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+<?php
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+
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+class sbo__relationship_table_formatter extends ChadoFieldFormatter {
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+
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+ // The default lable for this field.
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+ public static $default_label = 'Relationship Table by Type';
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+
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+ // The list of field types for which this formatter is appropriate.
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+ public static $field_types = array('sbo__relationship');
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+
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+ public static $default_settings = array(
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+ 'subject_caption' => 'This @content_type is <em>@rel_type</em> the following:',
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+ 'object_caption' => 'The following are <em>@rel_type</em> this @content_type:',
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+ );
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+
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+ /**
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+ *
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+ * @see TripalFieldFormatter::settingsForm()
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+ */
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+ public function settingsForm($view_mode, $form, &$form_state) {
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+
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+ $display = $this->instance['display'][$view_mode];
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+ $settings = $display['settings'];
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+
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+ // Ensure the default are set if the value is not configured.
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+ foreach ($this::$default_settings as $key => $value) {
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+ if (!isset($settings[$key])) { $settings[$key] = $value; }
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+ }
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+
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+ $element = array();
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+ $element['subject_caption'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Caption: where current entity is the subject.',
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+ '#description' => 'This labels the relationship tables where the current entity is the subject of the relationship.',
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+ '#default_value' => $settings['subject_caption'],
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+ );
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+
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+ $element['object_caption'] = array(
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+ '#type' => 'textfield',
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+ '#title' => 'Caption: where current entity is the object.',
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+ '#description' => 'This labels the relationship tables where the current entity is the object of the relationship.',
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+ '#default_value' => $settings['object_caption'],
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+ );
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+
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+ $element['tokens'] = array(
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+ '#type' => 'item',
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+ '#title' => 'Tokens',
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+ '#markup' => 'The following tokens should be used in <strong>both the above captions</strong>:</p>
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+ <ul>
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+ <li>@rel_type: the type name of the current relationship.</li>
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+ <li>@content_type: the human-readable name of the content type for the current entity.</li>
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+ </ul>',
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+ );
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+
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+ return $element;
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+ }
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+
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+ /**
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+ * @see TripalFieldFormatter::settingsSummary()
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+ */
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+ public function settingsSummary($view_mode) {
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+ $display = $this->instance['display'][$view_mode];
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+ $settings = $display['settings'];
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+
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+ // Ensure the default are set if the value is not configured.
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+ foreach ($this::$default_settings as $key => $value) {
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+ if (!isset($settings[$key])) { $settings[$key] = $value; }
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+ }
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+
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+ $summary = t('<strong>Subject Caption:</strong> @subject<br><strong>Object Caption:</strong> @object',
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+ array(
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+ '@subject' => $settings['subject_caption'],
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+ '@object' => $settings['object_caption'])
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+ );
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+
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+ return $summary;
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+ }
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+
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+ /**
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+ *
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+ * @see TripalFieldFormatter::view()
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+ */
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+ public function view(&$element, $entity_type, $entity, $langcode, $items, $display) {
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+
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+ // Get the settings and set defaults.
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+ $settings = $display['settings'];
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+ foreach ($this::$default_settings as $key => $value) {
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+ if (!isset($settings[$key])) { $settings[$key] = $value; }
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+ }
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+
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+ // Headers depending on which fields are available.
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+ $headers = array(
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+ 'all' => array('Name', 'Unique Name', 'Species', 'Type'),
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+ 'nst' => array('Name', 'Species', 'Type'),
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+ 'nut' => array('Name', 'Unique Name', 'Type'),
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+ 'nt' => array('Name', 'Type'),
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+ );
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+
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+ // This is an array of tables where each table corresponds to a relationship type.
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+ // The header is the same for all tables and the caption includes a sentence
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+ // stating the relationship type.
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+ $tables = array();
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+
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+ // For each relationship...
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+ foreach ($items as $delta => $item) {
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+ if (empty($item['value'])) {
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+ continue;
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+ }
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+
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+ $subject_name = $item['value']['local:relationship_subject']['schema:name'];
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+ $subject_uniquename = (isset($item['value']['local:relationship_subject']['data:0842'])) ? $item['value']['local:relationship_subject']['data:0842'] : NULL;
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+ $subject_type = $item['value']['local:relationship_subject']['rdfs:type'];
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+ $subject_species = (isset($item['value']['local:relationship_subject']['OBI:0100026'])) ? $item['value']['local:relationship_subject']['OBI:0100026'] : NULL;
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+
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+ $object_name = $item['value']['local:relationship_object']['schema:name'];
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+ $object_uniquename = (isset($item['value']['local:relationship_object']['data:0842'])) ? $item['value']['local:relationship_object']['data:0842'] : NULL;
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+ $object_type = $item['value']['local:relationship_object']['rdfs:type'];
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+ $object_species = (isset($item['value']['local:relationship_object']['OBI:0100026'])) ? $item['value']['local:relationship_object']['OBI:0100026'] : NULL;
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+
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+ $relationship_type = $item['value']['local:relationship_type'];
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+
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+ // Make types more readable.
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+ foreach(array('subject_type', 'object_type', 'relationship_type') as $var) {
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+ $$var = ucwords(str_replace('_',' ', $$var));
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+ }
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+
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+ // Handle some special cases.
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+ // For mRNA objects we don't want to show the CDS, exons, 5' UTR, etc.
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+ // we want to show the parent gene and the protein.
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+ if ($object_type == 'mRNA' and
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+ (in_array($subject_type, array('CDS', 'exon', 'five_prime_UTR', 'three_prime_UTR')))) {
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+ continue;
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+ }
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+
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+ // Set header type based on what values are available.
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+ if (!isset($tables[$relationship_type])) {
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+ $tables[$relationship_type]['header_type'] = 'all';
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+ if ($subject_uniquename === NULL AND $subject_species === NULL) {
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+ $tables[$relationship_type]['header_type'] = 'nt';
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+ }
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+ elseif ($subject_uniquename === NULL) {
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+ $tables[$relationship_type]['header_type'] = 'nst';
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+ }
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+ elseif ($subject_species === NULL) {
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+ $tables[$relationship_type]['header_type'] = 'nut';
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+ }
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+ }
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+
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+ // Convert the object/subject to a link if an entity exists for it.
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+ if (array_key_exists('entity', $item['value']['local:relationship_object'])) {
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+ list($entity_type, $object_entity_id) = explode(':', $item['value']['local:relationship_object']['entity']);
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+ if ($object_entity_id != $entity->id) {
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+ $object_name = l($object_name, 'bio_data/' . $object_entity_id);
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+ if ($object_uniquename) { $object_uniquename = l($object_uniquename, 'bio_data/' . $object_entity_id); }
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+ }
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+ }
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+ if (array_key_exists('entity', $item['value']['local:relationship_subject'])) {
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+ list($entity_type, $subject_entity_id) = explode(':', $item['value']['local:relationship_subject']['entity']);
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+ if ($subject_entity_id != $entity->id) {
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+ $subject_name = l($subject_name, 'bio_data/' . $subject_entity_id);
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+ if ($subject_uniquename) { $subject_uniquename = l($subject_uniquename, 'bio_data/' . $subject_entity_id); }
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+ }
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+ }
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+
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+ // Determine if the subject or object is the current entity.
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+ $is_subject = TRUE;
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+ if ($object_name == $entity->schema__name['und'][0]['value']) {
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+ $is_subject = FALSE;
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+ }
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+
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+
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+ // Add the related entity to the tables array by type of relationship.
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+ if ($is_subject) {
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+ $tables[$relationship_type]['caption'] = t($settings['subject_caption'],
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+ array('@rel_type' => $relationship_type, '@content_type' => $entity->rdfs__type['und'][0]['value']));
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+
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+ $row = array();
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+ $row['name'] = $object_name;
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+ if ($object_uniquename) { $row['uniquename'] = $object_uniquename; }
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+ if ($object_species) { $row['species'] = $object_species; }
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+ $row['type'] = $object_type;
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+
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+ $tables[$relationship_type]['rows'][] = $row;
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+ }
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+ else {
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+ $tables[$relationship_type]['caption'] = t($settings['object_caption'],
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+ array('@rel_type' => $relationship_type, '@content_type' => $entity->rdfs__type['und'][0]['value']));
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+
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+ $row = array();
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+ $row['name'] = $subject_name;
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+ if ($subject_uniquename) { $row['uniquename'] = $subject_uniquename; }
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+ if ($subject_species) { $row['species'] = $subject_species; }
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+ $row['type'] = $subject_type;
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+
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+ $tables[$relationship_type]['rows'][] = $row;
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+ }
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+ }
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+
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+ $element[0] = array(
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+ '#type' => 'markup',
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+ '#tree' => TRUE,
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+ );
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+
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+ foreach ($tables as $relationship_type => $details) {
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+
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+ $table_id = 'sbo__relationship-'.$item['value']['local:relationship_subject']['rdfs:type']; //$this->getPagerElementID();
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+ $element[0][$relationship_type] = array(
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+ '#type' => 'markup',
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+ '#theme' => 'table',
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+ '#header' => $headers[ $details['header_type'] ],
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+ '#rows' => $details['rows'],
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+ '#caption' => $details['caption'],
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+ '#sticky' => FALSE,
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+ '#attributes' => array(
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+ 'class' => 'tripal-data-table',
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+ 'id' => $table_id,
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+ ),
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+ );
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+ }
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+ }
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+}
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+
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+
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chunhuaicheng