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@@ -1,315 +1,354 @@
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<?php
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-/**
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- * Implements hook_info() for fields.
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- *
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- * This is a hook provided by the tripal_chado module for offloading the
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- * hook_field_info() hook for each field to specify.
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- */
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-function chado_linker__dbxref_info() {
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- return array(
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- 'label' => t('Cross references'),
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- 'description' => t('This record can be cross referenced with a record in
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- another online database. This field is intended for one or more
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- references. At a minimum, the database and accession must be provided.'),
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- 'default_widget' => 'chado_linker__dbxref_widget',
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- 'default_formatter' => 'chado_linker__dbxref_formatter',
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- 'settings' => array(),
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- 'storage' => array(
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- 'type' => 'field_chado_storage',
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- 'module' => 'tripal_chado',
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- 'active' => TRUE
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- ),
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- );
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-}
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-/**
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- * Implements hook_attach_info().
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- *
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- * This is a hook provided by the tripal_Chado module. It allows the field
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- * to specify which bundles it will attach to and to specify thee settings.
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- *
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- * @param $entity_type
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- * @param $entity
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- * @param $term
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- *
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- * @return
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- * A field array
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- */
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-function chado_linker__dbxref_attach_info($entity_type, $bundle, $target) {
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- $field_info = array();
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- $table_name = $target['data_table'];
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- $type_table = $target['type_table'];
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- $type_field = $target['field'];
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- $cv_id = $target['cv_id'];
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- $cvterm_id = $target['cvterm_id'];
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+class chado_linker_dbxref extends TripalField {
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+ /**
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+ * Implements hook_info() for fields.
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+ *
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+ * This is a hook provided by the tripal_chado module for offloading the
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+ * hook_field_info() hook for each field to specify.
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+ */
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+ function field_info() {
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+ return array(
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+ 'label' => t('Cross references'),
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+ 'description' => t('This record can be cross referenced with a record in
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+ another online database. This field is intended for one or more
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+ references. At a minimum, the database and accession must be provided.'),
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+ 'default_widget' => 'chado_linker__dbxref_widget',
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+ 'default_formatter' => 'chado_linker__dbxref_formatter',
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+ 'settings' => array(),
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+ 'storage' => array(
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+ 'type' => 'field_chado_storage',
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+ 'module' => 'tripal_chado',
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+ 'active' => TRUE
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+ ),
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+ );
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+ }
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+ /**
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+ * @see TripalField::attach_info()
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+ */
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+ function attach_info($entity_type, $bundle, $target) {
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+ $field_info = array();
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+
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+ $table_name = $target['data_table'];
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+ $type_table = $target['type_table'];
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+ $type_field = $target['field'];
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+ $cv_id = $target['cv_id'];
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+ $cvterm_id = $target['cvterm_id'];
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+
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+
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+ // If the linker table does not exists then we don't want to add attach.
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+ $dbxref_table = $table_name . '_dbxref';
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+ if (!chado_table_exists($dbxref_table)) {
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+ return $field_info;
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+ }
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+
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+ // We already have a dbxref_id field.
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+ $schema = chado_get_schema($dbxref_table);
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+ $pkey = $schema['primary key'][0];
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+
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+ // Initialize the field array.
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+ $field_info = array(
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+ 'field_name' => $dbxref_table,
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+ 'field_type' => 'chado_linker__dbxref',
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+ 'widget_type' => 'chado_linker__dbxref_widget',
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+ 'widget_settings' => array('display_label' => 1),
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+ 'description' => '',
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+ 'label' => 'Cross References',
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+ 'is_required' => 0,
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+ 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
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+ 'storage' => 'field_chado_storage',
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+ 'field_settings' => array(
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+ 'chado_table' => $dbxref_table,
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+ 'chado_column' => $pkey,
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+ 'base_table' => $table_name,
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+ 'semantic_web' => array(
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+ 'name' => '',
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+ 'accession' => '',
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+ 'ns' => '',
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+ 'nsurl' => '',
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+ ),
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+ ),
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+ );
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+ // If the base table has a 'dbxref_id' then change the label to
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+ // indicate these are secondary cross references.
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+ $schema = chado_get_schema($table_name);
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+ if (array_key_exists('dbxref_id', $schema['fields'])) {
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+ $field_info['label'] = 'Secondary Cross References';
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+ }
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- // If the linker table does not exists then we don't want to add attach.
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- $dbxref_table = $table_name . '_dbxref';
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- if (!chado_table_exists($dbxref_table)) {
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return $field_info;
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}
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-
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- // We already have a dbxref_id field.
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- $schema = chado_get_schema($dbxref_table);
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- $pkey = $schema['primary key'][0];
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-
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- // Initialize the field array.
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- $field_info = array(
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- 'field_name' => $dbxref_table,
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- 'field_type' => 'chado_linker__dbxref',
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- 'widget_type' => 'chado_linker__dbxref_widget',
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- 'widget_settings' => array('display_label' => 1),
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- 'description' => '',
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- 'label' => 'Cross References',
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- 'is_required' => 0,
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- 'cardinality' => FIELD_CARDINALITY_UNLIMITED,
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- 'storage' => 'field_chado_storage',
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- 'field_settings' => array(
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- 'chado_table' => $dbxref_table,
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- 'chado_column' => $pkey,
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- 'base_table' => $table_name,
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- 'semantic_web' => array(
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- 'name' => '',
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- 'accession' => '',
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- 'ns' => '',
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- 'nsurl' => '',
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+ /**
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+ * @see TripalField::widget_info()
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+ */
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+ function widget_info() {
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+ return array(
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+ 'label' => t('Cross references'),
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+ 'field types' => array('chado_linker__dbxref'),
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+ 'description' => t('This record can be cross referenced with a record
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+ in another online database. This field is intended for the most
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+ prominent reference. At a minimum, the database and accession
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+ must be provided.'),
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+ );
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+ }
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+ /**
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+ * @see TripalField::formatter_info()
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+ */
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+ function formatter_info() {
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+ return array(
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+ 'label' => t('Cross references'),
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+ 'field types' => array('chado_linker__dbxref'),
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+ 'settings' => array(
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),
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- ),
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- );
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-
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- // If the base table has a 'dbxref_id' then change the label to
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- // indicate these are secondary cross references.
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- $schema = chado_get_schema($table_name);
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- if (array_key_exists('dbxref_id', $schema['fields'])) {
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- $field_info['label'] = 'Secondary Cross References';
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+ );
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+ }
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+ /**
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+ * @see TripalField::formatter_view()
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+ */
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+ function formatter_view(&$element, $entity_type, $entity, $field,
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+ $instance, $langcode, $items, $display) {
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+
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+ $chado_table = $field['settings']['chado_table'];
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+ foreach ($items as $delta => $item) {
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+ $accession = '';
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+ if ($item[$chado_table . '__dbxref_id']) {
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+ $dbxref = chado_generate_var('dbxref', array('dbxref_id' => $item[$chado_table . '__dbxref_id']));
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+ $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
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+ if ($dbxref->db_id->urlprefix) {
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+ $accession = l($accession, $dbxref->db_id->urlprefix . '/' . $dbxref->accession, array('attributes' => array('target' => '_blank')));
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+ }
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+ }
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+ $element[$delta] = array(
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+ '#type' => 'markup',
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+ '#markup' => $accession,
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+ );
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+ }
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}
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- return $field_info;
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-}
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-/**
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- * Implements hook_widget_info.
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- *
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- * This is a hook provided by the tripal_chado module for offloading
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- * the hook_field_widget_info() hook for each field to specify.
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- */
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-function chado_linker__dbxref_widget_info() {
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- return array(
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- 'label' => t('Cross references'),
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- 'field types' => array('chado_linker__dbxref'),
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- 'description' => t('This record can be cross referenced with a record
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- in another online database. This field is intended for the most
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- prominent reference. At a minimum, the database and accession
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- must be provided.'),
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- );
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-}
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-/**
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- * Implements hook_formatter_info.
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- *
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- * This is a hook provided by the tripal_chado module for
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- * offloading the hook_field_formatter_info() for each field
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- * to specify.
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- *
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- */
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-function chado_linker__dbxref_formatter_info() {
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- return array(
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- 'label' => t('Cross references'),
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- 'field types' => array('chado_linker__dbxref'),
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- 'settings' => array(
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- ),
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- );
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-}
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-/**
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- *
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- * @param unknown $entity_type
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- * @param unknown $entity
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- * @param unknown $field
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- * @param unknown $instance
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- * @param unknown $langcode
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- * @param unknown $items
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- * @param unknown $display
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- */
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-function chado_linker__dbxref_formatter(&$element, $entity_type, $entity, $field,
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- $instance, $langcode, $items, $display) {
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-
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- $chado_table = $field['settings']['chado_table'];
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- foreach ($items as $delta => $item) {
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+ /**
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+ * @see TripalField::widget_form()
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+ */
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+ function widget_form(&$widget, $form, $form_state, $field,
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+ $instance, $langcode, $items, $delta, $element) {
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+
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+ $field_name = $field['field_name'];
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+ $field_type = $field['type'];
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+ $field_table = $field['settings']['chado_table'];
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+ $field_column = $field['settings']['chado_column'];
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+
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+ // Get the FK column that links to the base table.
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+ $chado_table = $field['settings']['chado_table'];
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+ $base_table = $field['settings']['base_table'];
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+ $schema = chado_get_schema($chado_table);
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+ $pkey = $schema['primary key'][0];
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+ $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
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+ $fkey = $fkeys[0];
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+
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+ // Get the field defaults.
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+ $record_id = '';
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+ $fkey_value = '';
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+ $dbxref_id = '';
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+ $db_id = '';
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$accession = '';
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- if ($item[$chado_table . '__dbxref_id']) {
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- $dbxref = chado_generate_var('dbxref', array('dbxref_id' => $item[$chado_table . '__dbxref_id']));
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- $accession = $dbxref->db_id->name . ':' . $dbxref->accession;
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- if ($dbxref->db_id->urlprefix) {
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- $accession = l($accession, $dbxref->db_id->urlprefix . '/' . $dbxref->accession, array('attributes' => array('target' => '_blank')));
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- }
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+ $version = '';
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+ $description = '';
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+
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+ // If the field already has a value then it will come through the $items
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+ // array. This happens when editing an existing record.
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+ if (array_key_exists($delta, $items)) {
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+ $record_id = $items[$delta]['value'];
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+ $fkey_value = $items[$delta][$field_name . '__' . $fkey];
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+ $dbxref_id = $items[$delta][$field_name . '__dbxref_id'];
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+ $db_id = $items[$delta][$field_name . '--dbxref__db_id'];
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+ $accession = $items[$delta][$field_name . '--dbxref__accession'];
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+ $version = $items[$delta][$field_name . '--dbxref__version'];
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+ $description = $items[$delta][$field_name . '--dbxref__description'];
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}
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- $element[$delta] = array(
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- '#type' => 'markup',
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- '#markup' => $accession,
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+
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+ // Check $form_state['values'] to see if an AJAX call set the values.
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+ if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
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+ $record_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name);
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+ $fkey_value = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '__' . $fkey);
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+ $dbxref_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '__dbxref_id');
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+ $db_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__db_id');
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+ $accession = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__accession');
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+ $version = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__version');
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+ $description = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__description');
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+ }
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+
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+ $schema = chado_get_schema('dbxref');
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+ $options = tripal_get_db_select_options();
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+
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+ $widget['#table_name'] = $chado_table;
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+ $widget['#fkey_field'] = $fkey;
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+ $widget['#element_validate'] = array('chado_linker__dbxref_widget_validate');
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+ $widget['#theme'] = 'chado_linker__dbxref_widget';
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+ $widget['#prefix'] = "<span id='$field_name-dbxref--db-id-$delta'>";
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+ $widget['#suffix'] = "</span>";
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+
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+
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+ $form['value'] = array(
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+ '#type' => 'value',
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+ '#value' => $items[$delta]['value'],
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);
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- }
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-}
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-/**
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- *
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- * @param unknown $field_name
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- * @param unknown $widget
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- * @param unknown $form
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- * @param unknown $form_state
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- * @param unknown $field
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- * @param unknown $instance
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- * @param unknown $langcode
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- * @param unknown $items
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- * @param unknown $delta
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- * @param unknown $element
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- */
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-function chado_linker__dbxref_widget(&$widget, $form, $form_state, $field,
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- $instance, $langcode, $items, $delta, $element) {
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-
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- $field_name = $field['field_name'];
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-
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- // Get the FK column that links to the base table.
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- $chado_table = $field['settings']['chado_table'];
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- $base_table = $field['settings']['base_table'];
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- $schema = chado_get_schema($chado_table);
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- $pkey = $schema['primary key'][0];
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- $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
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- $fkey = $fkeys[0];
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-
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- // Get the field defaults.
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- $record_id = '';
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- $fkey_value = '';
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- $dbxref_id = '';
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- $db_id = '';
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- $accession = '';
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- $version = '';
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- $description = '';
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-
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- // If the field already has a value then it will come through the $items
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- // array. This happens when editing an existing record.
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- if (array_key_exists($delta, $items)) {
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- $record_id = $items[$delta]['value'];
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- $fkey_value = $items[$delta][$field_name . '__' . $fkey];
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- $dbxref_id = $items[$delta][$field_name . '__dbxref_id'];
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|
|
- $db_id = $items[$delta][$field_name . '--dbxref__db_id'];
|
|
|
- $accession = $items[$delta][$field_name . '--dbxref__accession'];
|
|
|
- $version = $items[$delta][$field_name . '--dbxref__version'];
|
|
|
- $description = $items[$delta][$field_name . '--dbxref__description'];
|
|
|
- }
|
|
|
|
|
|
- // Check $form_state['values'] to see if an AJAX call set the values.
|
|
|
- if (array_key_exists('values', $form_state) and array_key_exists($delta, $form_state['values'])) {
|
|
|
- $record_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name);
|
|
|
- $fkey_value = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '__' . $fkey);
|
|
|
- $dbxref_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '__dbxref_id');
|
|
|
- $db_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__db_id');
|
|
|
- $accession = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__accession');
|
|
|
- $version = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__version');
|
|
|
- $description = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__description');
|
|
|
+ $widget[$field_table . '__' . $pkey] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $record_id,
|
|
|
+ );
|
|
|
+ $widget[$field_table . '__dbxref_id'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $dbxref_id,
|
|
|
+ );
|
|
|
+ $widget[$field_table . '__' . $fkey] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $fkey_value,
|
|
|
+ );
|
|
|
+ $widget[$field_table . '--dbxref__dbxref_id'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $dbxref_id,
|
|
|
+ );
|
|
|
+ $widget[$field_table . '--dbxref__db_id'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Database'),
|
|
|
+ '#options' => $options,
|
|
|
+ '#required' => $element['#required'],
|
|
|
+ '#default_value' => $db_id,
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
|
|
|
+ 'wrapper' => "$field_name-dbxref--db-id-$delta",
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'method' => 'replace'
|
|
|
+ ),
|
|
|
+ );
|
|
|
+ $widget[$field_table . '--dbxref__accession'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Accession'),
|
|
|
+ '#default_value' => $accession,
|
|
|
+ '#required' => $element['#required'],
|
|
|
+ '#maxlength' => array_key_exists('length', $schema['fields']['accession']) ? $schema['fields']['accession']['length'] : 255,
|
|
|
+ '#size' => 15,
|
|
|
+ '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/dbxref/' . $db_id,
|
|
|
+ '#ajax' => array(
|
|
|
+ 'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
|
|
|
+ 'wrapper' => "$field_name-dbxref--db-id-$delta",
|
|
|
+ 'effect' => 'fade',
|
|
|
+ 'method' => 'replace'
|
|
|
+ ),
|
|
|
+ '#disabled' => $db_id ? FALSE : TRUE,
|
|
|
+ );
|
|
|
+ $widget[$field_table . '--dbxref__version'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Version'),
|
|
|
+ '#default_value' => $version,
|
|
|
+ '#maxlength' => array_key_exists('length', $schema['fields']['version']) ? $schema['fields']['version']['length'] : 255,
|
|
|
+ '#size' => 5,
|
|
|
+ '#disabled' => $db_id ? FALSE : TRUE,
|
|
|
+ );
|
|
|
+ $widget[$field_table . '--dbxref__description'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Description'),
|
|
|
+ '#default_value' => $description,
|
|
|
+ '#size' => 20,
|
|
|
+ '#disabled' => $db_id ? FALSE : TRUE,
|
|
|
+ );
|
|
|
+ if (!$db_id) {
|
|
|
+ $widget['links'] = array(
|
|
|
+ '#type' => 'item',
|
|
|
+ '#markup' => l('Add a database', 'admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank')))
|
|
|
+ );
|
|
|
+ }
|
|
|
}
|
|
|
|
|
|
- $schema = chado_get_schema('dbxref');
|
|
|
- $options = tripal_get_db_select_options();
|
|
|
-
|
|
|
- $widget['#table_name'] = $chado_table;
|
|
|
- $widget['#fkey_field'] = $fkey;
|
|
|
- $widget['#element_validate'] = array('chado_linker__dbxref_widget_validate');
|
|
|
- $widget['#theme'] = 'chado_linker__dbxref_widget';
|
|
|
- $widget['#prefix'] = "<span id='$field_name-dbxref--db-id-$delta'>";
|
|
|
- $widget['#suffix'] = "</span>";
|
|
|
-
|
|
|
- $widget['value'] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $record_id,
|
|
|
- );
|
|
|
- $widget[$field_name . '__dbxref_id'] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $dbxref_id,
|
|
|
- );
|
|
|
- $widget[$field_name . '__' . $fkey] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $fkey_value,
|
|
|
- );
|
|
|
- $widget[$field_name . '--dbxref__dbxref_id'] = array(
|
|
|
- '#type' => 'value',
|
|
|
- '#default_value' => $dbxref_id,
|
|
|
- );
|
|
|
- $widget[$field_name . '--dbxref__db_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Database'),
|
|
|
- '#options' => $options,
|
|
|
- '#required' => $element['#required'],
|
|
|
- '#default_value' => $db_id,
|
|
|
- '#ajax' => array(
|
|
|
- 'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
|
|
|
- 'wrapper' => "$field_name-dbxref--db-id-$delta",
|
|
|
- 'effect' => 'fade',
|
|
|
- 'method' => 'replace'
|
|
|
- ),
|
|
|
- );
|
|
|
- $widget[$field_name . '--dbxref__accession'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Accession'),
|
|
|
- '#default_value' => $accession,
|
|
|
- '#required' => $element['#required'],
|
|
|
- '#maxlength' => array_key_exists('length', $schema['fields']['accession']) ? $schema['fields']['accession']['length'] : 255,
|
|
|
- '#size' => 15,
|
|
|
- '#autocomplete_path' => 'admin/tripal/storage/chado/auto_name/dbxref/' . $db_id,
|
|
|
- '#ajax' => array(
|
|
|
- 'callback' => "chado_linker__dbxref_widget_form_ajax_callback",
|
|
|
- 'wrapper' => "$field_name-dbxref--db-id-$delta",
|
|
|
- 'effect' => 'fade',
|
|
|
- 'method' => 'replace'
|
|
|
- ),
|
|
|
- '#disabled' => $db_id ? FALSE : TRUE,
|
|
|
- );
|
|
|
- $widget[$field_name . '--dbxref__version'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Version'),
|
|
|
- '#default_value' => $version,
|
|
|
- '#maxlength' => array_key_exists('length', $schema['fields']['version']) ? $schema['fields']['version']['length'] : 255,
|
|
|
- '#size' => 5,
|
|
|
- '#disabled' => $db_id ? FALSE : TRUE,
|
|
|
- );
|
|
|
- $widget[$field_name . '--dbxref__description'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Description'),
|
|
|
- '#default_value' => $description,
|
|
|
- '#size' => 20,
|
|
|
- '#disabled' => $db_id ? FALSE : TRUE,
|
|
|
- );
|
|
|
- if (!$db_id) {
|
|
|
- $widget['links'] = array(
|
|
|
- '#type' => 'item',
|
|
|
- '#markup' => l('Add a database', 'admin/tripal/chado/tripal_db/add', array('attributes' => array('target' => '_blank')))
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+
|
|
|
+ /**
|
|
|
+ * @see TripalField::load()
|
|
|
+ */
|
|
|
+ function load($field, $entity, $details) {
|
|
|
+
|
|
|
+ $record = $details['record'];
|
|
|
+
|
|
|
+ $field_name = $field['field_name'];
|
|
|
+ $field_type = $field['type'];
|
|
|
+ $chado_table = $field['settings']['chado_table'];
|
|
|
+ $schema = chado_get_schema($chado_table);
|
|
|
+ $pkey = $schema['primary key'][0];
|
|
|
+ $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
|
|
|
+ $fkey = $fkeys[0];
|
|
|
+
|
|
|
+ // Set some defaults for the empty record.
|
|
|
+ $entity->{$field_name}['und'][0] = array(
|
|
|
+ 'value' => '',
|
|
|
+ $chado_table . '__' . $pkey => '',
|
|
|
+ $chado_table . '__' . $fkey => '',
|
|
|
+ $chado_table . '__' . 'dbxref_id' => '',
|
|
|
+ $chado_table . '--' . 'dbxref__dbxref_id' => '',
|
|
|
+ $chado_table . '--' . 'dbxref__db_id' => '',
|
|
|
+ $chado_table . '--' . 'dbxref__accession' => '',
|
|
|
+ $chado_table . '--' . 'dbxref__version' => '',
|
|
|
+ $chado_table . '--' . 'dbxref__description' => '',
|
|
|
);
|
|
|
+
|
|
|
+ $linker_table = $base_table . '_dbxref';
|
|
|
+ $options = array('return_array' => 1);
|
|
|
+ $record = chado_expand_var($record, 'table', $linker_table, $options);
|
|
|
+ if (count($record->$linker_table) > 0) {
|
|
|
+ $i = 0;
|
|
|
+ foreach ($record->$linker_table as $index => $linker) {
|
|
|
+ $dbxref = $linker->dbxref_id;
|
|
|
+ $entity->{$field_name}['und'][$i] = array(
|
|
|
+ 'value' => array(),
|
|
|
+ $chado_table . '__' . $pkey => $linker->$pkey,
|
|
|
+ $chado_table . '__' . $fkey => $linker->$fkey->$fkey,
|
|
|
+ $chado_table . '__' . 'dbxref_id' => $dbxref->dbxref_id,
|
|
|
+ $chado_table . '--' . 'dbxref__dbxref_id' => $dbxref->dbxref_id,
|
|
|
+ $chado_table . '--' . 'dbxref__db_id' => $dbxref->db_id->db_id,
|
|
|
+ $chado_table . '--' . 'dbxref__accession' => $dbxref->accession,
|
|
|
+ $chado_table . '--' . 'dbxref__version' => $dbxref->version,
|
|
|
+ $chado_table . '--' . 'dbxref__description' => $dbxref->description,
|
|
|
+ );
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+ }
|
|
|
}
|
|
|
}
|
|
|
/**
|
|
|
- * An Ajax callback for the dbxref widget.
|
|
|
+ * Theme function for the dbxref_id_widget.
|
|
|
+ *
|
|
|
+ * @param $variables
|
|
|
*/
|
|
|
-function chado_linker__dbxref_widget_form_ajax_callback($form, $form_state) {
|
|
|
+function theme_chado_linker__dbxref_widget($variables) {
|
|
|
+ $element = $variables['element'];
|
|
|
|
|
|
- $field_name = $form_state['triggering_element']['#parents'][0];
|
|
|
- $delta = $form_state['triggering_element']['#parents'][2];
|
|
|
+ // These two fields were added to the widget to help identify the fields
|
|
|
+ // for layout.
|
|
|
+ $table_name = $element['#table_name'];
|
|
|
+ $fkey = $element['#fkey_field'];
|
|
|
|
|
|
- // Check to see if this dbxref already exists. If not then
|
|
|
- // give a notice to the user that the dbxref will be added.
|
|
|
- $db_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__db_id');
|
|
|
- $accession = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__accession');
|
|
|
- if ($db_id and $accession) {
|
|
|
- $values = array(
|
|
|
- 'db_id' => $db_id,
|
|
|
- 'accession' => $accession,
|
|
|
- );
|
|
|
- $options = array('is_duplicate' => TRUE);
|
|
|
- $has_duplicate = chado_select_record('dbxref', array('*'), $values, $options);
|
|
|
- if (!$has_duplicate) {
|
|
|
- drupal_set_message('The selected cross reference is new and will be added for future auto completions.');
|
|
|
- }
|
|
|
- }
|
|
|
+ $layout = "
|
|
|
+ <div class=\"secondary-dbxref-widget\">
|
|
|
+ <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '--dbxref__db_id']) . "
|
|
|
+ </div>
|
|
|
+ <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '--dbxref__accession']) . "
|
|
|
+ </div>
|
|
|
+ <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '--dbxref__version']) . "
|
|
|
+ </div>
|
|
|
+ <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '--dbxref__description']) . "
|
|
|
+ </div>
|
|
|
+ <div class=\"secondary-dbxref-widget-links\">" . drupal_render($element['links']) . "</div>
|
|
|
+ </div>
|
|
|
+ ";
|
|
|
|
|
|
- return $form[$field_name]['und'][$delta];
|
|
|
+ return $layout;
|
|
|
}
|
|
|
-
|
|
|
/**
|
|
|
* Callback function for validating the chado_linker__dbxref_widget.
|
|
|
*/
|
|
|
@@ -363,100 +402,36 @@ function chado_linker__dbxref_widget_validate($element, &$form_state) {
|
|
|
tripal_chado_set_field_form_values($field_name, $form_state, $dbxref->dbxref_id, $delta, $table_name . '__dbxref_id');
|
|
|
tripal_chado_set_field_form_values($field_name, $form_state, $dbxref->dbxref_id, $delta, $table_name . '--dbxref__dbxref_id');
|
|
|
}
|
|
|
-
|
|
|
}
|
|
|
else {
|
|
|
// If the db_id and accession are not set, then remove the linker FK value to the base table.
|
|
|
tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__' . $fkey);
|
|
|
}
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
- * Theme function for the dbxref_id_widget.
|
|
|
- *
|
|
|
- * @param $variables
|
|
|
+ * An Ajax callback for the dbxref widget.
|
|
|
*/
|
|
|
-function theme_chado_linker__dbxref_widget($variables) {
|
|
|
- $element = $variables['element'];
|
|
|
-
|
|
|
- // These two fields were added to the widget to help identify the fields
|
|
|
- // for layout.
|
|
|
- $table_name = $element['#table_name'];
|
|
|
- $fkey = $element['#fkey_field'];
|
|
|
-
|
|
|
- $layout = "
|
|
|
- <div class=\"secondary-dbxref-widget\">
|
|
|
- <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '--dbxref__db_id']) . "
|
|
|
- </div>
|
|
|
- <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '--dbxref__accession']) . "
|
|
|
- </div>
|
|
|
- <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '--dbxref__version']) . "
|
|
|
- </div>
|
|
|
- <div class=\"secondary-dbxref-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '--dbxref__description']) . "
|
|
|
- </div>
|
|
|
- <div class=\"secondary-dbxref-widget-links\">" . drupal_render($element['links']) . "</div>
|
|
|
- </div>
|
|
|
- ";
|
|
|
+function chado_linker__dbxref_widget_form_ajax_callback($form, $form_state) {
|
|
|
|
|
|
- return $layout;
|
|
|
-}
|
|
|
+ $field_name = $form_state['triggering_element']['#parents'][0];
|
|
|
+ $delta = $form_state['triggering_element']['#parents'][2];
|
|
|
|
|
|
-/**
|
|
|
- * Loads the field values with appropriate data.
|
|
|
- *
|
|
|
- * This function is called by the tripal_chado_field_storage_load() for
|
|
|
- * each property managed by the field_chado_storage storage type. This is
|
|
|
- * an optional hook function that is only needed if the field has
|
|
|
- * multiple form elements.
|
|
|
- *
|
|
|
- * @param $field
|
|
|
- * @param $entity
|
|
|
- * @param $base_table
|
|
|
- * @param $record
|
|
|
- */
|
|
|
-function chado_linker__dbxref_load($field, $entity, $base_table, $record) {
|
|
|
-
|
|
|
- $field_name = $field['field_name'];
|
|
|
- $field_type = $field['type'];
|
|
|
- $chado_table = $field['settings']['chado_table'];
|
|
|
- $schema = chado_get_schema($chado_table);
|
|
|
- $pkey = $schema['primary key'][0];
|
|
|
- $fkeys = array_values($schema['foreign keys'][$base_table]['columns']);
|
|
|
- $fkey = $fkeys[0];
|
|
|
-
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- // Set some defaults for the empty record.
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- $entity->{$field_name}['und'][0] = array(
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- 'value' => '',
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- $chado_table . '__' . $fkey => '',
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- $chado_table . '__' . 'dbxref_id' => '',
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- $chado_table . '--' . 'dbxref__dbxref_id' => '',
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- $chado_table . '--' . 'dbxref__db_id' => '',
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- $chado_table . '--' . 'dbxref__accession' => '',
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- $chado_table . '--' . 'dbxref__version' => '',
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- $chado_table . '--' . 'dbxref__description' => '',
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- );
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-
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- $linker_table = $base_table . '_dbxref';
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- $options = array('return_array' => 1);
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- $record = chado_expand_var($record, 'table', $linker_table, $options);
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- if (count($record->$linker_table) > 0) {
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|
- $i = 0;
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|
|
- foreach ($record->$linker_table as $index => $linker) {
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|
|
- $dbxref = $linker->dbxref_id;
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|
|
- $entity->{$field_name}['und'][$i] = array(
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- 'value' => $linker->$pkey,
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- $chado_table . '__' . $fkey => $linker->$fkey->$fkey,
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- $chado_table . '__' . 'dbxref_id' => $dbxref->dbxref_id,
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- $chado_table . '--' . 'dbxref__dbxref_id' => $dbxref->dbxref_id,
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- $chado_table . '--' . 'dbxref__db_id' => $dbxref->db_id->db_id,
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- $chado_table . '--' . 'dbxref__accession' => $dbxref->accession,
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- $chado_table . '--' . 'dbxref__version' => $dbxref->version,
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|
|
- $chado_table . '--' . 'dbxref__description' => $dbxref->description,
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|
|
- );
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|
|
- $i++;
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|
|
+ // Check to see if this dbxref already exists. If not then
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|
|
+ // give a notice to the user that the dbxref will be added.
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|
|
+ $db_id = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__db_id');
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|
|
+ $accession = tripal_chado_get_field_form_values($field_name, $form_state, $delta, $field_name . '--dbxref__accession');
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|
|
+ if ($db_id and $accession) {
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|
|
+ $values = array(
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|
|
+ 'db_id' => $db_id,
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|
|
+ 'accession' => $accession,
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|
|
+ );
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|
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+ $options = array('is_duplicate' => TRUE);
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|
|
+ $has_duplicate = chado_select_record('dbxref', array('*'), $values, $options);
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|
|
+ if (!$has_duplicate) {
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|
|
+ drupal_set_message('The selected cross reference is new and will be added for future auto completions.');
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|
|
}
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|
|
}
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|
|
+
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|
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+ return $form[$field_name]['und'][$delta];
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|
|
}
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Stephen Ficklin