function printFooterHTML($bCloseHTML = true)
{
// Print the LOVD footer, including the update checker and mapper (if $bFull == true).
global $_AUTH, $_SETT, $_STAT;
if (ROOT_PATH == '../' && !(defined('TAB_SELECTED') && TAB_SELECTED == 'docs')) {
// In the install directory, closing the tables opened by /install/index.php that /install/inc-bot.php used to close.
print "\n\n" . ' </TD>' . "\n" . ' </TR>' . "\n" . '</TABLE>' . "\n";
}
?>
</TD>
</TR>
</TABLE>
<?php
if (!$this->bFull) {
if ($bCloseHTML) {
// Close the <BODY> and <HTML> tags. Normal behaviour except when for instance the Progress Bar is used.
print "\n" . '</BODY>' . "\n" . '</HTML>' . "\n";
}
return true;
}
?>
</DIV>
<BR>
<TABLE border="0" cellpadding="0" cellspacing="0" width="100%" class="footer">
<TR>
<TD width="84">
</TD>
<TD align="center">
<?php
if (substr(lovd_getProjectFile(), 0, 6) == '/docs/') {
// In documents section.
print ' For the latest version of the LOVD manual, <A href="' . $_SETT['upstream_URL'] . $_SETT['system']['tree'] . '/docs/" target="_blank">check the online version</A>.<BR>' . "\n";
}
print ' Powered by <A href="' . $_SETT['upstream_URL'] . $_STAT['tree'] . '/" target="_blank">LOVD v.' . $_STAT['tree'] . '</A> Build ' . $_STAT['build'] . '<BR>' . "\n" . ' LOVD software ©2004-2016 <A href="http://www.lumc.nl/" target="_blank">Leiden University Medical Center</A>' . "\n";
?>
</TD>
<TD width="42" align="right">
<IMG src="gfx/lovd_mapping_99.png" alt="" title="" width="32" height="32" id="mapping_progress" style="margin : 5px;">
</TD>
<TD width="42" align="right">
<?php
if (!(defined('NOT_INSTALLED') || defined('MISSING_CONF') || defined('MISSING_STAT'))) {
if (time() - strtotime($_STAT['update_checked_date']) > 60 * 60 * 24) {
// Check for updates!
$sImgURL = 'check_update?icon';
} else {
// No need to re-check, use saved info.
if ($_STAT['update_version'] == 'Error') {
$sType = 'error';
} elseif (lovd_calculateVersion($_STAT['update_version']) > lovd_calculateVersion($_SETT['system']['version'])) {
$sType = 'newer';
} else {
$sType = 'newest';
}
$sImgURL = 'gfx/lovd_update_' . $sType . '_blue.png';
}
if ($_AUTH && ($_AUTH['level'] >= LEVEL_MANAGER || count($_AUTH['curates']))) {
print ' <A href="#" onclick="lovd_openWindow(\'' . lovd_getInstallURL() . 'check_update\', \'CheckUpdate\', 650, 175); return false;"><IMG src="' . $sImgURL . '" alt="" width="32" height="32" style="margin : 5px;"></A>' . "\n";
} else {
print ' <IMG src="' . $sImgURL . '" alt="" width="32" height="32" style="margin : 5px;">' . "\n";
}
}
?>
</TD>
</TR>
</TABLE>
</TD></TR></TABLE>
<SCRIPT type="text/javascript">
<!--
<?php
if (!(ROOT_PATH == '../' && !(defined('TAB_SELECTED') && TAB_SELECTED == 'docs') || defined('NOT_INSTALLED'))) {
// In install directory.
print '
function lovd_mapVariants ()
{
// This function requests the script that will do the actual work.
// First unbind any onclick handlers on the status image.
$("#mapping_progress").unbind();
// Now request the script.
$.get("ajax/map_variants.php", function (sResponse)
{
// The server responded successfully. Let\'s see what he\'s saying.
aResponse = sResponse.split("\\t");
$("#mapping_progress").attr({"src": "gfx/lovd_mapping_" + aResponse[1] + (aResponse[1] == "preparing"? ".gif" : ".png"), "title": aResponse[2]});
if (sResponse.indexOf("Notice") >= 0 || sResponse.indexOf("Warning") >= 0 || sResponse.indexOf("Error") >= 0 || sResponse.indexOf("Fatal") >= 0) {
// Something went wrong while processing the request, don\'t try again.
$("#mapping_progress").attr({"src": "gfx/lovd_mapping_99.png", "title": "There was a problem with LOVD while mapping variants to transcripts: " + sResponse});
} else if (aResponse[0] == "' . AJAX_TRUE . '") {
// More variants to map. Re-call.
setTimeout("lovd_mapVariants()", 50);
} else {
// No more variants to map. But allow the user to try.
$("#mapping_progress").click(lovd_mapVariants);
}
}
).fail(function (oObject, sStatus)
{
// Something went wrong while contacting the server, don\'t try again.
$("#mapping_progress").attr({"src": "gfx/lovd_mapping_99.png", "title": "There was a problem with LOVD while mapping variants to transcripts: " + sStatus});
}
);
}
';
// Not every page request should trigger the mapping...
if (!empty($_SESSION['mapping']['time_complete']) && $_SESSION['mapping']['time_complete'] >= time() - 60 * 60 * 24) {
// If it is less than one day ago that mapping was complete, don't start it automatically, but allow the user to start it himself.
print '$("#mapping_progress").click(lovd_mapVariants);' . "\n";
} elseif (!empty($_SESSION['mapping']['time_error']) && $_SESSION['mapping']['time_error'] >= time() - 60 * 60) {
// If it is less than one hour ago that an error occurred, don't start it either.
print '$("#mapping_progress").click(lovd_mapVariants);' . "\n";
print '$("#mapping_progress").attr("Title", "Mapping is temporarily suspended because of network problems on the last attempt. Click to retry.");' . "\n";
} else {
// Start mapping!
print 'setTimeout("lovd_mapVariants()", 500);' . "\n";
}
}
?>
// -->
</SCRIPT>
<?php
if ($bCloseHTML) {
// Close the <BODY> and <HTML> tags. Normal behaviour except when for instance the Progress Bar is used.
print '</BODY>' . "\n" . '</HTML>' . "\n";
} else {
flush();
@ob_end_flush();
// Can generate errors on the screen if no buffer found.
}
return true;
}
function viewList($sViewListID = false, $aColsToSkip = array(), $bNoHistory = false, $bHideNav = false, $bOptions = false, $bOnlyRows = false, $bFindReplace = false)
{
// Show a viewlist for the current object.
// Params:
// bFindReplace if true, find & replace option is shown in viewlist options menu.
// Views list of entries in the database, allowing search.
global $_DB, $_INI, $_SETT;
if (!defined('LOG_EVENT')) {
define('LOG_EVENT', $this->sObject . '::viewList()');
}
if (FORMAT == 'text/plain' && !defined('FORMAT_ALLOW_TEXTPLAIN')) {
die('text/plain not allowed here');
}
$bAjax = substr(lovd_getProjectFile(), 0, 6) == '/ajax/';
// ViewLists need an ID to identify the specific viewList, in case there are a few in one document.
if (!$sViewListID || !is_string($sViewListID)) {
$sViewListID = lovd_generateRandomID();
} else {
$sViewListID = preg_replace('/[^A-Z0-9._-]+/i', '', $sViewListID);
}
if (!is_array($aColsToSkip)) {
$aColsToSkip = array($aColsToSkip);
}
foreach ($this->aColumnsViewList as $sCol => $aCol) {
if (!$aCol['view'] && !in_array($sCol, $aColsToSkip)) {
$aColsToSkip[] = $sCol;
}
}
require_once ROOT_PATH . 'inc-lib-viewlist.php';
// First, check if entries are in the database at all.
$nTotal = $this->getCount();
if (!$nTotal && FORMAT == 'text/html') {
if ($bOnlyRows) {
die('0');
// Silent error.
}
lovd_showInfoTable('No entries in the database yet!', 'stop');
return 0;
}
// Process search fields (i.e. $_GET['search_...'] values) for viewlist.
list($WHERE, $HAVING, $aArguments, $aBadSyntaxColumns, $aColTypes) = $this->processViewListSearchArgs($_GET);
if ($WHERE) {
$this->aSQLViewList['WHERE'] .= ($this->aSQLViewList['WHERE'] ? ' AND ' : '') . $WHERE;
}
if ($HAVING) {
$this->aSQLViewList['HAVING'] .= ($this->aSQLViewList['HAVING'] ? ' AND ' : '') . $HAVING;
}
// SORT: Current settings, also implementing XSS check.
if (!empty($_GET['order']) && $_GET['order'] === strip_tags($_GET['order'])) {
$aOrder = explode(',', $_GET['order']);
} else {
$aOrder = array('', '');
}
// SORT: Verify request and set default.
if (empty($this->aColumnsViewList[$aOrder[0]]['db'][1])) {
$aOrder[0] = $this->sSortDefault;
}
if ($aOrder[1] != 'ASC' && $aOrder[1] != 'DESC') {
$aOrder[1] = $this->aColumnsViewList[$aOrder[0]]['db'][1];
}
$sSQLOrderBy = $this->aColumnsViewList[$aOrder[0]]['db'][0] . ' ' . $aOrder[1];
if (in_array($aOrder[0], array('chromosome', 'VariantOnGenome/DNA'))) {
// 2014-03-07; 3.0-10; We need to find the table alias of the VOG or genes table, because otherwise MySQL fails here ('chromosome' is ambiguous) if both are joined.
// 2014-04-28; 3.0-10; Prefer the genes table, since it joins to VOG as well, but may not have results which messes up the order.
$sAlias = '';
if (preg_match('/' . TABLE_GENES . ' AS ([a-z]+)/i', $this->aSQLViewList['FROM'], $aRegs)) {
$sAlias = $aRegs[1];
} elseif (preg_match('/' . TABLE_VARIANTS . ' AS ([a-z]+)/i', $this->aSQLViewList['FROM'], $aRegs)) {
$sAlias = $aRegs[1];
}
$this->aSQLViewList['FROM'] .= ' LEFT OUTER JOIN ' . TABLE_CHROMOSOMES . ' AS chr ON (' . (!$sAlias ? '' : $sAlias . '.') . 'chromosome = chr.name)';
$sSQLOrderBy = 'chr.sort_id ' . $aOrder[1];
if ($aOrder[0] == 'VariantOnGenome/DNA') {
$sSQLOrderBy .= ', position_g_start ' . $aOrder[1] . ', position_g_end ' . $aOrder[1] . ', `VariantOnGenome/DNA` ' . $aOrder[1];
}
} elseif ($aOrder[0] == 'VariantOnTranscript/DNA') {
$sSQLOrderBy = 'position_c_start ' . $aOrder[1] . ', position_c_start_intron ' . $aOrder[1] . ', position_c_end ' . $aOrder[1] . ', position_c_end_intron ' . $aOrder[1] . ', `VariantOnTranscript/DNA` ' . $aOrder[1];
}
// At this point, we're not sure if we'll actually use the ORDER BY at all.
$this->aSQLViewList['ORDER_BY'] = $sSQLOrderBy . (empty($this->aSQLViewList['ORDER_BY']) ? '' : ', ' . $this->aSQLViewList['ORDER_BY']);
// Only print stuff if we're not in Ajax right now.
if (!$bAjax && FORMAT == 'text/html') {
// Keep the URL clean; disable any fields that are not used.
lovd_includeJS('inc-js-viewlist.php' . (!$bNoHistory ? '' : '?nohistory'));
lovd_includeJS('inc-js-tooltip.php');
// Print form; required for sorting and searching.
// Because we don't want the form to submit itself while we are waiting for the Ajax response, we need to kill the native submit() functionality.
print ' <FORM action="' . CURRENT_PATH . '" method="get" id="viewlistForm_' . $sViewListID . '" style="margin : 0px;" onsubmit="return false;">' . "\n" . ' <INPUT type="hidden" name="viewlistid" value="' . $sViewListID . '">' . "\n" . ' <INPUT type="hidden" name="object" value="' . $this->sObject . '">' . "\n" . (!isset($this->sObjectID) ? '' : ' <INPUT type="hidden" name="object_id" value="' . $this->sObjectID . '">' . "\n") . (!isset($this->nID) ? '' : ' <INPUT type="hidden" name="id" value="' . $this->nID . '">' . "\n") . (!ACTION ? '' : ' <INPUT type="hidden" name="' . ACTION . '" value="">' . "\n") . ' <INPUT type="hidden" name="order" value="' . implode(',', $aOrder) . '">' . "\n";
// Skipping (permanently hiding) columns.
foreach ($aColsToSkip as $sCol) {
if (array_key_exists($sCol, $this->aColumnsViewList)) {
// Internet Explorer refuses to submit input with equal names. If names are different, everything works fine.
// Somebody please tell me it's a bug and nobody's logical thinking. Had to include $sCol to make it work.
print ' <INPUT type="hidden" name="skip[' . $sCol . ']" value="' . $sCol . '">' . "\n";
// Check if we're skipping columns, that do have a search value. If so, it needs to be sent on like this.
if (isset($_GET['search_' . $sCol])) {
print ' <INPUT type="hidden" name="search_' . $sCol . '" value="' . htmlspecialchars($_GET['search_' . $sCol]) . '">' . "\n";
}
}
}
if ($bHideNav) {
print ' <INPUT type="hidden" name="hidenav" value="true">' . "\n";
}
if ($bOptions) {
print ' <INPUT type="hidden" name="options" value="true">' . "\n";
}
print "\n";
}
// Make a reference variable of the session for cleaner code.
$aSessionViewList =& $_SESSION['viewlists'][$sViewListID];
// To make row ids persist when the viewList is refreshed, we must store the row id in $_SESSION.
if (!empty($aSessionViewList['row_id'])) {
$this->sRowID = $aSessionViewList['row_id'];
} else {
$aSessionViewList['row_id'] = $this->sRowID;
// Implies array creation.
}
// To make row links persist when the viewList is refreshed, we must store the row link in $_SESSION.
if (!empty($aSessionViewList['row_link'])) {
$this->sRowLink = $aSessionViewList['row_link'];
} else {
$aSessionViewList['row_link'] = $this->sRowLink;
// Implies array creation.
}
// Process input values regarding find & replace.
// User clicked preview.
$bFRPreview = !empty($_GET['FRPreviewClicked_' . $sViewListID]);
// Selected field name for replace.
$sFRFieldname = isset($_GET['FRFieldname_' . $sViewListID]) ? $_GET['FRFieldname_' . $sViewListID] : null;
// Display name of selected field.
$sFRFieldDisplayname = isset($_GET['FRFieldDisplayname_' . $sViewListID]) ? $_GET['FRFieldDisplayname_' . $sViewListID] : null;
// Search query for find & replace.
$sFRSearchValue = isset($_GET['FRSearch_' . $sViewListID]) ? $_GET['FRSearch_' . $sViewListID] : null;
// Replace value for find & replace.
$sFRReplaceValue = isset($_GET['FRReplace_' . $sViewListID]) ? $_GET['FRReplace_' . $sViewListID] : null;
// Type of matching.
$sFRMatchType = isset($_GET['FRMatchType_' . $sViewListID]) ? $_GET['FRMatchType_' . $sViewListID] : null;
// Flag stating whether all field content sould be replaced.
$bFRReplaceAll = !empty($_GET['FRReplaceAll_' . $sViewListID]);
// Predicted affected row count.
$nFRRowsAffected = null;
// Find & replace options parameter.
$aFROptions = array('sFRMatchType' => $sFRMatchType, 'bFRReplaceAll' => $bFRReplaceAll);
$nTotal = 0;
// Overwrites the previous $nTotal.
if (!count($aBadSyntaxColumns)) {
// Build argument list.
$aArgs = array_merge($aArguments['WHERE'], $aArguments['HAVING']);
if ($bFRPreview) {
// User clicked 'preview' in Find&Replace form, add F&R changes as a separate
// column in the query.
$nFRRowsAffected = $this->previewColumnFindAndReplace($sFRFieldname, $sFRFieldDisplayname, $sFRSearchValue, $sFRReplaceValue, $aArgs, $aFROptions);
}
// First find the amount of rows returned. We can use the SQL_CALC_FOUND_ROWS()
// function, but we'll try to avoid that due to extreme slowness in some cases.
// getRowCountForViewList() will take care of that.
// There is talk about a possible race condition using this technique on the mysql_num_rows man page, but I could find no evidence of it's existence on InnoDB tables.
// Just to be sure, I'm implementing a serializable transaction, which should lock the table between the two SELECT queries to ensure proper results.
// Last checked 2010-01-25, by Ivo Fokkema.
$_DB->query('SET TRANSACTION ISOLATION LEVEL SERIALIZABLE');
$_DB->beginTransaction();
// For ALL viewlists, we store the number of hits that we get, including the current filters.
// For large tables, getting a count can take a long time (especially when using SQL_CALC_FOUND_ROWS).
// ORDER BY is absolutely killing on large result sets.
// So, long time to retrieve count (>1s) => don't count again, and no sort.
// Count OK (<=1s), but big result set (250K) => no sort. ($_SETT['lists']['max_sortable_rows'])
// 1) If we don't have a count in memory, request count separately.
// Also if last count was >15min ago, request again.
$bTrueCount = false;
// Indicates whether or not we are sure about the number of results.
$sFilterMD5 = md5($WHERE . '||' . $HAVING . '||' . implode('|', $aArgs));
// A signature for the filters, NOTE that this depends on the column order!
// FIXME: If this count takes longer than 1s, we don't estimate anymore like we used to (see line 1543).
if (true || !isset($aSessionViewList['counts'][$sFilterMD5]['n'])) {
$t = microtime(true);
// Now, get the total number of hits if no LIMIT was used. Note that $nTotal gets overwritten here.
$nTotal = $this->getRowCountForViewList($this->aSQLViewList, $aArgs);
$tQ = microtime(true) - $t;
$aSessionViewList['counts'][$sFilterMD5]['n'] = $nTotal;
$aSessionViewList['counts'][$sFilterMD5]['t'] = $tQ;
$aSessionViewList['counts'][$sFilterMD5]['d'] = time();
$bTrueCount = true;
}
// Manipulate SELECT to include SQL_CALC_FOUND_ROWS.
$bSQLCALCFOUNDROWS = false;
// TODO: Remove this block. For now, this will be bypassed because $bTrueCount will always be true.
if (!$bTrueCount && $_INI['database']['driver'] == 'mysql' && ($aSessionViewList['counts'][$sFilterMD5]['t'] < 1 || $aSessionViewList['counts'][$sFilterMD5]['d'] < time() - 60 * 15)) {
// But only if we're using MySQL and it takes less than a second to get the correct number of results, or it's been more than 15 minutes since the last check!
$this->aSQLViewList['SELECT'] = 'SQL_CALC_FOUND_ROWS ' . $this->aSQLViewList['SELECT'];
$bSQLCALCFOUNDROWS = true;
}
if ($bOptions) {
// If the session variable does not exist, create it!
if (!isset($aSessionViewList['checked'])) {
$aSessionViewList['checked'] = array();
}
if (isset($_GET['ids_changed'])) {
if ($_GET['ids_changed'] == 'all') {
// If the select all button was clicked, fetch all entries and mark them as 'checked' in session.
// This query is the same as the viewList query, but without the ORDER BY and LIMIT, so that we can get the full result
// of the query.
$sSQL = $this->buildSQL(array('SELECT' => $this->aSQLViewList['SELECT'], 'FROM' => $this->aSQLViewList['FROM'], 'WHERE' => $this->aSQLViewList['WHERE'], 'GROUP_BY' => $this->aSQLViewList['GROUP_BY'], 'HAVING' => $this->aSQLViewList['HAVING']));
$q = $_DB->query($sSQL, $aArgs);
while ($zData = $q->fetchAssoc()) {
$zData = $this->generateRowID($zData);
// We only need the row_id here for knowing which ones we need to check.
// 2015-09-18; 3.0-14; We need to run rawurldecode() or else Columns are not selectable this way.
$aSessionViewList['checked'][] = rawurldecode($zData['row_id']);
}
} elseif ($_GET['ids_changed'] == 'none') {
// If the unselect all button was clicked, reset the 'checked' array.
$aSessionViewList['checked'] = array();
} else {
// Get the changed ids and remove them from or add them to the session.
$aIDsChanged = explode(';', $_GET['ids_changed']);
// Flip the keys & values, so that we can do a simple isset() to see if the id is already present.
$aSessionViewList['checked'] = array_flip($aSessionViewList['checked']);
// Determine the highest key number, so we can use that later when adding new values to the array.
$nIndex = count($aSessionViewList['checked']) ? max($aSessionViewList['checked']) + 1 : 0;
foreach ($aIDsChanged as $nID) {
if (isset($aSessionViewList['checked'][$nID])) {
// ID is found in the array, but is also in the 'ids_changed' array, so remove it!
unset($aSessionViewList['checked'][$nID]);
} else {
// ID is not found in the array, but IS in the 'ids_changed' array, so add it using the $nIndex as value we determined earlier.
// Also add 1 to the $nIndex so that the next id that needs to be added will not overwrite this one.
$aSessionViewList['checked'][$nID] = ++$nIndex;
}
}
// Flip the array back to its original state.
$aSessionViewList['checked'] = array_flip($aSessionViewList['checked']);
}
}
}
// ORDER BY will only occur when we estimate we have time for it.
if ($aSessionViewList['counts'][$sFilterMD5]['t'] < 1 && $aSessionViewList['counts'][$sFilterMD5]['n'] <= $_SETT['lists']['max_sortable_rows']) {
$bSortableVL = true;
} else {
// Not sortable, indicate this on the VL...
$aOrder = array('', '');
$bSortableVL = false;
// 2013-07-03; 3.0-07; However, we do try and sort because in principle, the order is random and this may cause confusion while paginating.
// So, as a result we'll try and sort on the PK. We attempt to determine this from the GROUP BY or ID col in the VL columns list.
$sCol = '';
if (isset($this->aSQLViewList['GROUP_BY'])) {
$sCol = $this->aSQLViewList['GROUP_BY'];
} elseif ($this->aColumnsViewList['id']) {
$sCol = $this->aColumnsViewList['id']['db'][0];
} elseif ($this->aColumnsViewList['id_']) {
$sCol = $this->aColumnsViewList['id_']['db'][0];
}
$this->aSQLViewList['ORDER_BY'] = $sCol;
}
if (!$bHideNav && FORMAT == 'text/html') {
// Implement LIMIT only if navigation is not hidden.
// We have a problem here, because we don't know how many hits there are,
// because we're using SQL_CALC_FOUND_ROWS which only gives us the number
// of hits AFTER we run the whole query. This means we should just assume
// the page number is possible.
$this->aSQLViewList['LIMIT'] = lovd_pagesplitInit();
// Function requires variable names $_GET['page'] and $_GET['page_size'].
}
$sSQL = $this->buildSQL($this->aSQLViewList);
// Run the viewList query.
// FIXME; what if using AJAX? Probably we should generate a number here, if this query fails, telling the system to try once more. If that fails also, the JS should throw a general error, maybe.
$q = $_DB->query($sSQL, $aArgs);
// Now, get the total number of hits as if no LIMIT was used (when we have used the proper SELECT syntax). Note that $nTotal gets overwritten here.
if ($bSQLCALCFOUNDROWS) {
// FIXME: 't' needs to be recalculated as well!
$nTotal = $_DB->query('SELECT FOUND_ROWS()')->fetchColumn();
$aSessionViewList['counts'][$sFilterMD5]['n'] = $nTotal;
$aSessionViewList['counts'][$sFilterMD5]['d'] = time();
$bTrueCount = true;
} else {
// Estimate the number of results!
$nTotal = $aSessionViewList['counts'][$sFilterMD5]['n'];
}
$_DB->commit();
// To end the transaction and the locks that come with it.
} else {
// Set certain values that are needed for hiding notices, applicable for the "incorrect syntax" error message.
$bTrueCount = true;
// Yes, we're sure we have 0 results.
$bSortableVL = false;
// Sorting makes no sense when you have no results.
}
// If no results are found, try to figure out if it was because of the user's searching or not.
if (!$nTotal) {
$bSearched = false;
$aHiddenSearch = array();
foreach ($_GET as $key => $value) {
if (substr($key, 0, 7) == 'search_') {
$sColumn = substr($key, 7);
if (!in_array($sColumn, $aColsToSkip)) {
$bSearched = true;
} elseif ($this->aColumnsViewList[$sColumn]['view']) {
$sColHeader = $this->aColumnsViewList[$sColumn]['view'][0];
// Make sure all hidden ID columns have "ID" in the header, so we can recognize them.
if (substr(rtrim($sColumn, '_'), -2) == 'id' && substr($sColHeader, -3) != ' ID') {
$sColHeader .= ' ID';
}
$aHiddenSearch[$sColHeader] = $value;
}
}
}
}
// FIXME; this is a temporary hack just to get the genes?authorize working when all users have been selected.
// There is no longer a viewList when all users have been selected, but we need one for the JS execution.
// Possibly, this code can be standardized a bit and, if necessary for other viewLists as well, can be kept here.
if (!$nTotal && !$bSearched && ($this->sObject == 'User' && !empty($_GET['search_id']))) {
// FIXME; Maybe check for JS contents of the rowlink?
// There has been searched, but apparently the ID column is forced hidden. This must be the authorize page.
$bSearched = true;
// This will trigger the creation of the viewList table.
}
if (FORMAT == 'text/html' && ($nTotal || $bSearched)) {
// Only print stuff if we're not just loading one entry right now.
if (!$bOnlyRows) {
if (!$bAjax) {
print ' <DIV id="viewlistDiv_' . $sViewListID . '">' . "\n";
// These contents will be replaced by Ajax.
}
// If we have a legend, create a hidden DIV that will be used for the full legend.
print ' <DIV id="viewlistLegend_' . $sViewListID . '" title="Legend" style="display : none;">' . "\n" . ' <H2 class="LOVD">Legend</H2>' . "\n\n" . ' <I class="S11">Please note that a short description of a certain column can be displayed when you move your mouse cursor over the column\'s header and hold it still. Below, a more detailed description is shown per column.</I><BR><BR>' . "\n\n";
$bLegend = false;
// We need to check if we have a legend at all.
foreach ($this->aColumnsViewList as $sField => $aCol) {
if (!empty($aCol['legend'])) {
$bLegend = true;
if (empty($aCol['legend'][1])) {
$aCol['legend'][1] = $aCol['legend'][0];
}
print ' <B>' . $aCol['view'][0] . '</B>: ' . $aCol['legend'][1];
if (substr($aCol['legend'][1], -5) == '</UL>') {
// No additional breaks, no possible listing of selection options. Column has its own UL already.
print "\n\n";
continue;
}
if (isset($this->aColumns[$sField]) && $this->aColumns[$sField]['form_type'][2] == 'select') {
// This is a custom column and it has a selection list with options. List the options below.
print '<BR>' . "\n" . ' All options:' . "\n" . ' <UL style="margin-top : 0px;">' . "\n";
foreach ($this->aColumns[$sField]['select_options'] as $sOption) {
print ' <LI>' . $sOption . '</LI>' . "\n";
}
print ' </UL>' . "\n\n";
} else {
print '<BR><BR>' . "\n\n";
}
}
}
print ' </DIV>' . "\n\n";
if (!$bHideNav) {
lovd_pagesplitShowNav($sViewListID, $nTotal, $bTrueCount, $bSortableVL, $bLegend);
}
// 'checked' attribute values for find & replace menu options.
$sFRMatchtypeCheck1 = !isset($sFRMatchType) || $sFRMatchType == '1' ? 'checked' : '';
$sFRMatchtypeCheck2 = $sFRMatchType == '2' ? 'checked' : '';
$sFRMatchtypeCheck3 = $sFRMatchType == '3' ? 'checked' : '';
$sFRReplaceAllCheck = $bFRReplaceAll ? 'checked' : '';
$sFRRowsAffected = !is_null($nFRRowsAffected) ? strval($nFRRowsAffected) : '';
$sFRFieldname = htmlspecialchars($sFRFieldname);
$sFRFieldDisplayname = htmlspecialchars($sFRFieldDisplayname);
$sFRSearchValue = htmlspecialchars($sFRSearchValue);
$sFRReplaceValue = htmlspecialchars($sFRReplaceValue);
// Print options menu for find & replace (hidden by default).
print <<<FROptions
<DIV id="viewlistFRFormContainer_{$sViewListID}" class="fnroptionsmenu" style="display: none;">
<SPAN><B style="color: red">Note that find & replace is still in BETA. Changes made using this feature are not checked for errors, therefore using find & replace may have destructive consequences.<BR>Make a download or backup of the data you're about to edit. If uncertain, use the edit form of the data entries instead.</B><BR>
Applying find & replace to column
"<B id="viewlistFRColDisplay_{$sViewListID}">{$sFRFieldname}</B>".
<INPUT id="FRFieldname_{$sViewListID}" type="hidden" name="FRFieldname_{$sViewListID}"
value="{$sFRFieldname}" />
<INPUT id="FRFieldDisplayname_{$sViewListID}" type="hidden"
name="FRFieldDisplayname_{$sViewListID}" value="{$sFRFieldDisplayname}" />
<INPUT id="FRRowsAffected_{$sViewListID}" type="hidden" value="{$sFRRowsAffected}" />
</SPAN>
<BR />
<TABLE>
<TR>
<TD>Text to find</TD>
<TD>
<INPUT type="text" name="FRSearch_{$sViewListID}" value="{$sFRSearchValue}"
style="width: 110px" />
</TD>
<TD>
<INPUT type="radio" name="FRMatchType_{$sViewListID}" value="1" {$sFRMatchtypeCheck1} />Match anywhere
<INPUT type="radio" name="FRMatchType_{$sViewListID}" value="2" {$sFRMatchtypeCheck2} />Match at beginning of field
<INPUT type="radio" name="FRMatchType_{$sViewListID}" value="3" {$sFRMatchtypeCheck3} />Match at end of field
</TD>
</TR>
<TR>
<TD>Replace with</TD>
<TD>
<INPUT type="text" name="FRReplace_{$sViewListID}" value="{$sFRReplaceValue}"
style="width: 110px" />
</TD>
<TD>
<INPUT type="checkbox" name="FRReplaceAll_{$sViewListID}" value="1" {$sFRReplaceAllCheck} />Replace everything in field
</TD>
</TR>
</TABLE>
<INPUT id="FRPreview_{$sViewListID}" type="button" value="Preview" />
<INPUT id="FRCancel_{$sViewListID}" type="button" value="Cancel" style="border : 1px solid #FF4422;" />
<DIV id="FRSubmitDiv_{$sViewListID}">
<BR>
Enter your password to apply find and replace:<BR>
<INPUT type="password" name="password" size="20" />
<INPUT id="FRSubmit_{$sViewListID}" type="submit" value="Submit" />
</DIV>
</DIV>
FROptions;
// Table and search headers (if applicable).
print ' <TABLE border="0" cellpadding="0" cellspacing="1" class="data" id="viewlistTable_' . $sViewListID . '">' . "\n" . ' <THEAD>' . "\n" . ' <TR>' . ($bOptions ? "\n" . ' <TH valign="center" style="text-align:center;">' . "\n" . ' <IMG id="viewlistOptionsButton_' . $sViewListID . '" src="gfx/options.png" width="16" height="16" style="cursor : pointer;"></TH>' : '');
foreach ($this->aColumnsViewList as $sField => $aCol) {
if (in_array($sField, $aColsToSkip)) {
continue;
}
$bSortable = !empty($aCol['db'][1]) && $bSortableVL;
// If we can't sort at all, nothing is sortable.
$bSearchable = !empty($aCol['db'][2]);
$nAllowFindAndReplace = (int) (!empty($aCol['allowfnr']));
// Later allow other columns as well, such as owned_by or statusid or so.
$sImg = '';
$sAlt = '';
if ($bSortable && $aOrder[0] == $sField) {
$sImg = $aOrder[1] == 'DESC' ? '_desc' : '_asc';
$sAlt = $aOrder[1] == 'DESC' ? 'Descending' : 'Ascending';
}
print "\n" . ' <TH valign="top"' . ($bSortable ? ' class="order' . ($aOrder[0] == $sField ? 'ed' : '') . '"' : '') . (empty($aCol['legend'][0]) ? '' : ' title="' . htmlspecialchars($aCol['legend'][0]) . '"') . ' data-allowfnr="' . $nAllowFindAndReplace . '" data-fieldname="' . $sField . '">' . "\n" . ' <IMG src="gfx/trans.png" alt="" width="' . $aCol['view'][1] . '" height="1" id="viewlistTable_' . $sViewListID . '_colwidth_' . $sField . '"><BR>' . (!$bSortable ? str_replace(' ', ' ', $aCol['view'][0]) . '<BR>' : "\n" . ' <DIV onclick="document.forms[\'viewlistForm_' . $sViewListID . '\'].order.value=\'' . $sField . ',' . ($aOrder[0] == $sField ? $aOrder[1] == 'ASC' ? 'DESC' : 'ASC' : $aCol['db'][1]) . '\'; if (document.forms[\'viewlistForm_' . $sViewListID . '\'].page) { document.forms[\'viewlistForm_' . $sViewListID . '\'].page.value=1; } lovd_AJAX_viewListSubmit(\'' . $sViewListID . '\');" style="position : relative;">' . "\n" . ' <IMG src="gfx/order_arrow' . $sImg . '.png" alt="' . $sAlt . '" title="' . $sAlt . '" width="13" height="12" style="position : absolute; top : 2px; right : 0px;">' . str_replace(' ', ' ', $aCol['view'][0]) . ' </DIV>') . (!$bSearchable ? '' : "\n" . ' <INPUT type="text" name="search_' . $sField . '" value="' . (!isset($_GET['search_' . $sField]) ? '' : htmlspecialchars($_GET['search_' . $sField])) . '" title="' . $aCol['view'][0] . ' field should contain...' . (!empty($_GET['search_' . $sField]) ? "\nCurrent search:\n\n" . htmlspecialchars(lovd_formatSearchExpression($_GET['search_' . $sField], $aColTypes[$sField])) : '') . '" style="width : ' . ($aCol['view'][1] - 6) . 'px; font-weight : normal;" onkeydown="if (event.keyCode == 13) { if (document.forms[\'viewlistForm_' . $sViewListID . '\'].page) { document.forms[\'viewlistForm_' . $sViewListID . '\'].page.value=1; } setTimeout(\'lovd_AJAX_viewListSubmit(\\\'' . $sViewListID . '\\\')\', 0); return false;}">') . '</TH>';
}
print '</TR></THEAD>';
}
} elseif (FORMAT == 'text/plain') {
// Download format: show headers.
$sObject = $this->sObject == 'Custom_ViewList' ? $this->sObjectID : $this->sObject . 's';
header('Content-type: text/plain; charset=UTF-8');
header('Content-Disposition: attachment; filename="LOVD_' . $sObject . '_' . date('Y-m-d_H.i.s') . '.txt"');
header('Pragma: public');
print '### LOVD-version ' . lovd_calculateVersion($_SETT['system']['version']) . ' ### ' . $sObject . ' Quick Download format ### This file can not be imported ###' . "\r\n";
// FIXME: this has to be done better, we can't see what we're filtering for, because it's in the arguments!
$sFilter = $WHERE . ($WHERE && $HAVING ? ' AND ' : '') . $HAVING;
if ($sFilter) {
if (count($aArgs) == substr_count($sFilter, '?')) {
foreach ($aArgs as $sArg) {
$sFilter = preg_replace('/\\?/', ctype_digit($sArg) ? $sArg : '"' . $sArg . '"', $sFilter, 1);
}
}
print '## Filter: ' . $sFilter . "\r\n";
}
if (ACTION == 'downloadSelected') {
print '## Filter: selected = ' . implode(',', $aSessionViewList['checked']) . "\r\n";
}
print '# charset=UTF-8' . "\r\n";
$i = 0;
foreach ($this->aColumnsViewList as $sField => $aCol) {
if (in_array($sField, $aColsToSkip)) {
continue;
}
print ($i++ ? "\t" : '') . '"{{' . $sField . '}}"';
}
print "\r\n";
}
if (!$nTotal && FORMAT == 'text/html') {
if ($bSearched) {
// Searched, but no results. FIXME: link to the proper documentation entry about search expressions
$sBadSyntaxColumns = implode(', ', array_unique($aBadSyntaxColumns));
// FIXME; use an IF here.
$sMessageNormal = 'No results have been found that match your criteria.<BR>Please redefine your search criteria.';
$sMessageBadSyntax = 'Your search column' . (count($aBadSyntaxColumns) > 1 ? 's contain' : ' contains') . ' incorrect search expression syntax at: ' . $sBadSyntaxColumns . '.';
$sMessage = empty($aBadSyntaxColumns) ? $sMessageNormal : $sMessageBadSyntax;
if ($bOnlyRows) {
die('0');
// Silent error.
}
// FIXME; This code is sort of duplicated, some 100 lines below we also print this, *if* results are found.
print '</TABLE><BR>' . "\n";
// <BR> is necessary to keep the InfoTable apart from the data headers.
if (!$bHideNav) {
print ' <INPUT type="hidden" name="total" value="' . $nTotal . '" disabled>' . "\n" . ' <INPUT type="hidden" name="page_size" value="' . $_GET['page_size'] . '">' . "\n" . ' <INPUT type="hidden" name="page" value="' . $_GET['page'] . '">' . "\n";
}
lovd_showInfoTable($sMessage, 'stop');
print ' </DIV></FORM>' . "\n\n";
} else {
if ($bOnlyRows) {
die('0');
// Silent error.
}
print ' <DIV id="viewlistDiv_' . $sViewListID . '">' . "\n";
// These contents will be replaced by Ajax.
if (substr($this->sObject, -7) == 'Variant') {
$sUnit = 'variants' . (substr($this->sObject, 0, 10) == 'Transcript' ? ' on transcripts' : '');
} elseif ($this->sObject == 'Custom_Viewlist') {
$sUnit = 'entries';
} elseif ($this->sObject == 'Shared_Column') {
$sUnit = 'active columns';
} else {
$sUnit = strtolower($this->sObject) . 's';
}
$sMessage = 'No ' . $sUnit . ' found';
if (!empty($aHiddenSearch)) {
$sWhere = '';
foreach ($aHiddenSearch as $sCol => $sValue) {
// If the hidden column has "ID" in its name, it is the primary filter column.
if (substr($sCol, -3) == ' ID') {
$sWhere .= ($sWhere ? ' and ' : ' ') . 'for this ' . strtolower(substr($sCol, 0, -3));
} else {
$sWhere .= ($sWhere ? ' and ' : ' where ') . strtolower($sCol) . ' is "' . str_replace('|', '" or "', trim($sValue, '="') . '"');
}
}
$sMessage .= $sWhere;
}
lovd_showInfoTable($sMessage . '!', 'stop');
print ' </DIV></FORM>' . "\n\n";
return 0;
}
}
// Now loop through the data and print. But check for $q to be set; if we had a bad search syntax, we end up here as well, but without an $q.
while (isset($q) && $nTotal && ($zData = $q->fetchAssoc())) {
// If row_id is not given by the database, but it should be created according to some format ($this->sRowID), put the data's ID in this format.
$zData = $this->generateRowID($zData);
// If row_link is not given by the database, but it should be created according to some format ($this->sRowLink), put the data's ID and the viewList's ID in this format.
if (!isset($zData['row_link'])) {
if ($this->sRowLink !== '' && $zData['row_id']) {
$zData['row_link'] = str_replace(array('{{ID}}', '{{ViewListID}}'), array(rawurlencode($zData['row_id']), $sViewListID), $this->sRowLink);
//$zData['row_link'] = preg_replace('/\{\{zData_(\w)+\}\}/', rawurlencode("$1"), $zData['row_link']);
//$zData['row_link'] = preg_replace_callback('/\{\{zData_(\w+)\}\}/', create_function('$aRegs', 'global $zData; return rawurlencode($zData[$aRegs[1]]);'), $zData['row_link']);
// FIXME; sorry, couldn't figure out how to do this in one line. Suggestions are welcome.
foreach ($zData as $key => $val) {
// Also allow data from $zData to be put into the row link & row id.
// FIXME; This is a temporary ugly solution, so we need to fix this later!!!!
$zData['row_link'] = preg_replace('/\\{\\{' . preg_quote($key, '/') . '\\}\\}/', rawurlencode($val), $zData['row_link']);
$zData['row_link'] = preg_replace('/\\{\\{zData_' . preg_quote($key, '/') . '\\}\\}/', rawurlencode($val), $zData['row_link']);
}
} else {
$zData['row_link'] = '';
}
}
$zData = $this->autoExplode($zData);
// Only the CustomViewList object has this 3rd argument, but other objects' prepareData()
// don't complain when called with this 3 argument they didn't define.
$zData = $this->prepareData($zData, 'list', $sViewListID);
if (FORMAT == 'text/html') {
// FIXME; rawurldecode() in the line below should have a better solution.
// IE (who else) refuses to respect the BASE href tag when using JS. So we have no other option than to include the full path here.
print "\n" . ' <TR class="' . (empty($zData['class_name']) ? 'data' : $zData['class_name']) . '"' . (!$zData['row_id'] ? '' : ' id="' . $zData['row_id'] . '"') . ' valign="top"' . (!$zData['row_link'] ? '' : ' style="cursor : pointer;"') . (!$zData['row_link'] ? '' : ' onclick="' . (substr($zData['row_link'], 0, 11) == 'javascript:' ? rawurldecode(substr($zData['row_link'], 11)) : 'window.location.href = \'' . lovd_getInstallURL(false) . $zData['row_link'] . '\';') . '"') . '>';
if ($bOptions) {
print "\n" . ' <TD align="center" class="checkbox" onclick="cancelParentEvent(event);"><INPUT id="check_' . $zData['row_id'] . '" class="checkbox" type="checkbox" name="check_' . $zData['row_id'] . '" onclick="lovd_recordCheckChanges(this, \'' . $sViewListID . '\');"' . (in_array($zData['row_id'], $aSessionViewList['checked']) ? ' checked' : '') . '></TD>';
}
foreach ($this->aColumnsViewList as $sField => $aCol) {
if (in_array($sField, $aColsToSkip)) {
continue;
}
print "\n" . ' <TD' . (!empty($aCol['view'][2]) ? ' ' . $aCol['view'][2] : '') . ($aOrder[0] == $sField ? ' class="ordered"' : '') . '>' . ($zData[$sField] === '' ? '-' : $zData[$sField]) . '</TD>';
}
print '</TR>';
} elseif (FORMAT == 'text/plain') {
// Download format: print contents.
if (ACTION == 'downloadSelected' && !in_array($zData['row_id'], $aSessionViewList['checked'])) {
// Only selected entries should be downloaded. And this one is not selected.
continue;
}
$i = 0;
foreach ($this->aColumnsViewList as $sField => $aCol) {
if (in_array($sField, $aColsToSkip)) {
continue;
}
print ($i++ ? "\t" : '') . '"' . str_replace(array("\r\n", "\r", "\n"), array('\\r\\n', '\\r', '\\n'), addslashes(html_entity_decode(strip_tags($zData[$sField])))) . '"';
}
print "\r\n";
}
}
// Only print stuff if we're not just loading one entry right now.
if ($nTotal && !$bOnlyRows && FORMAT == 'text/html') {
print '</TABLE>' . "\n";
if (!$bHideNav) {
print ' <INPUT type="hidden" name="total" value="' . $nTotal . '" disabled>' . "\n" . ' <INPUT type="hidden" name="page_size" value="' . $_GET['page_size'] . '">' . "\n" . ' <INPUT type="hidden" name="page" value="' . $_GET['page'] . '">' . "\n\n";
lovd_pagesplitShowNav($sViewListID, $nTotal, $bTrueCount, $bSortableVL, $bLegend);
}
if (!$bAjax) {
print ' </DIV></FORM><BR>' . "\n";
// These contents will be replaced by Ajax.
}
}
if (!$bAjax && FORMAT == 'text/html') {
// If sent using Ajax, the browser is not going to evaluate this code, anyways.
print ' <SCRIPT type="text/javascript">' . "\n" . ' // This has to be run when the document has finished loading everything, because only then can it get the proper width from IE7 and lower!' . "\n" . ' $( function () {lovd_stretchInputs(\'' . $sViewListID . '\');});' . "\n";
if ($bOptions) {
$sFRMenuOption = '';
if ($bFindReplace) {
// Add find & replace menu item to viewlist options menu.
$sFRMenuOption = <<<FRITEM
' <LI class="icon">' +
' <A click="lovd_FRColumnSelector(\\'{$sViewListID}\\');">' +
' <SPAN class="icon" style=""></SPAN>' +
' Find and replace text in column' +
' </A>' +
' </LI>' +
FRITEM;
}
print <<<OPMENU
// If menu's UL doesn't exist yet, create it.
if (\$('#viewlistMenu_{$sViewListID}').attr('id') == undefined) {
var oUL = window.document.createElement('ul');
oUL.setAttribute('id', 'viewlistMenu_{$sViewListID}');
oUL.className = 'jeegoocontext jeegooviewlist';
window.document.body.appendChild(oUL);
}
// Fix the top border that could not be set through jeegoo's style.css.
\$('#viewlistMenu_{$sViewListID}').attr('style', 'border-top : 1px solid #000;');
\$('#viewlistMenu_{$sViewListID}').prepend(
' <LI class="icon">' +
' <A click="check_list[\\'{$sViewListID}\\'] = \\'all\\'; lovd_AJAX_viewListSubmit(\\'{$sViewListID}\\');">' +
' <SPAN class="icon" style="background-image: url(gfx/check.png);"></SPAN>' +
' Select all <SPAN>entries</SPAN>' +
' </A>' +
' </LI>' +
' <LI class="icon">' +
' <A click="check_list[\\'{$sViewListID}\\'] = \\'none\\'; lovd_AJAX_viewListSubmit(\\'{$sViewListID}\\');">' +
' <SPAN class="icon" style="background-image: url(gfx/cross.png);"></SPAN>' +
' Unselect all' +
' </A>' +
' </LI>' +
{$sFRMenuOption}
' ');
\$('#viewlistMenu_{$sViewListID}').append(
' <LI class="icon">' +
' <A click="lovd_AJAX_viewListSubmit(\\'{$sViewListID}\\', function(){lovd_AJAX_viewListDownload(\\'{$sViewListID}\\', true);});">' +
' <SPAN class="icon" style="background-image: url(gfx/menu_save.png);"></SPAN>' +
' Download all entries (summary data)' +
' </A>' +
' </LI>' +
' <LI class="icon">' +
' <A click="lovd_AJAX_viewListSubmit(\\'{$sViewListID}\\', function(){lovd_AJAX_viewListDownload(\\'{$sViewListID}\\', false);});">' +
' <SPAN class="icon" style="background-image: url(gfx/menu_save.png);"></SPAN>' +
' Download selected entries (summary data)' +
' </A>' +
' </LI>');
lovd_activateMenu('{$sViewListID}');
OPMENU;
}
print ' check_list[\'' . $sViewListID . '\'] = [];' . "\n" . ' </SCRIPT>' . "\n\n";
}
return $nTotal;
}
} else {
// Error during update check.
lovd_writeLog('Error', 'CheckUpdate', 'Could not parse upstream server output:' . "\n" . $sUpdates);
$_DB->query('UPDATE ' . TABLE_STATUS . ' SET update_checked_date = ?, update_version = "Error", update_level = 0, update_description = "", update_released_date = NULL', array($sNow));
$_STAT['update_checked_date'] = $sNow;
$_STAT['update_version'] = 'Error';
$_STAT['update_released_date'] = '';
$_STAT['update_level'] = 0;
$_STAT['update_description'] = '';
}
}
// Process...
if ($_STAT['update_version'] == 'Error') {
$sType = 'error';
$sMessage = 'An error occured while checking for updates. For more information, see the error log. Please try again later.';
} elseif (lovd_calculateVersion($_STAT['update_version']) > lovd_calculateVersion($_SETT['system']['version'])) {
$sType = 'newer';
$sMessage = 'There is an update to LOVD available. More information is below.<BR>' . "\n" . '<B>Latest version</B>: ' . $_STAT['update_version'] . '<BR>' . "\n" . '<B>Release date</B>: ' . $_STAT['update_released_date'] . '<BR>' . "\n" . '<B>Priority level</B>: ' . $_SETT['update_levels'][$_STAT['update_level']] . '<BR>' . "\n" . '<B>Release info</B>: ' . str_replace("\n", '<BR>', $_STAT['update_description']) . '<BR>' . "\n" . '<B>Download</B>: <A href="' . dirname($_SETT['update_URL']) . '/download.php?version=' . $_STAT['update_version'] . '&type=tar.gz">GZIPped TARball</A> or <A href="' . dirname($_SETT['update_URL']) . '/download.php?version=' . $_STAT['update_version'] . '&type=zip">ZIP archive</A><BR>' . "\n" . '<A href="' . $_SETT['upstream_URL'] . $_SETT['system']['tree'] . '/changelog.txt" target="_blank">See the changelog</A>' . "\n";
} else {
$sType = 'newest';
$sMessage = 'There are currently no updates. Your LOVD installation is completely up to date.';
}
// If we're requested to show the icon, we will do that and quit. Else we will provide some info.
if (isset($_GET['icon'])) {
// Create icon.
header('Content-type: image/png');
readfile('gfx/lovd_update_' . $sType . '_blue.png');
exit;
} else {
// Print what we know about new versions...
$_T->printHeader(false);
$_BAR->setMessage('Other user upgrading the database is still not finished.<BR>' . (isset($_GET['force_lock']) ? 'Forcing upgrade as requested...' : 'This may indicate something went wrong during upgrade.'));
if (isset($_GET['force_lock'])) {
$bLocked = false;
}
} else {
$_BAR->setMessage('Upgrading database backend...');
}
flush();
if (!$bLocked) {
// There we go...
// This recursive count returns a higher count then we would seem to want at first glance,
// because each version's array of queries count as one as well.
// However, because we will run one additional query per version, this number will be correct anyway.
// 2012-02-02; 3.0-beta-02; But of course we should exclude the older versions...
foreach ($aUpdates as $sVersion => $aSQL) {
if (lovd_calculateVersion($sVersion) <= $sCalcVersionDB || lovd_calculateVersion($sVersion) > $sCalcVersionFiles) {
unset($aUpdates[$sVersion]);
}
}
$nSQL = count($aUpdates, true);
// Actually run the SQL...
$nSQLDone = 0;
$nSQLDonePercentage = 0;
$nSQLDonePercentagePrev = 0;
$nSQLFailed = 0;
$sSQLFailed = '';
foreach ($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...
$aDiseasesAlreadyWarnedFor = array();
// To prevent lots and lots of error messages for each phenotype entry created for the same disease that is not yet inserted into the database.
$aSectionsAlreadyWarnedFor = array();
// To prevent lots and lots of error messages for a section that cannot be updated in the database.
foreach ($aData as $i => $sLine) {
$sLine = trim($sLine);
if (!$sLine) {
if (!lovd_endLine()) {
break;
}
continue;
}
if (!$sFileVersion) {
// Still looking for the LOVD version! We have a line here, so this must be what we're looking for.
if (!preg_match('/^###\\s*LOVD-version\\s*([0-9]{4}\\-[0-9]{2}[a-z0-9])\\s*###\\s*([^#]+)\\s*###/', ltrim($sLine, '"'), $aRegs)) {
lovd_errorAdd('import', 'File format not recognized; the first line of the imported file should contain the LOVD version header (### LOVD-version ' . lovd_calculateVersion($_SETT['system']['version']) . ' ### ... etc).');
} else {
list(, $sFileVersion, $sFileType) = $aRegs;
$sFileType = trim($sFileType);
if (!isset($aTypes[$sFileType])) {
// We did not understand the file type (Full data download, custom columns, genes, etc).
lovd_errorAdd('import', 'File type not recognized; type "' . $sFileType . '" unknown.');
} else {
if (isset($aExcludedTypes[$sFileType])) {
// It is currently not possible to import owned data, see manual for details..
lovd_errorAdd('import', 'File type not allowed; ' . $aExcludedTypes[$sFileType] . ' ');
} else {
$sFileType = $aTypes[$sFileType];
// Clean $aParsed a bit, depending on the file type.
if ($sFileType == 'Col') {
$aParsed = array('Columns' => $aParsed['Columns']);
$sHeader = 'Custom column';
$sFilter = 'category';
$ID = $_PE[2];
lovd_requireAuth(LEVEL_MANAGER);
} elseif ($_PE[1] == 'genes' && empty($_PE[2])) {
// Download all genes.
$sFileName = 'genes';
$sHeader = 'Gene data';
lovd_requireAuth(LEVEL_MANAGER);
} else {
exit;
}
// If we get here, we can print the header already.
header('Content-Disposition: attachment; filename="LOVD_' . $sFileName . '_' . date('Y-m-d_H.i.s') . '.txt"');
header('Pragma: public');
print '### LOVD-version ' . lovd_calculateVersion($_SETT['system']['version']) . ' ### ' . $sHeader . ' download ### To import, do not remove or alter this header ###' . "\r\n";
if ($sFilter == 'owner') {
print '## Filter: (created_by = ' . $ID . ' || owned_by = ' . $ID . ')' . "\r\n";
} elseif ($sFilter == 'gene') {
print '## Filter: (gene = ' . $ID . ')' . "\r\n";
} elseif ($sFilter == 'category') {
print '## Filter: (category = ' . $ID . ')' . "\r\n";
}
print '# charset = UTF-8' . "\r\n\r\n";
// Prepare file creation by defining headers, columns and filters.
// All data types have same settings: optional ownership filter, no columns hidden.
$aDataTypeSettings = array('comments' => array(), 'data' => array(), 'filters' => array(), 'filter_other' => array(), 'hide_columns' => array(), 'prefetch' => false, 'settings' => array());
if ($sFilter == 'owner') {
// We need to prefetch the filtered data to be able to filter other objects (genes etc).
// Note: This will make all objects to be prefetched, which could be a bit of overkill here.
$aDataTypeSettings['prefetch'] = true;