9169db807b49113b231d35f2beec4e04c2fb1756
lrnassar
  Wed Jun 3 08:29:02 2026 -0700
Add dataVersion to Orphanet and ClinGen dosage tracks to show upstream release. refs #36455

Orphanet: parse the JDBOR release version (e.g. 1.3.42 / 4.1.8 [2025-03-03]) from
the downloaded XML and write it to a per-assembly version.txt that the orphadata
track points to via dataVersion.

ClinGen: write the ClinGen dosage 'results as of' date (e.g. 28 Apr,2026) from the
curation list header to a version file shared by the clinGenHaplo and clinGenTriplo
subtracks. The other ClinGen feeds publish no dataset-level date, so they are left
unversioned.

The version file is written per assembly only after that assembly's bigBed is
installed, surfacing the source's own release, which can differ from our otto
update timestamp.

diff --git src/hg/utils/otto/orphanet/checkOrphanet.sh src/hg/utils/otto/orphanet/checkOrphanet.sh
index 31acb138d60..8c5f78b2884 100755
--- src/hg/utils/otto/orphanet/checkOrphanet.sh
+++ src/hg/utils/otto/orphanet/checkOrphanet.sh
@@ -1,61 +1,68 @@
 #!/bin/bash
 set -beEu -o pipefail
 
 WORKDIR=$1
 
 cleanUpOnError () {
     echo "orphanet build failed, work directory:"
     echo "$WORKDIR"
 } 
 
 trap cleanUpOnError ERR
 trap "cleanUpOnError; exit 1" SIGINT SIGTERM
 umask 002
 
 if [ ! -d "${WORKDIR}" ]; then
     printf "ERROR in orphanet build, can not find the directory: %s\n" "${WORKDIR}"
     exit 255
 fi
 
 # the release directory, where gbdb symlinks will point
 if [ ! -d release ]; then
     mkdir -p ${WORKDIR}/release/{hg19,hg38}
 fi
 
 cd $WORKDIR
 today=$(date +%F)
 
 # orphanet updates every month so just make the new dir and download
 mkdir $today && cd $today
 wget --quiet http://www.orphadata.org/data/xml/en_product6.xml
 wget --quiet http://www.orphadata.org/data/xml/en_product4.xml
 wget --quiet http://www.orphadata.org/data/xml/en_product9_prev.xml
 wget --quiet http://www.orphadata.org/data/xml/en_product9_ages.xml
 
 # turn the xmls into one bed per assembly
 # Note that this script relies on $db.ensGene.gtf files existing
 # in $WORKDIR. You can generate these files like so:
 # cp /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/genes/hg19.ensGene.gtf.gz .
 # cp /usr/local/apache/htdocs-hgdownload/goldenPath/hg38/bigZips/genes/hg38.ensGene.gtf.gz .
 # gzip -d hg19.ensGene.gtf.gz 
 # gzip -d hg38.ensGene.gtf.gz
 ../parseOrphadata.py
 
 # Sort both files
 sort -k1,1 -k2,2n orphadata.hg19.bed > sortedOrphadata.hg19.bed
 sort -k1,1 -k2,2n orphadata.hg38.bed > sortedOrphadata.hg38.bed
 
 # Check not too much has changed
 oldHg19Count=$(bigBedInfo /gbdb/hg19/bbi/orphanet/orphadata.bb | grep itemCount | cut -d' ' -f2 | sed 's/,//g')
 newHg19Count=$(wc -l sortedOrphadata.hg19.bed | cut -d' ' -f1)
 oldHg38Count=$(bigBedInfo /gbdb/hg38/bbi/orphanet/orphadata.bb | grep itemCount | cut -d' ' -f2 | sed 's/,//g')
 newHg38Count=$(wc -l sortedOrphadata.hg38.bed | cut -d' ' -f1)
 echo $oldHg19Count $newHg19Count | awk '{diff=(($2-$1)/$1); if (diff > 0.1 || diff < -0.1) {printf "validate on hg19 Orphanet failed: old count: %d, new count: %d, difference: %0.2f\n", $1,$2,diff; exit 1;}}'
 echo $oldHg38Count $newHg38Count | awk '{diff=(($2-$1)/$1); if (diff > 0.1 || diff < -0.1) {printf "validate on hg38 Orphanet failed: old count: %d, new count: %d, difference: %0.2f\n", $1,$2,diff; exit 1;}}'
 
 # Make bigBed files
 bedToBigBed -tab -as=$WORKDIR/orphadata.as -type=bed9+20 sortedOrphadata.hg19.bed /hive/data/genomes/hg19/chrom.sizes orphadata.hg19.bb
 bedToBigBed -tab -as=$WORKDIR/orphadata.as -type=bed9+20 sortedOrphadata.hg38.bed /hive/data/genomes/hg38/chrom.sizes orphadata.hg38.bb
 
+# Grab Orphanet's own release version from the XML header for the trackDb dataVersion
+# file. Match the JDBOR line specifically; a bare version= would hit the line 1 XML
+# declaration version="1.0".
+ver=$(grep -m1 'JDBOR' en_product6.xml | grep -o 'version="[^"]*"' | sed 's/version="//; s/"$//')
+
 cp orphadata.hg19.bb $WORKDIR/release/hg19/orphadata.bb
+printf 'Orphadata version %s\n' "$ver" > $WORKDIR/release/hg19/version.txt
 cp orphadata.hg38.bb $WORKDIR/release/hg38/orphadata.bb
+printf 'Orphadata version %s\n' "$ver" > $WORKDIR/release/hg38/version.txt