<?php /** * Implements hook_entity_create(). * * This hook is called when brand new entities are created, but * they are not loaded so the hook_entity_load() is not yet called. We * can use this hook to add properties to the entity before saving. * * @param $entity * The entity being created. * @param $type * The type of entity being created. * @param $bundle (OPTIONAL) * The bundle object for the current entity. */ function tripal_chado_entity_create(&$entity, $type, $bundle = NULL) { if ($type == 'TripalEntity') { // Set some defaults on vars needed by this module. if (!property_exists($entity, 'chado_table')) { $entity->chado_table = NULL; $entity->chado_column = NULL; $entity->chado_linker = NULL; $entity->chado_type_id = NULL; $entity->chado_type_value = NULL; $entity->chado_base_type_id = NULL; // Add in the Chado table information for this entity type. if (!$bundle) { $bundle = tripal_load_bundle_entity(['name' => $entity->bundle]); } if ($bundle->data_table) { $entity->chado_table = $bundle->data_table; $entity->chado_column = $bundle->type_column; $entity->chado_linker = $bundle->type_linker_table; $entity->chado_type_id = $bundle->type_id; $entity->chado_type_value = $bundle->type_value; $entity->chado_base_type_id = $bundle->base_type_id; } } if (!property_exists($entity, 'chado_record')) { $entity->chado_record = NULL; $entity->chado_record_id = NULL; } } } /** * Implements hook_entity_presave(). */ function tripal_chado_entity_presave($entity, $type) { } /** * Implements hook_entity_postsave(). */ function tripal_chado_entity_postsave($entity, $type) { } /** * Implements hook_entity_load(). */ function tripal_chado_entity_load($entities, $type) { if ($type == 'TripalBundle') { foreach ($entities as $bundle) { // We want to add in the record ID to the entity. if (property_exists($bundle, 'id')) { $chado_bundle = db_select('chado_bundle', 'cb') ->fields('cb') ->condition('cb.bundle_id', $bundle->id) ->execute() ->fetchObject(); if ($chado_bundle) { $bundle->data_table = $chado_bundle->data_table; $bundle->type_linker_table = $chado_bundle->type_linker_table; $bundle->type_column = $chado_bundle->type_column; $bundle->type_id = $chado_bundle->type_id; $bundle->type_value = $chado_bundle->type_value; $bundle->base_type_id = $chado_bundle->base_type_id; } } } } if ($type == 'TripalEntity') { foreach ($entities as $entity) { // We want to add in the record ID to the entity. if (property_exists($entity, 'id')) { // Set some defaults on vars needed by this module. $entity->chado_table = NULL; $entity->chado_column = NULL; $entity->chado_record = NULL; $entity->chado_record_id = NULL; // Add in the Chado table information for this entity type. $bundle = tripal_load_bundle_entity(['name' => $entity->bundle]); if (!$bundle) { continue; } $entity->chado_table = $bundle->data_table; $entity->chado_column = $bundle->type_column; $chado_entity_table = chado_get_bundle_entity_table($bundle); $chado_entity = db_select($chado_entity_table, 'ce') ->fields('ce') ->condition('ce.entity_id', $entity->id) ->execute() ->fetchObject(); if ($chado_entity) { $schema = chado_get_schema($entity->chado_table); $record = chado_generate_var($entity->chado_table, [$schema['primary key'][0] => $chado_entity->record_id]); $entity->chado_record = $record; $entity->chado_record_id = $chado_entity->record_id; } } } } } /** * * Implements hook_entity_insert(). */ function tripal_chado_entity_insert($entity, $type) { } /** * * Implements hook_entity_update(). */ function tripal_chado_entity_update($entity, $type) { } /** * * Implements hook_entity_delete(). */ function tripal_chado_entity_delete($entity, $type) { if ($type !== 'TripalEntity') { return; } // Delete the removed entity from the corresponding chado_bio_data_x table $bundle = $entity->bundle; db_delete("chado_{$bundle}")->condition('entity_id', $entity->id)->execute(); } /** * Implements hook_tripal_default_title_format(). * * Overrides the default titles. */ function tripal_chado_tripal_default_title_format($bundle, $available_tokens) { $format = []; $table = $bundle->data_table; if ($table == 'organism') { if (chado_get_version() <= '1.2') { $format[] = [ 'format' => '[taxrank__genus] [taxrank__species]', 'weight' => -5, ]; } else { $format[] = [ 'format' => '[taxrank__genus] [taxrank__species] [taxrank__infraspecific_taxon,TAXRANK:0000045]', 'weight' => -5, ]; } } if ($table == 'arraydesign') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'assay') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'biomaterial') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'analysis') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'feature') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'featuremap') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'stock') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'pub') { $format[] = [ 'format' => '[tpub__title]', 'weight' => -5, ]; } if ($table == 'cvterm') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'project') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'contact') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'phylotree') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'library') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } if ($table == 'protocol') { $format[] = [ 'format' => '[schema__name]', 'weight' => -5, ]; } return $format; } /** * Implements hook_entity_view(). */ function tripal_chado_entity_view($entity, $type, $view_mode, $langcode) { // If this entity is a TripalEntity and is a full view, then // we want to support the legacy view, but only if the legacy // module is enabled (the functions exist). if ($type == 'TripalEntity') { // Use the generic template to render the fields if ($view_mode == 'full') { // Get the Chado table for this data type. $bundle = tripal_load_bundle_entity(['name' => $entity->bundle]); $chado_table = $bundle->data_table; $chado_field = $bundle->type_column; // Get the list of templates that should be used for entities and generatte // the key in the array for this entity type (using the chado table the // entity maps to). $enabled_templates = variable_get('tripal_chado_enabled_legacy_templates', []); $legacy_template = 'legacy_template--chado_' . $chado_table; // If the site admin has indicated that this entity type should use // a legacy tmplate then prepare the entity and content to fake a // node. if (key_exists($legacy_template, $enabled_templates) && $enabled_templates[$legacy_template]) { // Remove the fields added by the chado_field_storage. $fields = field_info_fields(); foreach ($fields as $field) { if ($field['storage']['type'] == 'field_chado_storage' or $field['storage']['type'] == 'tripal_no_storage') { $field_name = $field['field_name']; if (property_exists($entity, $field_name)) { $entity->$field_name = NULL; unset($entity->content[$field_name]); } } } // Make the entity look like a node. $entity->type = 'chado_' . $chado_table; $entity->$chado_table = $entity->chado_record; // Add any node specific fields to the entity to fake the node. $node_schema = drupal_get_schema('node'); foreach ($node_schema['fields'] as $field_name => $details) { if (!property_exists($entity, $field_name)) { $entity->$field_name = ''; if (array_key_exists('default', $details)) { $entity->$field_name = $details['default']; } } } // Now call the module's node_view hook to add additional // content to our 'fake' entity node. $modules = module_list(); foreach ($modules as $mname => $details) { $function_name = $mname . '_node_view'; if (function_exists($function_name)) { $function_name($entity, $view_mode, $langcode); } } } } } } /** * Implements hook_entity_view_alter(). * * This function is used to support legacy Tripal v2 templates * for use with Tripal v3 entities. */ function tripal_chado_entity_view_alter(&$build) { // For the legacy support, we need to make sure the TOC // is built. if ($build['#entity_type'] == 'TripalEntity') { $enabled_templates = variable_get('tripal_chado_enabled_legacy_templates', []); $entity = $build['#entity']; $legacy_template = 'legacy_template--' . $entity->type; if (key_exists($legacy_template, $enabled_templates) && $enabled_templates[$legacy_template]) { $build['#entity']->nid = NULL; $build['#node'] = $build['#entity']; $modules = module_list(); foreach ($modules as $mname => $details) { $function_name = $mname . '_node_view_alter'; if (function_exists($function_name)) { $function_name($build); } } } } }