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Fix the forbidden symbols when using unpackdb #467

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Merged
milot-mirdita merged 8 commits into from
Jul 7, 2021
Merged

Fix the forbidden symbols when using unpackdb #467

milot-mirdita merged 8 commits into from
Jul 7, 2021

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@cutecutecat cutecutecat commented Jul 2, 2021

fix issue #466

<>:"/ | ?* is not allowed in file path of Windows(all) and Linux(only /) when created separated database files with sequence names. Therefore, these symbols should be substituted with others.

At file src/util/unpack.cpp, substitute these forbidden symbols with others.
As '|' is frequently appeared in sequence name as:
A0A348AT68|unreviewed|Fluorescent
We change '|' to '!':
A0A348AT68!unreviewed!Fluorescent
Other symbols are changed to '@':
W5UC41|unreviewed|Nidogen-1|taxID/7998->W5UC41!unreviewed!Nidogen-1!taxID@7998

Then everything is ok!

@cutecutecat
fix bug of path forbidden chars
7bf0519 
<>:"/ \| ?* is not allowed in file path of Windows(all) and Linux(only /) when created separated database files with sequence names. Therefore, these symbols should be substituted with others.
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Merge branch 'soedinglab:master' into master
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Merge branch 'soedinglab:master' into master
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@cutecutecat cutecutecat mentioned this pull request Jul 2, 2021
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@cutecutecat cutecutecat changed the title Fix the forbidden symbols when using unpack Fix the forbidden symbols when using unpackdb Jul 2, 2021
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milot-mirdita commented Jul 2, 2021

Thanks a lot for your contribution and finding about this edge case.

We try to avoid Modern C++ features, could you please implement this without auto, lambdas and std::replace. I think FileUtil might be an appropriate place for this function.

The SSTR(key) branch is always numeric and doesn't require a call to path_substitution.

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cutecutecat commented Jul 5, 2021

Thanks a lot for your contribution and finding about this edge case.

We try to avoid Modern C++ features, could you please implement this without auto, lambdas and std::replace. I think FileUtil might be an appropriate place for this function.

The SSTR(key) branch is always numeric and doesn't require a call to path_substitution.

Thank you for your review. These C++ 11 features will be removed in a couple of days. I will push next request before this Friday.

@milot-mirdita milot-mirdita merged commit c663497 into soedinglab:master Jul 7, 2021
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milot-mirdita commented Jul 7, 2021

Thanks a lot!

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