diff --git a/src/annotation_service/main.py b/src/annotation_service/main.py index d96df730..13e5876c 100644 --- a/src/annotation_service/main.py +++ b/src/annotation_service/main.py @@ -29,7 +29,7 @@ def get_default_job_config(): # consequences 'do_consequence': True, - 'do_vep': False, + 'do_vep': True, #vcf annotate from vcf 'do_dbsnp': True, diff --git a/src/frontend_celery/start_keycloak.sh b/src/frontend_celery/start_keycloak.sh index 167a6938..3d173fd6 100755 --- a/src/frontend_celery/start_keycloak.sh +++ b/src/frontend_celery/start_keycloak.sh @@ -37,6 +37,8 @@ SCRIPT=$(readlink -f "$0") ROOT=$(dirname $(dirname $(dirname "$SCRIPT"))) TOOLS=$ROOT/tools KEYCLOAK_PATH=$TOOLS/keycloak +logs=$ROOT/logs/keycloak +mkdir -p $logs cd $ROOT pwd @@ -67,7 +69,9 @@ fi if [ "${WEBAPP_ENV}" == "prod" ] then - $KEYCLOAK_PATH/bin/kc.sh start --proxy=edge --hostname-strict=false --hostname=$KEYCLOAK_HOST #heredivar.uni-koeln.de --log-level INFO + $keycloak_path/bin/kc.sh start --auto-build --http-relative-path=/kc --db mysql --proxy=edge --hostname-strict=false --log-level INFO --http-host=localhost --db-url "jdbc:mysql://$KEYCLOAK_DB_HOST:$KEYCLOAK_DB_PORT/$KEYCLOAK_DB_SCHEME?allowPublicKeyRetrieval=true\&useSSL=false" --db-url-host $KEYCLOAK_DB_HOST --db-url-port $KEYCLOAK_DB_PORT --db-schema $KEYCLOAK_DB_SCHEME --http-port=$KEYCLOAK_PORT --db-username $KEYCLOAK_DB_USERNAME --db-password $KEYCLOAK_DB_PW --log console,file --log-file $logs/keycloak.log + + #$KEYCLOAK_PATH/bin/kc.sh start --proxy=edge --hostname-strict=false --hostname=$KEYCLOAK_HOST #heredivar.uni-koeln.de --log-level INFO fi diff --git a/tools/script/install_keycloak.sh b/tools/script/install_keycloak.sh index 1583e064..c2210cca 100755 --- a/tools/script/install_keycloak.sh +++ b/tools/script/install_keycloak.sh @@ -44,4 +44,12 @@ mv keycloak-$version $foldername #KEYCLOAK_ADMIN=xxx #KEYCLOAK_ADMIN_PASSWORD=xxx #keycloak-18.0.0/bin/kc.sh import --file /mnt/storage2/users/ahdoebm1/HerediVar/src/frontend_celery/keycloak_export/Heredivar-realm.json -#keycloak-18.0.0/bin/kc.sh build --http-relative-path /kc \ No newline at end of file +#keycloak-18.0.0/bin/kc.sh build --http-relative-path /kc + + +# production commands: +# follow this tutorial: https://gist.github.com/matissime/f9c6e72826862d5fd8a582289b2a2d5f +#mkdir -p keycloak/data/import/ +#cp $basedir/tools/data/init_keycloak.json keycloak/data/import/ +#keycloak/bin/kc.sh --verbose start --auto-build --import-realm --http-relative-path=/kc --db mysql --proxy=edge --hostname-strict=false --log-level INFO --http-host=localhost --db-url "jdbc:mysql://$KEYCLOAK_DB_HOST:$KEYCLOAK_DB_PORT/$KEYCLOAK_DB_SCHEME?allowPublicKeyRetrieval=true\&useSSL=false" --db-url-host $KEYCLOAK_DB_HOST --db-url-port $KEYCLOAK_DB_PORT --db-schema $KEYCLOAK_DB_SCHEME --http-port=$KEYCLOAK_PORT --db-username $KEYCLOAK_DB_USERNAME --db-password $KEYCLOAK_DB_PW +#rm keycloak/data/import/init_keycloak.json