'.$cvitjs_msg.'';
}
return $form;
}
function blastdb_form_validate($form, $form_state) {
if (isset($form_state['values']['regex']) AND !empty($form_state['values']['regex'])) {
// Check that any supplied regex includes //.
if (!preg_match('/\/.*\//', $form_state['values']['regex'])) {
form_set_error('regex', 'Regular Expressions require opening and closing slashes to delinate them. For example,
/^(\s+) .*/');
}
// Check that the supplied regex is valid.
elseif (@preg_match($form_state['values']['regex'], NULL) === FALSE) {
form_set_error('regex', 'Regular Expression not valid. See '
. '
PHP.net Regular '
. 'Expression Documentation for more information.');
}
}
// Check that the supplied db actually contains a URL prefix.
if (isset($form_state['values']['db_id'])) {
$db = tripal_get_db(array('db_id' => $form_state['values']['db_id']));
if (empty($db)) {
form_set_error('db_id', 'The database chosen no longer exists.');
}
if (empty($db->urlprefix)) {
form_set_error('db_id', 'The database choosen does not have a URL prefix '
. 'listed which means a link-out could not be created for BLAST hits. '
. 'Please edit the database '
. l('here', 'admin/tripal/chado/tripal_db/edit/' . $db->db_id,
array('attributes' => array('target' => '_blank')))
. ' to include a URL prefix before continuing'
);
}
}
// Check that there is a cvitjs section for the current
if (isset($form_state['values']['cvitjs_enabled']) AND $form_state['values']['cvitjs_enabled']) {
$conf_section = blast_ui_get_cvit_conf_text('data.'.$form_state['values']['db_name']);
if (!$conf_section) {
drupal_set_message('There is no section for this genome target defined in the CViTjs
configuration file.
No genome visualization will be shown until you define a
configuration section, "[data.'.$form_state['values']['db_name'].']", at '
.l('Admin > Tripal > Extensions > Tripal BLAST > BLAST UI', 'admin/tripal/extension/tripal_blast')
.'.',
'warning');
}
}
}
/**
* Implements hook_insert().
*/
function blastdb_insert($node) {
// Handle Link-out Rules.
$regex = '';
if (isset($node->dbxref_id_type)) {
if ($node->dbxref_id_type == 'custom') {
$regex = $node->regex;
}
else {
$regex = $node->dbxref_id_type;
}
}
$db_id = 0;
if (isset($node->db_id)) {
$db_id = $node->db_id;
}
if (!$node->dbxref_linkout_type) {
$node->dbxref_linkout_type = 'none';
}
if (!isset($node->cvitjs_enabled)) {
$node->cvitjs_enabled = 0;
}
// Actually insert the record.
db_insert('blastdb')->fields(array(
'nid' => $node->nid,
'name' => $node->db_name,
'path' => trim($node->db_path),
'dbtype' => $node->db_dbtype,
'dbxref_id_regex' => $regex,
'dbxref_db_id' => $db_id,
'dbxref_linkout_type' => $node->dbxref_linkout_type,
'cvitjs_enabled' => $node->cvitjs_enabled,
))->execute();
}
/**
* Implements hook_node_insert().
* This function acts on ALL NODES
*/
function blast_ui_node_insert($node) {
if ($node->type == 'blastdb') {
$node->title = $node->db_name;
}
}
/**
* Implements hook_update().
*/
function blastdb_update($node) {
// Handle Link-out Rules.
$regex = '';
if (isset($node->dbxref_id_type)) {
if ($node->dbxref_id_type == 'custom') {
$regex = $node->regex;
}
else {
$regex = $node->dbxref_id_type;
}
}
$db_id = 0;
if (isset($node->db_id)) {
$db_id = $node->db_id;
}
if (!$node->cvitjs_enabled) {
$node->cvitjs_enabled = 0;
}
if (!$node->dbxref_linkout_type) {
$node->dbxref_linkout_type = 'none';
}
// Update the record.
db_update('blastdb')->fields(array(
'name' => $node->db_name,
'path' => $node->db_path,
'dbtype' => $node->db_dbtype,
'dbxref_id_regex' => $regex,
'dbxref_db_id' => $db_id,
'dbxref_linkout_type' => $node->dbxref_linkout_type,
'cvitjs_enabled' => $node->cvitjs_enabled,
))->condition('nid', $node->nid)->execute();
}
/**
* Implements hook_node_update().
* This function acts on ALL NODES
*/
function blast_ui_node_update($node) {
if ($node->type == 'blastdb') {
$node->title = $node->db_name;
}
}
/**
* Implements hook_delete().
*/
function blastdb_delete($node) {
db_delete('blastdb')->condition('nid',$node->nid)->execute();
}
/**
* Implements hook_load().
*/
function blastdb_load($nodes) {
$sql = "
SELECT nid, name, path, dbtype, dbxref_id_regex, dbxref_db_id,
dbxref_linkout_type, cvitjs_enabled
FROM {blastdb}
WHERE nid IN (:nids)";
$result = db_query($sql, array(':nids' => array_keys($nodes)));
foreach ($result as $record) {
// Add basic blast node information.
$nodes[$record->nid]->db_name = $record->name;
$nodes[$record->nid]->db_path = $record->path;
$nodes[$record->nid]->title = $record->name;
$nodes[$record->nid]->db_dbtype = $record->dbtype;
// CViTjs status
$nodes[$record->nid]->cvitjs_enabled = $record->cvitjs_enabled;
// Determine the type of link-out chosen.
$types = module_invoke_all('blast_linkout_info');
$type = NULL;
if (isset($types[ $record->dbxref_linkout_type ])) {
$type = $types[ $record->dbxref_linkout_type ];
}
else {
tripal_report_error(
'blast_ui',
TRIPAL_ERROR,
'Unable to find details on the type of link-out choosen (%type). Have you defined hook_blast_linkout_info()? Make sure to clear the cache once you do so.',
array('%type' => $record->dbxref_linkout_type)
);
}
// Now determine if this node meets the requirements for the linkout
// chosen before adding linkout information.
$add_linkout = TRUE;
if (!$type OR $record->dbxref_linkout_type == 'none') {
$add_linkout = FALSE;
}
else {
if ($type['require_regex'] AND !$record->dbxref_id_regex) {
$add_linkout = FALSE;
}
if ($type['require_db'] AND !$record->dbxref_db_id) {
$add_linkout = FALSE;
}
}
// Add information related to link-outs to the node.
if ($add_linkout) {
$nodes[$record->nid]->linkout = new stdClass();
// If the link-out type requires a regex then provide one.
if ($type['require_regex']) {
if (preg_match('/\/.*\//', $record->dbxref_id_regex)) {
$nodes[$record->nid]->linkout->regex_type = 'custom';
$nodes[$record->nid]->linkout->regex = $record->dbxref_id_regex;
}
else {
$nodes[$record->nid]->linkout->regex_type = $record->dbxref_id_regex;
$nodes[$record->nid]->linkout->regex = get_blastdb_linkout_regex($nodes[$record->nid]);
}
}
else {
$nodes[$record->nid]->linkout->regex_type = 'none';
$nodes[$record->nid]->linkout->regex = NULL;
}
// If the link-out type requires a db then provide one.
if (isset($type['require_db'])) {
$nodes[$record->nid]->linkout->db_id = tripal_get_db(array('db_id' => $record->dbxref_db_id));
}
else {
$nodes[$record->nid]->linkout->db_id = NULL;
}
$nodes[$record->nid]->linkout->none = FALSE;
// Support complex link-outs.
$nodes[$record->nid]->linkout->type = $record->dbxref_linkout_type;
$nodes[$record->nid]->linkout->url_function = $type['process function'];
}
// If there is no linkout then provide some defaults.
else {
$nodes[$record->nid]->linkout = new stdClass();
$nodes[$record->nid]->linkout->regex = '';
$nodes[$record->nid]->linkout->db_id = 0;
$nodes[$record->nid]->linkout->none = TRUE;
}
}
}
/**
* AJAX Callback: Update Node Link-out Regex Textfield.
*
* On BlastDB node form the Link-out (dbxref) options allow for settings of a
* custom regex which should only be enabled when "Custom" is selected. This
* callback refreshes the regex textfield so it can change (ie: become enabled)
* when someone selects custom.
*/
function ajax_blast_ui_node_linkout_custom_callback($form, $form_state) {
return $form['dbxref']['details'];
}