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@@ -14,34 +14,314 @@ class so__transcript_formatter extends ChadoFieldFormatter {
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*/
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public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
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- // Get the settings
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- $settings = $display['settings'];
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+ $mRNA_fieldset = [];
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- $headers = ['Transcript Name', 'Identifier', 'Type', 'Location'];
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- $rows = [];
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+ // If there are no items return an empty element.
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+ if (count($items) == 0) {
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+ return $this->returnEmpty($element);
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+ }
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+
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+ // Get the list of fields that are t o be shown
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+ $fields_to_show = [];
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+ if (array_key_exists('transcript_fields', $this->instance['settings'])) {
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+ $fields_to_show = $this->fieldsToShow($this->instance['settings']['transcript_fields']);
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+ }
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+
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+ // For backwards compatibility if the 'transcript_fields' setting
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+ // is not available then return the default table.
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+ if (count($fields_to_show) == 0) {
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+ return $this->returnDefaultTable($element, $items);
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+ }
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+
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+ // If any of the transcripts are not published then just provide the
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+ // default view
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foreach ($items as $delta => $item) {
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+ // Skip empty items;
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if (!$item['value']) {
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continue;
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}
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- $transcript = $item['value'];
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- // Get the field values
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- $feature_name = $transcript['schema:name'];
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- $feature_uname = $transcript['data:0842'];
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- $loc = $transcript['SO:0000735'];
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- $type = $transcript['rdfs:type'];
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+ // If any transcript is not published (i.e. it doesn't have an entity)
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+ // then we want to just return the default table and stop.
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+ if (!array_key_exists('entity', $item['value'])) {
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+ return $this->returnDefaultTable($element, $items);
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+ }
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+ }
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+
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+ // Iterate through the list of fields so that we can load the mRNA
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+ // entity with all of the field requested by the site admin. If we
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+ // don't do this first then auto_attach fields won't be added.
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+ $field_ids = [];
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+ foreach ($fields_to_show as $field_name) {
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+ $field_info = field_info_field($field_name);
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+ $field_ids[] = $field_info['id'];
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+ }
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+
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+ // For backwards compatibility if no field IDs were provided then
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+ // return the original table of four rows.
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+ if (count($field_ids) == 0) {
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+ return $this->returnDefaultTable($element, $items);
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+ }
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+
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+ #return $this->returnFieldsets($items, $element, $field_ids, $fields_to_show);
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+ return $this->returnDropDown($items, $element, $field_ids, $fields_to_show);
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+
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+ }
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+
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+ /**
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+ * Returns a list of fields names that the site admin wants to show.
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+ */
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+ private function fieldsToShow($transcript_fields) {
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+ $to_show = [];
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+ foreach($transcript_fields as $field_name => $details) {
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+ if ($details['show'] == 1) {
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+ $to_show[] = $field_name;
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+ }
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+ }
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+ return $to_show;
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+ }
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+
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+ /**
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+ *
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+ */
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+ private function returnDropDown($items, &$element, $field_ids, $fields_to_show) {
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+
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+ drupal_add_js(drupal_get_path ('module', 'tripal_chado') . '/theme/js/so__transcript.js');
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+
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+ // Iterate through each mRNA (transcript).
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+ $options = [0 => '--Select a transcript to view--'];
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+ $transcripts = [];
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+ foreach ($items as $delta => $item) {
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+
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+ // Skip empty items;
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+ if (!$item['value']) {
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+ continue;
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+ }
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+
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+ list($entity_type, $mRNA_entity_id) = explode(':', $item['value']['entity']);
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+ $result = tripal_load_entity('TripalEntity', [$mRNA_entity_id], FALSE, $field_ids);
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+ reset($result);
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+ $mRNA_entity = $result[$mRNA_entity_id];
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+ $options[$mRNA_entity_id] = $mRNA_entity->title;
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+
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+ // Create the fieldset for this transcript.
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+ $transcripts[$mRNA_entity_id] = [
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+ '#type' => 'markup',
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+ '#prefix' => '<div id="' . 'tripal-chado-so__transcript-' . $mRNA_entity_id . '" class="tripal-chado-so__transcript-box">',
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+ '#suffix' => '</div>',
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+ ];
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+
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+ // Add a link to the mRNA page.
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+ $feature_name = $mRNA_entity->title;
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+ $feature_name = l($feature_name, "bio_data/" . $mRNA_entity->id, ['attributes' => ['target' => "_blank"]]);
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+ $transcripts[$mRNA_entity_id]['mRNA_link'] = [
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+ '#type' => 'markup',
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+ '#markup' => "<i>Click, " . $feature_name . ", for the full transcript page.</i>",
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+ '#weight' => -102
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+ ];
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+
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+ // Now add all fields to the fieldset.
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+ $this->addFields($mRNA_entity, $fields_to_show, $transcripts[$mRNA_entity_id]);
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+
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+ }
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+ $transcripts['transcript_dropdown'] = [
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+ '#type' => 'select',
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+ '#title' => 'Transcripts for this gene',
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+ '#options' => $options,
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+ '#weight' => -100,
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+ '#description' => 'Select a transcript to view more details.',
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+ '#attributes' => ['class' => ['tripal-chado-so__transcript-select']]
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+ ];
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+ $element[0] = $transcripts;
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+ }
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+
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+ /**
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+ *
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+ */
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+ private function returnFieldsets($items, &$element, $field_ids, $fields_to_show) {
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+
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+ // Iterate through each mRNA (transcript).
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+ $transcripts = [];
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+ foreach ($items as $delta => $item) {
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+
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+ // Skip empty items;
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+ if (!$item['value']) {
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+ continue;
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+ }
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+
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+ list($entity_type, $mRNA_entity_id) = explode(':', $item['value']['entity']);
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+
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+ // Now load the mRNA entity with all of the fields.
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+ $result = tripal_load_entity('TripalEntity', [$mRNA_entity_id], FALSE, $field_ids);
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+ reset($result);
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+ $mRNA_entity = $result[$mRNA_entity_id];
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+
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+ // Create the fieldset for this transcript.
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+ $transcripts[$mRNA_entity_id] = [
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+ '#type' => 'fieldset',
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+ '#title' => $mRNA_entity->title,
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+ '#description' => '',
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+ '#collapsible' => TRUE,
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+ '#collapsed' => TRUE,
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+ '#attributes' => ['class' => ['collapsible', 'collapsed']],
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+ ];
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+ drupal_add_library('system', 'drupal.collapse');
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+
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+
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+ // Add a link to the mRNA page.
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+ $feature_name = $mRNA_entity->title;
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+ $feature_name = l($feature_name, "bio_data/" . $mRNA_entity->id, ['attributes' => ['target' => "_blank"]]);
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+ $transcripts[$mRNA_entity_id]['mRNA_link'] = [
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+ '#type' => 'markup',
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+ '#markup' => "<i>Click, " . $feature_name . ", for the full transcript page.</i>",
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+ ];
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+
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+ // Now add all fields to the fieldset.
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+ $this->addFields($mRNA_entity, $fields_to_show, $transcripts[$mRNA_entity_id]);
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+
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+ }
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+ $element[0] = $transcripts;
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+ }
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+
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+ /**
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+ * Builds a fieldset for the entity.
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+ */
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+ private function addFields($mRNA_entity, $fields, &$fieldset) {
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+
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+ // Get some settings about the transcript content type.
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+ $mRNA_bundle = tripal_load_bundle_entity(['name'=> $mRNA_entity->bundle]);
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+ $hide_empty = tripal_get_bundle_variable('hide_empty_field', $mRNA_bundle->id);
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+
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+ // Get the Entity ID for the transcript.
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+ $entity_id = $mRNA_entity->id;
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+
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+ // We will use a summary table to house the fields that have a
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+ // cardinality of one. These will appear at the top of the fieldset.
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+ $summary_rows = [];
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+
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+ // Iterate through the list of fields that the site admin has indicated
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+ // that they want to show in the transcript fieldset. They are provided
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+ // in order that they should be shown.
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+ foreach ($fields as $field_name) {
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+
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+ // Load the field instance info. We'll need this to determine the
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+ // cardinality of the field and to render it for display.
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+ $field_info = field_info_field($field_name);
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+ $field_instance = field_info_instance('TripalEntity', $field_name, $mRNA_entity->bundle);
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+
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+ // For the display we want to honor the site admin's wishes and not
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+ // show fields that are empty if they have that setting turned on.
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+ $field_items = field_get_items('TripalEntity', $mRNA_entity, $field_name);
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+ $field_is_empty = tripal_field_is_empty($field_info, $field_items);
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+ if ($field_is_empty and $hide_empty) {
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+ continue;
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+ }
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+
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+ // If the default display is to hide this field then skip it too.
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+ if ($field_instance['display']['default']['type'] == 'hidden') {
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+ continue;
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+ }
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+
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+ // Get the render array for this field.
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+ $field_element = field_view_field('TripalEntity', $mRNA_entity, $field_name, $field_instance['display']['default']);
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+ $field_element['#label_display'] = 'hidden';
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+
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+ // We need to know the cardinality of this field. If it has a
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+ // cardinatliy of 1 we'll put it in the summary table for the
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+ // transcript that appears at the top of the fieldset. If not we'll
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+ // let it render as is, in the order it's provided to us here.
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+ $cardinality = array_key_exists('cardinality', $field_info) ? $field_info['cardinality'] : 1;
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+ if ($cardinality == 1) {
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- // Add a link if there is an entity.
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+ // add field to a special transcripts table, where fields have cardinality of 1
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+ $summary_rows[] = [
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+ [
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+ 'data' => $field_instance['label'],
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+ 'header' => TRUE,
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+ ],
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+ [
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+ 'data' => drupal_render($field_element),
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+ ]
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+ ];
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+ }
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+ // Else add the field as is.
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+ else {
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+ $fieldset[$field_name . '_header'] = [
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+ '#type' => 'markup',
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+ '#markup' => '<h3 class="tripal-chado-gene-transcript-fieldset-item">' . $field_instance['label'] . '</h3>',
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+ ];
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+ $fieldset[$field_name] = [
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+ '#type' => 'markup',
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+ '#markup' => drupal_render($field_element),
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+ ];
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+ }
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+ } // End looping over fields.
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+
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+ // If the summary table has values then
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+ if (count($summary_rows) > 0) {
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+ // display fields of single cardinality in a special transcripts table
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+ $summary_table = [
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+ 'header' => [],
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+ 'rows' => $summary_rows,
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+ 'attributes' => [
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+ 'id' => 'tripal_feature-table-transcript-fields-object',
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+ 'class' => 'tripal-data-table',
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+ ],
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+ 'sticky' => FALSE,
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+ 'caption' => "",
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+ 'colgroups' => [],
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+ 'empty' => 'This feature has no single cardinality transcript fields',
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+ ];
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+
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+ $fieldset['summary_header'] = [
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+ '#type' => 'markup',
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+ '#markup' => '<h3>Transcript ' . $mRNA_entity->title . '</h3>',
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+ '#weight' => -101,
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+ ];
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+ $fieldset['summary_table'] = [
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+ '#type' => 'markup',
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+ '#markup' => theme_table($summary_table),
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+ '#weight' => -100,
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+ ];
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+ }
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+ }
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+
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+ /**
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+ * Returns the default table.
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+ *
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+ * For backwards compatibility this function returns a table
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+ * of four columns and one row per transcript.
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+ */
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+ private function returnDefaultTable(&$element, $items) {
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+
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+ $default_headers = ['Transcript Name', 'Identifier', 'Type', 'Location'];
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+ $default_rows = [];
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+
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+ foreach ($items as $delta => $item) {
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+
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+ if (!$item['value']) {
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+ continue;
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+ }
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+
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+ // Get the field values.
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+ $feature_name = $item['value']['schema:name'];
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+ $feature_uname = $item['value']['data:0842'];
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+ $loc = $item['value']['SO:0000735'];
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+ $type = $item['value']['rdfs:type'];
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if (array_key_exists('entity', $item['value']) and $item['value']['entity']) {
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list($entity_type, $entity_id) = explode(':', $item['value']['entity']);
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$feature_name = l($feature_name, "bio_data/" . $entity_id, ['attributes' => ['target' => "_blank"]]);
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}
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- $rows[] = [$feature_name, $feature_uname, $type, $loc];
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+
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+
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+ $default_rows[] = [$feature_name, $feature_uname, $type, $loc];
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}
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- $table = [
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- 'header' => $headers,
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- 'rows' => $rows,
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+
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+ // Build the default table
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+ $default_table = [
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+ 'header' => $default_headers,
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+ 'rows' => $default_rows,
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'attributes' => [
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'id' => 'tripal_feature-table-transcripts-object',
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'class' => 'tripal-data-table',
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@@ -51,15 +331,21 @@ class so__transcript_formatter extends ChadoFieldFormatter {
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'colgroups' => [],
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'empty' => 'This feature has no transcripts',
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];
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- $content = theme_table($table);
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- // once we have our table array structure defined, we call Drupal's theme_table()
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- // function to generate the table.
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- if (count($items) > 0) {
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- $element[0] = [
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- '#type' => 'markup',
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- '#markup' => $content,
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- ];
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- }
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+ $element[0] = [
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+ '#type' => 'markup',
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+ '#markup' => theme_table($default_table),
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+ ];
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+ }
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+
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+ /**
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+ * Returns an empty element for the view.
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+ */
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+ private function returnEmpty(&$element){
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+ $element[0] = [
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+ '#type' => 'markup',
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+ '#markup' => '',
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+ ];
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}
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}
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+
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Stephen Ficklin
