tripal / tripald3

provides an API for developing consistent biological diagrams with a common configuration, as well as, providing some common diagrams such as pie, bar, column and pedigree diagrams.

Tripal 4 (Drupal 10)

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

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!

tripald3's Issues

Restrict node in pedigree tree

error on install: undefined function libraries_get_libraries

drush pm-enable -y tripald3
WD php: Error: Call to undefined function libraries_get_libraries() in tripald3_requirements() (line 71 of     [error]
/Users/bc/tripal/sites/all/modules/tripald3/tripald3.install).
Error: Call to undefined function libraries_get_libraries() in tripald3_requirements() (line 71 of /Users/bc/tripal/sites/all/modules/tripald3/tripald3.install).
Drush command terminated abnormally due to an unrecoverable error.

looks like libraries should be declared as a dependency

edit- i . see that it is listed as a requirement. Perhaps because you use a function in hte .install? i dunno.

You list in the README so probably OK to just close this issue.

Upgrade to Tripal 4 + Drupal 9

Work on this has been begun by @reynoldtan on branch 9.x-2.x. We have a PR open #14 for testing of the current upgrade and would appreciate feedback on this issue or the PR if you are interested in using this module for Tripal 4.

THIS ISSUE SHOULD NOT BE CLOSED UNTIL

• Tripal 4 stable is released
• 9.x-2.x branch is made the default branch
• all documentation has been upgraded to the Drupal 9 / Tripal 4 / Tripal D3 2.x

Example charts

Could anyone provide an example on how to use tripal3d to make eg bar chart?

Pedigree relationship tooltips are not always correctly ordered

Some of the relationship tooltips are not formed correctly. For example, in the following screenshot the tooltip should read CDC Impulse is_registered_cultivar_of IBC 479. I have checked the database + relationship fields which do have the relationship in the correct order thus the problem is with the pedigree js code in this library.

Make Tripal v3 compatible

This module should be made into a d3.js api for Tripal. All diagrams should perhaps move to other modules.

Few minor issues in pedigree tree

• Relationship not showing
• Only finding links for content with same Tripal content types as the root
• Nodes linking to # - top page
• Left border of top container box (for figure key legend) missing

Option to position figure legend key on top

Add option to position figure legend keys on top of a pedigree tree diagram

Create API to watermark visualizations

Colours re-used if more then 10+ categories

If there are more categories then colours, the colours are re-used. This may be the expected behaviour but causes unreadable charts... Should we add cross-hatching or some-such in this case?

Key spills off bottom of SVG

If there are too many categories for a chart to fit within the height specified, they simply get cut off. I'm not sure what we want the default to be. Should the SVG grow to fit the expanded key? This could throw off layouts... Should the key become two columns? There many not be room for this either.