$aForm = array_merge(array(array('POST', '', '', '', '40%', '14', '60%'), array('Emptying ' . $sID . ' gene database', 'All data associated to ' . $sID . ' will be deleted, as long as it\'s not associated with another gene. For instance, a variant that is mapped to ' . $sID . ' as well as another gene, will only lose the mapping to ' . $sID . '. A variant that is only described on ' . $sID . ' however, will be deleted. Also, an individual with a variant in ' . $sID . ', but also in another gene, will not be deleted, but the ' . $sID . ' variant data <I>will</I> be deleted. An individual that only has variants reported in ' . $sID . ' will be removed from the system.', 'print', 'Deleting ' . $nVariants . ' variant' . ($nVariants == 1 ? '' : 's') . ' and all associated data (screenings, individuals, phenotypes).<BR><B>All data (variants, screenings, individuals and phenotypes) only linked to ' . $sID . ' and not linked to any other gene will be deleted!</B>'), 'skip', array('Enter your password for authorization', '', 'password', 'password', 20), array('', '', 'submit', 'Empty gene database')));
lovd_viewForm($aForm);
print '</FORM>' . "\n\n";
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && preg_match('/^[a-z][a-z0-9#@-]*$/i', rawurldecode($_PE[1])) && ACTION == 'delete') {
// URL: /genes/DMD?delete
// Drop specific entry.
$sID = rawurldecode($_PE[1]);
define('PAGE_TITLE', 'Delete gene information entry ' . $sID);
define('LOG_EVENT', 'GeneDelete');
// Require manager clearance.
lovd_requireAUTH(LEVEL_MANAGER);
require ROOT_PATH . 'class/object_genes.php';
$_DATA = new LOVD_Gene();
$zData = $_DATA->loadEntry($sID);
// 2015-07-22; 3.0-14; Drop usage of CURRENT_PATH in favor of fixed $sID which may have a gene symbol with incorrect case.
// Now fix possible issues with capitalization. inc-init.php does this for $_SESSION['currdb'], but we're using $sID.
$sID = $zData['id'];
require ROOT_PATH . 'inc-lib-form.php';
// Check whether user has submitted and confirmed the form/action.
$bValidPassword = false;
$bConfirmation = !empty($_GET['confirm']);
if (POST) {
lovd_errorClean();
// Mandatory fields.
if (empty($_POST['password'])) {
lovd_errorAdd('password', 'Please fill in the \'Enter your password for authorization\' field.');
} elseif (!lovd_verifyPassword($_POST['password'], $_AUTH['password'])) {
lovd_errorAdd('password', 'Please enter your correct password for authorization.');
$aNavigation[CURRENT_PATH . '?edit'] = array('menu_edit.png', 'Edit screening information', 1);
if ($zData['variants_found']) {
$aNavigation['variants?create&target=' . $nID] = array('menu_plus.png', 'Add variant to screening', 1);
$aNavigation[CURRENT_PATH . '?removeVariants'] = array('cross.png', 'Remove variants from screening', $zData['variants_found_'] > 0 ? 1 : 0);
}
if ($_AUTH['level'] >= LEVEL_CURATOR) {
$aNavigation[CURRENT_PATH . '?delete'] = array('cross.png', 'Delete screening entry', 1);
}
}
lovd_showJGNavigation($aNavigation, 'Screenings');
if (!empty($zData['search_geneid'])) {
$_GET['search_geneid'] = html_entity_decode(rawurldecode($zData['search_geneid']));
print '<BR><BR>' . "\n\n";
$_T->printTitle('Genes screened', 'H4');
require ROOT_PATH . 'class/object_genes.php';
$_DATA = new LOVD_Gene();
$_DATA->setSortDefault('id');
$_DATA->viewList('Genes_for_S_VE', array(), true, true);
unset($_GET['search_geneid']);
}
if ($zData['variants_found'] || !empty($zData['variants'])) {
$_GET['search_screeningid'] = $nID;
print '<BR><BR>' . "\n\n";
$_T->printTitle('Variants found', 'H4');
require ROOT_PATH . 'class/object_custom_viewlists.php';
// VOG needs to be first, so it groups by the VOG ID.
$_DATA = new LOVD_CustomViewList(array('VariantOnGenome', 'Scr2Var', 'VariantOnTranscript'));
$_DATA->viewList('CustomVL_VOT_for_S_VE', array('transcriptid'), false, false, (bool) ($_AUTH['level'] >= LEVEL_MANAGER));
}
$_T->printFooter();
exit;
}
$sViewListID = 'Genes_SubmitVOT' . ($_GET['target'] ? '_' . $_GET['target'] : '');
$aOptionsList = array('width' => 600);
$aOptionsList['options'][0]['onclick'] = 'javascript:$(\'#container\').toggle(); lovd_stretchInputs(\'' . $sViewListID . '\');';
$aOptionsList['options'][0]['option_text'] = '<B>A variant that is located within a gene »»</B>';
$aOptionsList['options'][1]['onclick'] = 'variants?create&reference=Genome' . ($_GET['target'] ? '&target=' . $_GET['target'] : '');
$aOptionsList['options'][1]['option_text'] = '<B>A variant that was only described on genomic level »»</B>';
if ($_AUTH['level'] >= LEVEL_MANAGER) {
$aOptionsList['options'][2]['onclick'] = 'variants/upload?create' . ($_GET['target'] ? '&target=' . $_GET['target'] : '');
$aOptionsList['options'][2]['option_text'] = '<B>I want to upload a file with genomic variant data »»</B>';
}
print ' What kind of variant would you like to submit?<BR><BR>' . "\n\n";
print lovd_buildOptionTable($aOptionsList);
require ROOT_PATH . 'class/object_genes.php';
$_GET['page_size'] = 10;
$_DATA = new LOVD_Gene();
$_DATA->setRowLink($sViewListID, 'variants?create&reference=Transcript&geneid=' . $_DATA->sRowID . ($_GET['target'] ? '&target=' . $_GET['target'] : ''));
$_GET['search_transcripts'] = '>0';
print ' <DIV id="container" style="display : none;">' . "\n";
// Extra div is to prevent "No entries in the database yet!" error to show up if there are no genes in the database yet.
lovd_showInfoTable('Please find the gene for which you wish to submit this variant below, using the search fields if needed. <B>Click on the gene to proceed to the variant entry form</B>.<BR>If a gene is not shown in this display, but it does exist in this LOVD, then it does not have a transcript configured yet.', 'information', 600);
$_DATA->viewList($sViewListID, array('transcripts', 'variants', 'diseases_', 'updated_date_'));
print ' </DIV>' . "\n" . (!$bSubmit ? '' : ' <INPUT type="submit" value="Cancel" onclick="window.location.href=\'' . lovd_getInstallURL() . 'submit/screening/' . $_POST['screeningid'] . '\'; return false;" style="border : 1px solid #FF4422;">' . "\n");
$_T->printFooter();
exit;
} elseif (!in_array($_GET['reference'], array('Genome', 'Transcript')) || $_GET['reference'] == 'Transcript' && empty($_GET['geneid'])) {
exit;
}
// URL: /variants?create&reference=('Genome'|'Transcript')
// Create a variant on the genome.
if ($_GET['reference'] == 'Transcript') {