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@@ -30,8 +30,8 @@ class chado_linker__synonym extends TripalField {
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$chado_table = $this->field['settings']['chado_table'];
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foreach ($items as $delta => $item) {
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- if (array_key_exists($chado_table . '__synonym_id', $item) and
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- $item[$chado_table . '__synonym_id']) {
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+ if (array_key_exists('chado-' . $chado_table . '__synonym_id', $item) and
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+ $item['chado-' . $chado_table . '__synonym_id']) {
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$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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@@ -73,31 +73,29 @@ class chado_linker__synonym extends TripalField {
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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][$table_name . '__' . $pkey];
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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_id--name'];
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- $syn_type = $items[$delta][$table_name . '__synonym_id--type_id'];
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+ $record_id = $items[$delta]['chado-' . $table_name . '__' . $pkey];
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+ $fkey_value = $items[$delta]['chado-' . $table_name . '__' . $fkey];
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+ $synonym_id = $items[$delta]['chado-' . $table_name . '__synonym_id'];
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+ $pub_id = $items[$delta]['chado-' . $table_name . '__pub_id'];
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+ $is_current = $items[$delta]['chado-' . $table_name . '__is_current'];
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+ $is_internal = $items[$delta]['chado-' . $table_name . '__is_internal'];
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+ $syn_name = $items[$delta]['name'];
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+ $syn_type = $items[$delta]['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 . '__' . $pkey);
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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_id--name');
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-// $syn_type = tripal_chado_get_field_form_values($table_name, $form_state, $delta, $table_name . '__synonym_id--type_id');
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+ $record_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__' . $pkey];
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+ $fkey_value = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__' . $fkey];
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+ $synonym_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__synonym_id'];
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+ $pub_id = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__pub_id'];
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+ $is_current = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__is_current'];
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+ $is_internal = $form_state['values'][$field_name]['und'][$delta]['chado-' . $table_name . '__is_internal'];
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+ $syn_name = $form_state['values'][$field_name]['und'][$delta]['name'];
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+ $syn_type = $form_state['values'][$field_name]['und'][$delta]['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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+ $options = array();
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// Get the schema for the synonym table so we can make sure we limit the
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// size of the name field to the proper size.
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@@ -105,7 +103,6 @@ class chado_linker__synonym extends TripalField {
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$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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@@ -115,113 +112,158 @@ class chado_linker__synonym extends TripalField {
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'#value' => array_key_exists($delta, $items) ? $items[$delta]['value'] : '',
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);
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- $widget[$table_name . '__' . $pkey] = array(
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+ $widget['chado-' . $table_name . '__' . $pkey] = 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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+ $widget['chado-' . $table_name . '__synonym_id'] = array(
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+ '#type' => 'value',
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+ '#default_value' => $fkey_value,
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+ );
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+ $widget['chado-' . $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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// TODO: add a widget for selecting a publication.
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- $widget[$table_name . '__pub_id'] = array(
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+ $widget['chado-' . $table_name . '__pub_id'] = array(
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'#type' => 'value',
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'#default_value' => $pub_id,
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);
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- $widget[$table_name . '__synonym_id--type_id'] = array(
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+ $widget['type_id'] = array(
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'#type' => 'select',
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'#title' => t('Type'),
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'#options' => $options,
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'#default_value' => $syn_type,
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);
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- $widget[$table_name . '__synonym_id--name'] = array(
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+ $widget['name'] = array(
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'#type' => 'textfield',
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'#title' => t('Synonym Name'),
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'#default_value' => $syn_name,
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'#size' => 25,
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);
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- $widget[$table_name . '__is_current'] = array(
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+ $widget['chado-' . $table_name . '__is_current'] = array(
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'#type' => 'checkbox',
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'#title' => t('Is Current'),
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'#default_value' => $is_current,
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'#required' => $element['#required'],
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);
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- $widget[$table_name . '__is_internal'] = array(
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+ $widget['chado-' . $table_name . '__is_internal'] = array(
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'#type' => 'checkbox',
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'#title' => t('Is Internal'),
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'#default_value' => $is_internal,
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'#required' => $element['#required'],
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);
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}
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-
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- public function widgetFormSubmit($entity_type, $entity, $langcode, &$items, $form, &$form_state) {
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- $field_name = $element['#field_name'];
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- $delta = $element['#delta'];
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- $table_name = $element['#table_name'];
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- $fkey = $element['#fkey_field'];
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-
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- // If the form ID is field_ui_field_edit_form, then the user is editing the
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- // field's values in the manage fields form of Drupal. We don't want
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- // to validate it as if it were being used in a data entry form.
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- if ($form_state['build_info']['form_id'] =='field_ui_field_edit_form') {
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- return;
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- }
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-
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+ /**
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+ * @see TripalField::widgetFormValidate()
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+ */
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+ public function widgetFormValidate($entity_type, $entity, $field, $items, &$errors) {
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+
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+ $field_name = $this->field['field_name'];
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+ $field_type = $this->field['type'];
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+ $table_name = $this->field['settings']['chado_table'];
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+ $field_table = $this->field['settings']['chado_table'];
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+ $field_column = $this->field['settings']['chado_column'];
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+ $base_table = $this->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 values.
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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, $table_name . '--synonym__type_id');
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-
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- // Make sure that if a synonym is provided that a type is also
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- // provided.
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- if ($syn_name and !$syn_type) {
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- form_set_error(implode('][', $element ['#parents']) . '][' . $table_name . '--synonym__type_id', t("Please set a synonym type."));
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- }
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- if (!$syn_name and $syn_type) {
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- form_set_error(implode('][', $element ['#parents']) . '][' . $table_name . '--synonym__name', t("Please set a synonym name."));
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+ foreach ($items as $delta => $values) {
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+
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+ $record_id = $values['chado-' . $table_name . '__' . $pkey];
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+ $fkey_value = $values['chado-' . $table_name . '__' . $fkey];
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+ $synonym_id = $values['chado-' . $table_name . '__synonym_id'];
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+ $pub_id = $values['chado-' . $table_name . '__pub_id'];
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+ $is_current = $values['chado-' . $table_name . '__is_current'];
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+ $is_internal = $values['chado-' . $table_name . '__is_internal'];
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+ $syn_name = $values['name'];
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+ $syn_type = $values['type_id'];
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+
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+
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+ // Make sure that if a synonym is provided that a type is also
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+ // provided.
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+ if ($syn_name and !$syn_type) {
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+ $errors[$field_name][$delta]['und'][] = array(
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+ 'message' => t("Please set a synonym type."),
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+ 'error' => 'chado_linker__synonym',
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+ );
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+ }
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+ if (!$syn_name and $syn_type) {
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+ $errors[$field_name][$delta]['und'][] = array(
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+ 'message' => t("Please set a synonym name."),
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+ 'error' => 'chado_linker__synonym',
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+ );
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+ }
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}
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- // If the user provided a cv_id and a name then we want to set the
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- // foreign key value to be the chado_record_idd
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- if ($syn_name and $syn_type) {
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-
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- // Get the synonym. If one with the same name and type is already present
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- // then use that. Otherwise, insert a new one.
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- if (!$synonym_id) {
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- $synonym = chado_generate_var('synonym', array('name' => $syn_name, 'type_id' => $syn_type));
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- if (!$synonym) {
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- $synonym = chado_insert_record('synonym', array(
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- 'name' => $syn_name,
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- 'type_id' => $syn_type,
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- 'synonym_sgml' => '',
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- ));
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- $synonym = (object) $synonym;
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+ }
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+
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+ /**
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+ * @see TripalField::widgetFormSubmit()
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+ */
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+ public function widgetFormSubmit($entity_type, $entity, $langcode, &$items, $form, &$form_state) {
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+ $field_name = $this->field['field_name'];
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+ $field_type = $this->field['type'];
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+ $table_name = $this->field['settings']['chado_table'];
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+ $field_table = $this->field['settings']['chado_table'];
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+ $field_column = $this->field['settings']['chado_column'];
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+ $base_table = $this->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 = $fkeys[0];
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+
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+ // Get the field values.
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+ foreach ($items as $delta => $values) {
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+
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+ $record_id = $values['chado-' . $table_name . '__' . $pkey];
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+ $fkey_value = $values['chado-' . $table_name . '__' . $fkey];
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+ $synonym_id = $values['chado-' . $table_name . '__synonym_id'];
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+ $pub_id = $values['chado-' . $table_name . '__pub_id'];
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+ $is_current = $values['chado-' . $table_name . '__is_current'];
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+ $is_internal = $values['chado-' . $table_name . '__is_internal'];
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+ $syn_name = $values['name'];
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+ $syn_type = $values['type_id'];
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+
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+ // If the user provided a $syn_name and a $syn_type then we want to set
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+ // the foreign key value to be the chado_record_id.
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+ if ($syn_name and $syn_type) {
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+
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+ // Get the synonym. If one with the same name and type is already present
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+ // then use that. Otherwise, insert a new one.
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+ if (!$synonym_id) {
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+ $synonym = chado_generate_var('synonym', array('name' => $syn_name, 'type_id' => $syn_type));
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+ if (!$synonym) {
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+ $synonym = chado_insert_record('synonym', array(
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+ 'name' => $syn_name,
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+ 'type_id' => $syn_type,
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+ 'synonym_sgml' => '',
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+ ));
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+ $synonym = (object) $synonym;
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+ }
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+
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+ // Set the synonym_id and FK value
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+ $items[$delta]['chado-' . $table_name . '__synonym_id'] = $synonym->synonym_id;
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+ }
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+
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+ if (!$pub_id) {
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+ $pub = chado_generate_var('pub', array('uniquename' => 'null'));
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+ $items[$delta]['chado-' . $table_name . '__pub_id'] = $pub->pub_id;
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}
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-
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- // Set the synonym_id and FK value
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- tripal_chado_set_field_form_values($field_name, $form_state, $synonym->synonym_id, $delta, $table_name . '__synonym_id');
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- $fkey_value = $element['#entity']->chado_record_id;
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- tripal_chado_set_field_form_values($field_name, $form_state, $fkey_value, $delta, $table_name . '__' . $fkey);
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}
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-
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- if (!$pub_id) {
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- $pub = chado_generate_var('pub', array('uniquename' => 'null'));
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- tripal_chado_set_field_form_values($field_name, $form_state, $pub->pub_id, $delta, $table_name . '__pub_id');
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+ else {
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+ // If the $syn_name is not set, then remove the linker FK value to the base table.
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+ $items[$delta]['chado-' . $table_name . '__' . $fkey] = '';
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+ $items[$delta]['chado-' . $table_name . '__synonym_id'] = '';
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+ $items[$delta]['chado-' . $table_name . '__is_internal'] = '';
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+ $items[$delta]['chado-' . $table_name . '__is_current'] = '';
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}
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}
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- else {
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- // If the $syn_name is not set, then remove the linker FK value to the base table.
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- tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__' . $fkey);
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- tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__synonym_id');
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- tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__is_internal');
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- tripal_chado_set_field_form_values($field_name, $form_state, '', $delta, $table_name . '__is_current');
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- }
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}
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/**
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@@ -249,14 +291,14 @@ class chado_linker__synonym extends TripalField {
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// Set some defaults for the empty record.
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$entity->{$field_name}['und'][0] = array(
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'value' => array(),
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- $field_table . '__' . $pkey => '',
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- $field_table . '__' . $fkey_lcolumn => '',
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- $field_table . '__' . 'synonym_id' => '',
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- $field_table . '__' . 'pub_id' => '',
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|
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- $field_table . '__' . 'is_current' => TRUE,
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|
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- $field_table . '__' . 'is_internal' => '',
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|
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- $field_table . '__synonym_id--name' => '',
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|
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- $field_table . '__synonym_id--type_id' => '',
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|
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+ 'chado-' . $field_table . '__' . $pkey => '',
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|
|
+ 'chado-' . $field_table . '__' . $fkey_lcolumn => '',
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|
|
+ 'chado-' . $field_table . '__' . 'synonym_id' => '',
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|
|
+ 'chado-' . $field_table . '__' . 'pub_id' => '',
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|
|
+ 'chado-' . $field_table . '__' . 'is_current' => TRUE,
|
|
|
+ 'chado-' . $field_table . '__' . 'is_internal' => '',
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|
|
+ 'name' => '',
|
|
|
+ 'type_id' => '',
|
|
|
// Ignore the synonym_sgml column for now.
|
|
|
);
|
|
|
|
|
|
@@ -273,14 +315,14 @@ class chado_linker__synonym extends TripalField {
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|
|
'type' => $synonym->type_id->name,
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|
|
'name' => $synonym->name,
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|
|
),
|
|
|
- $field_table . '__' . $pkey = $linker->$pkey,
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|
|
- $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
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|
|
- $field_table . '__' . 'synonym_id' => $synonym->synonym_id,
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|
|
- $field_table . '__' . 'pub_id' => $linker->pub_id->pub_id,
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|
|
- $field_table . '__' . 'is_current' => $linker->is_current,
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|
|
- $field_table . '__' . 'is_internal' => $linker->is_internal,
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|
|
- $field_table . '__synonym_id--name' => $synonym->name,
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|
|
- $field_table . '__synonym_id--type_id' => $synonym->type_id->cvterm_id,
|
|
|
+ 'chado-' . $field_table . '__' . $pkey = $linker->$pkey,
|
|
|
+ 'chado-' . $field_table . '__' . $fkey_lcolumn => $linker->$fkey_lcolumn->$fkey_lcolumn,
|
|
|
+ 'chado-' . $field_table . '__' . 'synonym_id' => $synonym->synonym_id,
|
|
|
+ 'chado-' . $field_table . '__' . 'pub_id' => $linker->pub_id->pub_id,
|
|
|
+ 'chado-' . $field_table . '__' . 'is_current' => $linker->is_current,
|
|
|
+ 'chado-' . $field_table . '__' . 'is_internal' => $linker->is_internal,
|
|
|
+ 'name' => $synonym->name,
|
|
|
+ 'type_id' => $synonym->type_id->cvterm_id,
|
|
|
);
|
|
|
$i++;
|
|
|
}
|
|
|
@@ -304,16 +346,16 @@ function theme_chado_linker__synonym_widget($variables) {
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|
|
$layout = "
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|
|
<div class=\"synonym-widget\">
|
|
|
<div class=\"synonym-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '__synonym_id--name']) . "
|
|
|
+ drupal_render($element['name']) . "
|
|
|
</div>
|
|
|
<div>" .
|
|
|
- drupal_render($element[$table_name . '__synonym_id--type_id']) . "
|
|
|
+ drupal_render($element['type_id']) . "
|
|
|
</div>
|
|
|
<div class=\"synonym-widget-item\">" .
|
|
|
- drupal_render($element[$table_name . '__is_internal']) . "
|
|
|
+ drupal_render($element['chado-' . $table_name . '__is_internal']) . "
|
|
|
</div>
|
|
|
<div>" .
|
|
|
- drupal_render($element[$table_name . '__is_current']) . "
|
|
|
+ drupal_render($element['chado-' . $table_name . '__is_current']) . "
|
|
|
</div>
|
|
|
</div>
|
|
|
";
|
Stephen Ficklin