tripal/mainlab_tripal

Mainlab Tripal Data Display: extending the display of a Tripal database

Tripal 4 (Drupal 10)

               _   _                 _____                 _                                  _
     /\       | | (_)               |  __ \               | |                                | |
    /  \   ___| |_ ___   _____      | |  | | _____   _____| | ___  _ __  _ __ ___   ___ _ __ | |_
   / /\ \ / __| __| \ \ / / _ \     | |  | |/ _ \ \ / / _ \ |/ _ \| '_ \| '_ ` _ \ / _ \ '_ \| __|
  / ____ \ (__| |_| |\ V /  __/     | |__| |  __/\ V /  __/ | (_) | |_) | | | | | |  __/ | | | |_
 /_/    \_\___|\__|_| \_/ \___|     |_____/ \___| \_/ \___|_|\___/| .__/|_| |_| |_|\___|_| |_|\__|
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Compatibility

Tested on +

Drupal	10.2.x	10.3.x
PHP 8.1
PHP 8.2
PHP 8.3

Code Coverage

This project uses Code Climate to determine the quality of our codebase and the coverage of our test suite. Compatibility above is based on passing of this test suite.

Current Timeline

Required for Tripal 4.alpha3 Release

• Display suite / page work
• Importers: Publications
• Search (ElasticSearch + Views)

How to get involved!

This upgrade to Drupal 10 is a community effort. As such, we NEED YOUR HELP!

• To get involved, please join our Tripal Slack and comment in the #core-dev channel.
  • Alternatively, feel free to contact Lacey-Anne Sanderson through Slack direct message.
  • We can use help both with programming, documentation, outreach and welcome all individuals from all backgrounds!
• We prefer automated testing for all Pull Requests (PRs) and are happy to guide you through the process!
  • Just comment on the issue if you need help designing tests
  • If you need help implementing tests see our documentation
• If more documentation would be helpful, please create an issue here and we'll add it.

Documentation

Documentation for Tripal 4 has begun on ReadtheDocs.

• Installation
• Automated Testing
• Developer Guide
• Contribution Guide

Tripal Docker

Tripal Docker is currently focused on Development and Automated Testing. There will be a production focused Tripal Docker soon and if you're interested in helping or providing tips -please join us on our Slack channel!

For more information about how to use our fully functional development docker, see our documentation on ReadtheDocs!

mainlab_tripal's Issues

Undefined table: 7 ERROR: relation "chado_stock" does not exist LINE 1:

Notice: Undefined property: stdClass::$all_relationships in include() (line 22 of /var/www/html/sites/all/modules/mainlab_tripal/theme/cottongen/mainlab_organism_base.tpl.php). Warning: key_exists() expects parameter 2 to be array, null given in include() (line 27 of /var/www/html/sites/all/modules/mainlab_tripal/theme/cottongen/mainlab_organism_base.tpl.php). Warning: key_exists() expects parameter 2 to be array, null given in include() (line 32 of /var/www/html/sites/all/modules/mainlab_tripal/theme/cottongen/mainlab_organism_base.tpl.php). Warning: key_exists() expects parameter 2 to be array, null given in include() (line 37 of /var/www/html/sites/all/modules/mainlab_tripal/theme/cottongen/mainlab_organism_base.tpl.php). Warning: array_key_exists() expects parameter 2 to be array, null given in chado_expand_var() (line 753 of /var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_variables.api.inc). PDOException: SQLSTATE[42P01]: Undefined table: 7 ERROR: relation "chado_stock" does not exist LINE 1: ...cvterm_id = type_id) AS type, (SELECT nid FROM chado_stoc... ^: SELECT count(*) FROM (SELECT uniquename, (SELECT name FROM chado.cvterm WHERE cvterm_id = type_id) AS type, (SELECT nid FROM chado_stock WHERE stock_id = stock.stock_id) AS nid FROM chado.stock WHERE organism_id = (SELECT organism_id FROM chado.organism WHERE genus = :genus AND species = :species) AND (type_id NOT IN (SELECT cvterm_id FROM chado.cvterm WHERE name IN ('sample', 'clone') AND cv_id = (SELECT cv_id FROM chado.cv WHERE name = 'MAIN') ) )) A; Array ( [:genus] => Citrus [:species] => sinensis ) in chado_query() (line 1538 of /var/www/html/sites/all/modules/tripal/tripal_core/api/tripal_core.chado_query.api.inc).

single organism parameter not seen in mainlab_organism_base.tpl.php

If an organism has only one entry in the chado.organismprop table, this property will not appear on the organism summary page generated by theme/cottongen/mainlab_organism_base.tpl.php
bugfix is on line 14 of theme/cottongen/mainlab_organism_base.tpl.php