Monitoring Tasks

Please add to the documentation page, Monitoring Tasks Notes to add procedures and notes for specific jobs, then link back to the job in the list below. If editing this page you might find this HTML editor site helpful to graphical update the tables.

task	frequency	NOW	who April '16 -Feb '17	previous	previous	PROPOSED
from hgwdev qateam cron
Respond to items on the broken links report: Check to make sure that broken links reported are actually broken. If so, fix the link if it is clear what the new link should be and push to the RR. If not, contact the appropriate person at the web site in question to find out what the new link should be.	daily	ChrisV	Cath, Matt	Matt	Matt
Respond to the trackDbGlobal report: Make public and request a push of trackDb and friends for any assemblies that show up as changed in the trackDbGlobal report.	weekly	Jairo	Cath	Matt	Luvina
receive output from syncAday.csh; alert; if anything is out of sync (checks that tables are in sync between beta and RR for database of the day)	daily	Cath	ChrisV	Brian	Brian
receive output from checkMetaAday.csh; alert; if anything is out of sync (compares hgcentralbeta to hgcentral for db of the day)	daily	Cath	Cath, Matt	Matt	Matt
receive output from realTime.csh (previously gbLoaded) cron job and alert braney if anything seems very outdated No output for xenTro3, fr1, fr2, fr3, eboVir3, dm2	daily, problems every 3-6 months	Jairo	Cath, Luvina	Steve, Jonathan	Steve, Jonathan
receive output from showProcesslist.csh	daily, no action	Cath, Brian	Jairo, Matt	Steve, Jonathan	Steve, Jonathan
get output from checkTableStatus.csh on Mondays (this is a report on whether the genbank table dumps are up-to-date...if we could get rid of our dependence on those, we could get rid of this cron job)	weekly	Cath	Brian, Jonathan	Steve, Jonathan	Steve, Jonathan
get an email from backupCentral.csh each month that keeps a dump of hgcentral tables (there's a redmine ticket on whether we should change this one: http://redmine.soe.ucsc.edu/issues/7834)	monthly	Brian	Matt, Brian	Steve, Jonathan	Steve, Jonathan
receive an email on additions and subtractions to files in /gbdb on hgnfs1	daily	Matt	ChrisL, Luvina	Steve, Jonathan	Steve, Jonathan
receive an email from cron if qateam DailySandboxUpdate fails	daily	Matt, Brian	Matt, Brian	Steve, Jonathan	Steve, Jonathan
email request to build doPublicCrawl public.ix and public.ixx hub search files and push them.	runs quarterly	Jairo	ChrisL
increment databaseAday, /cluster/bin/scripts/databaseAday.csh	problems only	ChrisL, Matt, Brian	Brian, Jonathan	Steve, Jonathan	Steve, Jonathan
checkHgFindSpec -checkTermRegex, /cluster/bin/scripts/runCheckHgFindSpec go	problems only	ChrisL, Matt, Brian	Brian, Jonathan	Steve, Jonathan	Steve, Jonathan
check to see if there are new files to go with the CGI push /cluster/home/qateam/bin/scripts/findCgiFiles.csh go	problems only	ChrisL, Matt, Brian	Brian, Jonathan	Steve, Jonathan	Steve, Jonathan
get output from checkGenomeMysql	daily	Brian	ChrisL, Matt	Steve, Jonathan	Steve, Jonathan
[checkGbibMd5.sh] compares the md5sum of gbibBeta.zip on dev with the sum for gbib.zip on genome-store, complaining if they don't match.	runs weekly	Jairo, Cath	Brian, Cath, Jonathan	Brian, Steve, Jonathan
Check for unigene update for human SAGE track	daily	Cath, Braney	Luvina, Braney	Steve, Braney
look for broken symlinks in /gbdb:	daily	Browser Staff	Browser Staff	Browser Staff
look for broken symlinks in in (very large) visiGene directory	twice yearly	ChrisL	Cath, Galt	Steve, Galt
look for broken symlinks in htdocs-hgdownload/goldenpath	daily	Browser Staff	Browser Staff	Browser Staff
Check the source tree for duplicate case-independent filenames. These wreck havoc with git.	daily	Browser Staff	Browser Staff	Browser Staff
Check to see what kind of browsers and o/s people are using to access the public website	weekly	Ann, Jairo, ChrisL	Ann, ChrisL, Brian	Ann, Steve
sends a reminder to check the list of folks who have mirror sites. This list is created by a script of Hiram's and located here: http://genome-test.cse.ucsc.edu/admin/tools/useCount.html. The information comes from the phoneHome program in the CGIs. Sometimes companies set up mirrors, which is not OK.	monthly	Matt, Brian	Brian, Luvina	Matt	Pauline
run /cluster/bin/scripts/sessionStats.csh	monthly	Angie, Brian, Bob	Angie, Brian, Bob	Angie, Brian, Bob, Steve
ask Galt/Jim about blat updates	3x per year	ChrisV,Cath	Cath, Brian	Steve, Jonathan	Pauline, Steve, Jonathan
check that the ga4gh beacon server is running. Email Max if there is an issue.	daily	Jairo	Cath	Ann	Ann
check that blat servers are running ok	ongoing	Ann, Brian, Galt, Matt, Erich, ChrisL, ChrisV, Jairo, Cath	Ann, Brian, Donna, Galt, Luvina, Matt, Gary,	Ann, Brian, Donna, Galt, Luvina, Steve, Gary
receive output from hgTracksRandom cron; alert admins to problems	as needed	many: cath, chmalee, kuhn, brianlee, braney, ann,, jcasper, matt, jairo, chrisv	many: cath, chmalee, kuhn, brianlee, braney, luvina, gary, ann,, jcasper, matt	many: kuhn, katrina, brianlee, braney, luvina, gary, ann, steve, jcasper, matt	many: kuhn, pauline, katrina, brianlee, braney, luvina, gary, ann, steve, jcasper, matt
check that beta builds alright	3x week	Brian, Matt	Brian, ChrisL,Braney	Steve, Jonathan, Braney
hubPublicCheck complains when the hubPublic table doesn't have the same strings as the actual hub.txt file. (NOTE: To run only on Beta hubs requires these declarations: export HGDB_CONF=$HOME/.hg.conf.beta and SHELL=/bin/sh).	runs daily, complains rarely	Matt	Matt	Brian	Brian
Curl of http://genomewiki.ucsc.edu/index.php/Assembly_Hubs to test Public Wiki is accessible, output only if no response.	hourly	ChrisV	Brian	Brian
Cronjob reports checkUrlsInTable hg38 wgEncodeCell and cv.ra (likely infrequent results)	weekly	ChrisV	ChrisL	Brian	Brian
qaAutoTrack -script that does some auto-QA on the autopushed tracks.	daily	Matt
from build cron
receive cron output for tableDescriptions build errors	rare	Matt	Luvina	Steve, Luvina	Pauline, Matt
from galt's cron
run ReleaseLog script (this requires a copy of the kent repository)	daily	Galt	Galt	Galt	Galt
back up the qapushq	every 30 minutes M-F	Galt	Galt	Galt	Galt
non-cron jobs
Check for MLQs that may have slipped through the cracks with Google Groups to check for unanswered Q's. Check to make sure that the last response for every ticket came from one of us. If not, look it up in redmine to ensure that A) there is indeed a redmine ticket for it, and B) it has been responded to. If not, notify the appropriate MLM with as much information about the MLQ as possible.	weekly	Cath	Luvina	Luvina	Luvina
Monitor & report UCSC Genome Browser outages. See wiki procedures	hopefully, not much!	Alexa/ChrisV	Cath, Luvina	Steve, Jonathan	Steve, Jonathan
update crontab in genecats/qa/crontabs/*.crontab (and log in as qateam and restart the qateam crontab with updates)	as needed	Brian	Brian	Jonathan	Pauline, Jonathan
update UCSC Entrez LinkOut when necessary. Entrez LinkOut sends requests for changes (and statistics) to the browser-qa email address	rarely	ChrisL	Matt	Matt	Bob
Check genome-preview machine is still running	biweekly	Jairo	Brian	Brian	Brian
Updated Facebook with Announcements	As needed	Alexa/Team	Brian/Alexa/Team	Brian	Brian
Update Twitter with Announcements	As needed	Alexa/Team	Brian/Alexa/Team	Ann
otto cron jobs (/hive/data/outside/otto)
omimWrapper.sh checks for new OMIM data and downloads and loads it into hgwdev if so	runs daily, complains bi-weekly	jcasper	jcasper	braney	braney
omimUploadWrapper.sh uploads the OMIM tables to OMIM	runs daily, complains rarely	jcasper	jcasper	braney	braney
decipherWrapper.sh checks for new DECIPHER data and downloads and loads it into hgwdev if so	runs daily, complains monthly	jcasper	jcasper	braney	braney
iscaWrapper.sh checks for new ISCA data and downloads and loads it into hgwdev if so	runs daily, complains monthly	jcasper	jcasper	braney	braney
gwasWrapper.sh checks for new GWAS data and downloads and loads it into hgwdev if so	runs weekly, complains quarterly	jcasper	jcasper	braney	braney
geneReviewsWrapper.sh checks for new GeneReviews data and downloads and loads it into hgwdev if so	runs weekly, complains quarterly	jcasper	jcasper	braney	braney
otto cron jobs (/hive/data/outside/otto)
~jcasper/bin/scripts/updateHgConf.sh - checks for changes to hg.conf files and checks them in to the kent tree	runs weekly	jcasper	jcasper	nobody	nobody
~jcasper/bin/backup_hgconfprivate.sh - checks most recent versions of hg.conf.private files into a private repository (~jcasper/hgconf_private/)	runs twice a week	jcasper	jcasper	nobody	nobody