Merge pull request #1504 from pdtouch/tv4g1-issue1414-local-data-sour…

…ce-field

Tv4g1 issue1414 local data source field

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

@@ -0,0 +1,64 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+use Drupal\Core\Field\FieldItemListInterface;
+use Drupal\Core\Link;
+use Drupal\Core\Url;
+use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+/**
+ * Plugin implementation of default Tripal string type formatter.
+ *
+ * @FieldFormatter(
+ *   id = "chado_source_data_formatter_default",
+ *   label = @Translation("Chado Source Data Formatter"),
+ *   description = @Translation("The default source data widget which allows curators to manually enter analysis source data information on the content edit page."),
+ *   field_types = {
+ *     "chado_source_data_default"
+ *   }
+ * )
+ */
+class ChadoSourceDataFormatterDefault extends ChadoFormatterBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode)  {
+    $elements = [];
+    $content = '';
+
+    foreach ($items as $delta => $item) {
+      $sourcename_val = $item->get('sourcename')->getString();
+      if (!empty($sourcename_val)) {
+        $content .= "<dt>Source Name:</dt><dd>" . $sourcename_val . "</dd>";
+      }
+      $sourceversion_val = $item->get('sourceversion')->getString();
+      if (!empty($sourceversion_val)) {
+        $content .= "<dt>Source Version:</dt><dd>" . $sourceversion_val . "</dd>";
+      }
+      $sourceuri_val = $item->get('sourceuri')->getString();
+      if (!empty($sourceuri_val)) {
+        $url = $sourceuri_val;
+        if (preg_match('|://|', $sourceuri_val)) {
+          $url = Link::fromTextAndUrl($sourceuri_val, Url::fromUri($sourceuri_val, []))->toString();
+        }
+        $content .= "<dt>Source URI:</dt><dd>" . $url . "</dd>";
+      }
+    }
+
+    if ($content) {
+      $content = "<dl class=\"tripal-dl\">" . $content . "</dl>";
+    } else {
+      $content = 'The data source is not provided.';
+    }
+
+    // The cardinality of this field is always 1, so only create element for $delta of zero.
+    $elements[0] = [
+      '#type' => 'markup',
+      '#markup' => $content,
+    ];
+
+    return $elements;
+  }
+}

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

@@ -0,0 +1,100 @@
+<?php
+
+namespace Drupal\tripal_chado\Plugin\Field\FieldType;
+
+use Drupal\Core\Form\FormStateInterface;
+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 sequence data.
+ *
+ * @FieldType(
+ *   id = "chado_source_data_default",
+ *   label = @Translation("Chado Data Source"),
+ *   description = @Translation("The source and version of data used for this analysis"),
+ *   default_widget = "chado_source_data_widget_default",
+ *   default_formatter = "chado_source_data_formatter_default",
+ *   cardinality = 1,
+ * )
+ */
+class ChadoSourceDataDefault extends ChadoFieldItemBase {
+
+  public static $id = "chado_source_data_default";
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function mainPropertyName()  {
+    return 'sourcename';
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function defaultFieldSettings()  {
+    $settings = parent::defaultFieldSettings();
+    $settings['termIdSpace'] = 'local';
+    $settings['termAccession'] = 'source_data';
+    $settings['termFixed'] = FALSE;
+    return $settings;
+  }
+
+  /**  
+   * {@inheritdoc}
+   */
+  public static function defaultStorageSettings() {
+    $settings = parent::defaultStorageSettings();
+    $settings['storage_plugin_settings']['base_table'] = 'analysis';
+    return $settings;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function tripalTypes($field_definition)  {
+
+    // Create variables for easy access to settings.
+    $entity_type_id = $field_definition->getTargetEntityTypeId();
+
+    // 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 = $mapping->getColumnTermId('analysis', 'analysis_id');
+
+    $src_uri_term = $mapping->getColumnTermId('analysis', 'sourceuri');
+    $src_name_term = $mapping->getColumnTermId('analysis', 'sourcename');
+    $src_vers_term = $mapping->getColumnTermId('analysis', 'sourceversion');
+
+    // Get property terms using Chado table columns they map to. 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' => 'analysis',
+      'chado_column' => 'analysis_id',
+    ]);
+    $properties[] = new ChadoVarCharStoragePropertyType($entity_type_id, self::$id, 'sourceuri', $src_uri_term, 100, [
+      'action' => 'store',
+      'chado_table' => 'analysis',
+      'chado_column' => 'sourceuri',
+    ]);
+    $properties[] = new ChadoVarCharStoragePropertyType($entity_type_id, self::$id, 'sourcename', $src_name_term, 200, [
+      'action' => 'store',
+      'chado_table' => 'analysis',
+      'chado_column' => 'sourcename',
+      'delete_if_empty' => TRUE,
+      'empty_value' => '',
+    ]);
+    $properties[] = new ChadoVarCharStoragePropertyType($entity_type_id, self::$id, 'sourceversion', $src_vers_term, 100, [
+      'action' => 'store',
+      'chado_table' => 'analysis',
+      'chado_column' => 'sourceversion',
+    ]);
+
+    return ($properties);
+  }
+}

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

@@ -0,0 +1,78 @@
+<?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_source_data_widget_default",
+ *   label = @Translation("Chado Data Source Widget Default"),
+ *   description = @Translation("The default source data widget which allows curators to manually enter analysis source data information on the content edit page."),
+ *   field_types = {
+ *     "chado_source_data_default"
+ *   }
+ * )
+ */
+class ChadoSourceDataWidgetDefault extends ChadoWidgetBase {
+
+  /**
+   * {@inheritdoc}
+   */
+  public function formElement(FieldItemListInterface $items, $delta, array $element, array &$form, FormStateInterface $form_state)  {
+
+    $item_vals = $items[$delta]->getValue();
+
+    $elements = [];
+
+    $elements['datasourcegroup'] = [
+      '#type' => 'details',
+      '#title' => t("Data Source"),
+      '#description' => t('The source where data was obtained for this analysis.'),
+      '#open' => TRUE, // Controls the HTML5 'open' attribute. Defaults to FALSE.
+    ];
+
+    $elements['record_id'] = [
+      '#type' => 'value',
+      '#default_value' => $item_vals['record_id'] ?? 0,
+    ];
+    $elements['datasourcegroup']['sourcename'] =  [
+      '#title' => t("Name"),
+      '#type' => 'textfield',
+      '#description' => t('The name of the source where data was obtained for this analysis.'),
+      '#default_value' => $item_vals['sourcename'] ?? '',
+    ];
+    $elements['datasourcegroup']['sourceversion'] = [
+      '#title' => t('Version'),
+      '#type' => 'textfield',
+      '#description' => t('The version number of the data source (if applicable) for this analysis.'),
+      '#default_value' => $item_vals['sourceversion'] ?? '',
+    ];
+    $elements['datasourcegroup']['sourceuri'] =  [
+      '#title' => t("URI"),
+      '#type' => 'textfield',
+      '#description' => t('The URI (e.g. web URL) where the source data can be obtained.'),
+      '#default_value' => $item_vals['sourceuri'] ?? '',
+    ];
+
+    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]['sourceuri'] = $value['datasourcegroup']['sourceuri'];
+      $values[$val_key]['sourcename'] = $value['datasourcegroup']['sourcename'];
+      $values[$val_key]['sourceversion'] = $value['datasourcegroup']['sourceversion'];
+    }
+    return $values;
+  }
+}