92e0aa55b4aba9f659ca7fdbc6572c6c8ce356c9
jnavarr5
  Tue Aug 18 16:36:24 2026 -0700
Switch the MitoMap otto job to the fr.mitomap.org mirror and stop the run when a download fails or comes back empty, refs #38097

diff --git src/hg/utils/otto/mitoMap/checkMitoMapUpdate.sh src/hg/utils/otto/mitoMap/checkMitoMapUpdate.sh
index 1539da15bda..ca515ce3f80 100755
--- src/hg/utils/otto/mitoMap/checkMitoMapUpdate.sh
+++ src/hg/utils/otto/mitoMap/checkMitoMapUpdate.sh
@@ -1,23 +1,37 @@
 #! /bin/bash
 
 cd /hive/data/outside/otto/mitoMap
 
-wget -q https://mitomap.org/downloads/VariantsControl.tsv -O variantsControl.latest.tsv
-wget -q https://mitomap.org/downloads/VariantsCoding.tsv -O variantsCoding.latest.tsv
-wget -q https://mitomap.org/downloads/MutationsRNA.tsv -O mutationsRNA.latest.tsv
-wget -q https://mitomap.org/downloads/MutationsCodingControl.tsv -O mutationsCodingControl.latest.tsv
+# mitomap.org sits behind a Cloudflare bot check that answers our requests with 403,
+# so MitoMap told us to use their mirror until their IT sorts it out. See #38097.
+mitoMapUrl=https://fr.mitomap.org
+
+# Download a file, stopping the run if it fails or comes back empty. wget writes an
+# output file even on a 403, and without this the build would carry on from empty
+# input and only get caught later by the item count check.
+downloadFile() {
+  if ! wget -q "$mitoMapUrl/$1" -O "$2" || [ ! -s "$2" ]; then
+    echo "Error: could not download $mitoMapUrl/$1"
+    exit 1
+  fi
+}
+
+downloadFile downloads/VariantsControl.tsv variantsControl.latest.tsv
+downloadFile downloads/VariantsCoding.tsv variantsCoding.latest.tsv
+downloadFile downloads/MutationsRNA.tsv mutationsRNA.latest.tsv
+downloadFile downloads/MutationsCodingControl.tsv mutationsCodingControl.latest.tsv
 
 # Flag to track if any files are different
 run_script=false
 
 # Function to check if two files are the same
 check_files() {
   if ! cmp -s "$1" "$2"; then
     echo "Update needed for $2. Updating MitoMap track..."
     run_script=true
   fi
 }
 
 # Compare each pair of files
 check_files "mutationsCodingControl.latest.tsv" "mutationsCodingControl.tsv"
 check_files "mutationsRNA.latest.tsv" "mutationsRNA.tsv"
@@ -57,22 +71,29 @@
     echo "Difference in variants: $absDiffVars%"
     exit 1
 fi
 
 # If the difference is within the 20%, proceed
 mv mitoMapDiseaseMuts.new.bb mitoMapDiseaseMuts.bb
 mv mitoMapVars.new.bb mitoMapVars.bb
 mv mitoMapDiseaseMuts.hg19.new.bb mitoMapDiseaseMuts.hg19.bb
 mv mitoMapVars.hg19.new.bb mitoMapVars.hg19.bb
 
 mv mutationsCodingControl.latest.tsv mutationsCodingControl.tsv
 mv mutationsRNA.latest.tsv mutationsRNA.tsv
 mv variantsCoding.latest.tsv variantsCoding.tsv
 mv variantsControl.latest.tsv variantsControl.tsv
 
-wget -q https://mitomap.org/update-date.txt -O version.txt
+# Fetch MitoMap's own release date. Not fatal: the new tracks are already in place,
+# so a failure here just leaves the previous date showing in hgTrackUi.
+if wget -q $mitoMapUrl/update-date.txt -O version.new.txt && [ -s version.new.txt ]; then
+  mv version.new.txt version.txt
+else
+  echo "Warning: could not fetch $mitoMapUrl/update-date.txt, keeping $(cat version.txt)"
+  rm -f version.new.txt
+fi
 
 echo
 echo "Item counts for disease mutation old vs. new bigBed. Old: $oldCountDiseaseMuts New: $newCountDiseaseMuts"
 echo "Item counts for variants old vs. new bigBed. Old: $oldCountVars New: $newCountVars"
 echo
 echo "MitoMap tracks built successfully."