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