/**
* Show Genes
*
* Display all genes in the database, or only genes beginning
* with a certain letter.
*
* @param char First letter of desired gene
*/
public function show_genes($f_letter = NULL)
{
redirect_all_nonmembers();
$f_letter = ucfirst($f_letter);
$data['title'] = $f_letter ? 'Genes - ' . $f_letter : 'Genes';
$data['content'] = 'genes/genes';
$data['genes'] = $this->genes_model->get_genes($f_letter);
$data['letters'] = range('A', 'Z');
$this->load->view($this->editor_layout, $data);
}
/**
* Submit changes
*
* This has 2 different functions:
* 1.) Save the variant confirmation selection, OR
* 2.) Release all variant changes
*
* 1.) Saves the confirmation selection for variant change
* quality control.
*
* 2.) Releases all changes currently within the queue.
* A backup is first created, then the changes are made, and finally
* the changes are emptied from the queue.
*
* @author Sean Ephraim
* @access public
* @return void
*/
public function submit_changes()
{
redirect_all_nonmembers();
// Refuse access to wanderers
if (!isset($_POST['save-changes']) && !isset($_POST['release-changes'])) {
die("Hmmm... you must have wandered here by mistake.");
}
// Update confirmation status of all variants on this page
$post = $this->input->post();
$variants = isset($post['variants-on-this-page']) ? $post['variants-on-this-page'] : NULL;
if (is_array($variants)) {
foreach ($variants as $variant_id) {
$old_review = $this->variations_model->get_variant_review_info($variant_id);
$data['confirmed_for_release'] = TRUE;
if (isset($post['unconfirmed-variants']) && array_search($variant_id, $post['unconfirmed-variants']) !== FALSE) {
// variant was found in list of unconfirmed variants
$data['confirmed_for_release'] = FALSE;
}
$this->variations_model->update_variant_review_info($variant_id, $data);
// Log the activity if the review changed
if (!empty($old_review) && $data['confirmed_for_release'] != (bool) $old_review->confirmed_for_release) {
$username = $this->ion_auth->user()->row()->username;
$variation = $this->db->get_where($this->tables['vd_queue'], array('id' => $variant_id))->row_array();
$gene = empty($variation['gene']) ? 'MISSING_GENE' : $variation['gene'];
$protein = empty($variation['hgvs_protein_change']) ? 'MISSING_PROTEIN_CHANGE' : $variation['hgvs_protein_change'];
$variation = empty($variation['variation']) ? 'MISSING_VARIATION' : $variation['variation'];
if ($data['confirmed_for_release']) {
activity_log("User '{$username}' confirmed changes for variant {$gene}|{$protein}|{$variation}", 'confirm');
} else {
activity_log("User '{$username}' unconfirmed changes for variant {$gene}|{$protein}|{$variation}", 'unconfirm');
}
}
}
}
if (isset($_POST['save-changes'])) {
// Confirmation changes saved
$html = 'Changes saved.';
$this->session->set_flashdata('success', $html);
} else {
if (isset($_POST['release-changes'])) {
// Attempt to RELEASE all changes
/* NOTE: A release can only be successful if all variant changes have been
* confirmed for release. This means that 'unconfirmed-variants' must be
* empty. If any checkboxes in the name of 'unconfirmed-variants' are checked,
* then this element will not be empty, and the attempt to release will fail.
*/
if ($_POST['special-release'] === 'none') {
$found_unconfirmed = FALSE;
if (isset($_POST['unconfirmed-variants']) && count($_POST['unconfirmed-variants']) > 0) {
// ERROR: found unconfirmed variants on this page
$found_unconfirmed = TRUE;
}
// Check that all variants in queue have been confirmed for release
$all_queue_variants = $this->variations_model->get_unreleased_changes();
foreach ($all_queue_variants as $variant_id => $values) {
$variant_review = $this->variations_model->get_variant_review_info($variant_id);
if ($variant_review->confirmed_for_release == 0) {
// ERROR: found unconfirmed variants in the queue (not necessarily on this page)
$found_unconfirmed = TRUE;
}
}
if ($found_unconfirmed) {
// Release failed! Not all variants have been confirmed for release
$html = 'All changes must be confirmed prior to release. Check the boxes on the right side to confirm each change, or see the bottom of this page for special release options.';
$this->session->set_flashdata('error', $html);
redirect('variations/unreleased');
}
}
if ($_POST['special-release'] === 'force-all' || $this->version == 0) {
// Release all variants regardless of confirmation status
$success = $this->variations_model->push_data_live(FALSE);
} else {
// Only release the confirmed variants
$success = $this->variations_model->push_data_live();
}
if ($success === TRUE) {
// Successful release
$confirmed = '';
if ($_POST['special-release'] === 'force-confirmed') {
$confirmed = 'confirmed ';
}
$html = '<p>' . ' <p><i class="icon-ok"></i> Backup created</p>' . ' <p><i class="icon-ok"></i> All ' . $confirmed . 'changes released</p>' . '</p>';
$this->session->set_flashdata('success', $html);
} else {
// ERROR: Problem with releasing changes
$html = '<p>There was an error releasing changes. Please make sure that any changes you would like to release have been confirmed and/or any special release options have been selected.</p>';
$this->session->set_flashdata('error', $html);
}
}
}
// Redirect to proper page
$refer_url = $this->session->flashdata('refer_url');
if (isset($_POST['release-changes']) || empty($refer_url)) {
// Return to default URL if there's no reference URL or after releasing changes
redirect('variations/unreleased');
} else {
// Return to reference URL
redirect($refer_url);
}
}
