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submit_download_job.py
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import configparser
import argparse
import tempfile
import boto3
import sys
import utility
from collections import OrderedDict
def submit_download_job(job_config, cluster_id, dry_run, **kwargs):
job_configuration = "config/download_job.config"
if job_config is not None and job_config.strip() != "":
job_configuration = job_config.strip()
config = configparser.ConfigParser()
config.optionxform = str
config.read(job_configuration)
if cluster_id is None or cluster_id.strip() == "":
cluster_id = utility.get_cluster_id(dry_run)
else:
cluster_id = cluster_id.strip()
if cluster_id != "" and check_configuration(config):
if config["job_config"].get("upload_downloader_script", "False") == "True":
utility.upload_files_to_s3([(config["job_config"]["downloader_script"],
config["job_config"]["downloader_script_local_location"],
config["job_config"]["downloader_script_s3_location"])], dry_run)
job_argument = build_command(cluster_id, config)
if not dry_run:
emr_client = boto3.client("emr")
# warn user before removing any output
out = config["script_arguments"]["output_location"]
rep = config["script_arguments"]["report_location"]
# find out which output dirs, if any, exist
dirs_to_remove = utility.check_s3_path_exists([out, rep])
if dirs_to_remove:
response = input("About to remove any existing output directories." +
"\n\n\t{}\n\nProceed? [y/n]: ".format(
'\n\n\t'.join(dirs_to_remove)))
while response not in ['y', 'n']:
response = input('Proceed? [y/n]: ')
if response == 'n':
print("Program Terminated. Modify config file to change " +
"output directories.")
sys.exit(0)
# remove the output directories
if not utility.remove_s3_files(dirs_to_remove):
print("Program terminated")
sys.exit(1)
job_submission = emr_client.add_job_flow_steps(**job_argument)
print("Submitted download job to cluster {}. Job id is {}".format(cluster_id, job_submission["StepIds"][0]))
else:
print(job_argument)
def check_configuration(config):
if not utility.check_config(config, "job_config", ["name", "action_on_failure", "downloader_script",
"downloader_script_s3_location", "upload_downloader_script"]):
return False
if not utility.check_upload_config(config["job_config"], "upload_downloader_script", "downloader_script",
"downloader_script_local_location", "downloader_script_s3_location"):
return False
if not utility.check_config(config, "script_arguments", ["accession_list", "output_location", "report_location",
"region"]):
return False
if not utility.check_s3_region(config["script_arguments"]["region"]):
return False
return True
def set_mapper_number(manifest_file):
accession_counts = 0
if manifest_file.startswith("s3://"):
s3_client = boto3.resource("s3")
bucket_name, key_prefix = manifest_file.strip().strip("/")[5:].split("/", 1)
with tempfile.TemporaryDirectory() as tmpdirname:
s3_client.Object(bucket_name, key_prefix).download_file(tmpdirname+"/manifest")
for _ in open(tmpdirname+"/manifest"):
accession_counts += 1
else:
for _ in open(manifest_file):
accession_counts += 1
return accession_counts
def build_command(cluster_id, config):
job_arguments = OrderedDict()
job_arguments["JobFlowId"] = cluster_id
step_arguments = OrderedDict()
step_arguments['Name'] = config["job_config"]["name"]
step_arguments["ActionOnFailure"] = config["job_config"]["action_on_failure"]
hadoop_arguments = OrderedDict()
hadoop_arguments["Jar"] = "command-runner.jar"
command_args = ["hadoop-streaming",
"-D", 'mapreduce.job.name=SRA file downloader',
"-D", "mapreduce.task.timeout=86400000",
"-D", "mapreduce.map.speculative=false",
"-D", "mapreduce.reduce.speculative=false"]
mapper_number = set_mapper_number(config["script_arguments"]["accession_list"])
command_args.append("-D")
command_args.append("mapreduce.job.maps=" + str(mapper_number))
command_args.append("-files")
command_args.append(config["job_config"]["downloader_script_s3_location"].strip().strip("/") + "/" +
config["job_config"]["downloader_script"])
download_only_flag = "-d" if "download_only" in config["script_arguments"] and \
config["script_arguments"]["download_only"].lower() == "true" else ""
command_args.append("-mapper")
command_args.append('{} -o {} -r {} {}'.format(config["job_config"]["downloader_script"].strip(),
config["script_arguments"]["output_location"],
config["script_arguments"]["region"],
download_only_flag))
command_args.append("-reducer")
command_args.append("org.apache.hadoop.mapred.lib.IdentityReducer")
command_args.append("-numReduceTasks")
command_args.append("1")
command_args.append("-input")
command_args.append(config["script_arguments"]["accession_list"])
command_args.append("-output")
command_args.append(config["script_arguments"]["report_location"])
hadoop_arguments['Args'] = command_args
step_arguments["HadoopJarStep"] = hadoop_arguments
job_arguments["Steps"] = [step_arguments]
return job_arguments
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='Job submission script for spark-based RNA-seq Pipeline')
parser.add_argument('--config', '-c', action="store", dest="job_config", default="", help="Job configuration file")
parser.add_argument('--cluster-id', '-id', action="store", dest="cluster_id", help="Cluster ID for submission")
parser.add_argument('--dry-run', '-d', action="store_true", dest="dry_run",
help="Produce the configurations for the job flow to be submitted")
parser.set_defaults(method=submit_download_job)
parser_result = parser.parse_args()
parser_result.method(**vars(parser_result))