52357be3947a4643b735276094b8d01da8e3f8f0 braney Tue Sep 8 10:30:02 2026 -0700 ottoMonitor: check the last closed grace window, and let a job be owned by whoever is on duty Three changes, all from comments on the ticket. Lou: civic has no individual owner, so it belongs to the otto person. The owner column of ottoOwners.tsv now accepts ottoOnDuty, which the monitor resolves from the ottoOnDuty header at run time, so the rotation stays a one-line edit. The ticket body says the job has no individual owner, and the same person is not added as a watcher twice when the owner is also the person on duty. The grace window is now measured back from the last scheduled time whose window has already closed, instead of forward from the latest scheduled time. Written the other way, a daily job scheduled fewer than graceHours before the monitor's own 12:15 run could never be reported late, because every check landed inside a fresh window. Six of the forty jobs were in that hole: clinGen, genArkPushRR, grcIncidentDb, liftRequest, omim and pubtatorDbSnp. Max: a uniprot run can take days, and how long depends on the size of the release. Its stamp is created by a > redirect when the run starts, so the grace does not have to cover the run length, and a fresh stamp does not mean the run worked. That limit is now written down in the stamps table and the README, with the live case: the uniprot run dies after about 37 minutes on a missing lxml and has produced no output since January 2025, while the monitor reads it as on time. refs #38101 diff --git src/hg/utils/otto/ottoMonitor/README src/hg/utils/otto/ottoMonitor/README index dd90899e598..bbc23416771 100644 --- src/hg/utils/otto/ottoMonitor/README +++ src/hg/utils/otto/ottoMonitor/README @@ -1,104 +1,121 @@ ottoMonitor - a daily check that every otto job is still running. Refs #38101. WHY Otto jobs are silent when their source has published nothing. That is the design, and it is also why a job that stops running is invisible: no output, no mail, and the track quietly freezes. #38280 is the case that prompted this. A daily job whose source URL had disappeared ran about 1,100 times over three years without a word, and the wuhCor1 UniProt track has not moved since June 2023. WHAT IT ASKS One question per job: did it run when it was supposed to. It answers that from a run stamp, meaning something the job leaves behind whether or not the data changed. Of the 40 jobs in ottoMonitorStamps.tsv, twenty-four write a log, a dated directory, or a named file on every run. Eight leave only their working directory's mtime, because they write a temp file and delete it. Eight leave nothing at all, and those are reported as blind rather than as passing, so the gap stays visible instead of reading as good news. A late job is not automatically somebody's bug. So a late job with a source URL gets that URL fetched. If the source is down the job is left alone, and only a second run in a row that fails the same way becomes a ticket. If the source answers, the failure was something else and it files the same day. THE SURVEYS BEHIND IT ottoSourceUrls.tsv where each job's data comes from, the URL to probe, and the curl shape that URL actually answers. Every one was fetched, not read out of a script. ottoFailureSignatures.tsv what a run, a change and a failure look like on disk for each of the 47 jobs. ottoMonitorStamps.tsv is the machine-readable part of it; this is the reasoning. Both surveys cover all 47 jobs in otto.crontab. The monitor watches 40 of them. The other seven are the Cell Browser jobs, which ottoOwners.tsv marks monitor=no because the cells team owns them and a GB Bug would be the wrong tracker. Read the signature survey before changing a stamp glob. It says what each job writes and when, which is the difference between a stamp that tracks every run and one that only moves when the data changes. THE THREE INPUTS ottoOwners.tsv who owns each job, whether to watch it, its source URL, and its schedule. Canonical copy is in genecats at otto/ottoOwners.tsv. The team edits it there. ottoMonitorStamps.tsv where each job's run stamp lives. Kept beside this script, because it is about the monitor and not about ownership. state.json written under /hive/data/outside/otto/ottoMonitor/. Holds the last run seen, the last verdict, the number of runs in a row that failed the same way, and the ticket number when one is open. Without it a second strike cannot be told from a first. RUNNING IT ./ottoMonitor.py silent unless something is late ./ottoMonitor.py -v also lists the on-time jobs and the blind ones ./ottoMonitor.py --job clinvar one job ./ottoMonitor.py --file actually file tickets. OFF by default Filing is off by default on purpose. Run it without --file for a while and read what it would have filed. THE TWO COPIES Same rule as the rest of otto. Edit the copy in the kent tree at src/hg/utils/otto/ottoMonitor, commit, then copy it out to /hive/data/outside/otto/ottoMonitor, which is what cron runs. Never edit the hive copy directly. TRAPS WORTH KNOWING BEFORE YOU CHANGE A STAMP A file's mtime is not always the run time. hgsqlTableDate calls utime() to set a file's mtime to the database TABLE's date, on purpose, so a later -nt test asks about the data rather than the run. omimUpload's upload/*.date files look like an ideal run stamp and are not; the directory mtime is used instead. +A run stamp says the job started, not that it worked. Most of these globs are +written early in a run on purpose, so a job that dies half way still shows that +it tried. The cost is that a job which fails the same way every time looks on +time forever. uniprot is the live example: its monthly run dies after about 37 +minutes on a missing lxml, it has produced no output since January 2025, and the +browser serves UniProt release 2024_06 while the downloaded source is at 2026_02. +The monitor still reads it as on time, because lastRun.log is fresh every month. +Catching that needs a second kind of check, on the age of the job's OUTPUT +rather than on its schedule, and the monitor does not have one. + The eight directory-mtime jobs work today but nobody designed that signal. Copying a file into one of those directories by hand resets the clock and the monitor will read it as a run. +The grace window is measured from the last scheduled time whose window has +already closed, not from the latest scheduled time. Written the other way, a +daily job scheduled fewer than graceHours before the monitor's own run time can +never be called late, because every check lands inside a fresh window. Six of +the forty were in that hole: clinGen, genArkPushRR, grcIncidentDb, liftRequest, +omim and pubtatorDbSnp. + cron's day rule is an OR, not an AND: when both day-of-month and day-of-week are restricted the job runs when EITHER matches. A job like "14 13 * * mon" would look like it never runs if this were read the other way. A job with more than one crontab line has its schedules joined with ";" in the cron column of ottoOwners.tsv, and the monitor takes whichever fired last. ottoLastLog is the only one so far, because cron cannot say "the last day of the month" in one line. THE EIGHT BLIND JOBS gwas, mane, ncbiRefSeq, ottoGitVsHive, refSeqHistorical, strchive, uniprotWuhCor1, vcepVersions. Two of them are a one-line fix rather than a monitor problem. gwas already creates a dated directory, just after its change check instead of before. mane gates its whole body on whether an output file already exists. Moving either would put that job in reach. That is a suggestion for the owners, not something this ticket does.