upload-to-arvados

#!/bin/bash
#
# assumes ARVADOS_API_TOKEN and ARVADOS_API_HOST is set

project_uuid=`jq -r '.["public-database-project"].uuid' $HOME/.config/arvados/config.json`

echo "# uploading to project: $project_uuid"

rm -rf arv-stage

mkdir -p arv-stage
cd arv-stage

ln -s ../html .
ln -s ../db .

for x in `ls ../out-data`
do
  echo $x
  ln -s ../out-data/$x .
done

mv untap.sqlite3.gz hu-pgp.sqlite3.gz

dtstr=`date +'%Y-%m-%d+%H:%M:%S'`
arv-put --project-uuid $project_uuid --name HU-PGP-DB-$dtstr ./

cd ..