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50 lines
1.8 KiB
Python
Executable File
50 lines
1.8 KiB
Python
Executable File
#!/usr/bin/env python
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"""A simple script to redirect stderr to stdout when the return code is zero.
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See https://bitbucket.org/galaxy/galaxy-central/issue/325/
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Currently Galaxy ignores the return code from command line tools (even if it
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is non-zero which by convention indicates an error) and treats any output on
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stderr as an error (even though by convention stderr is used for errors or
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warnings).
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This script runs the given command line, capturing all stdout and stderr in
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memory, and gets the return code. For a zero return code, any stderr (which
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should be warnings only) is added to the stdout. That way Galaxy believes
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everything is fine. For a non-zero return code, we output stdout as is, and
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any stderr, plus the return code to ensure there is some output on stderr.
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That way Galaxy treats this as an error.
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Once issue 325 is fixed, this script will not be needed.
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"""
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import sys
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import subprocess
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#Avoid using shell=True when we call subprocess to ensure if the Python
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#script is killed, so too is the BLAST process.
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try:
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words = []
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for w in sys.argv[1:]:
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if " " in w:
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words.append('"%s"' % w)
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else:
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words.append(w)
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cmd = " ".join(words)
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child = subprocess.Popen(sys.argv[1:],
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stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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except Exception, err:
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sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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sys.exit(1)
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#Use .communicate as can get deadlocks with .wait(),
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stdout, stderr = child.communicate()
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return_code = child.returncode
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if return_code:
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sys.stdout.write(stdout)
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sys.stderr.write(stderr)
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sys.stderr.write("Return error code %i from command:\n" % return_code)
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sys.stderr.write("%s\n" % cmd)
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else:
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sys.stdout.write(stdout)
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sys.stdout.write(stderr)
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