$aFields = array('id', 'name', 'chromosome', 'chrom_band', 'imprinting', 'refseq_genomic', 'refseq_UD', 'reference', 'url_homepage', 'url_external', 'allow_download', 'allow_index_wiki', 'id_hgnc', 'id_entrez', 'id_omim', 'show_hgmd', 'show_genecards', 'show_genetests', 'note_index', 'note_listing', 'refseq', 'refseq_url', 'disclaimer', 'disclaimer_text', 'header', 'header_align', 'footer', 'footer_align', 'created_by', 'created_date');
// Prepare values.
$_POST['created_by'] = $_AUTH['id'];
if (empty($_POST['created_date']) || @strtotime($_POST['created_date']) > time()) {
$_POST['created_date'] = date('Y-m-d H:i:s');
}
$_POST['id'] = $zData['id'];
$_POST['name'] = $zData['name'];
$_POST['refseq_UD'] = $zData['refseq_UD'];
$_POST['chromosome'] = $zData['chromosome'];
$_POST['id_hgnc'] = $zData['id_hgnc'];
$_POST['id_entrez'] = $zData['id_entrez'] ? $zData['id_entrez'] : '';
$_POST['id_omim'] = $zData['id_omim'] ? $zData['id_omim'] : '';
$_DATA['Genes']->insertEntry($_POST, $aFields);
// Add the default custom columns to this gene.
lovd_addAllDefaultCustomColumns('gene', $_POST['id']);
// Write to log...
lovd_writeLog('Event', LOG_EVENT, 'Created gene information entry ' . $_POST['id'] . ' (' . $_POST['name'] . ')');
// Make current user curator of this gene.
$_DB->query('INSERT INTO ' . TABLE_CURATES . ' VALUES (?, ?, ?, ?)', array($_AUTH['id'], $_POST['id'], 1, 1));
// Add diseases.
$aSuccessDiseases = array();
if (!empty($_POST['active_diseases']) && is_array($_POST['active_diseases'])) {
foreach ($_POST['active_diseases'] as $nDisease) {
// Add disease to gene.
if ($nDisease) {
$q = $_DB->query('INSERT INTO ' . TABLE_GEN2DIS . ' VALUES (?, ?)', array($_POST['id'], $nDisease), false);
if (!$q) {
// Silent error.
lovd_writeLog('Error', LOG_EVENT, 'Disease information entry ' . $nDisease . ' - could not be added to gene ' . $_POST['id']);
} else {
require ROOT_PATH . 'inc-lib-actions.php';
require ROOT_PATH . 'class/object_diseases.php';
$_DATA = new LOVD_Disease();
require ROOT_PATH . 'inc-lib-form.php';
if (!empty($_POST)) {
lovd_errorClean();
$_DATA->checkFields($_POST);
if (!lovd_error()) {
// Fields to be used.
$aFields = array('symbol', 'name', 'id_omim', 'tissues', 'features', 'remarks', 'created_by', 'created_date');
// Prepare values.
$_POST['created_by'] = $_AUTH['id'];
$_POST['created_date'] = date('Y-m-d H:i:s');
$nID = $_DATA->insertEntry($_POST, $aFields);
// Add all standard custom columns to this new disease.
lovd_addAllDefaultCustomColumns('disease', $nID);
// Write to log...
lovd_writeLog('Event', LOG_EVENT, 'Created disease information entry ' . $nID . ' - ' . $_POST['symbol'] . ' (' . $_POST['name'] . ')');
// Add genes.
$aSuccess = array();
if (!empty($_POST['genes'])) {
foreach ($_POST['genes'] as $sGene) {
// Add gene to disease.
// FIXME; Nu dat PDO beschikbaar is, doe dit in een prepared statement met multiple executes.
$q = $_DB->query('INSERT INTO ' . TABLE_GEN2DIS . ' VALUES (?, ?)', array($sGene, $nID), false);
if (!$q) {
// Silent error.
lovd_writeLog('Error', LOG_EVENT, 'Disease information entry ' . $nID . ' - ' . $_POST['symbol'] . ' - could not be added to gene ' . $sGene);
} else {
$aSuccess[] = $sGene;
}
if (!empty($aFieldsTranscript)) {
// Mapping is going to succeed! Let's add this gene and transcript.
$aVariantOnTranscriptSQL = $aVariantOnTranscriptSQL[$aFieldsTranscript['id_ncbi']];
// But first check if the gene was already there without transcripts.
if (!$_DB->query('SELECT COUNT(*) FROM ' . TABLE_GENES . ' WHERE id = ?', array($sSymbol))->fetchColumn()) {
$aFields = array('id' => $sSymbol, 'name' => $sGeneName, 'chromosome' => $sChromosome, 'chrom_band' => $sChromBand, 'refseq_genomic' => $sRefseqGenomic, 'refseq_UD' => $sRefseqUD, 'reference' => '', 'url_homepage' => '', 'url_external' => '', 'allow_download' => 0, 'allow_index_wiki' => 0, 'id_hgnc' => $sHgncID, 'id_entrez' => $sEntrez, 'id_omim' => $sOmim, 'show_hgmd' => 1, 'show_genecards' => 1, 'show_genetests' => 1, 'note_index' => '', 'note_listing' => '', 'refseq' => '', 'refseq_url' => '', 'disclaimer' => 1, 'disclaimer_text' => '', 'header' => '', 'header_align' => -1, 'footer' => '', 'footer_align' => -1, 'created_by' => 0, 'created_date' => date('Y-m-d H:i:s'), 'updated_by' => 0, 'updated_date' => date('Y-m-d H:i:s'));
$_DB->query('INSERT INTO ' . TABLE_GENES . ' (' . implode(', ', array_keys($aFields)) . ') VALUES (?' . str_repeat(', ?', count($aFields) - 1) . ')', array_values($aFields));
// Only assign newly inserted genes to managers. If the creator of the variant is not a manager, make the database admin the curator for this gene.
if (empty($aManagerList)) {
// Building the list of managers only once.
$aManagerList = $_DB->query('SELECT id FROM ' . TABLE_USERS . ' WHERE level >= ' . LEVEL_MANAGER . ' ORDER BY level DESC')->fetchAllColumn();
}
$nCurator = array_search($aVariant['created_by'], $aManagerList) !== false ? $aVariant['created_by'] : $aManagerList[0];
$_DB->query('INSERT INTO ' . TABLE_CURATES . ' VALUES (?, ?, ?, ?)', array($nCurator, $sSymbol, 1, 1));
// Also activate default custom columns for this gene.
lovd_addAllDefaultCustomColumns('gene', $sSymbol, 0);
}
// Now insert the transcript.
$q = $_DB->query('INSERT IGNORE INTO ' . TABLE_TRANSCRIPTS . ' (' . implode(', ', array_keys($aFieldsTranscript)) . ') VALUES (?' . str_repeat(', ?', count($aFieldsTranscript) - 1) . ')', array_values($aFieldsTranscript));
if ($q->rowCount()) {
// Get the ID of the newly inserted transcript.
$nID = $_DB->lastInsertId();
} else {
// This transcript was just added by a concurrent call to the mapping script. Get its ID and map on.
$nID = $_DB->query('SELECT id FROM ' . TABLE_TRANSCRIPTS . ' WHERE id_ncbi = ?', array($aFieldsTranscript['id_ncbi']))->fetchColumn();
}
// Get the p. description too.
$aPrediction = lovd_getRNAProteinPrediction($sRefseqUD, $sSymbol, $aFieldsTranscript['id_ncbi'], $aVariantOnTranscriptSQL[1][7]);
$aVariantOnTranscriptSQL[1][8] = empty($aPrediction['predict']['RNA']) ? '' : $aPrediction['predict']['RNA'];
$aVariantOnTranscriptSQL[1][9] = empty($aPrediction['predict']['protein']) ? '' : $aPrediction['predict']['protein'];
// Map the variant to the newly inserted transcript.
