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This is a temporary repository for Drupal 9 upgrade for Tripal v4. It is meant to house issues related to the upgrade.

License: GNU General Public License v2.0

PHP 39.46% Dockerfile 0.23% Shell 0.41% JavaScript 0.84% PLpgSQL 58.78% CSS 0.27% Twig 0.03%

t4d8's Introduction

Tripal 4 (Drupal 9 + 10)

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

Compatibility

Drupal	9.2.x	9.3.x	9.4.x	9.5.x	10.0.x
PHP 8.0
PHP 8.1

Current Timeline

Required for Tripal 4.alpha2 Release

Publishing of the pages
Finish implementing Chado Storage for fields (#238, #239)
Drush generator/updator for fields
Update existing core fields
Finish Chado Vocabs/ID Spaces/Terms (#242, #243)
Legacy API
Move data type specific functionality into extension modules (#281)

Required for Tripal 4.alpha3 Release

Display suite / page work
Importers: Publications, Taxonomy, Newick
Search (ElasticSearch rather then Views)

How to get involved!

This upgrade to Drupal 9 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, let us know what is missing here and we'll add it

Documentation

Documentation for Tripal 4 has begun on ReadtheDocs. Please keep in mind the URL for this documentation will change once Tripal 4 is released.

Tripal Docker

Tripal Docker is currently focused on Development and Unit 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!

t4d8's People

Contributors

Stargazers

Watchers

Forkers

statonlab srobb1 katherynbuble par12005 daniel-shuy ferrisx4 risharde guignonv bradfordcondon yuenchan-usda

t4d8's Issues

Switch to Drupal 9!

Drupal 9.0 has been officially released so we should switch to it! :-D

Updates to Data Importing

Please tag all tickets and pr's with group 4 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

Group 1: Tripal Vocab & Tripal Term

This is to specify my intention to work on converting Tripal Vocab and Tripal Term entity types over to D8.

Group 9 - Documentation

The plan for Tripal 4 documentation is to provide a single resource for Tripal Users and Developers. Rather then documenting Tripal with the assumption you know Drupal, we are going to teach both Drupal/Tripal and provide links to core Drupal documentation for more information. This should make the Tripal 4 documentation an easier resource for PIs to point new developers at.

Idealistic Overview:

Install Tripal
Building your site: creating vocabularies, configuring pages...
Guiding your users: creating content, searching...
Site Administration: Importing data, administering users...
Extending Tripal
Upgrading Tripal
How to Contibute (Tripal Community)

This issue is meant to be a general guiding idea not a master plan 😉

Please feel free to use this issue to mention concepts or functionality which you would love to see well documented!

Group 1: TripalField

This issue deals with updating the TripalField infrastructure. The hope is to do this such that minimal to no work needs to be done on contributed fields. Specifically, these are the files being updated:

Small but critical fix for Tripal Administrative pages

Tripal administrative pages such as Data Storage does not populate sub menu links and instead displays "You do not have any administrative items" text. This means that users cannot get to the appropriate Tripal admin tools.

A fix has already been applied and will be published as a PR request.

Group 1: Upgrade Permissions (only checking needed)

I believe this is complete and stored in the tripal.permissions.yml file: All that is needed is double checking. This is a great opportunity to familiarize yourself with permissions in Drupal 8!

Resources:

chado_insert_cvterm() is slow

This issue is to remind us to speed up chado_insert_cvterm(). This function is used when creating Tripal Terms and chado cvterms and causes noticeable performance issues. Since Tripal Terms will be created during Installation of every Tripal site, this should be considered a high priority.

Group 1: FORMS Registration Form

In Tripal 3 we have a registration form for administrators to register with tripal.info. This is important for ongoing funding and presentations. This issue is to upgrade the Site Registration form shown below to Drupal 8:

Resources:

Choosing another schema for chado (for testing)

This was a great suggestion by Valentin Guignon in the Tripal Core Meeting on 2nd June 2020 in which I also think could be useful especially for preserving the data in live data implementations.

I am however wondering how we can go about getting this new functionality in, particularly if we are going to have a different schema for a test version of chado - how would we be able to link a specific content entity to use the test schema (this might be simple but due to my lack of experience at D8 and T4 at the moment).

CV Term accessions

When adding a controlled vocabulary to Tripal for content types, it automatically adds the short name as the prefix to any accession. For some vocabularies, such as EDAM, the short name can vary so automatically adding the short name will be incorrect for those types of vocabularies.

Create Icons for the Tripal Toolbar!

PR #87 added Tripal to the administration toolbar!

However, you'll notice the administrative toolbar typically has really awesome minimalistic icons... and we do not. This Issue is to remind us to make some :-)

Here they are in core: https://api.drupal.org/api/drupal/core%21modules%21toolbar%21css%21toolbar.icons.theme.css/8.2.x
Drupal uses these: https://github.com/ry5n/libricons/tree/master/src
Here is an example: https://git.drupalcode.org/project/devel/-/blob/4.x/src/ToolbarHandler.php#L103
Here is a tutorial on how: https://drupalcommerce.org/blog/10943/how-create-drupal-8-toolbar-icon

Group 3: Tripal Deamon

Please tag all tickets and pr's with group 3 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

Deprecation Notices for Drupal 9.1.x

The following deprecation notices are obtained when running the unit tests of Drupal 9.1.x. There were no deprecation notices for 9.0.x.

PHPUnit 9.5.0 by Sebastian Bergmann and contributors.

Warning:       Your XML configuration validates against a deprecated schema.
Suggestion:    Migrate your XML configuration using "--migrate-configuration"!

Testing 
................IIII..IIII.........SSS.                           39 / 39 (100%)

Time: 17:59.329, Memory: 16.00 MB

OK, but incomplete, skipped, or risky tests!
Tests: 39, Assertions: 4890, Skipped: 3, Incomplete: 8.

Remaining self deprecation notices (56)

  12x: The Drupal\Tests\tripal_chado\SchemaAPITest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    12x in DrupalListener::startTest from Drupal\Tests\Listeners

  9x: Calling Drupal\Tests\WebAssert::statusCodeEquals with more than one argument is deprecated in drupal:9.1.0 and will throw an \InvalidArgumentException in drupal:10.0.0. See https://www.drupal.org/node/3162537
    9x in TripalMenuPathsTest::testPaths from Drupal\Tests\tripal\Functional

  6x: The Drupal\Tests\tripal_chado\ChadoQueryAPITest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    6x in DrupalListener::startTest from Drupal\Tests\Listeners

  5x: Calling Drupal\Tests\UiHelperTrait::drupalPostForm() with $path set to NULL is deprecated in drupal:9.2.0 and the method is removed in drupal:10.0.0. Use $this->submitForm() instead. See https://www.drupal.org/node/3168858
    2x in TripalTermEntityTest::testTripalTermEntity from Drupal\Tests\tripal\Functional
    2x in TripalVocabEntityTest::testTripalVocabEntity from Drupal\Tests\tripal\Functional
    1x in chadoInstallerFormTest::testLoadInstallerForm from Drupal\Tests\tripal_chado\Functional

  4x: The Drupal\Tests\tripal\Functional\TripalTermEntityTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    4x in DrupalListener::startTest from Drupal\Tests\Listeners

  4x: The Drupal\Tests\tripal\Functional\TripalVocabEntityTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    4x in DrupalListener::startTest from Drupal\Tests\Listeners

  2x: The Drupal\Tests\tripal\Functional\bulkPgSchemaInstallerTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    2x in DrupalListener::startTest from Drupal\Tests\Listeners

  2x: The Drupal\Tests\tripal_chado\ChadoDbAPITest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    2x in DrupalListener::startTest from Drupal\Tests\Listeners

  2x: The Drupal\Tests\tripal_chado\ChadoCvAPITest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    2x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: The Drupal\Tests\tripal_chado\ChadoComplianceTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: The Drupal\Tests\tripal_chado\ChadoVariablesAPITest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: The Drupal\Tests\tripal\Functional\TripalContentTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: The Drupal\Tests\tripal_chado\Functional\chadoInstallerTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: The Drupal\Tests\tripal_chado\Functional\LoadTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: Declaring ::setUp without a void return typehint in Drupal\Tests\tripal_chado\Functional\LoadTest is deprecated in drupal:9.0.0. Typehinting will be required before drupal:10.0.0. See https://www.drupal.org/node/3114724
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: The Drupal\Tests\tripal\Functional\TripalMenuPathsTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: The Drupal\Tests\tripal_chado\Functional\chadoInstallerFormTest::$modules property must be declared protected. See https://www.drupal.org/node/2909426
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: Declaring ::setUp without a void return typehint in Drupal\Tests\tripal_chado\Functional\chadoInstallerFormTest is deprecated in drupal:9.0.0. Typehinting will be required before drupal:10.0.0. See https://www.drupal.org/node/3114724
    1x in DrupalListener::startTest from Drupal\Tests\Listeners

  1x: Calling Drupal\Tests\WebAssert::responseContains with more than one argument is deprecated in drupal:9.1.0 and will throw an \InvalidArgumentException in drupal:10.0.0. See https://www.drupal.org/node/3162537
    1x in chadoInstallerFormTest::testLoadInstallerForm from Drupal\Tests\tripal_chado\Functional

Note: we have to be careful with upgrading our phpunit.xml becuase we are still using earlier version of phpunit with drupal 8.9.x and 9.0.x

simple docker and integration

simple Docker to build Drupal site and install Tripal
Hook up to CI to test builds

Blank page (not WSOD) when adding Tripal Content when no Tripal Content Types exist

If an admin attempts to add Tripal Content and there have been no Tripal Content types added (with proper CV and CV term), a blank page is displayed. This is in relation to recently merged PR #62

Group 2: Chado Custom Tables API

This issue refers to upgrade of tripal_chado.api.inc To take on upgrade of one of these functions just comment below with the function you would like to take on.

chado_edit_custom_table() [Good first task]
chado_create_custom_table() [Good first task]
chado_validate_custom_table_schema() [Good first task]
chado_get_custom_table_id() [Good first task]
chado_get_custom_table_names() [Good first task]
chado_delete_custom_table() [Good first task]

Updates to Entities, Bundles, and Fields

Please tag all tickets and pr's with group 1 to denote it relates to this first group of updates.

Files this update will require to be reviewed and updated (in order):

Implement Test Coverage using GitHub Actions.

See https://docs.codeclimate.com/docs/github-actions-test-coverage
and https://github.com/paambaati/codeclimate-action

Updates to All Other Integrations

Please tag all tickets and pr's with group 8 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

How can we help you?

This upgrade to Drupal 8 is a community effort. As such, we NEED YOUR HELP!

This issue was created as a safe place for you to request documentation, point out barriers and share tips with the community. We will use this issue to improve our documentation and make contribution easier!

Chado install schema -custom name

Task based on #52

Excerpt:

For now, I'm focusing my thoughts on:

Ability to install chado in a different schema name.

Upgrade current hook system for chado queries perhaps supporting user-associated chado schema name.

Chado schema name in entity linking tables with associated Drupal permissions (including alter hook).

And of course, associated automated testing.

With backwards compatibility through smart defaults in mind.

This issue is focusing on allowing chado to be installed in a different chado schema name and allowing a new chado install beside an existing one.

Group 1: FORMS Tripal File Management forms

In Tripal 3 we have a file management system for users. This issue is to upgrade the administration forms for this file management system. Specifically,

Seeadmin/tripal/files and sub-pages on your Tripal3 site.

Resources:

Updates to Chado\Storage

Please tag all tickets and pr's with group 2 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

Group 3: Updates to Job Management

Please tag all tickets and pr's with group 3 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

Tripal Upgrade: Upgrade Tripal from Drupal 7 to Drupal 8

This issue holds the roadmap and resources for upgrading Tripal core from Drupal 7 to Drupal 8.

Upgrade Resources

Tripal 3/4 Table Changes

We are trying to keep data tables similar between Tripal 3/4 but in some cases they may need to change. When they do, add that information here:

tripal_bundle table changed to tripal_entity and the table structure has changed. This was to match the new Drupal Entity API.

Updates to the tripal_vocab table.

To be backwards compatible with the tripal_get_term_details API function the tripal_vocab tables need the url and urlprefix columns.

Have TripalDocker automatically build images and push to docker hub/github

It would be great to have images built automatically! Specifically,

on merge of PR to 9.x-4.x we want to update drupal8.9.x-dev, drupal9.0.x-dev, drupal9.1.x-dev and latest
on release we want to create release-tagged docker images for all the most recent release of drupal 8.9.x, 9.0.x and 9.1.x

The commands to currently create these images are:

git clone https://github.com/tripal/t4d8
cd t4d8
docker build --tag tripalproject/tripaldocker:drupal8.9.x-dev --build-arg drupalversion=8.9.x-dev tripaldocker/
docker build --tag tripalproject/tripaldocker:drupal9.0.x-dev --build-arg drupalversion=9.0.x-dev tripaldocker/
docker build --tag tripalproject/tripaldocker:drupal9.1.x-dev --build-arg drupalversion=9.1.x-dev tripaldocker/

Docker has a gihub action which should make setting this up pretty easy 🤞 🤞

This must be setup by collaborators in the Tripal 4 Core Dev Team as it requires access to Github Secrets. I will update here once I've added the secrets for this repository.

Issue template

Document an issue template for the given project

Group 1: Upgrade menu items

I believe this is actually complete so all that's needed here is to double check :-) This would be a great task to familiarize yourself with menu items in Drupal 8!

Resources:

Tripal Bundle and Tripal Entity

I'm starting to tackle Tripal Bundle and Tripal Entity; specifically,

Tripal Content Type Machine Name Bugs

Setting a custom machine name for Tripal Content Types that does not abide by the bio_data_n convention seems to be causing some issues.

For example, I had two Tripal content types on my dev site. The first was the "Gene" content type, and I allowed it to use the default bio_data_1 machine name. The second content type was the "Test Type" content type, and I set a custom machine name of bio_data_12.

Now I'm going to create a new content type, called "Test Type breaking". The default machine name works as expected, and shows me bio_data_13. I changed the machine name to tripal_content_test_type and created my breaking content type. This seems to cause two issues:

The default bio_data_N number no longer works for Tripal content type machine names. If I now click "Add Tripal Content Type" from the admin > structure > Tripal Content Types page, the default machine name now reads bio_data_1. If I proceed with this machine name, I get an exception:
Drupal\Core\Entity\EntityStorageException: 'tripal_entity_type' entity with ID 'bio_data_1' already exists.
The machine name of my "Test Type breaking" content type displays differently in the UI than it is in the database. If I create content with my "Test Type breaking" content type, then the type column in my tripal_entity table reads tripal_content_test_type, as expected. However, if I navigate to admin > structure > Tripal Content Types and click on the "Test Type breaking" type, it says the machine name is bio_data_13, which was the default machine name I saw when I was first filling out the add new content type form. This problem also seems to apply to the "Test Type" content type, which has a machine name of bio_data_12, but the one displayed in the UI is bio_data_2, which was the default in the add new content type form.

Perhaps users should not be allowed to create custom machine names for Tripal Content types? Or something should be done about the way that the default machine names are handled. My guess is that this is a problem in the tripal/src/Form/TripalEntityTypeForm.php file.

Updates to Views

Please tag all tickets and pr's with group 5 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

Group 1: API Entities api

This issue is specifically to upgrade tripal/tripal/api/tripal.entities.api.inc. To take on upgrade of one of these functions just comment below with the function you would like to take on.

Resources:

Hands-On Training: Controlled Vocabulary Terms Create/Load

Automated testing for entities

I'm working on adding automated testing for the base functionality of entities. This will provide a more stable base for adding field functionality.

We need a working OBO importer for Tripal 4

During the process of upgrading the GFF3 importer, it was noticed that the Sequence Ontology is needed during import hence the birth of this issue and corresponding branch to be created.

Group 1: Installation File

This issue is for upgrading the content of the tripal/tripal.install file. Really the only thing to be updated is hook_schema and not many changes were made in Drupal 8.

Notes:

We are not worrying about the upgrade process as this point.
We are keeping the tripal_variables infrastructure but no longer using them for core thus the tripal_add_variables function does not need to be upgraded.
Drupal 8 no longer supports hook_enable and at this point we don't need to worry about the drop/rename table dance you see going on there -skip tripal_enable when upgrading.
The schema should be the only part that needs to be upgraded. Again don't do the table rename part. Also skip tripal_vocab, tripal_term, tripal_entity and tripal_bundle as these are already managed by the entity api.
no need to keep the tripal_update_### functions.

Resources:

Updates to Display

Please tag all tickets and pr's with group 7 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

Integrate TripalVocab and TripalTerm with Chado

Currently TripalVocab and TripalTerm are completely database agnostic 🎉

Now we want to add functionality to these classes to allow extension modules to integrate with them. Specifically, to allow extension modules to hook into the save and load so they can also save additional information in their own database. Open question: How do we want to save these links? Do we want to leave that to the implementing module?

Core modules needing to integrate: tripal_chado and tripal_ws.

Additionally, we need to add some more properties to these classes:
TripalVocab:

url
urlprefix
semantic web url*
number of terms
TripalTerm:
url generated based on the vocab

We also need to allow extension modules to implement tripal_get_vocabulary_root_terms() and tripal_get_term_children() as currently TripalVocab and TripalTerm do not have a hierarchy... Maybe we should reconsider this?

Group 1: HTML5 File Upload Element

This issue is to handle upgrading the Tripal HTML5 upload form element used in all Tripal Importers.

Resources:

Group 2: Chado Setup/Prepare

We need to upgrade the prepare step which happens after chado is installed.

Tripal 3: https://github.com/tripal/tripal/blob/7.x-3.x/tripal_chado/includes/setup/tripal_chado.setup.inc

This will include

the simple form
Creating Tripal Vocabs, etc. Currently we'll focus only on those needed for content types.
Creating Tripal Content Types which map to the terms.
Materialized Views and custom tables not needed for alpha release.
Semweb will be done in Group 6

Resources:

Forms:
Vocabularies:
- Tripal4 Structure
- Tripal4 HowTo
Content Types:
- Tripal Content Types Class

Group 1: API Vocab/Terms api

This issue is specifically to upgrade tripal/tripal/api/tripal.terms.api.inc. To take on upgrade of one of these functions just comment below with the function you would like to take on.

Hooks near the top of the file
tripal_add_term() [Good first task]
tripal_get_term_details() [Good first task]
tripal_get_vocabulary_root_terms()
tripal_get_term_children()
tripal_get_vocabulary_details() [Good first task]
tripal_get_vocabulary_terms() [Good first task]
tripal_get_vocabularies() [Good first task]
tripal_get_term_lookup_form() and tripal_get_term_lookup_form_result() [Good first task]

Resources:

Group 1: Upgrade Tripal Core blocks

Blocks to be upgraded:

Notifications
Powered by Tripal
Content bar chart

Resources:

Group 1: Default Tripal Shortcuts

This has been partially implemented but commented out since it causes another dependency. I think default shortcut sets help new users tremendously and thus am tempted to add this anyway -what do others in the community think?

Group 1: Convert functions in tripal.module file

This was started and almost completed by @shawnawsu. The intent is to convert all functions in the tripal 3 tripal.module file to Drupal 8.

Here is the list of functions from Tripal 3:

Rename table tripal_admin_notfications

The table public.tripal_admin_notfications is spelled wrong. This is also true for Tripal 3. I assume it would not necessarily be feasible to correct this for Tripal 3, but we might want to correct this at least for Tripal 4. This should be pretty trivial since the table currently only appears in the tripal.install file as far as I can tell.

Group 2: Tripal Chado SCHEMA API

This issue was originally used for a small set of miscellaneous functions which need upgrading. That has been moved to #122 and this issue has been re-assigned for the discussion of the Chado Schema API. This was done since the Chado Schema API did not have a dedicated issue and @guignonv started a good discussion here.

ONLY discuss the Chado Schema API here. This should not include information on querying the Chado database which is a separate but related issue.

Tv3 Updates Needed in Tv4

I'm creating this issue as a place where we can add items that were added in Tv3 after we separated this t4d8 repository. As we review the pull request history for the Tv3 repository we can return here and add check boxes below link to the corresponding pull request.

The TripalField class got a new theme function for theming of the instance settings form, (PR coming soon).
An updated GFF3 Importer, tripal/tripal#1141
Date/Time incorrect time on display, tripal/tripal#1148

Group 1: Automated Testing for Permissions

We should have automated testing for our permissions to ensure they are working as expected.

Updates to Web Services

Please tag all tickets and pr's with group 6 to denote it relates to this group of updates.

Files this update will require to be reviewed and updated (in order):

tripal / t4d8 Goto Github PK

t4d8's Introduction

Tripal 4 (Drupal 9 + 10)

Compatibility

Current Timeline

Required for Tripal 4.alpha2 Release

Required for Tripal 4.alpha3 Release

How to get involved!

Documentation

Tripal Docker

t4d8's People

Contributors

Stargazers

Watchers

Forkers

t4d8's Issues

Upgrade Resources

Tripal 3/4 Table Changes

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Recommend Topics

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