What's Changed

Deprecations

• Actually deprecate the Chado Query API in favour of Tripal DBX. by @laceysanderson in #2294
• Remove deprecated functions from importers by @dsenalik in #2297
• New Controller Class to replace the ChadoOrganismAutocompleteController by @vidu-wil in #2293

Bug Fixes

• Update Symbolic Link for base Dockerfile by @laceysanderson in #1777
• GFF importer, fix loading gene sequence from FASTA section by @dsenalik in #1835
• Update chado prepare sql for automated tests by @dsenalik in #1849
• Catch adding Chado field to non-Chado content type by @dsenalik in #1846
• Fix data leak between publish calls by @laceysanderson in #1841
• Fix sequence coordinates widget when creating new feature by @dsenalik in #1874
• remove duplicated yaml by @dsenalik in #1901
• OBO importer - fix unsubstituted message by @dsenalik in #1905
• Fix ogi CV definition by @dsenalik in #1909
• Synonym field was broken on Drupal ≥ 10.2 by @dsenalik in #1918
• Set default terms for field properties when chado mapping is missing. by @laceysanderson in #1940
• ChadoAdditionalTypeTypeDefault can be manually added by @dsenalik in #1942
• don't add to render array if no value by @dsenalik in #1949
• Handle inline template and link for HTML replacements in the title by @laceysanderson in #1965
• Revert one change from PR #1882 by @dsenalik in #1921
• Ensure TripalFields can be added through UI and add some tests by @laceysanderson in #1968
• Fix dbxref "Add another item" bug by @dsenalik in #1962
• Publish update - no drupal records when no chado records by @dsenalik in #1977
• Github workflow forces people to accept chado :-p by @laceysanderson in #1998
• fix issue #2010 by @dsenalik in #2011
• Define third-party schema in tripal entity type as well by @laceysanderson in #2026
• Add character column type to string field type by @dsenalik in #2063
• Ensure it's not the same field when checking for existing terms. by @laceysanderson in #2093
• Ensure field has settings for view mode before adding them. by @laceysanderson in #2095
• Resolves duplicated field names during discover by @dsenalik in #2096
• Fix minor assay field bug by @dsenalik in #2099
• Implement approach to update Drupal field tables following a chado schema update. by @laceysanderson in #2109
• Ensure composer install works on all supported versions. by @laceysanderson in #2139
• Fix discovery on unit type field by @dsenalik in #2178
• Provide correct phpunit.xml version in 10.x docker images by @dsenalik in #2189
• ChadoIdSpace/ChadoVocabulary Missing Values by @laceysanderson in #2185
• Use phpunit 9.6 for any 10.x drupal version by @dsenalik in #2191
• Support Field group 4.0 semversion update by @laceysanderson in #2200
• Automated tests for property fields, widgets and formatters by @laceysanderson in #2133
• Fix brittle test by adding check for NCBI maintenance mode by @dsenalik in #2246
• Fix missing TripalEntityViewsData attribute by @dsenalik in #2264
• Editing single-hop property field fixed by @dsenalik in #2271
• Update Test Coverage Workflow to run on 4.x by @laceysanderson in #2277
• Update OBO importer to work for EDAM by @dsenalik in #2280
• Resolve missing germplasm cvterms in automated testing environment by @laceysanderson in #2288
• Newick importer file is required, and options match tripal 3 by @dsenalik in #2299
• Add missing optional parameter to getChadoForeignKeyDef() by @dsenalik in #2301
• Fix discover bug by checking for foreign key in both directions by @dsenalik in #2305
• Fixes "Organism Autocomplete adds trailing whitespace when infraspecific name is not present" by @laceysanderson in #2303

Content Pages, Fields + Display

• rename chado linker property field by @dsenalik in #1755
• Repair the field debugger by @dsenalik in #1766
• Default Layouts by @spficklin in #1792
• Tripal 4 sequence coordinate field by @pdtouch in #1700
• New base table third party setting + Drupal 10.2 fixes by @dsenalik in #1805
• CV terms on all fields by @spficklin in #1790
• Add missing terms for some chado columns, defining when necessary by @dsenalik in #1819
• Fix bug in publish showing up in testing environment by @dsenalik in #1854
• New Widgets for Property Fields by @laceysanderson in #1851
• Fixes validation missing values bug by @dsenalik in #1855
• Allow fields to link to their corresponding entity by @dsenalik in #1782
• Fix dbxref field, observed after GFF3 importer by @dsenalik in #1860
• Enable Wysiwyg toolbar for Tripal/Chado Text fields by @laceysanderson in #1862
• Fix the sequence coordinates field by @dsenalik in #1861
• Implement the fallback entity lookup by @dsenalik in #1865
• URL and name field filters default to plain text by @dsenalik in #1871
• Chado Contact by Role field by @laceysanderson in #1875
• Checking for new fields by @spficklin in #1869
• Add missing tripal icon for admin "Manage" toolbar by @dsenalik in #1887
• Render HTML tags in page titles, e.g. organism scientifc name by @dsenalik in #1878
• Fields move record_id_term to parent class by @dsenalik in #1889
• add formatting settings to ChadoStringType field by @dsenalik in #1896
• Unpublish UI by @spficklin in #1892
• Tv4g1 issue1843 publishing cardinality by @spficklin in #1882
• Tripal 4 yml typos by @dsenalik in #1903
• Automated Field Testing: focused on the field creation forms in Drupal 10.2+ by @laceysanderson in #1842
• Rename duplicated terms in tcontact.obo by @dsenalik in #1907
• ChadoStorage::deleteValues() by @spficklin in #1912
• Make sure the contact widget/formatter know they are compatible with both fields by @laceysanderson in #1943
• Resolve discovered field name length problems by @dsenalik in #1929
• Remove double-space collapse for publish by @dsenalik in #1931
• Fix the "Remove" button on field widgets by @dsenalik in #1958
• fix publish to store placeholders of proper type by @dsenalik in #1952
• Update ChadoProperty Text widget to support filtered HTML by @laceysanderson in #1978
• Provide validation for already-used field terms by @dsenalik in #1967
• Update Tripal Layout to support configuring the Form Display by @laceysanderson in #1982
• Add in schema for options all supported tripal_layout field group options. by @laceysanderson in #1993
• Publishing in batches by @dsenalik in #1983
• configurable mechanism for hiding fields when they have an "empty" value by @dsenalik in #1971
• Fix url template for custom content types by @dsenalik in #2002
• Add new third party settings needed by publish by @dsenalik in #1992
• Fixes bug in discovery, cv ...

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