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1 #!/usr/bin/env python
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2 """A simple script to redirect stderr to stdout when the return code is zero.
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3
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4 See https://bitbucket.org/galaxy/galaxy-central/issue/325/
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5
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6 Currently Galaxy ignores the return code from command line tools (even if it
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7 is non-zero which by convention indicates an error) and treats any output on
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8 stderr as an error (even though by convention stderr is used for errors or
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9 warnings).
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10
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11 This script runs the given command line, capturing all stdout and stderr in
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12 memory, and gets the return code. For a zero return code, any stderr (which
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13 should be warnings only) is added to the stdout. That way Galaxy believes
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14 everything is fine. For a non-zero return code, we output stdout as is, and
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15 any stderr, plus the return code to ensure there is some output on stderr.
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16 That way Galaxy treats this as an error.
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17
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18 Once issue 325 is fixed, this script will not be needed.
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19 """
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20 import sys
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21 import subprocess
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22
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23 #Avoid using shell=True when we call subprocess to ensure if the Python
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24 #script is killed, so too is the BLAST process.
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25 try:
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26 words = []
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27 for w in sys.argv[1:]:
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28 if " " in w:
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29 words.append('"%s"' % w)
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30 else:
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31 words.append(w)
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32 cmd = " ".join(words)
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33 child = subprocess.Popen(sys.argv[1:],
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34 stdout=subprocess.PIPE, stderr=subprocess.PIPE)
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35 except Exception, err:
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36 sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
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37 sys.exit(1)
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38 #Use .communicate as can get deadlocks with .wait(),
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39 stdout, stderr = child.communicate()
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40 return_code = child.returncode
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41
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42 if return_code:
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43 sys.stdout.write(stdout)
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44 sys.stderr.write(stderr)
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45 sys.stderr.write("Return error code %i from command:\n" % return_code)
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46 sys.stderr.write("%s\n" % cmd)
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47 else:
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48 sys.stdout.write(stdout)
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49 sys.stdout.write(stderr)
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