Convert lab field to term reference on lab test logs #603

CHANGELOG.md

@@ -38,6 +38,7 @@ If you would like to skip the automatic fix, add the following line to your
 - [Issue #3203129: Use GitHub Actions to build Docker Hub images](https://www.drupal.org/project/farm/issues/3203129)
 - [Announce new releases on Mastodon/Twitter via farmOS-microblog #599](https://github.com/farmOS/farmOS/pull/599)
 - [Improve dependency relationships of asset/log/quantity modules #601](https://github.com/farmOS/farmOS/pull/601)
+- [Convert lab field to term reference on lab test logs #603](https://github.com/farmOS/farmOS/pull/603)
 
 ### Fixed
 

modules/log/lab_test/farm_lab_test.info.yml

@@ -5,4 +5,5 @@ package: farmOS Logs
 core_version_requirement: ^9
 dependencies:
   - farm:farm_entity
+  - farm:farm_lab
   - log:log

modules/log/lab_test/farm_lab_test.post_update.php

@@ -5,6 +5,9 @@
  * Post update hooks for the farm_lab_test module.
  */
 
+use Drupal\Core\Utility\UpdateException;
+use Drupal\taxonomy\Entity\Term;
+
 /**
  * Add "Date received" and "Date processed" fields to lab test logs.
  */
@@ -36,3 +39,112 @@ function farm_lab_test_post_update_add_received_processed_date_fields(&$sandbox)
   $field_definition = \Drupal::service('farm_field.factory')->bundleFieldDefinition($options);
   \Drupal::entityDefinitionUpdateManager()->installFieldStorageDefinition('lab_processed_date', 'log', 'farm_lab_test', $field_definition);
 }
+
+/**
+ * Install the lab taxonomy module.
+ */
+function farm_lab_test_post_update_enable_farm_lab(&$sandbox) {
+  if (!\Drupal::service('module_handler')->moduleExists('farm_lab')) {
+    \Drupal::service('module_installer')->install(['farm_lab']);
+  }
+}
+
+/**
+ * Migrate laboratory names to taxonomy terms.
+ */
+function farm_lab_test_post_update_migrate_lab_terms(&$sandbox) {
+
+  // This function will be run as a batch operation to save the new term
+  // reference values on existing logs. On the first run, we will make
+  // preparations. This logic should only run once.
+  if (!isset($sandbox['current_log'])) {
+
+    // Query the database for all lab field data on logs.
+    // Save it to $sandbox for future reference.
+    $sandbox['log_map'] = \Drupal::database()->query('SELECT entity_id, lab_value FROM log__lab WHERE deleted = 0')->fetchAllKeyed(0);
+
+    // If there are no lab test logs, bail.
+    if (empty($sandbox['log_map'])) {
+      return NULL;
+    }
+
+    // Create taxonomy terms for each of the labs.
+    // Add them to a term map in $sandbox for future reference.
+    $unique_labs = array_unique($sandbox['log_map']);
+    $sandbox['term_map'] = [];
+    foreach ($unique_labs as $lab_name) {
+      $term = Term::create(['vid' => 'lab', 'name' => $lab_name]);
+      $term->save();
+      $sandbox['term_map'][$lab_name] = $term->id();
+    }
+
+    // Get the Drupal entity definition update manager.
+    $update_manager = \Drupal::entityDefinitionUpdateManager();
+
+    // Delete the old lab field.
+    $storage_definition = $update_manager->getFieldStorageDefinition('lab', 'log');
+    $update_manager->uninstallFieldStorageDefinition($storage_definition);
+
+    // Install the new lab field.
+    $options = [
+      'type' => 'entity_reference',
+      'label' => t('Laboratory'),
+      'description' => t('What laboratory performed this test?'),
+      'target_type' => 'taxonomy_term',
+      'target_bundle' => 'lab',
+      'auto_create' => TRUE,
+      'weight' => [
+        'form' => -40,
+        'view' => -40,
+      ],
+    ];
+    $field_definition = \Drupal::service('farm_field.factory')->bundleFieldDefinition($options);
+    $update_manager->installFieldStorageDefinition('lab', 'log', 'farm_lab_test', $field_definition);
+
+    // Track progress.
+    $sandbox['current_log'] = 0;
+    $sandbox['#finished'] = 0;
+  }
+
+  // Iterate over logs, 10 at a time.
+  $log_ids = array_keys($sandbox['log_map']);
+  $log_count = count($log_ids);
+  $end_log = $sandbox['current_log'] + 10;
+  $end_log = $end_log > $log_count ? $log_count : $end_log;
+  for ($i = $sandbox['current_log']; $i < $end_log; $i++) {
+
+    // Iterate the global counter.
+    $sandbox['current_log']++;
+
+    // Get the log ID.
+    $id = $log_ids[$i];
+
+    // If there is no taxonomy term to assign, skip.
+    if (empty($sandbox['log_map'][$id]) || empty($sandbox['term_map'][$sandbox['log_map'][$id]])) {
+      continue;
+    }
+
+    // Load the log.
+    $log = \Drupal::service('entity_type.manager')->getStorage('log')->load($id);
+
+    // If the log didn't load, throw an update exception.
+    if (empty($log)) {
+      throw new UpdateException('Could not load log. ID: @id', ['@id' => $id]);
+    }
+
+    // Assign the new lab taxonomy term.
+    $log->set('lab', $sandbox['term_map'][$sandbox['log_map'][$id]]);
+
+    // Save a new revision of the log.
+    $log->setNewRevision(TRUE);
+    $log->setRevisionLogMessage(t('Automatically migrated laboratory name to taxonomy term in the new Lab vocabulary.'));
+    $log->save();
+
+    // Declare that the log has been fixed.
+    \Drupal::logger('farm_lab_test')->notice(t('Log @id lab has been migrated.', ['@id' => $id]));
+  }
+
+  // Update progress.
+  $sandbox['#finished'] = $sandbox['current_log'] / count($sandbox['log_map']);
+  return NULL;
+}

modules/log/lab_test/src/Plugin/Log/LogType/LabTest.php

@@ -34,9 +34,12 @@ class LabTest extends FarmLogType {
 
     // Lab.
     $options = [
-      'type' => 'string',
+      'type' => 'entity_reference',
       'label' => $this->t('Laboratory'),
       'description' => $this->t('What laboratory performed this test?'),
+      'target_type' => 'taxonomy_term',
+      'target_bundle' => 'lab',
+      'auto_create' => TRUE,
       'weight' => [
         'form' => -40,
         'view' => -40,

modules/taxonomy/lab/config/install/taxonomy.vocabulary.lab.yml

@@ -0,0 +1,10 @@
+langcode: en
+status: true
+dependencies:
+  enforced:
+    module:
+      - farm_lab
+name: Labs
+vid: lab
+description: 'A list of labs.'
+weight: 0

modules/taxonomy/lab/farm_lab.info.yml

@@ -0,0 +1,7 @@
+name: Lab vocabulary
+description: Provides a Lab vocabulary.
+type: module
+package: farmOS Taxonomies
+core_version_requirement: ^9
+dependencies:
+  - drupal:taxonomy