From 7c432d03e8d9a9c0ea1a5a98bef18a63655957a1 Mon Sep 17 00:00:00 2001
From: Malladi <sm2699@xi19051258.sgc.loc>
Date: Mon, 28 Aug 2023 13:12:33 -0500
Subject: [PATCH] Removed ChadoLocalSourceData*.php files that were a repeat of
 ChadoSourceData*.php files

---
 .../ChadoLocalSourceDataFormatterDefault.php  |  67 -----------
 .../FieldType/ChadoLocalSourceDataDefault.php | 108 ------------------
 .../ChadoLocalSourceDataWidgetDefault.php     |  79 -------------
 3 files changed, 254 deletions(-)
 delete mode 100755 tripal_chado/src/Plugin/Field/FieldFormatter/ChadoLocalSourceDataFormatterDefault.php
 delete mode 100755 tripal_chado/src/Plugin/Field/FieldType/ChadoLocalSourceDataDefault.php
 delete mode 100755 tripal_chado/src/Plugin/Field/FieldWidget/ChadoLocalSourceDataWidgetDefault.php

diff --git a/tripal_chado/src/Plugin/Field/FieldFormatter/ChadoLocalSourceDataFormatterDefault.php b/tripal_chado/src/Plugin/Field/FieldFormatter/ChadoLocalSourceDataFormatterDefault.php
deleted file mode 100755
index 9798d7dd0..000000000
--- a/tripal_chado/src/Plugin/Field/FieldFormatter/ChadoLocalSourceDataFormatterDefault.php
+++ /dev/null
@@ -1,67 +0,0 @@
-<?php
-
-namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
-
-use Drupal\Core\Field\FieldItemListInterface;
-use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
-use Drupal\Core\Link;
-
-/**
- * Plugin implementation of default Tripal string type formatter.
- *
- * @FieldFormatter(
- *   id = "chado_local_source_data_formatter_default",
- *   label = @Translation("Chado Local Source Data Formatter"),
- *   description = @Translation("Analysis local source data formatter default"),
- *   field_types = {
- *     "chado_local_source_data_default"
- *   }
- * )
- */
-class ChadoLocalSourceDataFormatterDefault extends ChadoFormatterBase {
-
-  /**
-  * {@inheritdoc}
-  */
-  public function viewElements(FieldItemListInterface $items, $langcode) {
-    $elements = [];
-    $elements['#attached']['library'][] = 'tripal_chado/tripal_chado.field.ChadoLocalSourceDataFormatter';
-
-    $content = 'The data source is not provided.';
-
-    foreach($items as $delta => $item) {
-      $content = "<dl class=\"tripal-dl\">";
-<<<<<<< HEAD
-=======
-      $prog_vers_val = $item->get( 'programversion' )->getString() ;
-      if ( !empty( $prog_vers_val ) ) {
-        $content .= "<dt>Software version</dt><dd>: " . $prog_vers_val . " </dd>";
-      }
->>>>>>> b73440286faed0b3cf68dec7fdff3e2bb4528450
-      $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 (preg_match('/^https?:/i', $sourceuri_val ) ) {
-          $sourceuri_val = Link::fromTextAndUrl($sourceuri_val, $sourceuri_val);
-        }
-      */
-      if ( !empty( $sourceuri_val ) ) {
-        $content .= "<dt>Source URI</dt><dd>: " . $sourceuri_val . " </dd>";
-      }
-      $content .= "</dl>";
-    }
-    $elements[$delta] = [
-      '#type' => 'markup',
-      '#markup' => $content,
-    ];
-    
-    return $elements;
-  }
-}
diff --git a/tripal_chado/src/Plugin/Field/FieldType/ChadoLocalSourceDataDefault.php b/tripal_chado/src/Plugin/Field/FieldType/ChadoLocalSourceDataDefault.php
deleted file mode 100755
index 2ca8f71d8..000000000
--- a/tripal_chado/src/Plugin/Field/FieldType/ChadoLocalSourceDataDefault.php
+++ /dev/null
@@ -1,108 +0,0 @@
-<?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 sequence data.
- *
- * @FieldType(
- *   id = "chado_local_source_data_default",
- *   label = @Translation("Chado local analysis source data"),
- *   description = @Translation("The local source data used for this analysis"),
- *   default_widget = "chado_local_source_data_widget_default",
- *   default_formatter = "chado_local_source_data_formatter_default"
- * )
- */
-class ChadoLocalSourceDataDefault extends ChadoFieldItemBase {
-
-  public static $id = "chado_local_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');
-
-    $prog_vers_term = $mapping->getColumnTermId('analysis', 'programversion');
-    $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',
-    ]);
-<<<<<<< HEAD
-=======
-    $properties[] = new ChadoVarCharStoragePropertyType($entity_type_id, self::$id, 'programversion', $prog_vers_term, 100, [
-      'action' => 'store',
-      'chado_table' => 'analysis',
-      'chado_column' => 'programversion',
-    ]);
->>>>>>> b73440286faed0b3cf68dec7fdff3e2bb4528450
-    $properties[] = new ChadoVarCharStoragePropertyType($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);    
-  }
-
-}
diff --git a/tripal_chado/src/Plugin/Field/FieldWidget/ChadoLocalSourceDataWidgetDefault.php b/tripal_chado/src/Plugin/Field/FieldWidget/ChadoLocalSourceDataWidgetDefault.php
deleted file mode 100755
index 01adf86ad..000000000
--- a/tripal_chado/src/Plugin/Field/FieldWidget/ChadoLocalSourceDataWidgetDefault.php
+++ /dev/null
@@ -1,79 +0,0 @@
-<?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 widget.
- *
- * @FieldWidget(
- *   id = "chado_local_source_data_widget_default",
- *   label = @Translation("Chado analysis local source data Widget default"),
- *   description = @Translation("The default chado local source data widget which allows curators to manually enter analysis source on the content edit page."),
- *   field_types = {
- *     "chado_local_source_data_default"
- *   }
- * )
- */
-class ChadoLocalSourceDataWidgetDefault 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,
-    ];
-<<<<<<< HEAD
-=======
-
-    $elements['programversion'] =  [
-      '#title' => "Software version",
-      '#type' => 'textfield',
-      '#default_value' => $item_vals['programversion'] ?? '',
-    ];
->>>>>>> b73440286faed0b3cf68dec7fdff3e2bb4528450
-    $elements['sourceuri'] =  [
-      '#title' => "Local Source URI",
-      '#type' => 'textfield',
-      '#default_value' => $item_vals['sourceuri'] ?? '',
-    ];
-    $elements['sourcename'] =  [
-      '#title' => "Local Source Name",
-      '#type' => 'textfield',
-      '#default_value' => $item_vals['sourcename'] ?? '',
-    ];
-    $elements['sourceversion'] = [
-      '#type' => 'textfield',
-      '#default_value' => $item_vals['sourceversion'] ?? '',
-      '#title' => 'Local Source Version',
-    ];
-
-    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]['programversion'] = $value['programversion'];      
-      $values[$val_key]['sourceuri'] = $value['sourceuri'];      
-      $values[$val_key]['sourcename'] = $value['sourcename'];      
-      $values[$val_key]['sourceversion'] = $value['sourceversion'];
-    }
-    return $values;
-  }
-
-}
\ No newline at end of file