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Update file_setup Pipeline

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This commit is contained in:
Patrick Jentsch
2020-04-03 18:35:39 +02:00
parent 933136bd08
commit fa3b3cc556
5 changed files with 88 additions and 102 deletions
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29
wrapper/file_setup Executable file
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#!/usr/bin/env python3
# coding=utf-8
from argparse import ArgumentParser
import os
import subprocess
CONTAINER_IMAGE = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/file_setup:latest'
CONTAINER_INPUT_DIR = '/input'
CONTAINER_OUTPUT_DIR = '/output'
UID = str(os.getuid())
GID = str(os.getgid())
parser = ArgumentParser(add_help=False)
parser.add_argument('-i')
parser.add_argument('-o')
args, remaining_args = parser.parse_known_args()
cmd = ['docker', 'run', '--rm', '-it', '-u', '{}:{}'.format(UID, GID)]
if args.o is not None:
cmd += ['-v', '{}:{}'.format(os.path.abspath(args.o), CONTAINER_OUTPUT_DIR)]
remaining_args.insert(0, CONTAINER_OUTPUT_DIR)
if args.i is not None:
cmd += ['-v', '{}:{}'.format(os.path.abspath(args.i), CONTAINER_INPUT_DIR)]
remaining_args.insert(0, CONTAINER_INPUT_DIR)
cmd.append(CONTAINER_IMAGE)
cmd += remaining_args
subprocess.run(cmd)

39
wrapper/setup_files
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#!/usr/bin/env python3
# coding=utf-8
import argparse
import os
import subprocess
container_image = 'gitlab.ub.uni-bielefeld.de:4567/sfb1288inf/setup_files:latest'
container_input_dir = '/input'
container_output_dir = '/output'
uid = str(os.getuid())
gid = str(os.getgid())
parser = argparse.ArgumentParser(add_help=False)
parser.add_argument(
'-i',
dest='input_dir',
required=False
)
parser.add_argument(
'-o',
dest='output_dir',
required=False
)
args, remaining_args = parser.parse_known_args()
cmd = ['docker', 'run', '--rm', '-it', '-u', uid + ':' + gid]
if args.input_dir is not None:
host_input_dir = os.path.abspath(args.input_dir)
cmd += ['-v', host_input_dir + ':' + container_input_dir]
remaining_args += ['-i', container_input_dir]
if args.output_dir is not None:
host_output_dir = os.path.abspath(args.output_dir)
cmd += ['-v', host_output_dir + ':' + container_output_dir]
remaining_args += ['-o', container_output_dir]
cmd.append(container_image)
cmd += remaining_args
subprocess.run(cmd)