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Set default terms for field properties when chado mapping is missing. #1940

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Merged
merged 5 commits into from
Aug 1, 2024
Merged

Set default terms for field properties when chado mapping is missing. #1940

merged 5 commits into from
Aug 1, 2024

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@laceysanderson
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Bug Fix

Issue #1939

Tripal Version: 4

Description

Many field properties do not have defaults set for when chado mapping is not present. This causes field addition to fail whenever the column doesn't exist in the chado mapping. Instead this PR add a default for all properties and then if chado mapping provides a more specific term, we use it.

Testing?

  1. Start a new Tripaldocker container
  2. Add a type_id to the project table so that we have a column without a chado mapping.
docker exec CONTAINERNAME drush sql:query "ALTER TABLE chado.project ADD COLUMN type_id bigint"
docker exec CONTAINERNAME drush sql:query "ALTER TABLE chado.project ADD FOREIGN KEY (type_id) REFERENCES chado.cvterm (cvterm_id) ON DELETE SET NULL;"
  1. Update the chado schema yaml to ensure Tripal knows about this field. This is needed due to the bug mentioned in issue Field Settings form is not aware of updates to the schema #1936. Apply the following patch to tripal_chado/chado_schema/chado_schema-1.3.yml.
diff --git a/tripal_chado/chado_schema/chado_schema-1.3.yml b/tripal_chado/chado_schema/chado_schema-1.3.yml
index 7f482d32f..a73cb9c9d 100644
--- a/tripal_chado/chado_schema/chado_schema-1.3.yml
+++ b/tripal_chado/chado_schema/chado_schema-1.3.yml
@@ -4898,6 +4898,13 @@ project:
     description:
       type: text
       not null: FALSE
+    type_id:
+      type: integer
+  foreign keys:
+    cvterm:
+      table: cvterm
+      columns:
+        type_id: cvterm_id
   unique keys:
     project_c1: name
   primary key: project_id
  1. Clear the cache using drush cr
  2. Now in the UI, go to Tripal > Page Structure > Project > Manage Fields in the administrative toolbar.
  3. Click on "Create a new field" and add a label of "type", select "Chado Fields", then "Chado Integer Field Type" and click Continue.
  4. Thanks to the changes in step 2/3 you now see a "type_id" in the "table column" drop down. Select it and set a term for the field such as "rdfs:type".
  5. On 4.x you will now see a WSOD and error message as indicated in the linked issue. On this branch the field will add without error.
  6. Now create a project page and confirm the page saves without error and that you can set the type_id :-)

@laceysanderson laceysanderson linked an issue Jul 31, 2024 that may be closed by this pull request
Many field properties do not have defaults set for when chado mapping is not present. #1939
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@laceysanderson laceysanderson self-assigned this Jul 31, 2024
@laceysanderson laceysanderson added bug - confirmed For issues where a core developer has confirmed a bug exists. Group 1 - Tripal Content Types | Terms | Fields Any issue relating to Tripal Content including types, terms, and fields. labels Jul 31, 2024
@laceysanderson laceysanderson marked this pull request as ready for review July 31, 2024 20:37
dsenalik
dsenalik reviewed Aug 1, 2024
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That must have been a pain to add all those! But looks good.
Described test adding as a Chado Integer Field Type field worked as advertised.
Then I thought to try adding as a Chado Type Reference. When I go to create the project I see
The website encountered an unexpected error. Try again later.

TypeError: Drupal\tripal\TripalStorage\TripalStorageBase::addTypes(): Argument #2 ($types) must be of type array, null given, called in /var/www/drupal/web/modules/contrib/tripal/tripal/src/Entity/TripalEntity.php on line 425 in Drupal\tripal\TripalStorage\TripalStorageBase->addTypes() (line 115 of modules/contrib/tripal/tripal/src/TripalStorage/TripalStorageBase.php).

We are not getting anything from this in tripal/src/Entity/TripalEntity.php

        // Get the empty property values for this field item and the
        // property type objects.
        $prop_values = $item->tripalValuesTemplate($item->getFieldDefinition());
        $prop_types = get_class($item)::tripalTypes($item->getFieldDefinition());

dsenalik
dsenalik approved these changes Aug 1, 2024
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The bug I found is now issue #1941
So there is nothing wrong with this PR

@laceysanderson
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Thank you for the review @dsenalik! ❤️ Yes, it was tedious adding all of those 🤪 but the chado mapping UI helped to look them all up in the right format so it was better then it could have been!

@laceysanderson laceysanderson merged commit 85ca8c0 into 4.x Aug 1, 2024
@dsenalik dsenalik deleted the tv4g1-1939-setPropertyTermDefaults branch August 1, 2024 15:47
@dsenalik dsenalik mentioned this pull request Aug 8, 2024
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dsenalik
dsenalik reviewed Aug 8, 2024
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tripal_chado/src/Plugin/Field/FieldType/ChadoAdditionalTypeTypeDefault.php
Comment on lines -219 to +221
$type_table = $storage_settings['type_table'] ?? '';
$type_column = $storage_settings['type_column'] ?? '';
$type_fkey = $storage_settings['type_fkey'] ?? '';
$type_table = $storage_settings['type_table'] ?: '';
$type_column = $storage_settings['type_column'] ?: '';
$type_fkey = $storage_settings['type_fkey'] ?: '';
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@dsenalik dsenalik Aug 8, 2024 •
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This should not have been changed and will be reverted by PR #1942
This change causes a warning that array key does not exist in some cases.

@laceysanderson laceysanderson mentioned this pull request Oct 3, 2025
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@dsenalik dsenalik dsenalik approved these changes

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bug - confirmed For issues where a core developer has confirmed a bug exists. Group 1 - Tripal Content Types | Terms | Fields Any issue relating to Tripal Content including types, terms, and fields.

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Many field properties do not have defaults set for when chado mapping is not present.

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