tripal/tripal issues and pull requests

#1799 - Split the Taxonomy Importer

Issue - State: open - Opened by spficklin 5 months ago
Labels: Tripal 4, Group 4 - Data Importing

#1798 - Testing needed for Layouts

Issue - State: open - Opened by spficklin 5 months ago
Labels: Tripal 4, Group 7 - Page Display, Group 9 - Automated Testing

#1797 - Create YAML for all Content Types Layouts

Issue - State: open - Opened by spficklin 5 months ago
Labels: Tripal 4, Group 7 - Page Display

#1796 - Update README.md

Pull Request - State: closed - Opened by spficklin 5 months ago
Labels: Tripal 4, Group 0 - General Maintenance

#1795 - Fixes for the new Drupal 10.2 subform

Pull Request - State: closed - Opened by dsenalik 5 months ago - 7 comments
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1794 - Tripal Layout TODO

Issue - State: open - Opened by spficklin 5 months ago
Labels: Tripal 4, Group 7 - Page Display

#1793 - Checking for new fields

Issue - State: closed - Opened by spficklin 5 months ago - 4 comments
Labels: Community - Discussion, Tripal 4, PMC - Discussion, Group 1 - Tripal Content Types | Terms | Fields

#1792 - Default Layouts

Pull Request - State: closed - Opened by spficklin 5 months ago - 7 comments
Labels: Tripal 4, Group 7 - Page Display

#1791 - Edit Field Settings WSOD on Drupal 10.2

Issue - State: closed - Opened by laceysanderson 5 months ago - 4 comments
Labels: bug - confirmed, PR Submitted, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1790 - CV terms on all fields

Pull Request - State: closed - Opened by spficklin 5 months ago - 8 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Easy PR Review 😀

#1789 - Setting CV terms on non Tripal fields attached to Tripal content types

Issue - State: closed - Opened by spficklin 5 months ago - 1 comment
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1788 - ChadoStorage fix for joins that loop back to the root table

Pull Request - State: closed - Opened by spficklin 5 months ago - 1 comment
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1787 - Fix for error on job view and argument listing

Pull Request - State: closed - Opened by spficklin 5 months ago
Labels: Good First Issue, Tripal 4, Group 3 - Job Management, Easy PR Review 😀

#1786 - Can't view job log

Issue - State: closed - Opened by spficklin 5 months ago - 3 comments
Labels: Tripal 4, Group 3 - Job Management

#1785 - Change CV terms for Contact bundle

Pull Request - State: closed - Opened by benfrstr 5 months ago - 9 comments
Labels: Tripal 4, Group 0 - General Maintenance

#1784 - Modified 3 tripaldocker/Dockerfiles for PHP 8.1, 8.2 and 8.3 to accom…

Pull Request - State: closed - Opened by pdtouch 5 months ago - 1 comment
Labels: Tripal 4, Group 0 - General Maintenance, Group 4 - Data Importing, Easy PR Review 😀

#1783 - Change the CV term for the Contact bundle from local:contact to a real term NCIT:C47954

Issue - State: closed - Opened by dsenalik 5 months ago - 5 comments
Labels: Good First Issue, Tripal 4, Group 0 - General Maintenance

#1782 - Allow fields to link to their corresponding entity

Pull Request - State: closed - Opened by dsenalik 5 months ago - 9 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 7 - Page Display

#1781 - Add depreciation notices to legacy code

Issue - State: open - Opened by guignonv 5 months ago - 2 comments
Labels: Community - Enhancement, Good First Issue, Tripal 4, Group 0 - General Maintenance

#1780 - Chado CVTerm service: do we need one or do we just always use Tripal Terms?

Issue - State: open - Opened by laceysanderson 5 months ago - 2 comments
Labels: Community - Discussion, Tripal 4, Community - Codefest, Group 2 - Data Storage | Tripal DBX | Chado

#1779 - There are no custom tables by default even after preparing

Issue - State: closed - Opened by laceysanderson 5 months ago - 12 comments
Labels: bug - confirmed, Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1778 - Make sure admin route permissions are logical and consistent

Issue - State: open - Opened by dsenalik 5 months ago
Labels: Tripal 4, Group 0 - General Maintenance

#1777 - Update Symbolic Link for base Dockerfile

Pull Request - State: closed - Opened by laceysanderson 5 months ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1776 - Code coverage failure for pull requests from cloned repos

Issue - State: open - Opened by dsenalik 5 months ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 9 - Automated Testing

#1775 - Update Dockerfile Drupal version to 10.1.0 for PHP8.2

Pull Request - State: closed - Opened by exnehilo7 5 months ago - 5 comments
Labels: Tripal 4, Group 0 - General Maintenance

#1774 - 4.x dev

Pull Request - State: closed - Opened by exnehilo7 5 months ago

#1773 - Adds a test to actually ensure that getDefinitions() returns our core chado plugins

Pull Request - State: closed - Opened by laceysanderson 5 months ago - 1 comment
Labels: Tripal 4, Group 9 - Automated Testing, Easy PR Review 😀

#1772 - Testing for TripalImporter plugin manager is flawed

Issue - State: closed - Opened by laceysanderson 5 months ago
Labels: Group 9 - Automated Testing

#1771 - Tv4g2 issue1758 chado custom table functionality

Pull Request - State: closed - Opened by Ferrisx4 5 months ago - 5 comments
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1770 - Update Tripal Importer database rollback to apply to Chado, not the Drupal database

Pull Request - State: closed - Opened by carolyncaron 5 months ago - 1 comment
Labels: Tripal 4, Group 4 - Data Importing

#1769 - Add PHP8.3 + Drupal 10.2 to automated testing and docker builds

Pull Request - State: closed - Opened by dsenalik 5 months ago - 4 comments
Labels: Tripal 4, Group 9 - Automated Testing, PHP8

#1768 - Add function to get default schema and associated tests

Pull Request - State: closed - Opened by Ferrisx4 5 months ago
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1767 - Field path does not support reference back to base table

Issue - State: closed - Opened by dsenalik 5 months ago - 2 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1766 - Repair the field debugger

Pull Request - State: closed - Opened by dsenalik 5 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado, Easy PR Review 😀

#1765 - Field debugger was broken by PR #1723

Issue - State: closed - Opened by dsenalik 5 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado

#1764 - Tripal Importer class doesn't appear to be rolling back database transactions when exception is thrown

Issue - State: closed - Opened by carolyncaron 6 months ago - 2 comments
Labels: Tripal 4, Group 4 - Data Importing

#1763 - Tripal 3: Taxonomy importer name comparison now case insensitive

Pull Request - State: closed - Opened by dsenalik 6 months ago
Labels: Tripal 3, Group 4 - Data Importing, Easy PR Review 😀

#1762 - Tripal 4: Taxonomy importer name comparison now case insensitive

Pull Request - State: closed - Opened by dsenalik 6 months ago - 1 comment
Labels: Tripal 4, Group 4 - Data Importing, Easy PR Review 😀

#1761 - Organism name is incorrectly case sensitive for taxonomy loader

Issue - State: closed - Opened by dsenalik 6 months ago - 2 comments
Labels: bug - confirmed, Tripal 3, Tripal 4, Group 4 - Data Importing

#1760 - Add PHP8.3 + Drupal 10.2 to automated testing

Issue - State: closed - Opened by dsenalik 6 months ago
Labels: Tripal 4, Group 9 - Automated Testing, PHP8

#1759 - Make the default Chado schema clear and easy to grab

Issue - State: closed - Opened by laceysanderson 6 months ago - 1 comment
Labels: Good First Issue, Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1758 - Chado Custom Table functionality

Issue - State: closed - Opened by Ferrisx4 6 months ago - 5 comments
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1757 - SQLSTATE[42000]: Syntax error or access violation: 1071 Specified key was too long; max key length is 3072 bytes

Issue - State: closed - Opened by webfaqtory 6 months ago - 4 comments
Labels: waiting on submitter, bug - potential, Tripal 4

#1756 - Updating release numbers to 4.0.0-alpha3

Pull Request - State: closed - Opened by spficklin 6 months ago
Labels: Tripal 4

#1755 - rename chado linker property field

Pull Request - State: closed - Opened by dsenalik 6 months ago - 1 comment
Labels: PR - Reviewer #1 Approval, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Easy PR Review 😀

#1754 - "Linker" is no longer a needed field distinction

Issue - State: closed - Opened by dsenalik 6 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1753 - Tripal 4 alpha 2 typo fixes

Pull Request - State: closed - Opened by dsenalik 6 months ago
Labels: Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1752 - postLoad function for TripalField

Issue - State: open - Opened by spficklin 6 months ago - 4 comments
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1751 - Changes destroy() to delete() on the ChadoCustomTable class

Pull Request - State: closed - Opened by spficklin 6 months ago
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1750 - destroy destroy

Issue - State: closed - Opened by spficklin 6 months ago - 1 comment
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1749 - Increase of PHP memory to help upload larger FASTA files like scaffolds and genomes

Issue - State: closed - Opened by pdtouch 6 months ago - 4 comments
Labels: Tripal 4, Group 4 - Data Importing

#1748 - Chado fix for box_range

Pull Request - State: closed - Opened by spficklin 6 months ago - 2 comments
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1747 - GFF3 loader: landmarks defined in GFF3 file

Issue - State: open - Opened by dsenalik 6 months ago
Labels: Tripal 4, Group 4 - Data Importing

#1746 - create_point function is borked

Issue - State: closed - Opened by spficklin 6 months ago - 1 comment
Labels: PR Submitted, Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1745 - Fixes Usage of TripalJob

Pull Request - State: closed - Opened by spficklin 6 months ago
Labels: Tripal 4, Group 3 - Job Management

#1744 - Fixing inconsistent use of TripalJob service

Issue - State: closed - Opened by spficklin 6 months ago - 1 comment
Labels: Tripal 4, Group 3 - Job Management

#1743 - Update or add most remaining linking fields from issue #1381

Pull Request - State: closed - Opened by dsenalik 6 months ago - 4 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1742 - GFF3 loader validation

Pull Request - State: closed - Opened by spficklin 6 months ago - 2 comments
Labels: Tripal 4, Group 4 - Data Importing, Easy PR Review 😀

#1741 - GFF3 validation error

Issue - State: closed - Opened by spficklin 6 months ago - 1 comment
Labels: Tripal 4, Group 4 - Data Importing

#1740 - Fix for Quota Page

Pull Request - State: closed - Opened by spficklin 6 months ago
Labels: Tripal 4, Group 4 - Data Importing, Easy PR Review 😀

#1739 - File quota listing broken

Issue - State: closed - Opened by spficklin 6 months ago
Labels: Tripal 4, Group 4 - Data Importing

#1738 - Content Listing Session May be Problematic

Issue - State: open - Opened by spficklin 6 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1737 - Fix for Taxonomy Importer - removes the file upload field

Pull Request - State: closed - Opened by risharde 6 months ago - 1 comment
Labels: Tripal 4, Group 4 - Data Importing

#1736 - Fix to improve loading speed of content type listing

Pull Request - State: closed - Opened by spficklin 6 months ago - 1 comment
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado, Group 10 - Performance

#1735 - Fix unquoted leading zeros in yaml

Pull Request - State: closed - Opened by dsenalik 6 months ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Easy PR Review 😀

#1734 - Field not being added.

Issue - State: closed - Opened by spficklin 6 months ago
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1733 - Taxonomy importer is requesting a gff3 file

Issue - State: closed - Opened by dsenalik 6 months ago - 1 comment
Labels: Tripal 4, Group 4 - Data Importing

#1732 - Publishing content types and fields linked to a property type_id

Pull Request - State: closed - Opened by spficklin 6 months ago - 6 comments
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1731 - The challenge of the `fixed_value`

Issue - State: open - Opened by spficklin 6 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1730 - Fix for the fixed_value discrepancy that Doug pointed out on PR #1729

Pull Request - State: closed - Opened by laceysanderson 6 months ago - 6 comments

#1729 - Updates to ChadoStorage -- path argument and cleanup.

Pull Request - State: closed - Opened by spficklin 6 months ago - 43 comments
Labels: URGENT!, Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1728 - Generic way to Group Terms from multiple ontologies for a select list

Issue - State: open - Opened by laceysanderson 6 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado

#1727 - Cleanup Terms: move all chado_table focused local cvs into the main 'local' cv.

Pull Request - State: closed - Opened by laceysanderson 6 months ago - 2 comments
Labels: Group 0 - General Maintenance, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado

#1726 - Update the Taxonomy Importer to use real ontology terms.

Issue - State: open - Opened by laceysanderson 6 months ago - 1 comment
Labels: Tripal 4, Group 4 - Data Importing, Group 6 - Web Services

#1725 - Workflow working

Pull Request - State: closed - Opened by laceysanderson 6 months ago

#1724 - Revert "Finally have the github action working." AS THATS NOT THE BRANCH I MERGED

Pull Request - State: closed - Opened by laceysanderson 6 months ago

#1723 - Finally have the github action working.

Pull Request - State: closed - Opened by laceysanderson 6 months ago

#1722 - Forgot the file ending

Pull Request - State: closed - Opened by laceysanderson 6 months ago

#1721 - Create a Github Workflow to Sync Drupal.org on every push to 4.x

Pull Request - State: closed - Opened by laceysanderson 6 months ago - 1 comment
Labels: Tripal 4, Group 0 - General Maintenance, Group 8 - Other Integrations, Easy PR Review 😀

#1721 - Create a Github Workflow to Sync Drupal.org on every push to 4.x

Pull Request - State: closed - Opened by laceysanderson 6 months ago - 1 comment
Labels: Tripal 4, Group 0 - General Maintenance, Group 8 - Other Integrations, Easy PR Review 😀

#1720 - Workflow to keep github and drupal.org in sync

Issue - State: closed - Opened by laceysanderson 6 months ago
Labels: Tripal 4, Group 0 - General Maintenance, Group 8 - Other Integrations

#1719 - Support Joins for Finding Values

Issue - State: closed - Opened by spficklin 6 months ago - 9 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1718 - Fixed publication terms error

Pull Request - State: closed - Opened by spficklin 6 months ago - 5 comments
Labels: Tripal 4, Easy PR Review 😀

#1717 - Problem with Publication Fields

Issue - State: closed - Opened by spficklin 6 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1716 - Trying to publish 2+ content types in the same call to the Tripal job launcher fails

Issue - State: closed - Opened by laceysanderson 7 months ago - 1 comment
Labels: bug - confirmed, Release Blocker, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado

#1715 - Update matrix to build docker images for 10.0 and 10.1 only

Pull Request - State: closed - Opened by laceysanderson 7 months ago - 1 comment
Labels: Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1714 - Build Docker workflow still trying to create 9.4 and 9.5 images

Issue - State: closed - Opened by laceysanderson 7 months ago
Labels: Group 0 - General Maintenance

#1713 - Tripal 3 pub importer fixes for book type

Pull Request - State: closed - Opened by dsenalik 7 months ago - 1 comment
Labels: Tripal 3, Group 4 - Data Importing

#1712 - Tripal 3 pub importer "The Publication Type is a required property but is missing"

Issue - State: closed - Opened by dsenalik 7 months ago - 1 comment
Labels: Tripal 3, Group 4 - Data Importing

#1711 - ChadoTermsInit should take an arguement so it can be re-used

Pull Request - State: closed - Opened by laceysanderson 7 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Easy PR Review 😀

#1710 - Finally, the Database Cross Reference Field!

Pull Request - State: closed - Opened by dsenalik 7 months ago - 9 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1709 - Rename fields to standard naming convention

Pull Request - State: closed - Opened by dsenalik 7 months ago - 1 comment
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1708 - Ability to set field default value through YAML

Issue - State: open - Opened by dsenalik 7 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1707 - Make zero a valid integer for ChadoIntegerType field when it is required

Pull Request - State: closed - Opened by dsenalik 7 months ago
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Easy PR Review 😀

#1706 - Is zero a number? (ChadoIntegerType field)

Issue - State: closed - Opened by dsenalik 7 months ago
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1705 - No drush command given when importing content types

Issue - State: closed - Opened by spficklin 7 months ago - 1 comment
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 3 - Job Management

#1704 - Update or add all remaining linking fields from issue #1381

Pull Request - State: closed - Opened by dsenalik 7 months ago - 3 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado

#1703 - Chado storage again - The woes of too many joins

Issue - State: closed - Opened by dsenalik 7 months ago - 2 comments
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1702 - Improve maintainability chado upgrader complexity

Pull Request - State: closed - Opened by laceysanderson 7 months ago
Labels: Tripal 4, Group 0 - General Maintenance

#1701 - Tripal Pub Library implementation (part of Tripal Publications Importer implementation)

Pull Request - State: closed - Opened by risharde 7 months ago - 24 comments
Labels: Tripal 4, Group 4 - Data Importing, ready for review

GitHub / tripal/tripal issues and pull requests