334b92a7d3c7c61af8ea9facbc7ec1c2442025fa angie Thu Sep 30 09:59:38 2021 -0700 Update Nextstrain JSON URL. diff --git src/hg/utils/otto/nextstrainNcov/doUpdate.sh src/hg/utils/otto/nextstrainNcov/doUpdate.sh index 1f582aa..2b59b2c 100755 --- src/hg/utils/otto/nextstrainNcov/doUpdate.sh +++ src/hg/utils/otto/nextstrainNcov/doUpdate.sh @@ -1,27 +1,27 @@ #!/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/global' +ncovJsonUrl='https://nextstrain.org/charon/getDataset?prefix=/ncov/open/global' 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 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