$_T->printFooter(false);
// The false prevents the footer to actually close the <BODY> and <HTML> tags.
// Now we're still in the <BODY> so the progress bar can add <SCRIPT> tags as much as it wants.
flush();
// Now, start with ALTER TABLE if necessary, since that will take the longest time and ends a transaction anyway.
// If it fails directly after this, one can always just redo the add. LOVD will detect properly that it needs to be added to the ACTIVE_COLS table, then.
if (!$zData['active_checked']) {
$sSQL = 'ALTER TABLE ' . $aTableInfo['table_sql'] . ' ADD COLUMN `' . $zData['id'] . '` ' . $zData['mysql_type'];
$dStart = time();
$q = $_DB->exec($sSQL, false);
if ($q === false) {
$sError = $_DB->formatError();
// Save the PDO error before it disappears.
$tPassed = time() - $dStart;
$sMessage = $tPassed < 2 ? '' : ' (fail after ' . $tPassed . ' seconds - disk full maybe?)';
lovd_queryError(LOG_EVENT . $sMessage, $sSQL, $sError);
}
}
$_BAR->setProgress(80);
$_BAR->setMessage('Enabling column...');
$_DB->beginTransaction();
if (!$zData['active']) {
$sSQL = 'INSERT INTO ' . TABLE_ACTIVE_COLS . ' VALUES (?, ?, NOW())';
$_DB->query($sSQL, array($zData['id'], $_AUTH['id']));
}
// Write to log...
if (!$zData['active']) {
lovd_writeLog('Event', LOG_EVENT, 'Added column ' . $zData['id'] . ' (' . $zData['head_column'] . ') to ' . $aTableInfo['table_name'] . ' table');
}
$_BAR->setProgress(90);
$_BAR->setMessage('Registering column settings...');
function loadEntry($nID = false)
{
// Loads and returns an entry from the database.
global $_DB, $_T;
if (empty($nID)) {
// We were called, but the class wasn't initiated with an ID. Fail.
lovd_displayError('LOVD-Lib', 'Objects::(' . $this->sObject . ')::loadEntry() - Method didn\'t receive ID');
}
if ($this->sSQLPreLoadEntry !== '') {
// $sSQLPreLoadEntry is defined, execute it.
$_DB->query($this->sSQLPreLoadEntry);
}
// Build query.
if ($this->sSQLLoadEntry) {
$sSQL = $this->sSQLLoadEntry;
} else {
$sSQL = 'SELECT * FROM ' . constant($this->sTable) . ' WHERE id = ?';
}
$q = $_DB->query($sSQL, array($nID), false);
if ($q) {
$zData = $q->fetchAssoc();
}
if (!$q || !$zData) {
$sError = $_DB->formatError();
// Save the PDO error before it disappears.
$_T->printHeader();
if (defined('PAGE_TITLE')) {
$_T->printTitle();
}
if ($sError) {
lovd_queryError($this->sObject . '::loadEntry()', $sSQL, $sError);
}
lovd_showInfoTable('No such ID!', 'stop');
$_T->printFooter();
exit;
} else {
$this->nID = $nID;
}
$zData = $this->autoExplode($zData);
return $zData;
}
function loadAll($nID = false)
{
// Loads all variantOnTranscript entries from the database.
global $_DB, $_T;
if (empty($nID)) {
// We were called, but the class wasn't initiated with an ID. Fail.
lovd_displayError('LOVD-Lib', 'Objects::(' . $this->sObject . ')::loadEntry() - Method didn\'t receive ID');
}
$q = $_DB->query($this->sSQLLoadEntry, array($nID, $this->sObjectID), false);
if ($q) {
$z = $q->fetchAllAssoc();
}
if (!$q || !$z) {
$sError = $_DB->formatError();
// Save the PDO error before it disappears.
$_T->printHeader();
if (defined('PAGE_TITLE')) {
$_T->printTitle();
}
if ($sError) {
lovd_queryError($this->sObject . '::loadEntry()', $sSQL, $sError);
}
lovd_showInfoTable('No such ID!', 'stop');
$_T->printFooter();
exit;
}
$zData = array();
foreach ($z as $aVariantOnTranscript) {
$aVariantOnTranscript = $this->autoExplode($aVariantOnTranscript);
foreach ($this->aColumns as $sColClean => $aCol) {
$sCol = $aVariantOnTranscript['transcriptid'] . '_' . $sColClean;
if ($aCol['form_type'][2] == 'select' && $aCol['form_type'][3] > 1) {
$zData[$sCol] = explode(';', $aVariantOnTranscript[$sColClean]);
} else {
$zData[$sCol] = $aVariantOnTranscript[$sColClean];
}
}
$zData[$aVariantOnTranscript['transcriptid'] . '_effectid'] = $aVariantOnTranscript['effectid'];
$zData[$aVariantOnTranscript['transcriptid'] . '_position_c_start'] = $aVariantOnTranscript['position_c_start'];
$zData[$aVariantOnTranscript['transcriptid'] . '_position_c_start_intron'] = $aVariantOnTranscript['position_c_start_intron'];
$zData[$aVariantOnTranscript['transcriptid'] . '_position_c_end'] = $aVariantOnTranscript['position_c_end'];
$zData[$aVariantOnTranscript['transcriptid'] . '_position_c_end_intron'] = $aVariantOnTranscript['position_c_end_intron'];
}
return $zData;
}
$sSQLFailed = '';
foreach ($aUpdates as $sVersion => $aSQL) {
$_BAR->setMessage('To ' . $sVersion . '...');
// Also set update_checked_date to NULL, so LOVD will again check for updates as soon as possible.
$aSQL[] = 'UPDATE ' . TABLE_STATUS . ' SET version = "' . $sVersion . '", updated_date = NOW(), update_level = 0, update_checked_date = NULL';
// Loop needed queries...
foreach ($aSQL as $i => $sSQL) {
$i++;
if (!$nSQLFailed) {
$q = $_DB->query($sSQL, false, false);
// This means that there is no SQL injection check here. But hey - these are our own queries.
if (!$q) {
$nSQLFailed++;
// Error when running query.
$sError = $_DB->formatError();
lovd_queryError('RunUpgradeSQL', $sSQL, $sError, false);
$sSQLFailed = 'Error!<BR><BR>\\n\\n' . 'Error while executing query ' . $i . ':\\n' . '<PRE style="background : #F0F0F0;">' . htmlspecialchars($sError) . '</PRE><BR>\\n\\n' . 'This implies these MySQL queries need to be executed manually:<BR>\\n' . '<PRE style="background : #F0F0F0;">\\n<SPAN style="background : #C0C0C0;">' . sprintf('%' . strlen(count($aSQL)) . 'd', $i) . '</SPAN> ' . htmlspecialchars($sSQL) . ';\\n';
} else {
$nSQLDone++;
$nSQLDonePercentage = floor(100 * $nSQLDone / $nSQL);
// Don't want to show 100% when an error occurs at 99.5%.
if ($nSQLDonePercentage != $nSQLDonePercentagePrev) {
$_BAR->setProgress($nSQLDonePercentage);
$nSQLDonePercentagePrev = $nSQLDonePercentage;
}
flush();
usleep(1000);
}
} else {
// Something went wrong, so we need to print out the remaining queries...
$nSQLFailed++;
function execute($aSQL = array(), $bHalt = true, $bTrim = false)
{
// Wrapper around PDOStatement::execute().
global $_DB;
try {
if ($aSQL === (array) $aSQL) {
// Believe it or not, faster than is_array().
// lovd_queryDB() allowed the passing of arrays in the arguments.
foreach ($aSQL as $nKey => $Arg) {
if ($Arg === (array) $Arg) {
// Believe it or not, faster than is_array().
// We handle arrays gracefully.
$aSQL[$nKey] = implode(';', $bTrim ? array_map('trim', $Arg) : $Arg);
} elseif ($Arg === NULL) {
$this->bindValue($nKey + 1, $Arg, PDO::PARAM_INT);
} elseif ($bTrim) {
$aSQL[$nKey] = trim($aSQL[$nKey]);
}
}
}
// There is no else, we will catch the exception thrown by parent::execute().
parent::execute($aSQL);
} catch (PDOException $e) {
// Incorrect SQL, too few parameters, ...
if ($bHalt) {
try {
@$_DB->rollBack();
// In case we were in a transaction. // FIXME; we can know from PHP >= 5.3.3.
} catch (PDOException $eNoTransaction) {
}
// lovd_queryError() will call lovd_displayError() which will halt the system.
lovd_queryError(defined('LOG_EVENT') ? LOG_EVENT : 'Unknown', $this->queryString, 'Error in PDOStatement::execute() while executing prepared query: ' . $e->getMessage());
} else {
return false;
}
}
return true;
}
