New Controller Class to replace the ChadoOrganismAutocompleteController #2293

vidu-wil · 2025-09-23T22:11:48Z

New Feature

Issue #2284

Description

This PR introduces a new controller class, ChadoOrganismFormElementController, which replaces and extends the functionality of the existing ChadoOrganismAutocompleteController. It retains all existing methods while adding methods for generating the autocomplete/select elements used in the organism widget. Additionally, it includes a method to get the select options as a direct replacement for chado_get_organism_select_options() method.

Testing

Automated testing

ChadoOrganismFormElementControllerTest class containing the following methods:

testChadoOrganismFormElementController() - tests if the suggestions returned by the handleAutocomplete using the url request matches the expected number of options and whether the organism_id returned by getPkeyId is valid.
testFormElement() along with its data provider provideDataForTestFormElement() - tests the following test case scenarios to see if the returned element contains the expected keys and values:
1. Select element with valid default id given
2. Autocomplete with valid default id given
3. Autocomplete with valid default value given
4. Select element with valid default value given
5. Autocomplete with invalid default id given

…anismFormElementControllerTest, and the ChadoOrganismWidgetDefault is updated to use the new controller class instead of the ChadoOrganismAutocomplete controller

laceysanderson · 2025-09-25T20:46:53Z

The merging of #2294 should allow your tests to pass despite deprecations. However, be aware that #2297 will bring back failing on deprecations in D11 specifically. For any tests that directly test deprecated methods, you should add the #[IgnoreDeprecations] as shown in tripal_chado/tests/src/Functional/api/ChadoDbAPITest.php. This will allow these tests to throw deprecations but not fail while still ensuring any tests that indirectly call deprecated functionality fail.

…efault_id in getSelectElement

tripal_chado/src/Controller/ChadoOrganismFormElementController.php

dsenalik

Awesome work!
I think we should update the organism selects in the importers.
Specifically, the FASTA and GFF importers have organism select elements that could now use this new class.

tripal/tripal_chado/src/Plugin/TripalImporter/FASTAImporter.php

Lines 46 to 55 in 34e10c1

    
           // get the list of organisms 
        
           $organisms = chado_get_organism_select_options(); 
        
           $form['organism_id'] = [ 
        
             '#title' => t('Organism'), 
        
             '#type' => 'select', 
        
             '#description' => t("Choose the organism to which these sequences are associated"), 
        
             '#required' => TRUE, 
        
             '#options' => $organisms, 
        
           ];

tripal/tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php

Lines 397 to 412 in 34e10c1

    
           // get the list of organisms 
        
           $organisms = chado_get_organism_select_options(FALSE, TRUE); 
        
           // get the sequence ontology CV id 
        
           $conditions = ['cv.name' => 'sequence']; 
        
           $cv_records = $this->cvterm_buddy->getCv($conditions, []); 
        
           $sequence_cv_id = $cv_records[0]->getValue('cv.cv_id'); 
        
           $form['organism_id'] = [ 
        
             '#title' => t('Existing Organism'), 
        
             '#type' => 'select', 
        
             '#description' => t("Choose an existing organism to which the entries in the GFF file will be associated."), 
        
             '#required' => TRUE, 
        
             '#options' => $organisms, 
        
             '#empty_option' => t('- Select -'), 
        
           ];

Co-authored-by: Douglas Senalik <[email protected]>

tripal_chado/src/Controller/ChadoOrganismFormElementController.php

tripal_chado/src/Plugin/TripalImporter/FASTAImporter.php

tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php

Co-authored-by: Douglas Senalik <[email protected]>

dsenalik

I am very very sorry to say I request one more change.
The analysis field does not convert to autocomplete
I forgot that it is in the parent class
We need to change it here
never mind not relevant to this pr that only deals with the organism controller

tripal/tripal_chado/src/TripalImporter/ChadoImporterBase.php

Lines 254 to 282 in 34e10c1

    
           public function addAnalysis($form, &$form_state) { 
        
             $chado = $this->connection; 
        
             // Get the list of analyses. 
        
             $query = $chado->select('1:analysis', 'A'); 
        
             $query->fields('A', ['analysis_id', 'name']); 
        
             $query->orderBy('A.name'); 
        
             $analyses = []; 
        
             $results = $query->execute(); 
        
             while ($analysis = $results->fetchObject()) { 
        
               $analyses[$analysis->analysis_id] = $analysis->name; 
        
             } 
        
             // Add the form element. 
        
             $element['analysis_id'] = [ 
        
               '#title' => t('Analysis'), 
        
               '#type' => 'select', 
        
               '#description' => t('Choose the analysis to which the uploaded data ' . 
        
                 'will be associated. Why specify an analysis for a data load?  All ' . 
        
                 'data comes from some place, even if downloaded from a website. By ' . 
        
                 'specifying analysis details for all data imports it provides ' . 
        
                 'provenance and helps end user to reproduce the data set if needed. ' . 
        
                 'At a minimum it indicates the source of the data.'), 
        
               '#required' =>  $this->plugin_definition['require_analysis'], 
        
               '#options' => $analyses, 
        
             ]; 
        
             return $element;

laceysanderson

Some code comments --this is looking really good ❤️

tripal_chado/src/Controller/ChadoOrganismAutocompleteController.php

tripal_chado/src/Controller/ChadoOrganismFormElementController.php

tripal_chado/src/Plugin/TripalImporter/FASTAImporter.php

tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php

laceysanderson · 2025-09-29T23:17:45Z

Regarding the test failure: https://github.com/tripal/tripal/actions/runs/18112268169/job/51540955913?pr=2293#step:5:26

Drupal\Tests\tripal_chado\Functional\GFF3ImporterTest::testGFFImporterSimpleTest
TypeError: Drupal\tripal_chado\Controller\ChadoOrganismFormElementController::getPkeyId(): Argument Fix PHP warnings during Chado install #1 ($value) must be of type string, null given, called in /var/www/drupal/web/modules/contrib/tripal/tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php on line 634

/var/www/drupal/web/modules/contrib/tripal/tripal_chado/src/Controller/ChadoOrganismFormElementController.php:133
/var/www/drupal/web/modules/contrib/tripal/tripal_chado/src/Plugin/TripalImporter/GFF3Importer.php:634
/var/www/drupal/web/modules/contrib/tripal/tripal_chado/tests/src/Functional/Plugin/GFF3ImporterTest.php:122
/var/www/drupal/vendor/phpunit/phpunit/src/Framework/TestResult.php:729

This happens when the field is optional. I say we just allow the getPkeyId() to take NULL as a param and then return it without change. This way we don't need if's in every place this is called when it's optional.

Co-authored-by: Lacey-Anne Sanderson <[email protected]>

…and making the getPkeyId method to allow null as a parameter

laceysanderson

tldr; This is ready for merge! You addressed all the outstanding concerns, the code looks good, and the manual testing done below works perfectly. Good job and Thanks!!! ❤️ 🎉

Manual Testing

✅ Creating a germplasm variety through the UI (selecting its organism via the updated field; SELECT) works great as does editing and deleting it.

✅ Creating a germplasm variety through the UI (selecting its organism via the updated field; AUTO COMPLETE) works great as does editing and deleting it.

✅ Editing genes published via the GFF3 importer when either a SELECT or AUTOCOMPLETE on the organism widget is used works beautifully with no errors.

✅ Organisms with infraspecies provided work beautifully in both SELECT and AUTOCOMPLETE.

✅ GFF3 importer with updated form element works great.

✅ Fasta importer with updated form element also works great.

Changes addressed

vidu-wil added 3 commits September 23, 2025 16:46

ChadoOrganismFormElementController added with its test class ChadoOrg…

989c91f

…anismFormElementControllerTest, and the ChadoOrganismWidgetDefault is updated to use the new controller class instead of the ChadoOrganismAutocomplete controller

fixed and array with the getAutocompleteElement method

21d9422

updated the automated testing with new case scenarios

942c6bc

dsenalik added the Group 1 - Tripal Content Types | Terms | Fields Any issue relating to Tripal Content including types, terms, and fields. label Sep 23, 2025

dsenalik linked an issue Sep 23, 2025 that may be closed by this pull request

Updates needed for current tripal_chado API functions #2284

Closed

vidu-wil and others added 4 commits September 23, 2025 22:28

deprecated the ChadoOrganismAutocompleteController class

be9f687

Merge branch '4.x' into tv4g1-2284-updateOrganismAutocompleteController

e18a942

updated the deprecation notice link to tripal_doc PR link

34802be

Merge branch '4.x' into tv4g1-2284-updateOrganismAutocompleteController

ce8943e

added IgnoreDeprecations attribute to the test class

b24afe5

vidu-wil marked this pull request as ready for review September 26, 2025 16:32

updated docstring for getSelectOptions and added default option for d…

c48332c

…efault_id in getSelectElement

dsenalik reviewed Sep 27, 2025

View reviewed changes

tripal_chado/src/Controller/ChadoOrganismFormElementController.php Outdated Show resolved Hide resolved

dsenalik requested changes Sep 27, 2025

View reviewed changes

vidu-wil and others added 4 commits September 29, 2025 09:12

updated the comment with suggested changes.

15371c0

Co-authored-by: Douglas Senalik <[email protected]>

updated the FASTAImporter and GFF3Importer to use the new form element

3b9522c

updated the autocomplete route

6a16047

updated the code to obtain the organism id from autocomplete element

aec4b07