#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# delta_filter_wrapper.py
#
# This script is a wrapper for the MUMmer3.23 delta-filter script.
# It is required in order to catch STDOUT ahead of the SGE job
# runner so that pyani can run on SGE/OGE scheduling systems.
#
# The wrapper does not modify the output of delta-filter, and
# is called in exactly the same way, passing arguments through
# directly. The only departure from this is that the first
# argument is the path to delta-filter, and the final
# argument denotes the output filtered delta file path, so that
# redirection (which no longer works with SGE/OGE) is not
# necessary.
#
# For example, the delta-filter command
#
# delta-filter [options] <delta file> > <filtered delta file>
#
# becomes
#
# delta_filter_wrapper.py delta-filter [options] <delta file> <filtered delta file>
#
# This wrapper is not very robust, but will be improved in later
# versions of pyani.
#
# (c) The James Hutton Institute 2017
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@hutton.ac.uk
#
# Leighton Pritchard,
# Information and Computing Sciences,
# James Hutton Institute,
# Errol Road,
# Invergowrie,
# Dundee,
# DD2 5DA,
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2017 The James Hutton Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.

import shlex
import subprocess
import sys

# Parse command-line
df_exe = sys.argv[1]
args = sys.argv[2:-1]
outfname = sys.argv[-1]

sys.stdout.write("script called with %s" % sys.argv)

# Run delta-filter, routing output to the named file
with open(outfname, "w") as ofh:
    ofh.write(
        subprocess.run(
            [shlex.quote(_) for _ in [df_exe] + args], stdout=subprocess.PIPE
        ).stdout.decode("utf-8")
    )

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# delta_filter_wrapper.py
#
# This script is a wrapper for the MUMmer3.23 delta-filter script.
# It is required in order to catch STDOUT ahead of the SGE job
# runner so that pyani can run on SGE/OGE scheduling systems.
#
# The wrapper does not modify the output of delta-filter, and
# is called in exactly the same way, passing arguments through
# directly. The only departure from this is that the first
# argument is the path to delta-filter, and the final
# argument denotes the output filtered delta file path, so that
# redirection (which no longer works with SGE/OGE) is not
# necessary.
#
# For example, the delta-filter command
#
# delta-filter [options] <delta file> > <filtered delta file>
#
# becomes
#
# delta_filter_wrapper.py delta-filter [options] <delta file> <filtered delta file>
#
# This wrapper is not very robust, but will be improved in later
# versions of pyani.
#
# (c) The James Hutton Institute 2017
# Author: Leighton Pritchard
#
# Contact:
# leighton.pritchard@hutton.ac.uk
#
# Leighton Pritchard,
# Information and Computing Sciences,
# James Hutton Institute,
# Errol Road,
# Invergowrie,
# Dundee,
# DD2 5DA,
# Scotland,
# UK
#
# The MIT License
#
# Copyright (c) 2017 The James Hutton Institute
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.

import shlex
import subprocess
import sys

# Parse command-line
df_exe = sys.argv[1]
args = sys.argv[2:-1]
outfname = sys.argv[-1]

sys.stdout.write("script called with %s" % sys.argv)

# Run delta-filter, routing output to the named file
cmd = [shlex.quote(df_exe)] + [shlex.quote(_) for _ in args]
with open(outfname, "w") as ofh:
    ofh.write(
        subprocess.run(
            cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, check=True, shell=False
        ).stdout.decode("utf-8")
    )

make security-related change in delta-filter script