Tripal 4 files for sequence_coordinates-field: tv4g1-issue1414-data__…

…sequence_coordinates

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

@@ -1041,6 +1041,33 @@ fields:
               region: content
               weight: 10
 
+    -   name: gene_sequence_coordinates
+        content_type: gene
+        label: Sequence Coordinates
+        type: chado_sequence_coordinates_default
+        description: Locations on reference sequences where the feature is located.
+        cardinality: -1
+        required: false
+        storage_settings:
+            storage_plugin_id: chado_storage
+            storage_plugin_settings:
+                base_table: featureloc
+                linker_table: feature
+                linker_fkey_column: feature_id
+        settings:
+            termIdSpace: data
+            termAccession: "2012"
+        display:
+          view:
+            default:
+              region: content
+              label: above
+              weight: 10
+          form:
+            default:
+              region: content
+              weight: 10
+
     -   name: mrna_name
         content_type: mRNA
         label: Name

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

@@ -0,0 +1,75 @@
+<?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_sequence_coordinates_formatter_default",
+ *   label = @Translation("Chado sequence coordinates default formatter"),
+ *   description = @Translation("The default sequence coordinates formatter allows curators to view sequence coordinates (min, max, strand and phase) of the feature."),
+ *   field_types = {
+ *     "chado_sequence_coordinates_default"
+ *   }
+ * )
+ */
+class ChadoSequenceCoordinatesFormatterDefault extends ChadoFormatterBase
+{
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode)
+  {
+    $elements = [];
+    $reference_term = 'data:3002';
+
+    $locations = [];
+
+    foreach ($items as $item) {
+
+      if (!empty($item['value'])) {
+        $loc_rec = '';
+        $feature_ref_val = $item['value'][$reference_term];
+
+        $fmin_val = $item->get('fmin')->getString();
+        if (!empty($fmin_val)) {
+        $loc_rec .= $item['value'][$feature_ref_val] . ':' .$fmin_val . "..";
+        }
+        $fmax_val = $item->get('fmax')->getString();
+        if (!empty($fmax_val)) {
+            $loc_rec .= $item['value'][$fmax_val].'; ';
+        }
+        $phase_val = $item->get('phase')->getString();
+        if (!empty($phase_val)) {
+            $loc_rec .= $item['value'][$phase_val].'; ';
+        }
+        $strand_term = $item->get('strand')->getString();
+        if (!empty($strand_val)) {
+            $strand_symb = match( $item['value'][$strand_term] ) {
+                -1 => '-',
+                1 => '+',
+                default => '',
+            };
+            $loc_rec .= $strand_symb;
+        }
+        $locations[] = $loc_rec;
+      }
+    }
+    if ( !$locations ) {
+        $content = 'This feature is not located on any sequence.';
+    }
+    else {
+        $content = implode('<br />', $locations);
+    }
+    // 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/FieldFormatter/ChadoSequenceCoordinatesFormatterTable.php

@@ -0,0 +1,94 @@
+<?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_sequence_coordinates_formatter_table",
+ *   label = @Translation("Chado sequence coordinates table formatter"),
+ *   description = @Translation("The sequence coordinates widget allows curators to manually enter feature sequence coordinates information on the content edit page."),
+ *   field_types = {
+ *     "chado_sequence_coordinates_default"
+ *   }
+ * )
+ */
+class ChadoSequenceCoordinatesFormatterTable extends ChadoFormatterBase {
+
+  public static $default_settings = [
+    'caption' => 'This @content_type has the following sequence coordinates:',
+    'expand_strand' => TRUE,
+  ];
+
+  /**
+   * {@inheritdoc}
+   */
+  public function viewElements(FieldItemListInterface $items, $langcode) {
+    $elements = [];
+    $reference_term = 'data:3002';
+
+    // Get the settings and set defaults.
+    $settings = $display['settings'];
+    foreach ($this::$default_settings as $key => $value) {
+      if (!isset($settings[$key])) {
+        $settings[$key] = $value;
+      }
+    }
+
+    // Replace tokens in the caption.
+    $settings['caption'] = t($settings['caption'],
+      ['@content_type' => $entity->rdfs__type['und'][0]['value']]);
+
+    // For each location, add it to the table.
+    $header = ['Name', 'Location', 'Strand', 'Phase'];
+
+    $locations = [];
+
+    foreach ($items as $item) {
+
+      if (!empty($item['value'])) {
+        $fmin_term = $item->get('fmin')->getString();
+        $fmax_term = $item->get('fmax')->getString();
+        $strand_term = $item->get('strand')->getString();
+        $phase_term = $item->get('phase')->getString();
+
+        $strand_val = $item['value'][$strand_term];
+        if ($settings['expand_strand']) {
+          $strand_symb = match( $strand_val ) {
+            -1 => '-',
+            1 => '+',
+            default => '<span style="color:#B3B3B3">unknown</span>',
+          };
+        }
+      }
+
+      $locations[] = [
+        $item['value'][$reference_term],
+        $item['value'][$fmin_term] . '..' . $fmax = $item['value'][$fmax_term],
+        $strand_symb, $item['value'][$phase_term],
+      ];
+    }
+
+    if ( !$locations ) {
+      $content = 'This feature is not located on any sequence.';
+    } 
+    else {
+      $content = $locations;
+    }
+
+    // The cardinality of this field is always 1, so only create element for $delta of zero.
+    $elements[0] = [
+      '#type' => 'markup',
+      '#theme' => 'table',
+      '#header' => $header,
+      '#rows' => $content,
+      '#caption' => $settings['caption'],        
+    ];
+
+    return $elements;
+  }
+}