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/makeDosage.sh src/hg/utils/otto/clinGen/makeDosage.sh
index e1f8e377167..a4cb947c293 100755
--- src/hg/utils/otto/clinGen/makeDosage.sh
+++ src/hg/utils/otto/clinGen/makeDosage.sh
@@ -92,18 +92,16 @@
         fi
 
         bedToBigBed -type=bed9+17 -as=../../clinGenDosageHaplo.as -tab ../output/${db}.clinGenHaplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenHaplo.bb
         bedToBigBed -type=bed9+17 -as=../../clinGenDosageTriplo.as -tab ../output/${db}.clinGenTriplo.bed /hive/data/genomes/${db}/chrom.sizes ../output/${db}.clinGenTriplo.bb
         cp ../output/${db}.clinGenHaplo.bb ${WORKDIR}/release/${db}/clinGenHaplo.bb
         cp ../output/${db}.clinGenTriplo.bb ${WORKDIR}/release/${db}/clinGenTriplo.bb
 
         # ClinGen stamps the curation list with its own "results as of" date (line 2,
         # e.g. "#28 Apr,2026"). Expose it via dataVersion (shared by the Haplo and Triplo
         # subtracks) so users can tie the browser data to a specific ClinGen dosage
         # release rather than our otto run date.
         dosageDate=$(sed -n 2p ClinGen_region_curation_list_${grc}.tsv | tr -d '#\r')
         printf 'ClinGen Dosage Sensitivity Map, %s\n' "$dosageDate" > ${WORKDIR}/release/${db}/clinGenDosageVersion.txt
     done
     cd ../..
-else
-    echo "No ClinGen CNV update"
 fi