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@@ -178,34 +178,25 @@ function tripal_fields_field_formatter_view($entity_type, $entity, $field,
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}
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break;
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case 'tripal_fields_primary_dbxref_formatter':
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- foreach ($items as $delta => $item) {
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- $accession = '';
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- if ($item['value']) {
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- $dbxref = chado_generate_var('dbxref', array('dbxref_id' => $item['value']));
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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);
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- }
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- }
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- // TODO: add hook here to allow other modules to change this display
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- // if they want.
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- $element[$delta] = array(
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- // We create a render array to produce the desired markup,
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- '#type' => 'markup',
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- '#markup' => $accession,
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- );
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- }
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+ module_load_include('inc', 'tripal_fields', 'includes/tripal_fields/fields/primary_dbxref');
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+ $content = tripal_fields_primary_dbxref_formatter($entity_type, $entity, $field,
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+ $instance, $langcode, $items, $display);
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+
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+ $element[$delta] = array(
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+ // We create a render array to produce the desired markup,
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+ '#type' => 'markup',
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+ '#markup' => $content,
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+ );
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break;
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case 'tripal_fields_md5checksum_formatter':
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- foreach ($items as $delta => $item) {
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- // TODO: add hook here to allow other modules to change this display
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- // if they want.
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- $element[$delta] = array(
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- // We create a render array to produce the desired markup,
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- '#type' => 'markup',
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- '#markup' => key_exists('value', $item) ? $item['value'] : '',
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- );
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- }
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+ module_load_include('inc', 'tripal_fields', 'includes/tripal_fields/fields/md5checksum');
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+ $content = tripal_fields_md5checksum_checkbox_formatter($entity_type, $entity, $field,
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+ $instance, $langcode, $items, $display);
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+ $element[$delta] = array(
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+ // We create a render array to produce the desired markup,
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+ '#type' => 'markup',
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+ '#markup' => $content,
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+ );
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break;
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case 'tripal_fields_residues_formatter':
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foreach ($items as $delta => $item) {
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@@ -265,99 +256,19 @@ function tripal_fields_field_widget_form(&$form, &$form_state, $field,
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$element['value'] = $widget;
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break;
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case 'tripal_fields_primary_dbxref_widget':
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- // Get the field defaults from the database if a record exists.
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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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- $description = '';
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- if (count($items) > 0 and $items[0]['value']) {
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- $dbxref = chado_generate_var('dbxref', array('dbxref_id' => $items[0]['value']));
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- $dbxref_id = $dbxref->dbxref_id;
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- $db_id = $dbxref->db_id->db_id;
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- $accession = $dbxref->accession;
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- $version = $dbxref->version;
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- $description = $dbxref->description;
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- }
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- $temp = tripal_fields_get_field_form_values($field_name, $form_state, 'dbxref__db_id');
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- if (count($temp) > 0) {
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- $db_id = $temp[0];
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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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- $widget += array(
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- '#element_validate' => array('tripal_fields_primary_dbxref_widget_validate'),
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- '#type' => 'fieldset',
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- '#title' => $element['#title'],
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- '#description' => $element['#description'],
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- '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
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- '#delta' => $delta,
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- '#theme' => 'tripal_fields_primary_dbxref_widget',
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- '#group' => 'entity_vetical_tabs',
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- array(
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- $element['#field_name'] => array(
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- '#type' => 'hidden',
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- '#default_value' => $dbxref_id,
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- ),
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- 'dbxref__db_id' => array(
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- '#type' => 'select',
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- '#title' => t('Database'),
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- '#options' => $options,
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- '#required' => $element['#required'],
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- '#default_value' => $db_id,
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- '#ajax' => array(
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- 'callback' => "tripal_fields_primary_dbxref_widget_form_ajax_callback",
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- 'wrapper' => "$field_name-dbxref--db-id",
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- 'effect' => 'fade',
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- 'method' => 'replace'
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- )
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- ),
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- 'dbxref__accession' => array(
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- '#type' => 'textfield',
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- '#title' => t('Accession'),
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- '#default_value' => $accession,
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- '#required' => $element['#required'],
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- '#maxlength' => array_key_exists('length', $schema['fields']['accession']) ? $schema['fields']['accession']['length'] : 255,
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- '#size' => 15,
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- '#autocomplete_path' => "admin/tripal/chado/tripal_db/dbxref/auto_name/$db_id",
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- '#ajax' => array(
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- 'callback' => "tripal_fields_primary_dbxref_widget_form_ajax_callback",
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- 'wrapper' => "$field_name-dbxref--db-id",
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- 'effect' => 'fade',
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- 'method' => 'replace'
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- )
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- ),
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- 'dbxref__version' => array(
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- '#type' => 'textfield',
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- '#title' => t('Version'),
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- '#default_value' => $version,
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- '#maxlength' => array_key_exists('length', $schema['fields']['version']) ? $schema['fields']['version']['length'] : 255,
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- '#size' => 5,
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- ),
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- 'dbxref__description' => array(
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- '#type' => 'textfield',
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- '#title' => t('Description'),
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- '#default_value' => $description,
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- '#size' => 20,
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- ),
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- ),
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- '#prefix' => "<span id='$field_name-dbxref--db-id'>",
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- '#suffix' => "</span>"
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- );
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+ // Make sure the include files get parsed now and for the form submits.
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+ form_load_include($form_state, 'inc', 'tripal_fields', 'includes/fields/primary_dbxref');
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+ module_load_include('inc', 'tripal_fields', 'includes/fields/primary_dbxref');
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+ // Update the widget with the new field.
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+ tripal_fields_primary_dbxref_widget($field_name, $widget, $form,
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+ $form_state, $field, $instance, $langcode, $items, $delta, $element);
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$element['value'] = $widget;
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break;
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case 'tripal_fields_md5checksum_checkbox_widget':
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- $widget += array(
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- '#type' => 'checkbox',
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- '#title' => $element['#title'],
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- '#description' => $element['#description'],
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- '#options' => array(0, 1),
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- '#default_value' => 1,
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- '#weight' => isset($element['#weight']) ? $element['#weight'] : 0,
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- '#delta' => $delta,
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- '#element_validate' => array('tripal_fields_md5checksum_checkbox_widget_validate'),
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- );
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+ form_load_include($form_state, 'inc', 'tripal_fields', 'includes/tripal_fields/fields/md5checksum');
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+ module_load_include('inc', 'tripal_fields', 'includes/tripal_fields/fields/md5checksum');
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+ tripal_fields_md5checksum_checkbox_widget($field_name, $widget,
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+ $form, $form_state, $field, $instance, $langcode, $items, $delta, $element);
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$element['value'] = $widget;
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break;
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case 'tripal_fields_residues_textarea_widget':
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@@ -440,45 +351,7 @@ function tripal_fields_organism_select_widget_validate($element, &$form_state) {
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form_error($element, t("Please specify an organism that already exists in the database."));
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}
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}
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-/**
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- * Callback function for validating the tripal_fields_organism_select_widget.
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- */
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-function tripal_fields_primary_dbxref_widget_validate($element, &$form_state) {
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- $field_name = $element['#field_name'];
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-
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- // If the form ID is field_ui_field_edit_form, then the user is editing the
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- // field's values in the manage fields form of Drupal. We don't want
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- // to validate it as if it were being used in a data entry form.
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- if ($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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- // Get the field values.
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- $db_id = tripal_fields_get_field_form_values($field_name, $form_state, "dbxref__db_id");
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- $accession = tripal_fields_get_field_form_values($field_name, $form_state, "dbxref__accession");
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- $version = tripal_fields_get_field_form_values($field_name, $form_state, "dbxref__version");
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- $description = tripal_fields_get_field_form_values($field_name, $form_state, "dbxref__description");
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- // Make sure that if a database ID is provided that an accession is also
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- // provided. Here we use the form_set_error function rather than the
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- // form_error function because the form_error will add a red_highlight
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- // around all of the fields in the fieldset which is confusing as it's not
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- // clear to the user what field is required and which isn't. Therefore,
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- // we borrow the code from the 'form_error' function and append the field
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- // so that the proper field is highlighted on error.
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- if (count($db_id) == 0 and count($accession) > 0) {
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- form_set_error(implode('][', $element ['#parents']) . '][0][dbxref__db_id', t("A database and the accession must both be provided for the primary cross reference."));
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- }
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- if (count($db_id) > 0 and count($accession) == 0) {
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- form_set_error(implode('][', $element ['#parents']) . '][0][dbxref__accession', t("A database and the accession must both be provided for the primary cross reference."));
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- }
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-
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- // If user did not select a database, we want to remove dbxref_id from the
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- // field.
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- if (count($db_id) == 0) {
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- tripal_fields_set_field_form_values($field_name, $form_state, '__NULL__', $field_name);
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- }
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-}
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/**
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* Callback function for validating the tripal_fields_kvproperty_widget.
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*/
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@@ -486,22 +359,7 @@ function tripal_fields_kvproperty_widget_validate($element, &$form_state) {
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// Add the new field to the entity
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$form_state['rebuild'] = TRUE;
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}
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-/**
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- * Callback function for validating the tripal_fields_md5checksum_checkbox_widget.
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- */
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-function tripal_fields_md5checksum_checkbox_widget_validate($element, &$form_state) {
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- $field_name = $element['#field_name'];
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- // Calculate the md5 checksum for the sequence only if md5 box is checked and the residues exist
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- $residues = tripal_fields_get_field_form_values('feature__residues', $form_state);
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- if (count($residues) > 0 && trim($residues[0]) != '') {
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- tripal_fields_set_field_form_values ($field_name, $form_state, md5($residues[0]));
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- }
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- else {
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- // Otherwise, remove the md5 value
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- tripal_fields_set_field_form_values ($field_name, $form_state, '__NULL__');
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- }
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-}
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/**
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* Callback function for validating the tripal_fields_residues_textarea_widget.
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@@ -605,23 +463,3 @@ function tripal_fields_set_field_form_values($field_name, &$form_state, $newvalu
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return $values;
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}
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-/**
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- * An Ajax callback for the tripal_fields_admin_publish_form..
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- */
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-function tripal_fields_primary_dbxref_widget_form_ajax_callback($form, $form_state) {
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- $field_name = $form_state['triggering_element']['#parents'][0];
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- $db_id = tripal_fields_get_field_form_values($field_name, $form_state, 'dbxref__db_id');
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- $accession = tripal_fields_get_field_form_values($field_name, $form_state, 'dbxref__accession');
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- if (count($db_id) > 0 and count($accession) > 0) {
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- $values = array(
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- 'db_id' => $db_id[0],
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- 'accession' => $accession[0],
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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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- return $form[$field_name];
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-}
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Stephen Ficklin