5b5ab5deac3d892d181614dc496156ad7b688d7e brianlee Wed Nov 10 17:03:59 2021 -0800 Adding a note about invisible trackDb architecture caching and updating udcTimeout to 5 seconds from 1 second refs #28487 diff --git src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html index 4e47416..17dc89a 100755 --- src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html +++ src/hg/htdocs/goldenPath/help/hgTrackHubHelp.html @@ -646,38 +646,46 @@ description file is not present, the corresponding sections of the track settings and details pages are left blank. Only one description page can be associated with composite and multiWig tracks; the file name should correspond to the symbolic name of the top-level track in the composite.</p> <!-- ========== Debugging and Updating Track Hubs ============================== --> <a name="Debug"></a> <h2>Debugging Track Hubs</strong></h2> <h3>Not updating? Change udcTimeout</h3> <p> As part of the track hub mechanism, UCSC caches data from the hub on the local server. The hub utility periodically checks the time stamps on the hub files, and downloads them again only if they have a time stamp newer than the UCSC one. For performance reasons, UCSC checks the time stamps every 300 seconds, which can result in a 5-minute delay between the time a hub file is updated and the change appears on the Genome Browser. Hub providers can work around this delay by inserting the -CGI variable <em><strong>udcTimeout=1</strong></em> into the Genome Browser URL, which will reduce -the delay to one second. To add this variable, open the Genome Browser tracks page and zoom or +CGI variable <em><strong>udcTimeout=5</strong></em> into the Genome Browser URL, which will reduce +the delay to five seconds. To add this variable, open the Genome Browser tracks page and zoom or scroll the image to display a full browser URL in which the CGI variables visible. Insert the CGI variable just after the "hgTracks" portion of the URL so that it reads -<em>http://genome.ucsc.edu/cgi-bin/hgTracks?<b>udcTimeout=1&</b></em> (with the remainder of the URL +<em>http://genome.ucsc.edu/cgi-bin/hgTracks?<b>udcTimeout=5&</b></em> (with the remainder of the URL following the ampersand). To restore the default timeout, a warning message will appear on hgTracks with a link to clear the udcTimeout variable.</p> - +<h4>I used udcTimeout, why is it still not updating?</h4> +<p> +Browser software attempts to speed performance by reading the trackDb architecture into +a separate cache. This software assumes that the timestamp on a file like a hub's trackDb.txt should +always be increasing in time and never decreasing (i.e., a new update to the file should not have +an earlier timestamp). We did discover that if someone were to copy an older file (say with +<code>cp -p</code> to preserve file timestamp), for example to restore a trackDb.txt to an earlier +version, they might get stuck with a hub that is not updating. To resolve this specific problem the +person would only need to edit or touch the file and give it a new timestamp.</p> <a name="validate"></a> <h3>Check hub settings using Hub Development tool</h3> <p> Hubs can be checked for valid file configuration, trackDb keywords, and composite or super track settings with the Hub Development tool. This tool can be accessed from the Track Hub page under <a href="../../cgi-bin/hgHubConnect?#hubDeveloper">the Hub Development tab</a>. After entering your URL in the search box, the tool runs the <a href="http://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">hubCheck utility</a> program equivalent to:</p> <pre>hubCheck -noTracks http://url.to.hub.txt</pre> <p> The noTracks setting speeds up the validation process but does not check for the presence or validity of your remotely hosted data track files. This tool checks your hub.txt, genome.txt, and trackDb.txt settings and displays warnings and errors in bright red font, such as "<font color="red">Missing required setting...</font>" and