Created
August 7, 2018 08:47
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source /homes/dbolser/EG_Places/Devel/lib/libensembl-94/setup.sh | |
release=41 | |
# $ENSEMBL_ROOT_DIR/ensembl-production/scripts/process_division.sh \ | |
# EPl mysql-pan-prod ensembl_production $release \ | |
# > db_to_copy.txt | |
ENDPOINT=http://eg-prod-01.ebi.ac.uk:7000/hc/ | |
SERVER=$( mysql-prod-2 details url) | |
PRODUCTION=$( mysql-pan-prod details url) | |
STAGING=$( mysql-staging-1 details url) | |
LIVE=$( mysql-publicsql details url) | |
COMPARA_MASTER=$( mysql-pan-prod details url) | |
#GROUP=EGCoreHandover | |
#GROUP=EGCore | |
#TEST=DensityFeatures | |
#TEST=BlanksInsteadOfNulls | |
#TEST=CoreForeignKeys | |
TEST=InterproDescriptions | |
GREST='' | |
if [ ! -z ${GROUP} ]; then | |
echo "USING GROUP $GROUP" | |
GREST="$GREST --hc_groups $GROUP" | |
fi | |
if [ ! -z ${TEST} ]; then | |
echo "USING TEST $TEST" | |
GREST="$GREST --hc_names $TEST" | |
fi | |
DATA_FILE_PATH=/nfs/panda/ensembl/production/ensemblftp/data_files/ | |
#TAG=pre_handover_hc_bulk_run | |
TAG=one_off_test-"$(date +%Y%m%d%H%M%S)" | |
BASE_DIR=/homes/dbolser/EG_Places/Devel/lib/ensembl-prodinf-core | |
time \ | |
while read -r db; do | |
echo $SERVER$db | |
#echo \ | |
python \ | |
$BASE_DIR/ensembl_prodinf/hc_client.py \ | |
--uri $ENDPOINT \ | |
--action submit \ | |
--tag "$TAG" \ | |
--db_uri "${SERVER}${db}" \ | |
--production_uri "${PRODUCTION}ensembl_production" \ | |
--staging_uri $STAGING \ | |
--live_uri $LIVE \ | |
--compara_uri "${COMPARA_MASTER}ensembl_compara_master" \ | |
$GREST \ | |
--data_files_path $DATA_FILE_PATH \ | |
--email ${USER}@ebi.ac.uk | |
echo | |
done \ | |
< <( grep _core_ db_to_copy.txt ) | |
echo $TAG; echo $TAG; echo $TAG; | |
# one_off_test-2018-07-20T09:45:16+01:00 | |
## Get results... | |
python \ | |
$BASE_DIR/ensembl_prodinf/hc_client.py \ | |
--uri $ENDPOINT \ | |
--action collate \ | |
--tag "$TAG" \ | |
--output_file results.json | |
cat results.json| json_pp | less -S | |
# ## Delete jobs... | |
# python \ | |
# $BASE_DIR/ensembl_prodinf/hc_client.py \ | |
# --uri $ENDPOINT \ | |
# --action delete \ | |
# --tag "$TAG" |
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