#!/usr/bin/env bash
#
# Licensed to Big Data Genomics (BDG) under one
# or more contributor license agreements.  See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership.  The BDG licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.  You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

set -e

# does the user have ADAM_OPTS set? if yes, then warn
if [[ -z $@ && -n "$ADAM_OPTS" ]]; then
    echo "WARNING: Passing Spark arguments via ADAM_OPTS was recently removed." 1>&2
    echo "Run adam-shell instead as adam-shell <spark-args>" 1>&2
fi

SOURCE_DIR=$(dirname ${BASH_SOURCE[0]})

ADAM_CLI_JAR=$(${SOURCE_DIR}/find-adam-assembly.sh)

SPARK_SHELL=$(${SOURCE_DIR}/find-spark.sh spark-shell)
echo "Using SPARK_SHELL=$SPARK_SHELL" 1>&2

# submit the job to Spark
"$SPARK_SHELL" \
    --conf spark.serializer=org.apache.spark.serializer.KryoSerializer \
    --conf spark.kryo.registrator=org.bdgenomics.adam.serialization.ADAMKryoRegistrator \
    --jars ${ADAM_CLI_JAR} \
    "$@"
