tripal / fields_generator

A composer tool for easily generating Tripal Fields

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!

fields_generator's Issues

Error connecting to DB

current version cant connect to DB properly/ has trouble finding settings.php

Zenodo DOI release

I've added DOI integration via Zenodo. Let's make sure the next release is descriptive.

Field (load) stub has a typo

There is a comma where a semi colon should be

We need help text

I think migrating to symfony console would be great for this module. It'll make the command much more intuitive to use.

Creating two fields in a row will overwite the stub file

If you use the generator twice in a row pointed at teh same output location, the fields stub file intended to go in module_name.fields.inc will get overwitten.

Move term adding function to the install

We currently generate the term insertion code in the .fields.inc file but the badges guideline specifically asks for this to be in the install file. Would a simple comment suffice? Or do we need to create a new file for it?

typo in stub file generated

$field_name = 'obi__microarray platform'; instead of $field_name = 'obi__microarray_platform';

More accurately, it could automtically introduce white space for machine names, or throw a warning

simpler rule for CV vs DB?

Use the EBI breadcrumb.

so teal box = CV, orange box = DB. IF obo namespace is provided in the sidebar, that will override the CV

This works for all DB/CVs except where capitalization is inconsistent between db and cv.

Reformat the stub classes to satisfy code sniffer

Example, change array() to [].

dead links in readme

tripal.info documentation has moved. http://tripal.info/tutorials/v3.x/developers_handbook/custom_field for example

style incompatibility

The drupal code sniffer reformats the static variable documentation and its kind of not good.

• can we use @see like we do for the method definitions?
• if not, what should we do?
  • remove the comments and perhaps put @see at the top of the class?
  • reformat the comments to follow the Drupal style standard?

Update git commands in docs

the git clone command stills refers to the old statonlab repo

move static overrides int othe constructor?

I'm not a big fan of our stubs returning the super verbose public $static everything with the comments etc.

I was messing around with extending an importer and took this approach: overriding the parent static methods in the __construct method:

  /**
   * how we previously set it.  no longer necessary, you get style complaints.
   */
  public static $methods = array(
    'file_upload' => FALSE,
    'file_local' => FALSE,
    'file_remote' => FALSE,
  );
  public static $file_required = FALSE;

  /**
   * EutilsImporter constructor.
   *
   * @param \TripalJob|null $job
   */
  public function __construct(TripalJob $job = NULL) {
    parent::__construct($job);
    static::$name = 'NCBI EUtils Accession loader';
    static::$machine_name = 'eutils_loader';
    static::$description = 'Import a BLAST XML file into Chado';
    static::$use_analysis = FALSE;
    static::$button_text = 'Import NCBI Record';
    static::$methods = [
      'file_upload' => FALSE,
      'file_local' => FALSE,
      'file_remote' => FALSE,
    ];
  }

Do we like this more? You get a lot of less code sniffer complaints this way and its a lot more compact.

I also think it will partially resolve #46

improving CVterm suggestions

since OLS tends to show you lots of garbage from garbage CVs...

Elasticsearch integration

• Pick which CVs to search?

How to attach newly generated field to bundle?

Hi @bradfordcondon , I don't understand how to attach the generated field to my specific bundle. I can't seem to locate information/documentation regarding this, can you help me out? Thanks!

ask what bundle to attach field to by default

right now automatically attaches to organism

Update stubs

Stephen has added more functionality to fields.

I need to update the stub files to reflect this.

CV guide update

stephen has updated the CV guide to clarify the language, particularly what is Tripal, what is Chado, and what is general CV. good stuff. I should incorporate changes.

http://tripal.info/tutorials/v3.x/developers_handbook/custom-field/vocabulary

library contributed fields need to have "tripal_chado"

for library, the module should be 'tripal_chado'. That's because we dont have the fields.inc file that tells drupal about our field, so someone has to tell drupal about it: and we want that to be Tripal.

To fix, change the 'module' prompt to advise people of this.

Changes to the TripalField class

I have just made a change to the TripalField class (on the collections branch of Tripal) which moves the download_formatters out of the $default_instance_settings variable and into it's own static variable. This is because it would be really hard to add new formatters to a field without manually rewritting the settings for existing fields.... too much effort. Once the 'collections' branch gets merged into the 7.x-3.x branch then this change will be active.

add @see to stubs

for the formatter view for example: * @see TripalFieldFormatter::view()

I like having the stubs generated have the full text, but maybe we should do something like:

/**
* @see TripalFieldFormatter::view()
* the full description for this method is provided below.  You should delete it, and only leave the @see annotation above, when you are ready to contribute your code.
* full 
* description...
**/

broken build

phpunit
PHP Fatal error:  Declaration of GeneratorEngineTest::setUp() must be compatible with PHPUnit\Framework\TestCase::setUp(): void in /home/travis/build/tripal/fields_generator/tests/Generator.php.test on line 34
PHP Stack trace:
PHP   1. {main}() /home/travis/.phpenv/versions/7.2.15/bin/phpunit:0
PHP   2. PHPUnit\TextUI\Command::main() /home/travis/.phpenv/versions/7.2.15/bin/phpunit:619
PHP   3. PHPUnit\TextUI\Command->run() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/TextUI/Command.php:164
PHP   4. PHPUnit\TextUI\Command->handleArguments() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/TextUI/Command.php:175
PHP   5. PHPUnit\Util\Configuration->getTestSuiteConfiguration() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/TextUI/Command.php:910
PHP   6. PHPUnit\Util\Configuration->getTestSuite() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Util/Configuration.php:870
PHP   7. PHPUnit\Framework\TestSuite->addTestFiles() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Util/Configuration.php:1013
PHP   8. PHPUnit\Framework\TestSuite->addTestFile() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Framework/TestSuite.php:625
PHP   9. PHPUnit\Util\FileLoader::checkAndLoad() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Framework/TestSuite.php:546
PHP  10. PHPUnit\Util\FileLoader::load() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Util/FileLoader.php:47
Fatal error: Declaration of GeneratorEngineTest::setUp() must be compatible with PHPUnit\Framework\TestCase::setUp(): void in /home/travis/build/tripal/fields_generator/tests/Generator.php.test on line 34
Call Stack:
    0.0008     561248   1. {main}() /home/travis/.phpenv/versions/7.2.15/bin/phpunit:0
    0.0721    9831616   2. PHPUnit\TextUI\Command::main() /home/travis/.phpenv/versions/7.2.15/bin/phpunit:619
    0.0721    9840408   3. PHPUnit\TextUI\Command->run() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/TextUI/Command.php:164
    0.0721    9840408   4. PHPUnit\TextUI\Command->handleArguments() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/TextUI/Command.php:175
    0.0793    9843040   5. PHPUnit\Util\Configuration->getTestSuiteConfiguration() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/TextUI/Command.php:910
    0.0793    9843624   6. PHPUnit\Util\Configuration->getTestSuite() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Util/Configuration.php:870
    0.0798    9881960   7. PHPUnit\Framework\TestSuite->addTestFiles() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Util/Configuration.php:1013
    0.0798    9881960   8. PHPUnit\Framework\TestSuite->addTestFile() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Framework/TestSuite.php:625
    0.0798    9881960   9. PHPUnit\Util\FileLoader::checkAndLoad() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Framework/TestSuite.php:546
    0.0799    9882248  10. PHPUnit\Util\FileLoader::load() phar:///home/travis/.phpenv/versions/7.2.15/bin/phpunit/phpunit/Util/FileLoader.php:47
The command "phpunit" exited with 255.

https://travis-ci.org/tripal/fields_generator/builds/500085780?utm_medium=notification&utm_source=email

don't clear prompt when backspacking!

pressing backspace when being asked a question clears the prompt question!

code demonstrating SO in CV guide missing

set max length for machien name

the whole field name ie database__term_name must be 32 characters or less. let's halt if created term would be more.

h for help?

Right now the questions we ask the user to generate the field are too verbose making it not clear where the cursor is which is a bit disorienting (for me at least). For a better experience, I suggest adding the following:

• A -v option to enable verbose mode which is the mode it is currently using
• Typing h or help as the answer to any question should generate help text

Yes it's a little bit of work but a good improvement imo.