e1df6d7bb91a0f8027129677be73ad720d79449d
angie
  Fri Aug 26 11:38:42 2022 -0700
Update nextstrain URL and use curl --compressed (thanks @tsibley).

diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh
index 2b59b2c..1afd407 100755
--- src/hg/utils/otto/nextstrainNcov/doUpdate.sh
+++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh
@@ -1,34 +1,33 @@
 #!/bin/bash
 source ~/.bashrc
 set -beEu -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/nextstrainNcov/doUpdate.sh
 
 ottoDir=/hive/data/outside/otto/nextstrainNcov
 chromSizes=/hive/data/genomes/wuhCor1/chrom.sizes
 gbdbDir=/gbdb/wuhCor1/nextstrain
 
-ncovJsonUrl='https://nextstrain.org/charon/getDataset?prefix=/ncov/open/global'
+ncovJsonUrl='https://nextstrain.org/charon/getDataset?prefix=/ncov/open/global/6m'
 
 cd $ottoDir
 
-# The file is named .json, but is actually gzipped, so gunzip it.
 rm -f ncov.json
-curl -s "$ncovJsonUrl" \
-| gunzip -c > ncov.json
+# HT Thomas Sibley: use --compressed flag to send "Accept-Encoding: gzip" and auto-decompress:
+curl -sS --compressed "$ncovJsonUrl" > ncov.json
 curl -s -I "$ncovJsonUrl" \
 | grep Last-Mod | sed -re 's/Last-Modified: //; s/\r//;' \
    > ncov.json.date
 latestDate=$(cat ncov.json.date)
 oldDate=$(cat old.ncov.json.date)
 if [ $(date -d "$latestDate" +%s) -le $(date -d "$oldDate" +%s)  ]; then
     exit 0
 fi
 
 today=`date +%F`
 mkdir -p $today
 ncovTime=$(date -d "$latestDate" +%F-%H:%M)
 cp -p ncov.json $today/ncov.$ncovTime.json
 mv -f ncov.json old.ncov.json
 mv ncov.json.date old.ncov.json.date