0bcea84e83ceef4cccba34202e1792e8ad05d980
lrnassar
  Fri Jul 31 18:09:53 2026 -0700
Adding monthly otto notifier that compares our VCEP hub spec versions against the ClinGen CSpec registry. refs #37795

New script src/hg/utils/otto/vcepVersions/checkVcepVersions.py scrapes the
published version from each VCEP hub description page on hgdownload (ENIGMA
BRCA1/BRCA2 and InSiGHT Lynch syndrome) and compares it to the current released
version in the ClinGen CSpec registry, which embeds its specification list as
inline JSON on the affiliation page. Silent when the versions agree, prints a
report when a hub is behind or when the check itself fails.

Only released specs for the genes a hub actually displays are compared, since
an affiliation can carry specs for more genes than we show, on their own
schedule. InSiGHT 50099 for instance also holds APC and MUTYH.

Also adds the monthly crontab entry, mailing otto-group.

diff --git src/hg/utils/otto/otto.crontab src/hg/utils/otto/otto.crontab
index 2fe655dc489..9c32cadf840 100644
--- src/hg/utils/otto/otto.crontab
+++ src/hg/utils/otto/otto.crontab
@@ -78,30 +78,35 @@
 #OMIM
 17 4 * * *  /hive/data/outside/otto/omim/omimWrapper.sh 2>&1
 
 #LOVD
 14 13 * * mon /hive/data/outside/otto/lovd/doUpdate.sh
 
 #MitoMap
 55 8 *  * 3 /hive/data/outside/otto/mitoMap/checkMitoMapUpdate.sh
 
 #RefSeq Historical update notifier (RM #35766) - silent unless NCBI has a new release
 40 8 * * 3 /hive/data/outside/otto/refSeqHistorical/checkRefSeqHistoricalUpdate.sh
 
 # InSiGHT VCEP ClinVar curated variants weekly update
 08 03 * * 2 umask 002; /hive/data/outside/otto/insight/doUpdate.sh
 
+# VCEP hub spec version notifier (RM #37795) - monthly, silent unless one of our
+# VCEP hub description pages is behind the ClinGen CSpec registry
+MAILTO=otto-group@ucsc.edu
+40 06 15 * * /hive/data/outside/otto/vcepVersions/checkVcepVersions.py
+
 # UniProt massive 110+ database update, takes 3-4 days.
 #Format: Minute - Hour - DayofMonth month Day-of-week
 MAILTO=max@soe.ucsc.edu,otto-group@ucsc.edu
 00 07 26 * * /hive/data/outside/otto/uniprot/doUpdate.sh run
 
 #wuhCor1 uniprot otto cron by Max, May 2021
 00 4 * * * /hive/data/outside/otto/uniprot/covidCheck.sh
 
 #ClinGen
 00 9 * * * /hive/data/outside/otto/clinGen/clinGenWrapper.sh
 
 #ClinGen CSpec
 11 11 * * 3 /hive/data/outside/otto/clinGen/clinGenCspec/makeClinGenCspec.sh
 
 #VarChat