Ecosyste.ms: Issues

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GitHub / tripal/tripal issues and pull requests

#1584 - Full Test Suite for ChadoStorage: Single Property Field

Pull Request - State: closed - Opened by laceysanderson about 1 year ago - 3 comments
Labels: Tripal 4, Group 9 - Automated Testing

#1583 - REVEAL: Adding the title Templates to the content type YAML

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

#1582 - REVEAL: Fix Content Type listing

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

#1581 - Debug level logging is not documented and has a gotchya

Issue - State: closed - Opened by dsenalik about 1 year ago - 3 comments
Labels: Tripal 3, Community - Discussion, PR Submitted, Tripal 4, Group 0 - General Maintenance

#1580 - Tripal Importer Plugin Submit Button

Issue - State: closed - Opened by reynoldtan about 1 year ago - 1 comment
Labels: bug - confirmed, Good First Issue, Tripal 4, Group 4 - Data Importing

#1579 - Tripal 4 importer logging enhancement

Issue - State: closed - Opened by dsenalik about 1 year ago - 2 comments
Labels: Tripal 4, Group 4 - Data Importing

#1578 - Tripal 4 ChadoAnalysisDefault field

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

#1577 - Tripal 4 tripal logger string substitution not done in some cases

Pull Request - State: closed - Opened by dsenalik about 1 year ago - 2 comments
Labels: bug - confirmed, Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1576 - Tripal 4 tripal logger string substitution not done in some cases

Issue - State: closed - Opened by dsenalik about 1 year ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 0 - General Maintenance

#1575 - Expand automated docker build set to include images without Chado

Pull Request - State: closed - Opened by laceysanderson about 1 year ago - 1 comment
Labels: Tripal 4, Group 9 - Automated Testing

#1574 - Tripal 3 Fix php8.1 deprecations

Pull Request - State: closed - Opened by dsenalik about 1 year ago
Labels: bug - confirmed, Tripal 3, Group 0 - General Maintenance, PHP8, Easy PR Review 😀

#1573 - Tripal 3 PHP 8.1 deprecation notices

Issue - State: closed - Opened by dsenalik over 1 year ago - 3 comments
Labels: bug - confirmed, Tripal 3, Group 0 - General Maintenance, PHP8

#1572 - Docker builds are too restrictive for automated testing in extension modules

Issue - State: closed - Opened by laceysanderson over 1 year ago - 1 comment
Labels: Tripal 4, Group 9 - Automated Testing

#1571 - Cvterm autocomplete needs filter by cv

Issue - State: closed - Opened by laceysanderson over 1 year ago - 1 comment
Labels: PR Submitted, Good First Issue, Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado, Group 4 - Data Importing

#1570 - Tripal 4 issue1568 add missing legacy_ro.obo

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 6 comments
Labels: bug - confirmed, Tripal 4, Group 4 - Data Importing

#1569 - OBO Importer: Cannot find term: 'NCIT:C25693' when importing into 2nd chado schema

Issue - State: open - Opened by laceysanderson over 1 year ago - 1 comment
Labels: bug - potential, Group 4 - Data Importing

#1568 - OBO Importer: legacy_ro.obo does not exist or cannot be read.

Issue - State: closed - Opened by laceysanderson over 1 year ago - 2 comments
Labels: bug - confirmed, Good First Issue, Tripal 4, Group 4 - Data Importing

#1567 - REVEAL: Smaller Bug Fixes / Changes

Issue - State: open - Opened by laceysanderson over 1 year ago
Labels: Group 0 - General Maintenance

#1566 - REVEAL: Fixes to the Content Terms creation

Issue - State: open - Opened by laceysanderson over 1 year ago
Labels: Group 1 - Tripal Content Types | Terms | Fields

#1565 - REVEAL: Remove `bio_data` assumption from content types

Issue - State: closed - Opened by laceysanderson over 1 year ago - 3 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1564 - REVEAL: Fix Content Type listing

Issue - State: closed - Opened by laceysanderson over 1 year ago - 1 comment
Labels: PR Submitted, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1563 - REVEAL: Adding the title Templates to the content type YAML

Issue - State: closed - Opened by laceysanderson over 1 year ago - 2 comments
Labels: PR Submitted, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1562 - Tripal4 issue1561 fix parallel message

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 3 - Job Management, Easy PR Review 😀

#1561 - Tripal 4 drush trp-run-jobs --parallel does not take a parameter

Issue - State: closed - Opened by dsenalik over 1 year ago
Labels: bug - confirmed, Good First Issue, Tripal 4, Group 3 - Job Management

#1560 - Tripal 4 - NCBI Taxonomy Loader

Pull Request - State: closed - Opened by risharde over 1 year ago - 7 comments
Labels: Tripal 4, Group 4 - Data Importing

#1559 - Tripal 4 php8 warning fix in OBO loader

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: Tripal 4, Group 4 - Data Importing, PHP8, Easy PR Review 😀

#1558 - Tripal 4 change hook invocation to module handler service

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 0 - General Maintenance

#1557 - Tripal 4 OBOImporter warnings under PHP8

Issue - State: closed - Opened by dsenalik over 1 year ago
Labels: bug - confirmed, PR Submitted, Tripal 4, Group 4 - Data Importing, PHP8

#1556 - Tripal 4 Drupal 10: All hook invocation delegated to Module Handler service

Issue - State: closed - Opened by dsenalik over 1 year ago - 2 comments
Labels: bug - confirmed, Tripal 4, Group 0 - General Maintenance

#1555 - Tripal 4 add a chado boolean field

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 3 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1554 - Project Autocomplete Controller

Pull Request - State: closed - Opened by reynoldtan over 1 year ago - 4 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1553 - Chado project autocomplete

Issue - State: closed - Opened by reynoldtan over 1 year ago - 1 comment
Labels: Community - Enhancement, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1552 - New infrastructure for Kernel Testing Chado Storage + Property Field Tests

Pull Request - State: closed - Opened by laceysanderson over 1 year ago - 2 comments
Labels: Tripal 4, Group 9 - Automated Testing

#1551 - Tripal 4 is missing chado_boolean_type field

Issue - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: PR Submitted, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1550 - Tripal 4: Implement some of the missing core fields and add to content types

Issue - State: open - Opened by dsenalik over 1 year ago - 8 comments
Labels: bug - confirmed, Group 1 - Tripal Content Types | Terms | Fields

#1549 - Dependency injection for Chado Storage + Storage Property Types/Values

Pull Request - State: closed - Opened by laceysanderson over 1 year ago - 1 comment
Labels: Tripal 4, Group 9 - Automated Testing

#1548 - Port tripal_version() api function and drush trp-version to Tripal 4

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 2 comments
Labels: Tripal 4, Group 0 - General Maintenance

#1547 - Tripal 4 change chado storage handling of empty fields

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 3 comments
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1546 - Kernel tests for Chado Storage

Issue - State: closed - Opened by laceysanderson over 1 year ago - 3 comments
Labels: Tripal 4, Group 9 - Automated Testing

#1545 - Tripal 4 tripal_report_error() is deprecated

Issue - State: open - Opened by dsenalik over 1 year ago
Labels: Good First Issue, Group 0 - General Maintenance

#1544 - Tripal 4 chado storage validation error with form fields where null is allowed

Issue - State: closed - Opened by dsenalik over 1 year ago - 3 comments
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1543 - Issue 1520 fix deprecated dynamic property

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 0 - General Maintenance, PHP8, Easy PR Review 😀

#1542 - Move Extensions into Tripal 4 Core

Issue - State: open - Opened by spficklin over 1 year ago
Labels: Group 8 - Other Integrations

#1541 - Restructure Kernel Tests

Pull Request - State: closed - Opened by laceysanderson over 1 year ago - 2 comments
Labels: Tripal 4, Group 9 - Automated Testing

#1540 - tripal 3 issue 1538 local__contact widget ajax error fix

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: bug - confirmed, Group 1 - Tripal Content Types | Terms | Fields, PHP8, Easy PR Review 😀

#1539 - Test Directory Structure

Issue - State: open - Opened by laceysanderson over 1 year ago
Labels: Group 9 - Automated Testing

#1538 - Tripal 3 ajax error in local__contact widget

Issue - State: closed - Opened by dsenalik over 1 year ago
Labels: bug - confirmed, Tripal 3, Group 1 - Tripal Content Types | Terms | Fields, PHP8

#1537 - Tripal 4 port of tripal 3 chado_get_organism_id_from_scientific_name()

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 8 comments
Labels: Tripal 4, Group 0 - General Maintenance

#1536 - Port pull #1328 to Tripal 4

Issue - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: Tripal 4, Group 0 - General Maintenance

#1523 - Tripal 4 Drupal 10.1 compatibility

Issue - State: closed - Opened by dsenalik over 1 year ago - 2 comments
Labels: bug - confirmed, Tripal 4, Group 9 - Automated Testing

#1522 - Remove use of \Drupal from Class settings in favour of dependency injection

Issue - State: open - Opened by laceysanderson over 1 year ago - 2 comments
Labels: Group 0 - General Maintenance

#1521 - Tripal 4 - Fix all the PHP 8.2 deprecations

Pull Request - State: open - Opened by dsenalik over 1 year ago - 1 comment

#1520 - Tripal 4 - Fix PHP 8.2 dynamic property deprecations

Issue - State: closed - Opened by dsenalik over 1 year ago - 7 comments
Labels: Tripal 4, Group 0 - General Maintenance, Group 9 - Automated Testing, PHP8

#1519 - Adds a Dockerfile for PHP 8.2 and testing for Drupal 10.1.x

Pull Request - State: open - Opened by laceysanderson over 1 year ago
Labels: Tripal 4, Group 0 - General Maintenance, Group 9 - Automated Testing, Easy PR Review 😀

#1518 - Tripal 4 error on "Tripal Content Terms" page

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

#1517 - Compatibility with Drupal 10.0 🎉 (and keeping 9.4 and 9.5)

Pull Request - State: closed - Opened by laceysanderson over 1 year ago - 5 comments
Labels: Release Blocker, Tripal 4, Group 0 - General Maintenance, Group 2 - Data Storage | Tripal DBX | Chado, Group 9 - Automated Testing

#1516 - install chado report SQL syntax error

Issue - State: closed - Opened by jmzhuzhonghua over 1 year ago - 3 comments
Labels: Community - Question, Tripal 4

#1515 - Tripal 4 - Publish Chado Content

Issue - State: closed - Opened by Ferrisx4 over 1 year ago - 3 comments
Labels: PR Submitted, Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1514 - Unpublished/Deleted Items (e.g. organisms) still visible

Issue - State: open - Opened by Ferrisx4 over 1 year ago - 1 comment
Labels: bug - potential, Group 1 - Tripal Content Types | Terms | Fields, Group 2 - Data Storage | Tripal DBX | Chado

#1513 - Tripal 4 - NCBI Taxonomy and Newick Loader

Issue - State: closed - Opened by risharde over 1 year ago - 2 comments
Labels: Tripal 4, Group 4 - Data Importing

#1512 - Tripal 4 rename some remaining .inc files to .php - issue1502

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 0 - General Maintenance

#1511 - Remove deprecated functionality to move us closer to D10 support

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

#1510 - Get Tests to pass on Drupal 10

Issue - State: closed - Opened by laceysanderson over 1 year ago - 2 comments
Labels: Tripal 4, Group 9 - Automated Testing

#1509 - Tripal 4 update YAML for various missing fields

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

#1508 - Tv4g1 issue1507 fix pylotree typo

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

#1507 - Tripal 4 yml typos

Issue - State: closed - Opened by dsenalik over 1 year ago - 2 comments
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1506 - Remove default select from chado_get_organism_select_options()

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1505 - Remove built-in "Select an organism" option from chado_get_organism_select_options()

Issue - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: PR Submitted, Good First Issue, Tripal 4, Group 0 - General Maintenance

#1504 - Tv4g1 issue1414 local data source field

Pull Request - State: open - Opened by pdtouch over 1 year ago - 4 comments
Labels: waiting on submitter, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1503 - Some API functions are still hardcoded to 'chado'

Issue - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1502 - All PHP files should end in `.php` for Drupal 9/10

Issue - State: open - Opened by laceysanderson over 1 year ago - 3 comments
Labels: Tripal 4, Group 0 - General Maintenance, Group 9 - Automated Testing

#1501 - Add a retry for failed requests to remote URLs

Issue - State: open - Opened by dsenalik over 1 year ago - 6 comments
Labels: bug - confirmed, Group 4 - Data Importing, Group 9 - Automated Testing

#1500 - Version number updates

Pull Request - State: closed - Opened by spficklin over 1 year ago
Labels: Tripal 3, Easy PR Review 😀

#1499 - Update testing badge urls and other t4d8 references in the README

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

#1498 - Tripal 4 chado_unabbreviate_infraspecific_rank (port tripal 3 pull 1244)

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 4 comments
Labels: Community - Enhancement, Tripal 4, Group 0 - General Maintenance, Group 2 - Data Storage | Tripal DBX | Chado

#1497 - Tripal 4 issue1496 fix old workflow versions

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 2 comments
Labels: bug - confirmed, Tripal 4, Group 4 - Data Importing, Group 9 - Automated Testing

#1496 - Tripal 4 testing badges do not work

Issue - State: closed - Opened by dsenalik over 1 year ago - 3 comments
Labels: bug - confirmed, PR Submitted, Tripal 4, Group 9 - Automated Testing

#1495 - Issue 1414 local source data field for Analysis

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 2 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1494 - Create ChadoLocalSourceDataFormatterDefault.php

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 1 comment

#1493 - Create ChadoLocalSourceDataWidgetDefault.php

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 1 comment

#1492 - Create ChadoLocalSourceDataDefault.php

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 1 comment

#1491 - Create ChadoLocalSourceDataWidgetDefault.php

Pull Request - State: closed - Opened by pdtouch over 1 year ago

#1490 - Create ChadoLocalSourceDataDefault.php

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 1 comment

#1489 - Tv4 merge tripal3 pull 1369 gff loader changes

Pull Request - State: closed - Opened by dsenalik over 1 year ago
Labels: Tripal 4, Group 4 - Data Importing

#1488 - Tripal 4 - FASTA loader

Pull Request - State: closed - Opened by risharde over 1 year ago - 8 comments
Labels: Tripal 4, Group 4 - Data Importing

#1487 - Issue 1318 Add autocompletes for upcoming chado_linker module

Pull Request - State: closed - Opened by dsenalik over 1 year ago
Labels: Community - Enhancement, Tripal 3, Group 1 - Tripal Content Types | Terms | Fields, PHP8

#1486 - Chado CV Term Autocomplete Functionality

Pull Request - State: closed - Opened by reynoldtan over 1 year ago - 1 comment
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1485 - Port pull #1244 to Tripal 4

Issue - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: PR Submitted, Tripal 4, Group 0 - General Maintenance

#1484 - Tv4g4 issue1483 organism lists for select

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

#1483 - Port pull #1311 to Tripal 4

Issue - State: closed - Opened by dsenalik over 1 year ago - 8 comments
Labels: PR Submitted, Tripal 4, Group 4 - Data Importing

#1482 - Chado cvterm autocomplete

Issue - State: closed - Opened by laceysanderson over 1 year ago
Labels: Tripal 4, Group 2 - Data Storage | Tripal DBX | Chado

#1481 - Tripal 4 additional type field bug with "term_name"

Issue - State: closed - Opened by dsenalik over 1 year ago - 2 comments
Labels: bug - confirmed, Tripal 4, Group 1 - Tripal Content Types | Terms | Fields

#1480 - Update Dockerfile-php8-pgsql13

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 3 comments
Labels: Community - Enhancement, Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1479 - Update Dockerfile-php8.1-pgsql13

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 1 comment
Labels: Community - Enhancement, Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1478 - Change Automated PHPunit testing workflow to be triggered on pull requests

Pull Request - State: closed - Opened by laceysanderson over 1 year ago - 4 comments
Labels: Tripal 4, Group 9 - Automated Testing

#1477 - Phpunit workflows not running on PRs from a forked repo

Issue - State: closed - Opened by laceysanderson over 1 year ago - 3 comments

#1476 - Update Dockerfile-php8.1-pgsql13

Pull Request - State: closed - Opened by pdtouch over 1 year ago - 6 comments
Labels: Community - Enhancement, Tripal 4, Group 0 - General Maintenance, Easy PR Review 😀

#1475 - Redo of "Content Types and Fields defined by YAML" focused on minimal changes

Pull Request - State: closed - Opened by laceysanderson over 1 year ago - 2 comments
Labels: Tripal 4, Group 1 - Tripal Content Types | Terms | Fields, Easy PR Review 😀

#1474 - Tripal 4 Issue 1472 $form_state bugfix

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: bug - confirmed, Tripal 4, Group 4 - Data Importing, Easy PR Review 😀

#1473 - Tv4g4 issue1472 form state bug - Abandoned, wrong starting branch

Pull Request - State: closed - Opened by dsenalik over 1 year ago - 1 comment
Labels: wontfix