Updated User's and Developer's documentation to include module rating system, usage3 of pythlotree visualizations, fields and AJAX, creating your own RTD docs for a custom module, how to contribute to Tripal core development, improvements to the setup of a genomics web site, manging user file quotas, a new list of extension modules,
2. Added additional unit testing
3. Multiple bug fixes with chado querying
4. Fixes to bugs in icons of the panels display
5. Fixed access permissions in web services if the field permissions module is installed.
6. Fixed bugs with cvterm entity types.
7. Fixed bugs where some fields disappear even if they are not empty.
8. Fixed multiple problems with the relationship field.
9. Fixed bug with bulk setting of URL aliases for entities.
10. Fixes to the linker contact field.
11. Fixes to fields not being removed when emptied.
12. Support for creation of database cross references inside of entity edit forms.
13. Fixes to the FASTA importer related if a regex is not needed to specify a relationship.
14. New functionality to unpublish orphaned entities.

This release represents the first stable release for Tripal v3.0 and succeeds all previous release candidate releases. 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.

This is the third release candidate prior to a stable release. There may still be bugs and issues.