Merge pull request #1388 from tripal/tv4g1-292-sequenceField

Tripal 4 Field: Sequence Residues

tripal_chado/src/Plugin/Field/FieldFormatter/ChadoSequenceFormatterDefault.css

@@ -0,0 +1,10 @@
+#tripal-chado-sequence-format {
+  font-family: Consolas, monaco, monospace;
+  font-size: 12px;
+  height: 195px; /* height set to bisect characters in last row as visible scroll feedback */
+  max-width: 400px;
+  overflow: scroll;
+  line-height: normal !important;
+  border: 1px solid #DDDDDD;
+  padding: 10px;
+}

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

@@ -0,0 +1,42 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+use Drupal\tripal\TripalField\TripalFormatterBase;
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\Core\Form\FormStateInterface;
+use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+/**
+ * Plugin implementation of Default Tripal field formatter for sequence data
+ *
+ * @FieldFormatter(
+ *   id = "chado_sequence_formatter_default",
+ *   label = @Translation("Chado Sequence Residues Display"),
+ *   description = @Translation("Displays chado sequence residues from the feature table on the page."),
+ *   field_types = {
+ *     "chado_sequence_default"
+ *   }
+ * )
+ */
+class ChadoSequenceFormatterDefault extends ChadoFormatterBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode) {
+    $elements = [];
+    $elements['#attached']['library'][] = 'tripal_chado/tripal_chado.field.ChadoSequenceFormatterDefault';
+
+    foreach($items as $delta => $item) {
+      $residues = $item->get('residues')->getString();
+      if (!empty($residues)) {
+        $elements[$delta] = [
+          "#markup" => "<pre id='tripal-chado-sequence-format'>" . wordwrap($residues,50,'<br>',TRUE) . "</pre>",
+        ];
+      }
+    }
+
+    return $elements;
+  }
+}

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

@@ -0,0 +1,82 @@
+<?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\ChadoTextStoragePropertyType;
+use Drupal\core\Form\FormStateInterface;
+use Drupal\core\Field\FieldDefinitionInterface;
+
+/**
+ * Plugin implementation of Default Tripal field for sequence data.
+ *
+ * @FieldType(
+ *   id = "chado_sequence_default",
+ *   label = @Translation("Chado Sequence Residues"),
+ *   description = @Translation("Manages sequence residues for content types storing data in the chado feature table."),
+ *   default_widget = "chado_sequence_widget_default",
+ *   default_formatter = "chado_sequence_formatter_default"
+ * )
+ */
+class ChadoSequenceDefault extends ChadoFieldItemBase {
+
+  public static $id = "chado_sequence_default";
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function mainPropertyName() {
+    return 'residues';
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function defaultFieldSettings() {
+    $settings = parent::defaultFieldSettings();
+    $settings['termIdSpace'] = 'data';
+    $settings['termAccession'] = '2044';
+    return $settings;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function defaultStorageSettings() {
+    $settings = parent::defaultStorageSettings();
+    $settings['storage_plugin_settings']['base_table'] = 'feature';
+    return $settings;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function tripalTypes($field_definition) {
+    $entity_type_id = $field_definition->getTargetEntityTypeId();
+
+    // Get the base table columns needed for this field.
+    $settings = $field_definition->getSetting('storage_plugin_settings');
+
+    // Get the property terms by using the Chado table columns they map to.
+    $storage = \Drupal::entityTypeManager()->getStorage('chado_term_mapping');
+    $mapping = $storage->load('core_mapping');
+    $record_id_term = 'SIO:000729';
+    $residues_term = $mapping->getColumnTermId('feature', 'residues');
+
+    // Return the properties for this field.
+    $properties = [];
+    $properties[] = new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'record_id', $record_id_term, [
+        'action' => 'store_id',
+        'drupal_store' => TRUE,
+        'chado_table' => 'feature',
+        'chado_column' => 'feature_id'
+    ]);
+    $properties[] =  new ChadoTextStoragePropertyType($entity_type_id, self::$id, 'residues', $residues_term, [
+      'action' => 'store',
+      'chado_column' => 'residues',
+      'chado_table' => 'feature'
+    ]);
+    return $properties;
+  }
+}

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

@@ -0,0 +1,60 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldWidget;
+
+use Drupal\tripal\Plugin\Field\FieldWidget\TripalTextTypeWidget;
+use Drupal\tripal\TripalField\TripalWidgetBase;
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\Core\Form\FormStateInterface;
+use Drupal\tripal_chado\TripalField\ChadoWidgetBase;
+
+/**
+ * Plugin implementation of default Chado Sequence widget.
+ *
+ * @FieldWidget(
+ *   id = "chado_sequence_widget_default",
+ *   label = @Translation("Chado Sequence Residues Widget"),
+ *   description = @Translation("The default chado sequence widget which allows curators to manually enter sequence residues on the content edit page."),
+ *   field_types = {
+ *     "chado_sequence_default"
+ *   }
+ * )
+ */
+class ChadoSequenceWidgetDefault extends ChadoWidgetBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function formElement(FieldItemListInterface $items, $delta, array $element, array &$form, FormStateInterface $form_state) {
+
+    $item_vals = $items[$delta]->getValue();
+    $elements = [];
+    $elements['record_id'] = [
+      '#type' => 'value',
+      '#default_value' => $item_vals['record_id'] ?? 0,
+    ];
+
+    $elements['residues'] = $element + [
+      '#type' => 'textarea',
+      '#default_value' => $item_vals['residues'] ?? '',
+      '#placeholder' => $this->getSetting('placeholder'),
+      '#attributes' => ['class' => ['js-text-full', 'text-full']],
+    ];
+
+    return $elements;
+  }
+
+
+  /**
+   * {@inheritDoc}
+   */
+  public function massageFormValues(array $values, array $form, FormStateInterface $form_state) {
+
+    // Remove any empty values that aren't mapped to a record id.
+    foreach ($values as $val_key => $value) {
+      $values[$val_key]['residues'] = preg_replace('/\s/', '', $value['residues']);
+    }
+    return $values;
+  }
+
+}

tripal_chado/tripal_chado.libraries.yml

@@ -4,3 +4,8 @@ tripal_chado.chado_table:
       css/chado_table.css: {}
   js:
     js/chado_table.js: {}
+
+tripal_chado.field.ChadoSequenceFormatterDefault:
+  css:
+    component:
+      src/Plugin/Field/FieldFormatter/ChadoSequenceFormatterDefault.css: {}