4654fecc7b9d5d905365bd72fee9d3fa4cb6724f
chmalee
  Thu Jan 13 12:38:46 2022 -0800
Staging updates to clingen tracks: slightly rework the otto job after changes to the clinGen website, get out links on description pages correct, refs #28453

diff --git src/hg/utils/otto/clinGen/makeGeneValidity.sh src/hg/utils/otto/clinGen/makeGeneValidity.sh
index 03472db..84ddb6e 100755
--- src/hg/utils/otto/clinGen/makeGeneValidity.sh
+++ src/hg/utils/otto/clinGen/makeGeneValidity.sh
@@ -2,32 +2,47 @@
 
 # downloads and builds the ClinGen Gene Validity track
 # assumes running in the build directory:
 # /hive/data/outside/otto/clinGen/
 set -beEu -o pipefail
 
 WORKDIR=$1
 mkdir -p ${WORKDIR}/clinGenGeneValidity
 cd ${WORKDIR}/clinGenGeneValidity
 
 # the release directory, where gbdb symlinks will point
 if [ ! -d release ]; then
     mkdir -p ${WORKDIR}/release/{hg19,hg38}
 fi
 
-#	see if anything is changing, if so, email notify, download, and build
-wget -q https://raw.githubusercontent.com/RedRiver1816/ClinGen_UCSC_Hub/master/hg19/hg19ClinGenBigBed.bb -O tempUpdate
-if [[ ! -e lastUpdate || tempUpdate -nt lastUpdate ]]; then
-    printf "New ClinGen Gene-Disease tracks hub:\nhttps://github.com/RedRiver1816/ClinGen_UCSC_Hub\n"
+echo "user anonymous
+ls hg*ClinGenBigBed.bb
+bye" > ftp.geneDiseaseValidity.cmds
+
+if [ -e release.list ]
+then
+    mv release.list prev.release.list
+fi
+touch prev.release.list
+rm -f release.list
+
+# connect and list a directory, result to file: ls.check
+ftp -n -v -i ftp.clinicalgenome.org 2>&1 < ftp.geneDiseaseValidity.cmds &> ls.check
+grep "hg.*ClinGenBigBed.bb" ls.check | sort > release.list || echo "Error - no bigBed files found"
+
+# 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
-    hubClone -download https://raw.githubusercontent.com/RedRiver1816/ClinGen_UCSC_Hub/master/hub.txt
+    wget -N -q "ftp://ftp.clinicalgenome.org/hg19ClinGenBigBed.bb"
+    wget -N -q "ftp://ftp.clinicalgenome.org/hg38ClinGenBigBed.bb"
     cp ClinGenHub/hg19/hg19ClinGenBigBed.bb ${WORKDIR}/release/hg19/clinGenGeneDisease.bb
     cp ClinGenHub/hg38/hg38ClinGenBigBed.bb ${WORKDIR}/release/hg38/clinGenGeneDisease.bb
     cd ..
-    mv tempUpdate lastUpdate
     echo "ClinGen Gene-Disease update done: `date`"
 else
-    rm tempUpdate
     echo "No update"
 fi