}
return $sLogMessage;
}
if (PATH_COUNT == 1 && !ACTION) {
// URL: /genes
// View all entries.
// Managers are allowed to download this list...
if ($_AUTH['level'] >= LEVEL_MANAGER) {
define('FORMAT_ALLOW_TEXTPLAIN', true);
}
define('PAGE_TITLE', 'View all genes');
$_T->printHeader();
$_T->printTitle();
require ROOT_PATH . 'class/object_genes.php';
$_DATA = new LOVD_Gene();
$_DATA->viewList('Genes', array(), false, false, (bool) ($_AUTH['level'] >= LEVEL_MANAGER));
$_T->printFooter();
exit;
}
if (PATH_COUNT == 2 && preg_match('/^[a-z][a-z0-9#@-]*$/i', rawurldecode($_PE[1])) && !ACTION) {
// URL: /genes/DMD
// View specific entry.
$sID = rawurldecode($_PE[1]);
define('PAGE_TITLE', 'View ' . $sID . ' gene homepage');
$_T->printHeader();
$_T->printTitle();
lovd_printGeneHeader();
// Load appropriate user level for this gene.
lovd_isAuthorized('gene', $sID);
require ROOT_PATH . 'class/object_genes.php';
$_DATA = new LOVD_Gene();
$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));
}
$_T->printFooter();
exit;
}
if (PATH_COUNT == 1 && ACTION == 'create' && isset($_GET['target']) && ctype_digit($_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') {
// On purpose not checking for format of $_GET['geneid']. If it's not right, we'll automatically get to the error message below.
$sGene = $_DB->query('SELECT id FROM ' . TABLE_GENES . ' WHERE id = ?', array($_GET['geneid']))->fetchColumn();
if (!$sGene) {
define('PAGE_TITLE', 'Create a new variant entry');
$_T->printHeader();
$_T->printTitle();
