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/mastermind/buildMastermind.sh src/hg/utils/otto/mastermind/buildMastermind.sh
index b2b1552ab8b..7eaae532038 100755
--- src/hg/utils/otto/mastermind/buildMastermind.sh
+++ src/hg/utils/otto/mastermind/buildMastermind.sh
@@ -1,42 +1,46 @@
 #wget 'https://mastermind.genomenon.com/cvr/download?format=csv' -O - > mastermind.2018.11.26.csv.gz
 #unzip mastermind.2018.11.26.csv.zip
 #mv mastermind_cited_variants_reference-2018.11.26-csv/ 2018-11-26
 #hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > chromAlias.tab
 #ln -s `pwd`/mastermind.bb /gbdb/hg19/bbi/mastermind.bb
 #python mastermindToBed.py 2018-11-26/mastermind_cited_variants_reference-2018.11.26.csv 
 #bedSort mastermind.bed mastermind.bed
 #bedToBigBed -type=bed9+ -as=mastermind.as -tab mastermind.bed //hive/data/genomes/hg19/chrom.sizes  mastermind.bb
 
-set -e -o pipefail
+set -eE -o pipefail
+# Emit an error line on any failure so cron actually sends mail. wget -q is silent and
+# set -e would otherwise abort with no output, which cron treats as nothing to report.
+# -E (errtrace) makes the ERR trap fire for failures inside functions/subshells too.
+trap 'echo "ERROR: mastermind build failed (exit $?) at line $LINENO" >&2' ERR
 cd /hive/data/outside/otto/mastermind
 date=`date --iso-8601`
 mkdir -p hg19 hg38
 mkdir -p archive/$date
 hgsql hg19 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > hg19/chromAlias.tab
 hgsql hg38 -NB -e 'select alias, chrom from chromAlias where source = "refseq";' > hg38/chromAlias.tab
 wget -q 'https://mastermind.genomenon.com/cvr/download?build=grch37&format=csv' -O archive/$date/hg19.zip
 wget -q 'https://mastermind.genomenon.com/cvr/download?build=grch38&format=csv' -O archive/$date/hg38.zip
 unzip -o archive/$date/hg19.zip -d archive/$date
 unzip -o archive/$date/hg38.zip -d archive/$date
 python mastermindToBed.py hg19/chromAlias.tab archive/$date/mastermind_cited_variants_reference-*-grch37.csv hg19/mastermind.bed
 python mastermindToBed.py hg38/chromAlias.tab archive/$date/mastermind_cited_variants_reference-*-grch38.csv hg38/mastermind.bed
 bedSort hg19/mastermind.bed hg19/mastermind.bed
 bedSort hg38/mastermind.bed hg38/mastermind.bed
 bedToBigBed -type=bed9+ -as=mastermind.as -tab hg19/mastermind.bed /hive/data/genomes/hg19/chrom.sizes  hg19/mastermind.new.bb
 bedToBigBed -type=bed9+ -as=mastermind.as -tab hg38/mastermind.bed /hive/data/genomes/hg38/chrom.sizes  hg38/mastermind.new.bb
-curl -s https://mastermind.genomenon.com/cvr/version | cut -d\" -f4 > mastermindRelease.new.txt
+curl -sf https://mastermind.genomenon.com/cvr/version | cut -d\" -f4 > mastermindRelease.new.txt
 mv mastermindRelease.new.txt mastermindRelease.txt
 mv hg19/mastermind.new.bb hg19/mastermind.bb
 mv hg38/mastermind.new.bb hg38/mastermind.bb
 
 # build archive
 REL=`cat mastermindRelease.txt`
 ARCH=/hive/data/inside/archive
 mkdir -p $ARCH/{hg19,hg38}/mastermind/$REL
 cp hg19/mastermind.bb $ARCH/hg19/mastermind/$REL/
 cp hg38/mastermind.bb $ARCH/hg38/mastermind/$REL/
 hgsql hg19 -e 'select * from trackDb where tableName="mastermind"' > $ARCH/hg19/mastermind/$REL/trackDb.tab
 hgsql hg38 -e 'select * from trackDb where tableName="mastermind"' > $ARCH/hg38/mastermind/$REL/trackDb.tab
 cp archive/$date/LICENSE.pdf $ARCH/hg19/mastermind/$REL/
 cp archive/$date/LICENSE.pdf $ARCH/hg38/mastermind/$REL/
 echo "These file were derived from Genomenom CVR, see https://www.genomenon.com/cvr/" > $ARCH/hg19/mastermind/$REL/README.txt