|
|
@@ -145,16 +145,6 @@ class GFF3Importer extends TripalImporter {
|
|
|
expression would be "$1-P$2".'),
|
|
|
];
|
|
|
|
|
|
- $form['advanced']['use_transaction'] = [
|
|
|
- '#type' => 'checkbox',
|
|
|
- '#title' => t('Use a transaction'),
|
|
|
- '#required' => FALSE,
|
|
|
- '#description' => t('Use a database transaction when loading the GFF file. If an error occurs
|
|
|
- the entire datset loaded prior to the failure will be rolled back and will not be available
|
|
|
- in the database. If this option is unchecked and failure occurs all records up to the point
|
|
|
- of failure will be present in the database.'),
|
|
|
- '#default_value' => 1,
|
|
|
- ];
|
|
|
$form['advanced']['add_only'] = [
|
|
|
'#type' => 'checkbox',
|
|
|
'#title' => t('Import only new features'),
|
|
|
@@ -266,7 +256,6 @@ class GFF3Importer extends TripalImporter {
|
|
|
$update = $form_state['values']['update'];
|
|
|
$refresh = 0; //$form_state['values']['refresh'];
|
|
|
$remove = 0; //$form_state['values']['remove'];
|
|
|
- $use_transaction = $form_state['values']['use_transaction'];
|
|
|
$line_number = trim($form_state['values']['line_number']);
|
|
|
$landmark_type = trim($form_state['values']['landmark_type']);
|
|
|
$alt_id_attr = trim($form_state['values']['alt_id_attr']);
|
|
|
@@ -319,7 +308,6 @@ class GFF3Importer extends TripalImporter {
|
|
|
$update = $arguments['update'];
|
|
|
$refresh = FALSE;
|
|
|
$remove = FALSE;
|
|
|
- $use_transaction = $arguments['use_transaction'];
|
|
|
$target_organism_id = $arguments['target_organism_id'];
|
|
|
$target_type = $arguments['target_type'];
|
|
|
$create_target = $arguments['create_target'];
|
|
|
@@ -337,7 +325,7 @@ class GFF3Importer extends TripalImporter {
|
|
|
|
|
|
|
|
|
$this->loadGFF3($file_path, $organism_id, $analysis_id,
|
|
|
- $add_only, $update, $refresh, $remove, $use_transaction,
|
|
|
+ $add_only, $update, $refresh, $remove,
|
|
|
$target_organism_id, $target_type, $create_target,
|
|
|
$start_line, $landmark_type, $alt_id_attr, $create_organism,
|
|
|
$re_mrna, $re_protein, $skip_protein);
|
|
|
@@ -367,9 +355,6 @@ class GFF3Importer extends TripalImporter {
|
|
|
* @param $remove
|
|
|
* Set to 1 to remove features present in the GFF file that exist in the
|
|
|
* database. Default is 0.
|
|
|
- * @param $use_transaction
|
|
|
- * Set to 1 to use a transaction when loading the GFF. Any failure during
|
|
|
- * loading will result in the rollback of any changes. Default is 1.
|
|
|
* @param $target_organism_id
|
|
|
* If the GFF file contains a 'Target' attribute then the feature and the
|
|
|
* target will have an alignment created, but to find the proper target
|
|
|
@@ -426,7 +411,7 @@ class GFF3Importer extends TripalImporter {
|
|
|
* @ingroup gff3_loader
|
|
|
*/
|
|
|
private function loadGFF3($gff_file, $organism_id, $analysis_id,
|
|
|
- $add_only = 0, $update = 1, $refresh = 0, $remove = 0, $use_transaction = 1,
|
|
|
+ $add_only = 0, $update = 1, $refresh = 0, $remove = 0,
|
|
|
$target_organism_id = NULL, $target_type = NULL, $create_target = 0,
|
|
|
$start_line = 1, $landmark_type = '', $alt_id_attr = '', $create_organism = FALSE,
|
|
|
$re_mrna = '', $re_protein = '', $skip_protein = 0) {
|
Peter Richter