Merge pull request #1607 from pdtouch/tv4g1-issue1414-data__sequence_…

…length

Tripal 4 Fields: Sequence Length + Sequence Checksum

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

@@ -0,0 +1,39 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+/**
+ * Plugin implementation of Default Tripal field formatter for sequence data 
+ *
+ * @FieldFormatter(
+ *   id = "chado_sequence_checksum_formatter_default",
+ *   label = @Translation("Chado Sequence checksum Formatter"),
+ *   description = @Translation("A chado sequence checksum formatter"),
+ *   field_types = {
+ *     "chado_sequence_checksum_default"
+ *   }
+ * )
+ */
+class ChadoSequenceChecksumFormatterDefault extends ChadoFormatterBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode) {
+    $elements = [];
+    foreach($items as $delta => $item) {
+      $seqlen_val = $item->get('seqlen')->getString();
+      if ( intval($seqlen_val) > 0 ) {
+        $elements[$delta] = [
+          "#markup" => $item->get('md5checksum')->getString()
+        ];
+      } 
+    }
+
+    return $elements;
+  }
+
+}

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

@@ -0,0 +1,37 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+/**
+ * Plugin implementation of Default Tripal field formatter for sequence data 
+ *
+ * @FieldFormatter(
+ *   id = "chado_sequence_length_formatter_commas",
+ *   label = @Translation("Chado Sequence Length with Commas Formatter 1,000,000"),
+ *   description = @Translation("A chado sequence length commas (ex. 1,000,000) formatter"),
+ *   field_types = {
+ *     "chado_sequence_length_default"
+ *   }
+ * )
+ */
+class ChadoSequenceLengthFormatterCommas extends ChadoFormatterBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode) {
+    $elements = [];
+    $elements['#attached']['library'][] = 'tripal_chado/tripal_chado.field.ChadoSequenceLengthFormatterCommas';
+
+    foreach($items as $delta => $item) {
+      $elements[$delta] = [
+        "#markup" => number_format(floatval($item->get('seqlen')->getString()))
+      ];
+    }
+
+    return $elements;
+  }
+}

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

@@ -0,0 +1,37 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+/**
+ * Plugin implementation of Default Tripal field formatter for sequence data 
+ *
+ * @FieldFormatter(
+ *   id = "chado_sequence_length_formatter_default",
+ *   label = @Translation("Chado Sequence Length Formatter"),
+ *   description = @Translation("A chado sequence length formatter"),
+ *   field_types = {
+ *     "chado_sequence_length_default"
+ *   }
+ * )
+ */
+class ChadoSequenceLengthFormatterDefault extends ChadoFormatterBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode) {
+    $elements = [];
+    $elements['#attached']['library'][] = 'tripal_chado/tripal_chado.field.ChadoSequenceLengthFormatterDefault';
+
+    foreach($items as $delta => $item) {
+      $elements[$delta] = [
+        "#markup" => $item->get('seqlen')->getString()
+      ];
+    }
+
+    return $elements;
+  }
+}

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

@@ -0,0 +1,93 @@
+<?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\ChadoBpCharStoragePropertyType;
+
+/**
+ * Plugin implementation of Default Tripal field for sequence data.
+ *
+ * @FieldType(
+ *   id = "chado_sequence_checksum_default",
+ *   label = @Translation("Chado Feature Sequence Checksum"),
+ *   description = @Translation("A chado feature sequence md5 checksum"),
+ *   default_widget = "chado_sequence_checksum_widget_default",
+ *   default_formatter = "chado_sequence_checksum_formatter_default"
+ * )
+ */
+class ChadoSequenceChecksumDefault extends ChadoFieldItemBase {
+
+  public static $id = "chado_sequence_checksum_default";
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function mainPropertyName() {
+    return 'md5checksum';
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function defaultFieldSettings() {
+    $settings = parent::defaultFieldSettings();
+    $settings['termIdSpace'] = 'data';
+    $settings['termAccession'] = '2190';
+    $settings['fixed_value'] = TRUE;
+    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';
+    $md5checksum_term = $mapping->getColumnTermId('feature', 'md5checksum');
+    $seqlen_term = $mapping->getColumnTermId('feature', 'seqlen');
+
+    // Get the length of the database fields so we don't go over the size limit.
+    $chado = \Drupal::service('tripal_chado.database');
+    $schema = $chado->schema();
+    $feature_def = $schema->getTableDef('feature', ['format' => 'Drupal']);
+    $md5_checksum_len = $feature_def['fields']['md5checksum']['size'];
+
+    // 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'
+    ]);
+    $properties[] =  new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'seqlen', $seqlen_term, [
+      'action' => 'store',
+      'chado_column' => 'seqlen',
+      'chado_table' => 'feature'
+    ]);
+    $properties[] =  new ChadoBpCharStoragePropertyType($entity_type_id, self::$id, 'md5checksum', $md5checksum_term, $md5_checksum_len, [
+      'action' => 'store',
+      'chado_column' => 'md5checksum',
+      'chado_table' => 'feature'
+    ]);
+    return $properties;
+  }
+}

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

@@ -5,8 +5,7 @@
 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;
+use Drupal\tripal_chado\TripalStorage\ChadoBpCharStoragePropertyType;
 
 /**
  * Plugin implementation of Default Tripal field for sequence data.
@@ -16,7 +15,8 @@
  *   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"
+ *   default_formatter = "chado_sequence_formatter_default",
+ *   cardinality = 1,
  * )
  */
 class ChadoSequenceDefault extends ChadoFieldItemBase {
@@ -46,6 +46,7 @@ public static function defaultFieldSettings() {
   public static function defaultStorageSettings() {
     $settings = parent::defaultStorageSettings();
     $settings['storage_plugin_settings']['base_table'] = 'feature';
+
     return $settings;
   }
 
@@ -63,6 +64,8 @@ public static function tripalTypes($field_definition) {
     $mapping = $storage->load('core_mapping');
     $record_id_term = 'SIO:000729';
     $residues_term = $mapping->getColumnTermId('feature', 'residues');
+    $seqlen_term = $mapping->getColumnTermId('feature', 'seqlen');
+    $md5checksum_term = $mapping->getColumnTermId('feature', 'md5checksum');
 
     // Return the properties for this field.
     $properties = [];
@@ -77,6 +80,21 @@ public static function tripalTypes($field_definition) {
       'chado_column' => 'residues',
       'chado_table' => 'feature'
     ]);
+
+    $properties[] =  new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'seqlen', $seqlen_term, [
+      'action' => 'store',
+      'chado_column' => 'seqlen',
+      'chado_table' => 'feature'
+    ]);
+
+    // Hard-coded as the length of MD3Checksum supported by the chado feature.md5checksum column.
+    $md5checksum_len = 32;
+    $properties[] =  new ChadoBpCharStoragePropertyType($entity_type_id, self::$id, 'md5checksum', $md5checksum_term, $md5checksum_len, [
+      'action' => 'store',
+      'chado_column' => 'md5checksum',
+      'chado_table' => 'feature'
+    ]);
+
     return $properties;
   }
 }

tripal_chado/src/Plugin/Field/FieldType/ChadoSequenceLengthDefault.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;
+
+/**
+ * Plugin implementation of Default Tripal field for sequence data.
+ *
+ * @FieldType(
+ *   id = "chado_sequence_length_default",
+ *   label = @Translation("Chado Feature Sequence Length"),
+ *   description = @Translation("A chado feature sequence length"),
+ *   default_widget = "chado_sequence_length_widget_default",
+ *   default_formatter = "chado_sequence_length_formatter_default"
+ * )
+ */
+
+
+class ChadoSequenceLengthDefault extends ChadoFieldItemBase {
+
+  public static $id = "chado_sequence_length_default";
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function mainPropertyName() {
+    return 'seqlen';
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function defaultFieldSettings() {
+    $settings = parent::defaultFieldSettings();
+    $settings['termIdSpace'] = 'data';
+    $settings['termAccession'] = '1249';
+    $settings['fixed_value'] = TRUE;
+    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';
+    $seqlen_term = $mapping->getColumnTermId('feature', 'seqlen');
+
+    // 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'
+    ]);
+    $properties[] =  new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'seqlen', $seqlen_term, [
+      'action' => 'store',
+      'chado_column' => 'seqlen',
+      'chado_table' => 'feature'
+    ]);
+    return $properties;
+  }
+}

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

@@ -0,0 +1,38 @@
+<?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 Sequence Checksum widget.
+ *
+ * @FieldWidget(
+ *   id = "chado_sequence_checksum_widget_default",
+ *   label = @Translation("Chado Sequence Checksum Widget"),
+ *   description = @Translation("The default chado sequence checksum widget."),
+ *   field_types = {
+ *     "chado_sequence_checksum_default"
+ *   }
+ * )
+ */
+class ChadoSequenceChecksumWidgetDefault 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,
+    ];
+
+    return $elements;
+  }
+
+}