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Ensembl / Bio-DB-HTS

Git repo for Bio::DB::HTS module on CPAN, providing Perl links into HTSlib
Apache License 2.0
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Request to honour POSIX ACLs #89

Closed CanWood closed 1 day ago

CanWood commented 4 years ago

Hi folks.

Would it be possible to have the access checks on bam files enhanced to check whether or not POSIX ACLs will allow users to access files? HTS.pm line 1387 uses filetest access and, according to the perldoc for filetest

...you may encounter surprises if your program runs on a system that uses ACLs, since the stat() information won't reflect the actual permissions.

Any chance these tests could be enhanced to allow use of ACL on supporting systems?

Thanks!

jmarshall commented 4 years ago

Honouring ACLs is precisely what use filetest 'access' does, as added (by you) in PR #49.

Or are you saying there are other places in the code that the pragma could also usefully be used? If so, where?

CanWood commented 4 years ago

Wow. Long enough ago that I did not remember submitting that! I'll run some more tests but it's looking to me like my original fix may not have been sufficient. My apologies. I'll be in touch.

sgiorgetti commented 1 day ago

Closing because of aging. Please, re-open this if you feel it's still current