Hi everyone,

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I���m currently having problems with executing bash commands through OSSubprocess (version: #stable, as of today) on OS X 10.11.6. I���m using the command line tools of a program called ParseCit to extract metadata from .txt files. It works well for about 75% of all txt files I���ve tested it with, but fails on the remaining 25%. This isn���t due to ParseCit though, since it works on all input files, when I issue the command directly from a bash. I���ve prepared two test txt files ��� one that works fine (goodExample.txt) and one that doesn���t work (badExample.txt) with OSSubprocess. The conversion for both files works fine when issuing the following respective commands in a shell or bash:

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������������������������������ /Users/silas/Documents/TestWithOSS/tools/mac/parsecit/bin/citeExtract.pl -m extract_all /Users/silas/Documents/TestWithOSS/test_txt/badExample.txt

/Users/silas/Documents/TestWithOSS/tools/mac/parsecit/bin/citeExtract.pl -m extract_all /Users/silas/Documents/TestWithOSS/test_txt/goodExample.txt

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Using OSSubprocess, it works well for goodExample.txt, the result looks like this:

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Unfortunately, that exact same method/command fails, if the target file is badExample.txt instead.

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Below, you can find two methods I���ve tried for badExaple.txt, neither of which work. Method 2 (which is the one I used in the above screenshot for goodExample.txt) has a stderr stream, its contents are just above the Method 2 screenshot. It looks like it should be a ParseCit problem, but, as I���ve mentioned above, it works fine when done directly in a bash or shell.

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In this GitHub repo there are the ���tools��� folder containing a compiled version of ParseCit, a corresponding INSTALL.md with all the necessary install steps for ParseCit, and a folder ���test_txt���, which contains goodExample.txt and badExample.txt. The EES-INSTALL.md in the same repo is not relevant in this context.

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If anyone has an idea what could be the problem or how I could get it to work, I���d be very happy.

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Best,

Silas

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*** Methods I���ve tried ***

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Method 1

Result: Empty stdout, empty stderr, exit status 65280

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Method 2

Result: Empty stdout, exit status 65280,

Stderr:

/Users/silas/Documents/TestWithOSS/tools/mac/parsecit/bin/sectLabel/genericSect/extractFeature.rb:35:in `split': invalid byte sequence in US-ASCII (ArgumentError)

������������������������������ from /Users/silas/Documents/TestWithOSS/tools/mac/parsecit/bin/sectLabel/genericSect/extractFeature.rb:35:in `<main>'

Die: SectLabel::Controller::getGenericHeaders different in number of headers 8 vs. the number of generic headers 0

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*** The commands ***

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p1 := OSSUnixSubprocess new

������ command: '/Users/silas/Documents/TestWithOSS/tools/mac/parsecit/bin/citeExtract.pl';

������ arguments: #('-m' 'extract_all' '/Users/silas/Documents/TestWithOSS/test_txt/badExample.txt');

������ redirectStdout;

������������������������������ redirectStderr;

������ runAndWaitOnExitDo: [ :process :outString�� |

�������������� outString inspect

������ ].

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p3 := OSSUnixSubprocess new

������������������������������ shell: '/bin/bash'

������ command: '/Users/silas/Documents/TestWithOSS/tools/mac/parsecit/bin/citeExtract.pl -m extract_all /Users/silas/Documents/TestWithOSS/test_txt/badExample.txt';

������ redirectStdout;

������������������������������ redirectStderr;

������ runAndWaitOnExitDo: [ :process :outString�� |

�������������� outString inspect

������ ].