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check for errors while writing to disk - #856

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luizirber merged 3 commits into
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fix/write_exceptions
Apr 14, 2015
Merged

check for errors while writing to disk#856
luizirber merged 3 commits into
masterfrom
fix/write_exceptions

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@mr-c

@mr-c mr-c commented Feb 26, 2015

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Will fix #443

@mr-c

mr-c commented Mar 30, 2015

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  • Is it mergeable?
  • Did it pass the tests?
  • If it introduces new functionality in scripts/ is it tested?
    Check for code coverage with make clean diff-cover
  • Is it well formatted? Look at make pep8, make diff_pylint_report,
    make cppcheck, and make doc output. Use make format and manual
    fixing as needed.
  • Did it change the command-line interface? Only additions are allowed
    without a major version increment. Changing file formats also requires a
    major version number increment.
  • Is it documented in the ChangeLog?
    http://en.wikipedia.org/wiki/Changelog#Format
  • Was a spellchecker run on the source code and documentation after
    changes were made?

@mr-c
mr-c force-pushed the fix/write_exceptions branch from 014021c to 817192b Compare March 30, 2015 14:11
@mr-c

mr-c commented Mar 30, 2015

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This PR lowers coverage due to extra IO error checking code and how hard it is to test that.

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mr-c commented Mar 30, 2015

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Jenkins, please retest this

@mr-c
mr-c force-pushed the fix/write_exceptions branch from 3c0062d to 4124cfc Compare April 3, 2015 11:35
@mr-c

mr-c commented Apr 3, 2015

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@luizirber @camillescott @ctb ready for review and merge

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mr-c force-pushed the fix/write_exceptions branch from 4124cfc to fd93397 Compare April 4, 2015 16:12
@mr-c mr-c mentioned this pull request Apr 4, 2015
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luizirber
luizirber reviewed Apr 6, 2015
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Comment thread khmer/__init__.py

@luizirber luizirber Apr 6, 2015

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Can this check be used on extract_hashbits_info too?

(at first I thought this could be more strict and catch only struct.error, but there might be IOError too and in the end they are all a kind of corrupted input, so I think that's fine)

@mr-c mr-c Apr 6, 2015

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Done, thanks for the suggestion.

@luizirber

luizirber commented Apr 6, 2015

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It would be good to open an issue to add tests for these extra IO error checking code (per #856 (comment) )

@mr-c mr-c mentioned this pull request Apr 6, 2015
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mr-c force-pushed the fix/write_exceptions branch from fd93397 to 3881bad Compare April 6, 2015 10:10
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mr-c commented Apr 6, 2015

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Jenkins, retest this please

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mr-c force-pushed the fix/write_exceptions branch from 3881bad to 1c7b728 Compare April 14, 2015 13:26
luizirber added a commit that referenced this pull request Apr 14, 2015
@luizirber
Merge pull request #856 from ged-lab/fix/write_exceptions
e099926 
check for errors while writing to disk
@luizirber
luizirber merged commit e099926 into master Apr 14, 2015
@mr-c
mr-c deleted the fix/write_exceptions branch April 14, 2015 13:32
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Update C++ writing code to handle write exceptions properly.

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