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Merge pull request #1578 from tripal/tv4g1-issue1414-ChadoAnalysisDef…
…ault Tripal 4 ChadoAnalysisDefault field
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38 changes: 38 additions & 0 deletions
38
tripal_chado/src/Plugin/Field/FieldFormatter/ChadoAnalysisFormatterDefault.php
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,38 @@ | ||
| <?php | ||
|
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| namespace Drupal\tripal_chado\Plugin\Field\FieldFormatter; | ||
|
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| use Drupal\tripal\TripalField\TripalFormatterBase; | ||
| use Drupal\Core\Field\FieldItemListInterface; | ||
| use Drupal\Core\Form\FormStateInterface; | ||
| use Drupal\tripal_chado\TripalField\ChadoFormatterBase; | ||
|
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| /** | ||
| * Plugin implementation of default Tripal analysis formatter. | ||
| * | ||
| * @FieldFormatter( | ||
| * id = "chado_analysis_formatter_default", | ||
| * label = @Translation("Chado analysis formatter"), | ||
| * description = @Translation("A chado analysis formatter"), | ||
| * field_types = { | ||
| * "chado_analysis_default" | ||
| * } | ||
| * ) | ||
| */ | ||
| class ChadoAnalysisFormatterDefault extends ChadoFormatterBase { | ||
|
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public function viewElements(FieldItemListInterface $items, $langcode) { | ||
| $elements = []; | ||
|
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| foreach($items as $delta => $item) { | ||
| $elements[$delta] = [ | ||
| "#markup" => $item->get('analysis_name')->getString() | ||
| ]; | ||
| } | ||
|
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| return $elements; | ||
| } | ||
| } |
168 changes: 168 additions & 0 deletions
168
tripal_chado/src/Plugin/Field/FieldType/ChadoAnalysisDefault.php
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,168 @@ | ||
| <?php | ||
|
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| namespace Drupal\tripal_chado\Plugin\Field\FieldType; | ||
|
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| use Drupal\tripal_chado\TripalField\ChadoFieldItemBase; | ||
| use Drupal\tripal_chado\TripalStorage\ChadoVarCharStoragePropertyType; | ||
| use Drupal\tripal_chado\TripalStorage\ChadoIntStoragePropertyType; | ||
| use Drupal\tripal_chado\TripalStorage\ChadoTextStoragePropertyType; | ||
| use Drupal\tripal\TripalField\TripalFieldItemBase; | ||
| use Drupal\tripal\TripalStorage\StoragePropertyValue; | ||
| use Drupal\Core\Field\FieldStorageDefinitionInterface; | ||
| use Drupal\core\Form\FormStateInterface; | ||
| use Drupal\core\Field\FieldDefinitionInterface; | ||
|
|
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| /** | ||
| * Plugin implementation of default Tripal analysis field type. | ||
| * | ||
| * @FieldType( | ||
| * id = "chado_analysis_default", | ||
| * label = @Translation("Analysis"), | ||
| * description = @Translation("Application of analytical methods to existing data of a specific type"), | ||
| * default_widget = "chado_analysis_widget_default", | ||
| * default_formatter = "chado_analysis_formatter_default", | ||
| * cardinality = 1 | ||
| * ) | ||
| */ | ||
| class ChadoAnalysisDefault extends ChadoFieldItemBase { | ||
|
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| public static $id = 'chado_analysis_default'; | ||
|
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public static function mainPropertyName() { | ||
| // Overrides the default of 'value' | ||
| return 'analysis_name'; | ||
| } | ||
|
|
||
| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public static function defaultFieldSettings() { | ||
| $settings = parent::defaultFieldSettings(); | ||
| $settings['termIdSpace'] = 'operation'; | ||
| $settings['termAccession'] = '2945'; | ||
| return $settings; | ||
| } | ||
|
|
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public static function defaultStorageSettings() { | ||
| $settings = parent::defaultStorageSettings(); | ||
| return $settings; | ||
| } | ||
|
|
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public function storageSettingsForm(array &$form, FormStateInterface $form_state, $has_data) { | ||
|
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| $elements = parent::storageSettingsForm($form, $form_state, $has_data); | ||
| $storage_settings = $this->getSetting('storage_plugin_settings'); | ||
| $base_table = $form_state->getValue(['settings', 'storage_plugin_settings', 'base_table']); | ||
|
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| // Only present base tables that have a foreign key to analysis. | ||
| $elements['storage_plugin_settings']['base_table']['#options'] = $this->getBaseTables('analysis'); | ||
|
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| // Add a validation to make sure the base table has a foreign | ||
| // key to analysis_id in the chado.analysis table. | ||
| $elements['storage_plugin_settings']['base_table']['#element_validate'] = [[static::class, 'storageSettingsFormValidate']]; | ||
| return $elements; | ||
| } | ||
|
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public static function tripalTypes($field_definition) { | ||
| $entity_type_id = $field_definition->getTargetEntityTypeId(); | ||
|
|
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| // Get the Chado table and column this field maps to. | ||
| $storage_settings = $field_definition->getSetting('storage_plugin_settings'); | ||
| $base_table = $storage_settings['base_table']; | ||
|
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| // If we don't have a base table then we're not ready to specify the | ||
| // properties for this field. | ||
| if (!$base_table) { | ||
| $record_id_term = 'operation:2945'; | ||
| return [ | ||
| new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'record_id', $record_id_term, [ | ||
| 'action' => 'store_id', | ||
| 'drupal_store' => TRUE, | ||
| ]) | ||
| ]; | ||
| } | ||
|
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| // Get the connecting information for the foreign key from the | ||
| // base table to the analysis table. | ||
| $chado = \Drupal::service('tripal_chado.database'); | ||
| $schema = $chado->schema(); | ||
| $base_table_def = $schema->getTableDef($base_table, ['format' => 'Drupal']); | ||
| $analysis_table_def = $schema->getTableDef('analysis', ['format' => 'Drupal']); | ||
| $base_pkey_col = $base_table_def['primary key']; | ||
| $base_fkey_col = 'analysis_id'; | ||
|
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| // Create variables to store the terms for the analysis. | ||
| $storage = \Drupal::entityTypeManager()->getStorage('chado_term_mapping'); | ||
| $mapping = $storage->load('core_mapping'); | ||
| $record_id_term = 'SIO:000729'; | ||
| $analysis_id_term = $mapping->getColumnTermId('analysis', 'analysis_id'); | ||
| $analysis_name_term = $mapping->getColumnTermId('analysis', 'name'); | ||
| $analysis_name_length = $analysis_table_def['fields']['name']['size']; | ||
|
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| // Define field properties, this is a simple lookup in the analysis table | ||
| $properties = []; | ||
| $properties[] = new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'record_id', $record_id_term, [ | ||
| 'action' => 'store_id', | ||
| 'drupal_store' => TRUE, | ||
| 'chado_table' => $base_table, | ||
| 'chado_column' => $base_pkey_col, | ||
| ]); | ||
| $properties[] = new ChadoIntStoragePropertyType($entity_type_id, self::$id, 'analysis_id', $analysis_id_term, [ | ||
| 'action' => 'store', | ||
| 'chado_table' => $base_table, | ||
| 'chado_column' => $base_fkey_col, | ||
| ]); | ||
| $properties[] = new ChadoVarCharStoragePropertyType($entity_type_id, self::$id, 'analysis_name', $analysis_name_term, $analysis_name_length, [ | ||
| 'action' => 'join', | ||
| 'path' => $base_table . '.' . $base_fkey_col . '>analysis.analysis_id', | ||
| 'chado_column' => 'name', | ||
| 'as' => 'analysis_name', | ||
| ]); | ||
|
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| return $properties; | ||
| } | ||
|
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| /** | ||
| * Form element validation handler | ||
| * | ||
| * @param array $form | ||
| * The form where the settings form is being included in. | ||
| * @param \Drupal\Core\Form\FormStateInterface $form_state | ||
| * The form state of the (entire) configuration form. | ||
| */ | ||
| public static function storageSettingsFormValidate(array $form, FormStateInterface $form_state) { | ||
| $settings = $form_state->getValue('settings'); | ||
| if (!array_key_exists('storage_plugin_settings', $settings)) { | ||
| return; | ||
| } | ||
|
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| // Validation confirms that the base table has a foreign key | ||
| // to analysis_id in the chado.analysis table. | ||
| // This validation might be redundant, since we only present | ||
| // valid base tables to the user, but let's play it safe. | ||
| $base_table = $settings['storage_plugin_settings']['base_table']; | ||
| $chado = \Drupal::service('tripal_chado.database'); | ||
| $schema = $chado->schema(); | ||
| $base_table_def = $schema->getTableDef($base_table, ['format' => 'Drupal']); | ||
| $base_fkey_col = 'analysis_id'; | ||
| $fkeys = $base_table_def['foreign keys']['analysis']['columns'] ?? []; | ||
| if (!in_array($base_fkey_col, $fkeys)) { | ||
| $form_state->setErrorByName('storage_plugin_settings][base_table', | ||
| 'The selected base table does not have a foreign key to analysis_id,' | ||
| . ' this field cannot be used on this content type.'); | ||
| } | ||
| } | ||
|
|
||
| } |
73 changes: 73 additions & 0 deletions
73
tripal_chado/src/Plugin/Field/FieldWidget/ChadoAnalysisWidgetDefault.php
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| <?php | ||
|
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| namespace Drupal\tripal_chado\Plugin\Field\FieldWidget; | ||
|
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| use Drupal\tripal\TripalField\TripalWidgetBase; | ||
| use Drupal\Core\Field\FieldItemListInterface; | ||
| use Drupal\Core\Form\FormStateInterface; | ||
| use Drupal\tripal_chado\TripalField\ChadoWidgetBase; | ||
|
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| /** | ||
| * Plugin implementation of default Chado analysis widget. | ||
| * | ||
| * @FieldWidget( | ||
| * id = "chado_analysis_widget_default", | ||
| * label = @Translation("Chado Analysis Widget"), | ||
| * description = @Translation("The default analysis widget."), | ||
| * field_types = { | ||
| * "chado_analysis_default" | ||
| * } | ||
| * ) | ||
| */ | ||
| class ChadoAnalysisWidgetDefault extends ChadoWidgetBase { | ||
|
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| /** | ||
| * {@inheritdoc} | ||
| */ | ||
| public function formElement(FieldItemListInterface $items, $delta, array $element, array &$form, FormStateInterface $form_state) { | ||
|
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| // Get the list of analyses. | ||
| $analyses = []; | ||
| $chado = \Drupal::service('tripal_chado.database'); | ||
|
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| // In addition to getting a sorted list of analyses, include | ||
| // the analysisprop rdfs:type when it is present, e.g. | ||
| // genome assembly or genome annotation. | ||
| $sql = 'SELECT A.analysis_id, A.name, TYPE.value FROM {1:analysis} A | ||
| LEFT JOIN ( | ||
| SELECT AP.analysis_id, AP.value FROM {1:analysisprop} AP | ||
| LEFT JOIN {1:cvterm} T ON AP.type_id=T.cvterm_id | ||
| LEFT JOIN {1:cv} CV ON T.cv_id=CV.cv_id | ||
| WHERE T.name=:cvterm | ||
| AND CV.name=:cv | ||
| ) AS TYPE | ||
| ON A.analysis_id=TYPE.analysis_id | ||
| ORDER BY A.name'; | ||
| $results = $chado->query($sql, [':cvterm' => 'type', ':cv' => 'rdfs']); | ||
|
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| while ($analysis = $results->fetchObject()) { | ||
| $type_text = $analysis->value ? ' (' . $analysis->value . ')' : ''; | ||
| $analyses[$analysis->analysis_id] = $analysis->name . $type_text; | ||
| } | ||
|
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| $item_vals = $items[$delta]->getValue(); | ||
| $record_id = $item_vals['record_id'] ?? 0; | ||
| $analysis_id = $item_vals['analysis_id'] ?? 0; | ||
|
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| $elements = []; | ||
| $elements['record_id'] = [ | ||
| '#type' => 'value', | ||
| '#default_value' => $record_id, | ||
| ]; | ||
| $elements['analysis_id'] = $element + [ | ||
| '#type' => 'select', | ||
| '#options' => $analyses, | ||
| '#default_value' => $analysis_id, | ||
| '#placeholder' => $this->getSetting('placeholder'), | ||
| '#empty_option' => '-- Select --', | ||
| ]; | ||
|
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| return $elements; | ||
| } | ||
|
|
||
| } |
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