Updates to the tripal fields documentation

docs/dev_guide/module_dev.rst

@@ -11,7 +11,7 @@ Custom Module Development
    module_dev/file_structure
    module_dev/routing
    module_dev/entities
-   module_dev/fields
+   module_dev/tripal_fields
    module_dev/forms
    module_dev/jobs
    module_dev/logging

docs/dev_guide/module_dev/fields/auto_attach.rst

@@ -0,0 +1,13 @@
+Add Fields to Content Types
+============================
+
+In order for a field to be used, it needs to be added to a specific content type. This can be done through the "Manage Fields" interface for a given Content Type. More specifically, go to Tripal > Page Structure and then choose "Manage Fields" for the Content Type you want to add a field to.
+
+This can also be done programmatically, however documentation for this is still being developed.
+
+.. warning::
+
+  This documentation is still being developed. In the meantime there are
+  examples for programmatically adding TripalFields in the Tripal core codebase.
+  Specifically, look in the Chado Preparer class in
+  `tripal_chado/src/Task/ChadoPreparer.php`.

docs/dev_guide/module_dev/fields/custom_field_backend.rst

@@ -0,0 +1,10 @@
+Non-Chado Field Storage
+=========================
+
+The TripalStorage plugin supports providing custom backends for fields. You can have fields with different storage backends on the same Content Type.
+
+.. warning::
+
+  This documentation is still being developed. Currently ChadoStorage provides
+  an example for implementing the TripalStorage data store extension. It can be
+  found in `tripal_chado/src/Plugin/TripalStorage/ChadoStorage.php`.

docs/dev_guide/module_dev/fields/formatters.rst

@@ -0,0 +1,266 @@
+Field Formatters
+==================
+
+Implementing a ChadoFormatterBase Class
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+When creating a new Tripal field, the class responsible for displaying
+information to the site users is the "Formatter" class.
+This class extends the `ChadoFormatterBase` class.
+
+To illustrate with a simple example, we will create a simple field to display the
+organism's scientific name on a germplasm page.
+We earlier created a property to store this, ``organism_scientific_name``,
+so the formatter will use the value from that property.
+
+Formatter Class Setup
+```````````````````````
+To create a new field, we will extend the `ChadoFormatterBase` class.
+For a new field named `MyField` we would create a new file in our module here:
+`src/Plugin/Field/FieldFormatter/MyfieldFormatter.php`
+The following is a simple class example:
+
+.. code-block:: php
+
+  <?php
+  namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter;
+
+  use Drupal\Core\Field\FieldItemListInterface;
+  use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+  /**
+   * Plugin implementation of an organism scientific name formatter.
+   *
+   * @FieldFormatter(
+   *   id = "my_field_formatter",
+   *   label = @Translation("Organism scientific name formatter"),
+   *   description = @Translation("A chado organism scientific name formatter"),
+   *   field_types = {
+   *     "my_field"
+   *   },
+   * )
+   */
+  class MyFieldFormatter extends ChadoFormatterBase {
+
+    /**
+     * {@inheritdoc}
+     */
+    public static function defaultSettings() {
+      $settings = parent::defaultSettings();
+      return $settings;
+    }
+
+    /**
+     * {@inheritdoc}
+     */
+    public function viewElements(FieldItemListInterface $items, $langcode) {
+      $elements = [];
+      $list = [];
+      $lookup_manager = \Drupal::service('tripal.tripal_entity.lookup');
+
+      foreach ($items as $delta => $item) {
+        $values = [
+          'entity_id' => $item->get('entity_id')->getString(),
+          'scientific_name' => $item->get('organism_scientific_name')->getString(),
+        ];
+
+        // Create a clickable link to the corresponding entity when one exists.
+        $renderable_item = $lookup_manager->getRenderableItem($values['scientific_name'], $values['entity_id']);
+
+        $list[$delta] = $renderable_item;
+      }
+
+      // If only one element has been found, don't make into a list.
+      if (count($list) == 1) {
+        $elements = $list;
+      }
+      // If more than one value has been found, display all values in an
+      // unordered list.
+      elseif (count($list) > 1) {
+        $elements[0] = [
+          '#theme' => 'item_list',
+          '#list_type' => 'ul',
+          '#items' => $list,
+          '#wrapper_attributes' => ['class' => 'container'],
+        ];
+      }
+
+      return $elements;
+    }
+
+  }
+
+Below is a line-by-line explanation of each section of the code snippet above.
+
+Formatter Namespace and Use Statements
+````````````````````````````````````````
+
+The following should always be present and specifies the namespace for this
+field.
+
+.. code-block:: php
+
+  namespace Drupal\mymodule\Plugin\Field\FieldFormatter;
+
+
+.. note::
+
+  Be sure to change `mymodule` in the `namespace` to the name of your module.
+
+.. warning::
+
+  If you misspell the `namespace` your field will not work properly.
+
+The following "use" statement is required for all Chado fields.
+
+.. code-block:: php
+
+  use Drupal\tripal_chado\TripalField\ChadoFormatterBase;
+
+Unless you are sure that your field will only handle a single value in all
+cases, you will likely want the following use statement to allow the
+formatter to handle a list of multiple items.
+
+.. code-block:: php
+
+  use Drupal\Core\Field\FieldItemListInterface;
+
+Formatter Annotation Section
+``````````````````````````````
+The annotation section in the class file is the set of in-line comments for the class.
+This annotation is required.
+This section is similar to the annotation section in the previous Type class.
+Note the ``field_types`` annotation, which specifies what field types this formatter can be used
+for. This should match the ``id`` annotation in the Type class.
+
+.. code-block:: php
+
+  /**
+   * Plugin implementation of an organism scientific name formatter.
+   *
+   * @FieldFormatter(
+   *   id = "my_field_formatter",
+   *   label = @Translation("Organism scientific name formatter"),
+   *   description = @Translation("A chado organism scientific name formatter"),
+   *   field_types = {
+   *     "my_field"
+   *   },
+   * )
+   */
+
+.. note::
+
+   Multiple formatters can exist for a given field, and the site
+   administrator can select which formatter is appropriate for a
+   particular content type.
+
+.. warning::
+
+   If the annotation section is not present, has misspellings, or is not
+   complete, the field will not be recognized by Drupal.
+
+Formatter Class Definition
+````````````````````````````
+
+Next, the class definition line must extend the `ChadoFormatterBase` class. You
+must name your class the same as the filename in which it is contained (minus
+the `.php` extension).
+
+.. code-block:: php
+
+  class MyFieldFormatter extends ChadoFormatterBase {
+
+.. warning::
+
+    If you misspell the class name such that it is not the same as the filename
+    of the file in which it is contained, then the field will not be recognized by
+    Drupal.
+
+The defaultSettings() Function
+````````````````````````````````
+This is an optional function. If your field requires some additional settings
+for content display. An example might be how many decimal places to display
+for a real number. This example does not add any settings.
+
+.. code-block:: php
+
+  public static function defaultSettings() {
+    $settings = parent::defaultSettings();
+    return $settings;
+  }
+
+The viewElements() Function
+`````````````````````````````
+
+The `viewElements()` function is used to retrieve one or more property types
+managed by this field, and prepare them for display. Our example will just display
+a single value, but some fields can be configured for a cardinality greater than
+one, meaning multiple values may be present, so the values can be made into a
+list or a table as appropriate.
+
+In the example code block below you can see the steps where the property values
+are retrieved from the ``$items`` array..
+
+.. code-block:: php
+
+    public function viewElements(FieldItemListInterface $items, $langcode) {
+      $elements = [];
+      $list = [];
+      $lookup_manager = \Drupal::service('tripal.tripal_entity.lookup');
+
+      foreach ($items as $delta => $item) {
+        $values = [
+          'entity_id' => $item->get('entity_id')->getString(),
+          'scientific_name' => $item->get('organism_scientific_name')->getString(),
+        ];
+
+Then for each retrieved item, we convert the returned value into a
+`render array <https://www.drupal.org/docs/drupal-apis/render-api/render-arrays>`_
+item using the `tripal.tripal_entity.lookup` service. When possible, the item
+includes a link to the corresponding organism entity page, and if not, then
+plain markup is generated. Either way, it is then added to the array 
+``$list`` of values to display.
+
+.. code-block:: php
+
+        // Create a clickable link to the corresponding entity when one exists.
+        $renderable_item = $lookup_manager->getRenderableItem($values['scientific_name'],
+                                                              $values['entity_id']);
+        $list[$delta] = $renderable_item;
+      }
+
+The last step is to populate the ``$elements`` array. If there is only one value,
+as will be the case for this example, it becomes the only value in the array.
+However, when multiple values are present, we can present them as a list.
+Alternatively, you might want to display them in a table format.
+For an example of a table formatter, see the `ChadoSequenceCoordinatesFormatterTable` formatter.
+
+.. code-block:: php
+
+      // If only one element has been found, don't make into a list.
+      if (count($list) == 1) {
+        $elements = $list;
+      }
+      // If more than one value has been found, display all values in an
+      // unordered list.
+      elseif (count($list) > 1) {
+        $elements[0] = [
+          '#theme' => 'item_list',
+          '#list_type' => 'ul',
+          '#items' => $list,
+          '#wrapper_attributes' => ['class' => 'container'],
+        ];
+      }
+
+      return $elements;
+    }
+
+This completes your field formatter!
+
+The next section :ref:`Field Widgets` will describe how to create a widget
+for this new field to allow editing content.
+
+.. note::
+
+  A good way to learn about fields is to look at examples of fields in the Tripal
+  core codebase. Specifically, look in the
+  `tripal_chado/src/Plugin/Field/FieldFormatter` directory.