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Remove shebang options - Improve apply_regex_substitution log output#2906

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boegel merged 6 commits intoeasybuilders:developfrom
vanzod:fix_shebang_regex
Jun 4, 2019
Merged

Remove shebang options - Improve apply_regex_substitution log output#2906
boegel merged 6 commits intoeasybuilders:developfrom
vanzod:fix_shebang_regex

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@vanzod vanzod commented Jun 3, 2019

The problem with the changes in #2905 is that with coreutils < 0.30 everything that follows the first word in the shebang is treated as a single argument. Hence something like #!/usr/bin/env perl -w fails with:

/usr/bin/env: 'perl -w': No such file or directory

This fix removes any flag from the shebang.

Changes to filetools.py are also proposed to provide a complete log of the strings replaced by apply_regex_substitutions. The log output will be:

INFO Fixing 'perl' shebang to '#!/usr/bin/env perl' for files that match 'bin/SVDetect': ['/opt/easybuild/software/Compiler/GCC/6.4.0-2.28/SVDetect/0.8b-Perl-5.26.0/bin/SVDetect']
INFO Applying following regex substitutions to /opt/easybuild/software/Compiler/GCC/6.4.0-2.28/SVDetect/0.8b-Perl-5.26.0/bin/SVDetect: [('^#!.*/perl[0-9.]*\\s+.*', '#!/usr/bin/env perl')]
INFO Replacing line 1 in /opt/easybuild/software/Compiler/GCC/6.4.0-2.28/SVDetect/0.8b-Perl-5.26.0/scripts/BAM_preprocessingPairs.pl: '#!/usr/bin/perl -w' -> '#!/usr/bin/env perl'

vanzod added 2 commits June 3, 2019 12:15
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Ignore options
0f679bb 
With coreutils < 0.30 everything that follows the first word in the shebang is treated as a single argument
@vanzod
Print string substitution details in log
a510e69
@vanzod vanzod added this to the 3.x milestone Jun 3, 2019
@vanzod vanzod requested a review from boegel June 3, 2019 17:21
@vanzod vanzod changed the title Fix shebang regex Remove shebang options - Improve apply_regex_substitution log output Jun 3, 2019
@boegel boegel modified the milestones: 3.x, next release (3.9.2) Jun 3, 2019
boegel
boegel requested changes Jun 3, 2019
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@easybuilders easybuilders deleted a comment from boegelbot Jun 3, 2019
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boegel previously approved these changes Jun 3, 2019
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lgtm

@easybuilders easybuilders deleted a comment from boegelbot Jun 4, 2019
@easybuilders easybuilders deleted a comment from boegelbot Jun 4, 2019
@boegel boegel merged commit 0af131d into easybuilders:develop Jun 4, 2019
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