Merge pull request #1588 from tripal/7v4g1-1565-Remove_bio_data

Remove 'bio_data' from Tripal
tripal · Aug 9, 2023 · 0ee074f · 0ee074f
2 parents d584796 + 0cc4704
commit 0ee074f
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Showing 27 changed files with 1,572 additions and 1,691 deletions.
diff --git a/tripal/config/schema/tripal.schema.yml b/tripal/config/schema/tripal.schema.yml
@@ -162,7 +162,7 @@ tripal.tripalentitytype_collection.*:
                  type: string
                  label: "Category"
                  nullable: false
-               name:
+               id:
                  type: string
                  label: "A machine readable content type id (a.k.a., the bundle ID or Entity Type ID)"
                  nullable: false

diff --git a/tripal/config/schema/tripal_entity_type.schema.yml b/tripal/config/schema/tripal_entity_type.schema.yml
@@ -1,13 +1,10 @@
-tripal.bio_data.*:
+tripal.content_type.*:
   type: config_entity
   label: 'Tripal Content Type'
   mapping:
     id:
-      type: integer
-      label: 'ID'
-    name:
       type: string
-      label: 'Name'
+      label: 'ID'
     label:
       type: label
       label: 'Label'

diff --git a/tripal/js/tripal.js b/tripal/js/tripal.js
@@ -116,7 +116,7 @@
    */
   TripalAjaxField.prototype.attach = function () {
     $.ajax({
-      url     : baseurl + '/bio_data/ajax/field_attach/' + this.id,
+      url     : baseurl + '/tripal/ajax/field_attach/' + this.id,
       dataType: 'json',
       type    : 'GET',
       success : this.setFieldContent.bind(this)
@@ -212,7 +212,7 @@ function tripal_navigate_field_pager(id, page) {
   jQuery('#' + id + '-spinner').show();
   jQuery.ajax({
     type   : 'GET',
-    url    : Drupal.settings['basePath'] + 'bio_data/ajax/field_attach/' + id,
+    url    : Drupal.settings['basePath'] + 'tripal/ajax/field_attach/' + id,
     data   : {'page': page},
     success: function (response) {
       jQuery('#' + id + ' .field-items').replaceWith(response['content']);

diff --git a/tripal/src/Controller/TripalEntityUIController.php b/tripal/src/Controller/TripalEntityUIController.php
@@ -43,7 +43,7 @@ public function tripalContentAddPage() {
       $bundles[$category]['members'][] = [
         'title' => $entity->getLabel(),
         'help' => $entity->getHelpText(),
-        'url' => Url::fromRoute('entity.tripal_entity.add_form', ['tripal_entity_type' => $entity->getName()]),
+        'url' => Url::fromRoute('entity.tripal_entity.add_form', ['tripal_entity_type' => $entity->id()]),
       ];
     }
 
@@ -84,7 +84,7 @@ public function tripalContentAddPage() {
    */
   public function tripalCheckForFields($tripal_entity_type) {
 
-    $bundle_name = $tripal_entity_type->getName();
+    $bundle_name = $tripal_entity_type->id();
     $term = $tripal_entity_type->getTerm();
 
     //$added = tripal_create_bundle_fields($bundle, $term);

diff --git a/tripal/src/Entity/TripalEntity.php b/tripal/src/Entity/TripalEntity.php
@@ -10,6 +10,7 @@
 use Drupal\user\UserInterface;
 use Drupal\tripal\TripalField\Interfaces\TripalFieldItemInterface;
 use Drupal\field\Entity\FieldConfig;
+use Symfony\Component\Routing\Route;
 
 
 /**
@@ -47,12 +48,12 @@
  *     "status" = "status",
  *   },
  *   links = {
- *     "canonical" = "/bio_data/{tripal_entity}",
- *     "add-page" = "/bio_data/add",
- *     "add-form" = "/bio_data/add/{tripal_entity_type}",
- *     "edit-form" = "/bio_data/{tripal_entity}/edit",
- *     "delete-form" = "/bio_data/{tripal_entity}/delete",
- *     "collection" = "/admin/content/bio_data",
+ *     "canonical" = "/tripal/{tripal_entity}",
+ *     "add-page" = "/tripal/add",
+ *     "add-form" = "/tripal/add/{tripal_entity_type}",
+ *     "edit-form" = "/tripal/{tripal_entity}/edit",
+ *     "delete-form" = "/tripal/{tripal_entity}/delete",
+ *     "collection" = "/admin/content/tripal",
  *   },
  *   bundle_entity_type = "tripal_entity_type",
  *   field_ui_base_route = "entity.tripal_entity_type.edit_form"
@@ -69,7 +70,7 @@ class TripalEntity extends ContentEntityBase implements TripalEntityInterface {
    * @code
       $values = [
         'title' => 'laceytest'.time(),
-        'type' => 'bio_data_1',
+        'type' => 'organism',
         'uid' => 1,
       ];
       $entity = \Drupal\tripal\Entity\TripalEntity::create($values);
@@ -79,7 +80,7 @@ class TripalEntity extends ContentEntityBase implements TripalEntityInterface {
    * @param array $values
    *   - *title: the title of the entity.
    *   - *user_id: the user_id of the user who authored the content.
-   *   - *type: the type of tripal entity this is (e.g. bio_data_1)
+   *   - *type: the type of tripal entity this is (e.g. organism)
    *   - status: whether the entity is published or not (boolean)
    *   - created: the unix timestamp for when this content was created.
    * @return object
@@ -153,35 +154,20 @@ public function getTitle() {
    *   The alias to use. It can contain tokens the correspond to field values.
    *   Token should be be compatible with those returned by
    *   tripal_get_entity_tokens().
-   * @param array $cache
-   *   This array is used to store objects you want to cache for performance
-   *   reasons, as well as, cache related options. The following are supported:
-   *   - TripalEntityType $bundle
-   *       The bundle for the current entity.
    */
-  public function setAlias($path_alias = NULL, $cache = []) {
+  public function setAlias($path_alias = NULL) {
 
-    $system_path = "/bio_data/" . $this->getID();
-    $langcode = \Drupal::languageManager()->getCurrentLanguage()->getId();
+
+    $system_path = "/tripal/" . $this->getID();
 
     // If no alias was supplied then we should try to generate one using the
     // default format set by admins.
     if (!$path_alias) {
 
-      // Load the TripalEntityType entity for this TripalEntity (if it's not
-      // cached). First get the format for the url alias based on the bundle
-      // of the entity. Then replace all the tokens with values from the entity fields.
-      if (isset($cache['bundle'])) {
-        $bundle = $cache['bundle'];
-      }
-      else {
-        $bundle = \Drupal\tripal\Entity\TripalEntityType::load($this->getType());
-      }
-
+      $bundle = \Drupal\tripal\Entity\TripalEntityType::load($this->getType());
       $path_alias = $bundle->getURLFormat();
       $path_alias = $this->replaceTokens($path_alias,
         ['tripal_entity_type' => $bundle]);
-
     }
 
     // Ensure there is a leading slash.
@@ -196,7 +182,6 @@ public function setAlias($path_alias = NULL, $cache = []) {
     $path = \Drupal::entityTypeManager()->getStorage('path_alias')->create([
       'path' => $system_path,
       'alias' => $path_alias,
-      'langcode' => $langcode,
     ]);
     $path->save();
   }

diff --git a/tripal/src/Entity/TripalEntityType.php b/tripal/src/Entity/TripalEntityType.php
@@ -29,23 +29,22 @@
  *       "html" = "Drupal\tripal\Routing\TripalEntityTypeHtmlRouteProvider",
  *     },
  *   },
- *   config_prefix = "bio_data",
+ *   config_prefix = "content_type",
  *   admin_permission = "manage tripal content types",
  *   bundle_of = "tripal_entity",
  *   entity_keys = {
- *     "id" = "name",
+ *     "id" = "id",
  *     "label" = "label",
  *   },
  *   links = {
- *     "canonical" = "/admin/structure/bio_data/{tripal_entity_type}",
- *     "add-form" = "/admin/structure/bio_data/add",
- *     "edit-form" = "/admin/structure/bio_data/manage/{tripal_entity_type}",
- *     "delete-form" = "/admin/structure/bio_data/manage/{tripal_entity_type}/delete",
- *     "collection" = "/admin/structure/bio_data"
+ *     "canonical" = "/admin/structure/tripal/{tripal_entity_type}",
+ *     "add-form" = "/admin/structure/tripal/add",
+ *     "edit-form" = "/admin/structure/tripal/manage/{tripal_entity_type}",
+ *     "delete-form" = "/admin/structure/tripal/manage/{tripal_entity_type}/delete",
+ *     "collection" = "/admin/structure/tripal"
  *   },
  *   config_export = {
  *     "id",
- *     "name",
  *     "label",
  *     "termIdSpace",
  *     "termAccession",
@@ -67,13 +66,6 @@ class TripalEntityType extends ConfigEntityBundleBase implements TripalEntityTyp
    */
   protected $id;
 
-  /**
-   * The Tripal Content machine name.
-   *
-   * @var string
-   */
-  protected $name;
-
   /**
    * The Tripal Content type label.
    *
@@ -207,15 +199,6 @@ public static function create(array $values = []) {
    */
    public function save() {
 
-     // First we want to set an id for this content type.
-     if ($this->isNew()) {
-       $config = \Drupal::service('config.factory')->getEditable('tripal.settings');
-       $max_id = $config->get('tripal_entity_type.max_id');
-       $this->id = $max_id + 1;
-       $this->name = 'bio_data_' . $this->id;
-       $config->set('tripal_entity_type.max_id', $this->id)->save();
-     }
-
      // Set defaults for anything not already set.
      $this->setDefaults();
 
@@ -240,8 +223,8 @@ public function validate() {
     if ($this->label === NULL) {
       throw new \Exception("The label is required when creating a TripalEntityType.");
     }
-    if ($this->name === NULL) {
-      throw new \Exception("The name is required when creating a TripalEntityType.");
+    if ($this->id === NULL) {
+      throw new \Exception("The id is required when creating a TripalEntityType.");
     }
     if ($this->help_text === NULL) {
       throw new \Exception("The help text is required when creating a TripalEntityType.");
@@ -287,7 +270,7 @@ public function setDefaults() {
    * {@inheritdoc}
    */
   public function id() {
-    return $this->name;
+    return $this->id;
   }
 
   /**
@@ -297,27 +280,6 @@ public function getID() {
     return $this->id;
   }
 
-  /**
-   * {@inheritdoc}
-   */
-  public function setID($id) {
-    $this->id = $id;
-  }
-
-  /**
-   * {@inheritdoc}
-   */
-  public function getName() {
-    return $this->name;
-  }
-
-  /**
-   * {@inheritdoc}
-   */
-  public function setName($name) {
-    $this->name = $name;
-  }
-
   /**
    * {@inheritdoc}
    */
@@ -595,8 +557,7 @@ public function getTokens($options = []) {
       'required' => TRUE,
     ];
 
-    $instances = \Drupal::service('entity_field.manager')
-      ->getFieldDefinitions('tripal_entity', $this->name);
+    $instances = \Drupal::service('entity_field.manager')->getFieldDefinitions('tripal_entity', $this->id);
     foreach ($instances as $instance_name => $instance) {
 
       $use_field = TRUE;
@@ -718,4 +679,5 @@ public static function sortByCategory(TripalEntityTypeInterface $a, TripalEntity
       return strnatcasecmp($b_value, $a_value);
     }
   }
+
 }
diff --git a/tripal/src/Entity/TripalEntityTypeInterface.php b/tripal/src/Entity/TripalEntityTypeInterface.php
@@ -9,43 +9,6 @@
  */
 interface TripalEntityTypeInterface extends ConfigEntityInterface {
 
-  /**
-   * Gets the index of the machine name (e.g. 1).
-   *
-   * @return string
-   *   Index of the machine name of the Tripal Entity Type.
-   */
-  public function getID();
-
-  /**
-   * Sets the index of the machine name.
-   *
-   * @param integer $id
-   *   The index of the machine name of the Tripal Entity Type.
-   *
-   * @return \Drupal\tripal\Entity\TripalEntityTypeInterface
-   *   The called Tripal Entity Type entity.
-   */
-  public function setID($id);
-
-  /**
-   * Gets the machine name of the Tripal Entity Type (e.g. bio_data_1).
-   *
-   * @return string
-   *   Machine name of the Tripal Entity Type.
-   */
-  public function getName();
-
-  /**
-   * Sets the machine name of the Tripal Entity Type.
-   *
-   * @param string $name
-   *   The machine name of the Tripal Entity Type.
-   *
-   * @return \Drupal\tripal\Entity\TripalEntityTypeInterface
-   *   The called Tripal Entity Type entity.
-   */
-  public function setName($name);
 
   /**
    * Gets the Tripal Entity Type label (e.g. gene).

diff --git a/tripal/src/Form/TripalEntityForm.php b/tripal/src/Form/TripalEntityForm.php
@@ -40,7 +40,7 @@ public function save(array $form, FormStateInterface $form_state) {
     $entity->setTitle($values['title'][0]['value']);
     $entity->setOwnerId($values['uid'][0]['target_id']);
     $status = parent::save($form, $form_state);
-    // $entity->setAlias();
+    $entity->setAlias();
 
     switch ($status) {
       case SAVED_NEW: