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- <?php
- class schema__publication extends ChadoField {
- // --------------------------------------------------------------------------
- // EDITABLE STATIC CONSTANTS
- //
- // The following constants SHOULD be set for each descendent class. They are
- // used by the static functions to provide information to Drupal about
- // the field and it's default widget and formatter.
- // --------------------------------------------------------------------------
- // The default lable for this field.
- public static $default_label = 'Publication';
- // The default description for this field.
- public static $description = 'Associates a publication (e.g. journal article,
- conference proceedings, book chapter, etc.) with this record.';
- // Provide a list of instance specific settings. These can be access within
- // the instanceSettingsForm. When the instanceSettingsForm is submitted
- // then Drupal with automatically change these settings for the instnace.
- // It is recommended to put settings at the instance level whenever possible.
- // If you override this variable in a child class be sure to replicate the
- // term_name, term_vocab, term_accession and term_fixed keys as these are
- // required for all TripalFields.
- public static $default_instance_settings = [
- // The short name for the vocabulary (e.g. shcema, SO, GO, PATO, etc.).
- 'term_vocabulary' => 'schema',
- // The name of the term.
- 'term_name' => 'publication',
- // The unique ID (i.e. accession) of the term.
- 'term_accession' => 'publication',
- // Set to TRUE if the site admin is allowed to change the term
- // type. This will create form elements when editing the field instance
- // to allow the site admin to change the term settings above.
- 'term_fixed' => FALSE,
- ];
- // The default widget for this field.
- public static $default_widget = 'schema__publication_widget';
- // The default formatter for this field.
- public static $default_formatter = 'schema__publication_formatter';
- // --------------------------------------------------------------------------
- // PROTECTED CLASS MEMBERS -- DO NOT OVERRIDE
- // --------------------------------------------------------------------------
- // An array containing details about the field. The format of this array
- // is the same as that returned by field_info_fields()
- protected $field;
- // An array containing details about an instance of the field. A field does
- // not have to have an instance. But if dealing with an instance (such as
- // when using the widgetForm, formatterSettingsForm, etc.) it should be set.
- protected $instance;
- /**
- * @see TripalField::elementInfo()
- */
- public function elementInfo() {
- $field_term = $this->getFieldTermID();
- return [
- $field_term => [
- 'operations' => [],
- 'sortable' => FALSE,
- 'searchable' => FALSE,
- 'type' => 'xs:string',
- 'readonly' => TRUE,
- ],
- ];
- }
- /**
- *
- * @see TripalField::load()
- */
- public function load($entity) {
- $record = $entity->chado_record;
- $field_name = $this->field['field_name'];
- $field_type = $this->field['type'];
- $field_table = $this->instance['settings']['chado_table'];
- $field_column = $this->instance['settings']['chado_column'];
- $base_table = $this->instance['settings']['base_table'];
- // These fields are used when the publications come through a linker table.
- $pkey = '';
- $fkey_lcolumn = '';
- $fkey_rcolumn = '';
- $linker_table = '';
- // If we don't have a chado record return before creating a stub for this field!
- if (!$record) {
- return;
- }
- // If the field table and the base table are not the same thing then
- // we are going through a linker table.
- if ($field_table != $base_table) {
- // Get the FK that links to the base record.
- $schema = chado_get_schema($field_table);
- $pkey = $schema['primary key'][0];
- $fkey_lcolumn = key($schema['foreign keys'][$base_table]['columns']);
- $fkey_rcolumn = $schema['foreign keys'][$base_table]['columns'][$fkey_lcolumn];
- $linker_table = $base_table . '_pub';
- // Set some defaults for the empty record.
- $entity->{$field_name}['und'][0] = [
- 'value' => [],
- 'chado-' . $field_table . '__' . $pkey => '',
- 'chado-' . $field_table . '__' . $fkey_lcolumn => '',
- 'chado-' . $field_table . '__' . 'pub_id' => '',
- ];
- }
- // Otherwise, the base table has a pub_id field.
- else {
- $entity->{$field_name}['und'][0] = [
- 'value' => [],
- 'chado-' . $field_table . '__' . $field_column => '',
- ];
- }
- // Get the list of publications
- $pubs = [];
- if ($linker_table) {
- $options = [
- 'return_array' => 1,
- ];
- $record = chado_expand_var($record, 'table', $linker_table, $options);
- if (property_exists($record, $linker_table) and is_array($record->$linker_table) and count($record->$linker_table) > 0) {
- $i = 0;
- foreach ($record->$linker_table as $index => $linker) {
- $pub = $linker->pub_id;
- $pubs[$pub->pub_id] = $pub;
- }
- }
- }
- else {
- $pub = $record->{$field_column};
- if ($pub) {
- $pubs[$pub->pub_id] = $pub;
- }
- }
- $i = 0;
- foreach ($pubs as $pub_id => $pub) {
- $pub_details = chado_get_minimal_pub_info($pub);
- $entity->{$field_name}['und'][$i]['value'] = $pub_details;
- if ($linker_table) {
- $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $pkey] = $linker->$pkey;
- $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $fkey_lcolumn] = $linker->$fkey_lcolumn->$fkey_lcolumn;
- $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . 'pub_id'] = $pub_id;
- }
- else {
- $entity->{$field_name}['und'][$i]['chado-' . $field_table . '__' . $field_column] = $pub_id;
- }
- if (property_exists($pub, 'entity_id')) {
- $entity->{$field_name}['und'][$i]['value']['entity'] = 'TripalEntity:' . $pub->entity_id;
- }
- $i++;
- }
- }
- }
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