Merge pull request tripal#1680 from pdtouch/tv4g1-issue1414-uo__unit

Tripal 4 Chado Unit field tv4g1-issue1414-uo__unit

tripal_chado/config/install/tripal.tripalfield_collection.default_chado.yml

@@ -1496,7 +1496,7 @@ fields:
     -   name: physical_map_unit_type
         content_type: physical_map
         label: Unit Type
-        type: chado_additional_type_default
+        type: chado_unit_default
         description: A unit of measurement is a standardized quantity of a physical quality.
         cardinality: 1
         required: false
@@ -2222,7 +2222,7 @@ fields:
     -   name: genetic_map_unit_type
         content_type: genetic_map
         label: Unit Type
-        type: chado_additional_type_default
+        type: chado_unit_default
         description: A unit of measurement is a standardized quantity of a physical quality.
         cardinality: 1
         required: false

tripal_chado/src/Plugin/Field/FieldFormatter/ChadoUnitFormatterDefault.php

@@ -0,0 +1,36 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+/**
+ * Plugin implementation of default Tripal string type formatter.
+ *
+ * @FieldFormatter(
+ *   id = "chado_unit_formatter_default",
+ *   label = @Translation("Chado unit type formatter"),
+ *   description = @Translation("A Chado unit type formatter."),
+ *   field_types = {
+ *     "chado_unit_default"
+ *   }
+ * )
+ */
+class ChadoUnitFormatterDefault extends ChadoFormatterBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode)  {
+
+    $elements = [];
+    foreach($items as $delta => $item) {
+      $elements[$delta] = [
+        "#markup" => $item->get('cv_name')->getString()
+      ];
+    }
+
+    return $elements;
+  }
+}

tripal_chado/src/Plugin/Field/FieldType/ChadoUnitDefault.php

@@ -0,0 +1,107 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldType;
+
+use Drupal\tripal_chado\TripalField\ChadoFieldItemBase;
+use Drupal\tripal_chado\TripalStorage\ChadoIntStoragePropertyType;
+use Drupal\tripal_chado\TripalStorage\ChadoVarCharStoragePropertyType;
+
+/**
+ * Plugin implementation of Default Tripal field for unit of measurement.
+ *
+ * @FieldType(
+ *   id = "chado_unit_default",
+ *   label = @Translation("Chado unit of measurement"),
+ *   description = @Translation("Provide unit of measurement of content, for example, Genetic Map."),
+ *   default_widget = "chado_unit_widget_default",
+ *   default_formatter = "chado_unit_formatter_default"
+ * )
+ */
+
+class ChadoUnitDefault extends ChadoFieldItemBase {
+
+  public static $id = "chado_unit_default";
+
+  /**
+   * {@inheritdoc}
+  */
+  public static function mainPropertyName() {
+    return 'unittype_id';
+  }
+
+  /**
+  * {@inheritdoc}
+  */
+  public static function defaultFieldSettings() {
+    $settings = parent::defaultFieldSettings();
+    $settings['termIdSpace'] = 'UO';
+    $settings['termAccession'] = '0000000';
+    return $settings;
+  }
+
+  /**  
+   * {@inheritdoc}
+   */
+  public static function defaultStorageSettings() {
+    $settings = parent::defaultStorageSettings();
+    return $settings;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function tripalTypes($field_definition)  {
+
+    $entity_type_id = $field_definition->getTargetEntityTypeId();
+
+    $chado = \Drupal::service('tripal_chado.database');
+    $schema = $chado->schema();
+
+    $cvterm_def = $schema->getTableDef('cvterm', ['format' => 'Drupal']);
+    $cv_name_len = $cvterm_def['fields']['name']['size'];
+
+    $field_settings = $field_definition->getSetting('storage_plugin_settings');
+    $base_table = $field_settings['base_table'];
+
+    if (!$base_table) {
+      $record_id_term = 'data:1280';
+      return [
+        new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'record_id', $record_id_term, [
+          'action' => 'store_id',
+          'drupal_store' => TRUE,
+        ])
+      ];
+    }
+
+    $storage = \Drupal::entityTypeManager()->getStorage('chado_term_mapping');
+    $mapping = $storage->load('core_mapping');
+    $record_id_term = $mapping->getColumnTermId('featuremap', 'featuremap_id');
+    $unittype_id_term = $mapping->getColumnTermId( 'featuremap', 'unittype_id' ) ;    
+    $cv_name_term = $mapping->getColumnTermId('cvterm', 'name');
+
+    $properties = [];
+
+    $properties[] = new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'record_id', $record_id_term, [
+      'action' => 'store_id',
+      'drupal_store' => TRUE,
+      'chado_table' => 'featuremap',
+      'chado_column' => 'featuremap_id',
+    ]);
+
+    $properties[] = new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'unittype_id', $unittype_id_term, [
+      'action' => 'store',
+      'chado_table' => 'featuremap',
+      'chado_column' => 'unittype_id',
+    ]);
+
+    $properties[] = new ChadoVarCharStoragePropertyType($entity_type_id, self::$id, 'cv_name', $cv_name_term, $cv_name_len, [
+      'action' => 'read_value',
+      'path' => 'featuremap.unittype_id>cvterm.cvterm_id',
+      'chado_column' => 'name',
+      'as' => 'cv_name'
+    ]);
+
+    return( $properties );
+  }
+
+}

tripal_chado/src/Plugin/Field/FieldWidget/ChadoUnitWidgetDefault.php

@@ -0,0 +1,77 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldWidget;
+
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\Core\Form\FormStateInterface;
+use Drupal\tripal_chado\TripalField\ChadoWidgetBase;
+
+/**
+ * Plugin implementation of default Chado Data Source widget.
+ *
+ * @FieldWidget(
+ *   id = "chado_unit_widget_default",
+ *   label = @Translation("Chado Unit Widget Default"),
+ *   description = @Translation("The default unit widget which allows curators to enter unit on the Gene Map content edit page."),
+ *   field_types = {
+ *     "chado_unit_default"
+ *   }
+ * )
+ */
+class ChadoUnitWidgetDefault extends ChadoWidgetBase {
+  /**
+   * {@inheritdoc}
+   */
+  public function formElement(FieldItemListInterface $items, $delta, array $element, array &$form, FormStateInterface $form_state)  {
+
+    $unit_vals = [];
+
+    $chado = \Drupal::service('tripal_chado.database');
+
+    $query = $chado->select( 'cvterm', 'cvt' );
+    $query->leftJoin ('cv', 'cv', 'cvt.cv_id = cv.cv_id ');
+    $query->addField( 'cvt', 'name', 'cvt_name' );
+    $query->addField( 'cvt', 'cvterm_id', 'unittype_id' );
+    $query->condition('cv.name', 'featuremap_units', '=');
+    $results = $query->execute();
+
+    while ( $unit_rec = $results->fetchObject() ) {
+      $unit_vals[$unit_rec->unittype_id] = $unit_rec->cvt_name;
+    }
+
+    $item_vals = $items[$delta]->getValue() ;
+    $record_id = $item_vals['record_id'] ?? 0 ;
+    $unittype_id = $item_vals['unittype_id'] ?? 0 ;
+
+    $elements = [];
+
+    $elements['record_id'] = [
+      '#default_value' => $record_id,
+      '#type' => 'value',
+    ];
+
+    $elements['unittype_id'] = $element + [
+      '#type' => 'select',
+      '#description' =>  t("Select map unit from dropdown."),
+      '#options' => $unit_vals,
+      '#default_value' => $unittype_id,
+      '#empty_option' => '-- Select --',
+    ];
+
+    return $elements;
+  }  
+
+  /**
+   * {@inheritDoc}
+   */
+  public function massageFormValues(array $values, array $form, FormStateInterface $form_state) {
+    // Remove any empty values that don't have a unit type
+     foreach ($values as $delta => $item) {
+       if ($item['unittype_id'] == '') {
+         unset($values[$delta]);
+       }
+     }
+     return $values;
+   }
+
+}