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/makeGeneValidity.sh src/hg/utils/otto/clinGen/makeGeneValidity.sh
index 5d8318da8c5..96e19af8d68 100755
--- src/hg/utils/otto/clinGen/makeGeneValidity.sh
+++ src/hg/utils/otto/clinGen/makeGeneValidity.sh
@@ -31,18 +31,16 @@
 
 # see if anything is changing, if so, notify, download, and build
 diff prev.release.list release.list > release.diff || true
 count=`wc -l release.diff | cut -d' ' -f1`
 if [ "${count}" -gt 1 ]; then
     printf "New ClinGen Gene-Disease tracks\n"
     today=`date +%F`
     mkdir -p $today
     cd $today
     wget -N -q "ftp://ftp.clinicalgenome.org/hg19ClinGenBigBed.bb"
     wget -N -q "ftp://ftp.clinicalgenome.org/hg38ClinGenBigBed.bb"
     cp hg19ClinGenBigBed.bb ${WORKDIR}/release/hg19/clinGenGeneDisease.bb
     cp hg38ClinGenBigBed.bb ${WORKDIR}/release/hg38/clinGenGeneDisease.bb
     cd ..
     echo "ClinGen Gene-Disease update done: `date`"
-else
-    echo "No update"
 fi