1fbf0a4bf3e1a40b9a117893d61b395561779d7a
chmalee
  Mon Sep 23 13:45:20 2019 -0700
Adding archiving commands to otto build scripts, refs #21825

diff --git src/hg/utils/otto/geneReviews/checkGeneReviews.sh src/hg/utils/otto/geneReviews/checkGeneReviews.sh
index 53f6fb5..95f2da7 100755
--- src/hg/utils/otto/geneReviews/checkGeneReviews.sh
+++ src/hg/utils/otto/geneReviews/checkGeneReviews.sh
@@ -1,58 +1,75 @@
 #!/bin/sh -e
 
 #	Do not modify this script, modify the source tree copy:
 #	src/utils/geneReviews/checkGeneReviews.sh
 #	This script is used via a cron job and kept in $HOME/bin/scripts/
 
 #	cron jobs need to ensure this is true
 #       current login requires the user be chinhli
 umask 002
 
 WORKDIR=$1
 export WORKDIR
 
 function installGeneReviewTables() {
 for i in `cat ../geneReviews.tables`
     do
     n=$i"New"
     o=$i"Old"
     hgsqlSwapTables $1 $n $i $o -dropTable3
     done
     echo "GENEREVIEWS Installed `date` in $1"
 }
 
 
 #	this is where we are going to work
 if [ ! -d "${WORKDIR}" ]; then
     echo "ERROR in GENEREVIEWS release watch, Can not find the directory:
     ${WORKDIR}" 
     exit 255
 fi
 
 cd "${WORKDIR}"
 wget -q --timestamping ftp://ftp.ncbi.nih.gov/pub/GeneReviews/*.txt
 chmod 660 *.txt
 if test NBKid_shortname_genesymbol.txt -nt lastUpdate
 then
     today=`date +%F`
     mkdir -p $today
     mv *.txt $today
 
     cd $today
 
     # build the new GENEREVIEWS track tables
     ../buildGeneReviews.sh
     ../validateGeneReviews.sh hg38
     ../validateGeneReviews.sh hg19
     ../validateGeneReviews.sh hg18
     # now install
     installGeneReviewTables "hg38"  
     installGeneReviewTables "hg19"    
     installGeneReviewTables "hg18"
+    # now archive
+    for db in "hg18" "hg19" "hg38"
+    do
+        if [ ! -d ${WORKDIR}/archive/${db} ]; then
+            mkdir -p ${WORKDIR}/archive/${db}
+        fi
+        cd ${WORKDIR}/archive/${db}
+        mkdir ${today}
+        cd ${today}
+        printf "This directory contains a backup of the geneReviews track built on %s" "${today}" > README 
+        for i in `cat ${WORKDIR}/geneReviews.tables`
+        do
+            hgsql -Ne "show create table ${i}" ${db} > ${i}.sql
+            hgsql -Ne "select * from ${i}" ${db} | gzip >  ${i}.txt.gz
+        done
+    done
+    cd ${WORKDIR}/${today}
 
     rm -f ../lastUpdate
     cp -p NBKid_shortname_genesymbol.txt ../lastUpdate
 
 fi
 
 exit 0