351ed2fc24a13b86cf2a1fc9695309e2c0da9de5
lrnassar
  Wed Jun 3 09:33:28 2026 -0700
Make otto fetch failures loud and clinGen silent on no-update. refs #37697

Several otto jobs used 'wget -q'/'curl -s' under 'set -e', so a broken download
aborted with no output and cron (which mails on output, not exit code) sent nothing
-- the mode by which mastermind failed silently for months.

- mastermind, malacards: add an ERR trap that echoes a failure message; switch
mastermind's 'curl -s' to 'curl -sf' so an HTTP error fails loudly instead of
writing a challenge page into the release file.
- geneReviews: add an ERR trap (kept silent on no-update via the wrapper's mail -E).
- All three use 'set -eE' (errtrace) so the ERR trap also fires for failures inside
functions/subshells, not just top-level commands.
- clinGen: capture each sub-build's exit status instead of swallowing it under
'set +e', and report which sub-build failed. Also drop the routine 'No ... update'
echoes and the unconditional 'ClinGen update done.' line, and switch the wrapper to
'mail -E', so clinGen is now silent on no-update and only emails on a real update
or a failure.

diff --git src/hg/utils/otto/clinGen/clinGenWrapper.sh src/hg/utils/otto/clinGen/clinGenWrapper.sh
index bff4d84f168..c7df6fdb5d7 100755
--- src/hg/utils/otto/clinGen/clinGenWrapper.sh
+++ src/hg/utils/otto/clinGen/clinGenWrapper.sh
@@ -1,7 +1,7 @@
 #!/bin/sh -e
 PATH=/cluster/bin/x86_64:$PATH
 EMAIL="otto-group@ucsc.edu"
 WORKDIR="/hive/data/outside/otto/clinGen"
 
 cd $WORKDIR
-./checkClinGen.sh $WORKDIR 2>&1 |  mail -s "ClinGen Build" $EMAIL
+./checkClinGen.sh $WORKDIR 2>&1 |  mail -E -s "ClinGen Build" $EMAIL