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@@ -1,251 +1,303 @@
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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__synonym_info() {
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- return array(
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- 'label' => t('Synonyms'),
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- 'description' => t('Adds an alternative name (synonym or alias) to this record.'),
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- 'default_widget' => 'chado_linker__synonym_widget',
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- 'default_formatter' => 'chado_linker__synonym_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 $term
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- *
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- * @return
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- * A field array
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- */
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-function chado_linker__synonym_attach_info($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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- // If the linker table does not exists then we don't want to add attach.
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- $syn_table = $table_name . '_synonym';
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- if (!chado_table_exists($syn_table)) {
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- return $field_info;
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+
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+class chado_linker__synonym extends TripalField {
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+
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+ /**
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+ * @see TripalField::field_info()
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+ */
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+ function field_info() {
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+ return array(
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+ 'label' => t('Synonyms'),
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+ 'description' => t('Adds an alternative name (synonym or alias) to this record.'),
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+ 'default_widget' => 'chado_linker__synonym_widget',
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+ 'default_formatter' => 'chado_linker__synonym_formatter',
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+ 'settings' => array(),
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+ 'storage' => array(
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+ 'type' => 'field_chado_storage',
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+ 'module' => 'tripal_chado',
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+ 'active' => TRUE
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+ ),
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+ );
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}
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+ /**
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+ * @see TripalField::attach_info()
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+ */
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+ function attach_info($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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+ // If the linker table does not exists then we don't want to add attach.
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+ $syn_table = $table_name . '_synonym';
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+ if (!chado_table_exists($syn_table)) {
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+ return $field_info;
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+ }
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- $schema = chado_get_schema($syn_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' => $table_name . '__synonym',
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- 'field_type' => 'chado_linker__synonym',
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- 'widget_type' => 'chado_linker__synonym_widget',
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- 'widget_settings' => array('display_label' => 1),
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- 'description' => '',
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- 'label' => 'Synonyms',
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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' => $syn_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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+ $schema = chado_get_schema($syn_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' => $table_name . '__synonym',
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+ 'field_type' => 'chado_linker__synonym',
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+ 'widget_type' => 'chado_linker__synonym_widget',
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+ 'widget_settings' => array('display_label' => 1),
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+ 'description' => '',
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+ 'label' => 'Synonyms',
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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' => $syn_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' => 'alternateName',
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+ 'accession' => 'alternateName',
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+ 'ns' => 'schema',
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+ 'nsurl' => 'https://schema.org/',
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+ ),
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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__synonym_widget_info() {
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- return array(
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- 'label' => t('Synonyms'),
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- 'field types' => array('chado_linker__synonym'),
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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__synonym_formatter_info() {
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- return array(
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- 'label' => t('Synonyms'),
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- 'field types' => array('chado_linker__synonym'),
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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 $display
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- */
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-function chado_linker__synonym_formatter(&$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 => $item) {
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- if ($item[$chado_table . '__synonym_id']) {
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- $synonym = chado_generate_var('synonym', array('synonym_id' => $item[$chado_table . '__synonym_id']));
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- $name = $synonym->name;
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- if ($synonym->type_id->name != 'exact') {
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- $name .= ' (<i>' . $synonym->type_id->name . '</i>)';
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+ );
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+ return $field_info;
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+ }
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+ /**
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+ * @see TripalField::widget_info()
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+ */
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+ function widget_info() {
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+ return array(
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+ 'label' => t('Synonyms'),
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+ 'field types' => array('chado_linker__synonym'),
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+ );
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+ }
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+ /**
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+ * @see TripalField::formatter_info()
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+ */
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+ function formatter_info() {
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+ return array(
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+ 'label' => t('Synonyms'),
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+ 'field types' => array('chado_linker__synonym'),
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+ 'settings' => array(
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+ ),
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+ );
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+ }
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+ /**
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+ * @see TripalField::formatter_view()
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+ */
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+ function formatter_view(&$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 => $item) {
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+ if ($item[$chado_table . '__synonym_id']) {
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+ $synonym = chado_generate_var('synonym', array('synonym_id' => $item[$chado_table . '__synonym_id']));
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+ $name = $synonym->name;
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+ if ($synonym->type_id->name != 'exact') {
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+ $name .= ' (<i>' . $synonym->type_id->name . '</i>)';
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+ }
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+ $element[$delta] = array(
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+ '#type' => 'markup',
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+ '#markup' => $name,
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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' => $name,
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- );
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}
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}
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-}
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-/**
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- *
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- */
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-function chado_linker__synonym_widget(&$widget, $form, $form_state, $field,
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- $instance, $langcode, $items, $delta, $element) {
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-
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- $entity = $form['#entity'];
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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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- $table_name = $field['settings']['chado_table'];
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- $base_table = $field['settings']['base_table'];
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- $schema = chado_get_schema($table_name);
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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 = $element['#entity']->chado_record_id;
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- $synonym_id = '';
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- $pub_id = '';
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- $is_current = TRUE;
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- $is_internal = FALSE;
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- $syn_name = '';
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- $syn_type = '';
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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][$table_name . '__' . $fkey];
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- $synonym_id = $items[$delta][$table_name . '__synonym_id'];
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- $pub_id = $items[$delta][$table_name . '__pub_id'];
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- $is_current = $items[$delta][$table_name . '__is_current'];
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- $is_internal = $items[$delta][$table_name . '__is_internal'];
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- $syn_name = $items[$delta][$table_name . '--synonym__name'];
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- $syn_type = $items[$delta][$table_name . '--synonym__type_id'];
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- }
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+ /**
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+ * @see TripalField::widget_form()
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+ */
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+ function widget_form(&$widget, $form, $form_state, $field,
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+ $instance, $langcode, $items, $delta, $element) {
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+
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+ $entity = $form['#entity'];
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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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+ $table_name = $field['settings']['chado_table'];
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+ $base_table = $field['settings']['base_table'];
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+ $schema = chado_get_schema($table_name);
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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 = $element['#entity']->chado_record_id;
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+ $synonym_id = '';
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+ $pub_id = '';
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+ $is_current = TRUE;
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+ $is_internal = FALSE;
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+ $syn_name = '';
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+ $syn_type = '';
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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][$table_name . '__' . $fkey];
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+ $synonym_id = $items[$delta][$table_name . '__synonym_id'];
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+ $pub_id = $items[$delta][$table_name . '__pub_id'];
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+ $is_current = $items[$delta][$table_name . '__is_current'];
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+ $is_internal = $items[$delta][$table_name . '__is_internal'];
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+ $syn_name = $items[$delta][$table_name . '--synonym__name'];
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+ $syn_type = $items[$delta][$table_name . '--synonym__type_id'];
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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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- $record_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name);
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- $fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
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- $synonym_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__synonym_id');
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- $pub_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__pub_id');
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- $is_current = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_current');
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- $is_internal = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_internal');
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- $syn_name = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__name');
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- $syn_type = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__type_id');
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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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+ $record_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name);
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+ $fkey_value = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__' . $fkey);
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+ $synonym_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__synonym_id');
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+ $pub_id = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__pub_id');
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+ $is_current = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_current');
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+ $is_internal = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__is_internal');
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+ $syn_name = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__name');
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+ $syn_type = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '--synonym__type_id');
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+ }
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- // Get the synonym type terms. There shouldn't be too many.
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- $cv = tripal_get_default_cv('synonym', 'type_id');
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- $options = tripal_get_cvterm_select_options($cv->cv_id);
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-
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- // Get the schema for the synonym table so we can make sure we limit the
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- // size of the name field to the proper size.
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- $schema = chado_get_schema('synonym');
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-
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- $widget['#table_name'] = $table_name;
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- $widget['#fkey_field'] = $fkey;
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- $widget['#element_validate'] = array('chado_linker__synonym_widget_validate');
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- $widget['#theme'] = 'chado_linker__synonym_widget';
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- $widget['#prefix'] = "<span id='$table_name-$delta'>";
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- $widget['#suffix'] = "</span>";
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-
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- $widget['value'] = array(
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- '#type' => 'value',
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- '#default_value' => $record_id,
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- );
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- $widget[$table_name . '__' . $fkey] = array(
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- '#type' => 'value',
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- '#default_value' => $fkey_value,
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- );
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-
|
|
|
- $widget[$table_name . '--synonym__type_id'] = array(
|
|
|
- '#type' => 'select',
|
|
|
- '#title' => t('Type'),
|
|
|
- '#options' => $options,
|
|
|
- '#default_value' => $syn_type,
|
|
|
- );
|
|
|
- $widget[$table_name . '--synonym__name'] = array(
|
|
|
- '#type' => 'textfield',
|
|
|
- '#title' => t('Synonym Name'),
|
|
|
- '#default_value' => $syn_name,
|
|
|
- '#size' => 25,
|
|
|
- );
|
|
|
-
|
|
|
- $widget[$table_name . '__is_current'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Is Current'),
|
|
|
- '#default_value' => $is_current,
|
|
|
- '#required' => $element['#required'],
|
|
|
- );
|
|
|
-
|
|
|
- $widget[$table_name . '__is_internal'] = array(
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Is Internal'),
|
|
|
- '#default_value' => $is_internal,
|
|
|
- '#required' => $element['#required'],
|
|
|
- );
|
|
|
+ // Get the synonym type terms. There shouldn't be too many.
|
|
|
+ $cv = tripal_get_default_cv('synonym', 'type_id');
|
|
|
+ $options = tripal_get_cvterm_select_options($cv->cv_id);
|
|
|
+
|
|
|
+ // Get the schema for the synonym table so we can make sure we limit the
|
|
|
+ // size of the name field to the proper size.
|
|
|
+ $schema = chado_get_schema('synonym');
|
|
|
+
|
|
|
+ $widget['#table_name'] = $table_name;
|
|
|
+ $widget['#fkey_field'] = $fkey;
|
|
|
+ $widget['#element_validate'] = array('chado_linker__synonym_widget_validate');
|
|
|
+ $widget['#theme'] = 'chado_linker__synonym_widget';
|
|
|
+ $widget['#prefix'] = "<span id='$table_name-$delta'>";
|
|
|
+ $widget['#suffix'] = "</span>";
|
|
|
+
|
|
|
+ $widget['value'] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $record_id,
|
|
|
+ );
|
|
|
+ $widget[$table_name . '__' . $fkey] = array(
|
|
|
+ '#type' => 'value',
|
|
|
+ '#default_value' => $fkey_value,
|
|
|
+ );
|
|
|
+
|
|
|
+ $widget[$table_name . '--synonym__type_id'] = array(
|
|
|
+ '#type' => 'select',
|
|
|
+ '#title' => t('Type'),
|
|
|
+ '#options' => $options,
|
|
|
+ '#default_value' => $syn_type,
|
|
|
+ );
|
|
|
+ $widget[$table_name . '--synonym__name'] = array(
|
|
|
+ '#type' => 'textfield',
|
|
|
+ '#title' => t('Synonym Name'),
|
|
|
+ '#default_value' => $syn_name,
|
|
|
+ '#size' => 25,
|
|
|
+ );
|
|
|
+
|
|
|
+ $widget[$table_name . '__is_current'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Is Current'),
|
|
|
+ '#default_value' => $is_current,
|
|
|
+ '#required' => $element['#required'],
|
|
|
+ );
|
|
|
+
|
|
|
+ $widget[$table_name . '__is_internal'] = array(
|
|
|
+ '#type' => 'checkbox',
|
|
|
+ '#title' => t('Is Internal'),
|
|
|
+ '#default_value' => $is_internal,
|
|
|
+ '#required' => $element['#required'],
|
|
|
+ );
|
|
|
|
|
|
+ }
|
|
|
+
|
|
|
+ /**
|
|
|
+ * @see TripalField::load()
|
|
|
+ */
|
|
|
+ function load($field, $entity, $details) {
|
|
|
+
|
|
|
+ $record = $details['record'];
|
|
|
+ $base_table = $field['settings']['base_table'];
|
|
|
+
|
|
|
+ $field_name = $field['field_name'];
|
|
|
+ $field_type = $field['type'];
|
|
|
+ $field_table = $field['settings']['chado_table'];
|
|
|
+ $field_column = $field['settings']['chado_column'];
|
|
|
+
|
|
|
+ // 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];
|
|
|
+
|
|
|
+ // Set some defaults for the empty record.
|
|
|
+ $entity->{$field_name}['und'][0] = array(
|
|
|
+ 'value' => '',
|
|
|
+ $field_table . '__' . $fkey_lcolumn => '',
|
|
|
+ $field_table . '__' . 'synonym_id' => '',
|
|
|
+ $field_table . '__' . 'pub_id' => '',
|
|
|
+ $field_table . '__' . 'is_current' => TRUE,
|
|
|
+ $field_table . '__' . 'is_internal' => '',
|
|
|
+ $field_table . '--' . 'synonym__name' => '',
|
|
|
+ $field_table . '--' . 'synonym__type_id' => '',
|
|
|
+ // Ignore the synonym_sgml column for now.
|
|
|
+ );
|
|
|
+
|
|
|
+ $linker_table = $base_table . '_synonym';
|
|
|
+ $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) {
|
|
|
+ $synonym = $linker->synonym_id;
|
|
|
+ $entity->{$field_name}['und'][$i] = array(
|
|
|
+ 'value' => $linker->$pkey,
|
|
|
+ $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
|
|
|
+ $field_table . '__' . 'synonym_id' => $synonym->synonym_id,
|
|
|
+ $field_table . '__' . 'pub_id' => $linker->pub_id->pub_id,
|
|
|
+ $field_table . '__' . 'is_current' => $linker->is_current,
|
|
|
+ $field_table . '__' . 'is_internal' => $linker->is_internal,
|
|
|
+ $field_table . '--' . 'synonym__name' => $synonym->name,
|
|
|
+ $field_table . '--' . 'synonym__type_id' => $synonym->type_id->cvterm_id,
|
|
|
+ );
|
|
|
+ $i++;
|
|
|
+ }
|
|
|
+ }
|
|
|
+ }
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
- * An Ajax callback for the synonym widget.
|
|
|
+ * Theme function for the synonym widget.
|
|
|
+ *
|
|
|
+ * @param $variables
|
|
|
*/
|
|
|
-function chado_linker__synonym_widget_form_ajax_callback($form, $form_state) {
|
|
|
+function theme_chado_linker__synonym_widget($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'];
|
|
|
|
|
|
- return $form[$field_name]['und'][$delta];
|
|
|
-}
|
|
|
+ $layout = "
|
|
|
+ <div class=\"synonym-widget\">
|
|
|
+ <div class=\"synonym-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '--synonym__name']) . "
|
|
|
+ </div>
|
|
|
+ <div>" .
|
|
|
+ drupal_render($element[$table_name . '--synonym__type_id']) . "
|
|
|
+ </div>
|
|
|
+ <div class=\"synonym-widget-item\">" .
|
|
|
+ drupal_render($element[$table_name . '__is_internal']) . "
|
|
|
+ </div>
|
|
|
+ <div>" .
|
|
|
+ drupal_render($element[$table_name . '__is_current']) . "
|
|
|
+ </div>
|
|
|
+ </div>
|
|
|
+ ";
|
|
|
|
|
|
+ return $layout;
|
|
|
+}
|
|
|
/**
|
|
|
* Callback function for validating the chado_linker__synonym_widget.
|
|
|
*/
|
|
|
@@ -317,97 +369,14 @@ function chado_linker__synonym_widget_validate($element, &$form_state) {
|
|
|
}
|
|
|
|
|
|
}
|
|
|
+
|
|
|
/**
|
|
|
- * Theme function for the synonym widget.
|
|
|
- *
|
|
|
- * @param $variables
|
|
|
+ * An Ajax callback for the synonym widget.
|
|
|
*/
|
|
|
-function theme_chado_linker__synonym_widget($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'];
|
|
|
-
|
|
|
- $layout = "
|
|
|
- <div class=\"synonym-widget\">
|
|
|
- <div class=\"synonym-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '--synonym__name']) . "
|
|
|
- </div>
|
|
|
- <div>" .
|
|
|
- drupal_render($element[$table_name . '--synonym__type_id']) . "
|
|
|
- </div>
|
|
|
- <div class=\"synonym-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '__is_internal']) . "
|
|
|
- </div>
|
|
|
- <div>" .
|
|
|
- drupal_render($element[$table_name . '__is_current']) . "
|
|
|
- </div>
|
|
|
- </div>
|
|
|
- ";
|
|
|
+function chado_linker__synonym_widget_form_ajax_callback($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 $record
|
|
|
- */
|
|
|
-function chado_linker__synonym_load($field, $entity, $base_table, $record) {
|
|
|
-
|
|
|
- $field_name = $field['field_name'];
|
|
|
- $field_type = $field['type'];
|
|
|
- $field_table = $field['settings']['chado_table'];
|
|
|
- $field_column = $field['settings']['chado_column'];
|
|
|
-
|
|
|
- // 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];
|
|
|
-
|
|
|
- // Set some defaults for the empty record.
|
|
|
- $entity->{$field_name}['und'][0] = array(
|
|
|
- 'value' => '',
|
|
|
- $field_table . '__' . $fkey_lcolumn => '',
|
|
|
- $field_table . '__' . 'synonym_id' => '',
|
|
|
- $field_table . '__' . 'pub_id' => '',
|
|
|
- $field_table . '__' . 'is_current' => TRUE,
|
|
|
- $field_table . '__' . 'is_internal' => '',
|
|
|
- $field_table . '--' . 'synonym__name' => '',
|
|
|
- $field_table . '--' . 'synonym__type_id' => '',
|
|
|
- // Ignore the synonym_sgml column for now.
|
|
|
- );
|
|
|
-
|
|
|
- $linker_table = $base_table . '_synonym';
|
|
|
- $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) {
|
|
|
- $synonym = $linker->synonym_id;
|
|
|
- $entity->{$field_name}['und'][$i] = array(
|
|
|
- 'value' => $linker->$pkey,
|
|
|
- $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
|
|
|
- $field_table . '__' . 'synonym_id' => $synonym->synonym_id,
|
|
|
- $field_table . '__' . 'pub_id' => $linker->pub_id->pub_id,
|
|
|
- $field_table . '__' . 'is_current' => $linker->is_current,
|
|
|
- $field_table . '__' . 'is_internal' => $linker->is_internal,
|
|
|
- $field_table . '--' . 'synonym__name' => $synonym->name,
|
|
|
- $field_table . '--' . 'synonym__type_id' => $synonym->type_id->cvterm_id,
|
|
|
- );
|
|
|
- $i++;
|
|
|
- }
|
|
|
- }
|
|
|
+ return $form[$field_name]['und'][$delta];
|
|
|
}
|
|
|
-
|
Stephen Ficklin