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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1128 ] timestamps not preserved when untarring files
    03/11/11 14:32
    Submitted by:
    Assigned to:
    Ticket group:
    timestamps not preserved when untarring files
    Original submission:
    It looks like tarfile.extract() does not preserve the modification
    times of files that get extracted. My reading of the Python API is that
    tarfile.extractall() does preserver these times. I can't tell whether
    permissions are being preserved or not. That is, all files seem to
    be world readable and directories world readable-executable, but
    I don't know if that's because the permissions are being preserved, or
    just because the umask for /Users/birch has those permissions.

    In any case, it might be worth trying tarfile.extractall(). The other
    reason is that tarfile.extract() is very very slow on canolaoil. It
    took 8 hours to do an update on canola oil. That, of course, is a
    real worst case situation, but if, by chance tarfile.extract() performs
    better, that would be a plus.
    Please log in to add comments and receive followups via email.
    Comment Date By
    There is probably no way around the timestamp issue that won't substantially hinder performance. Since this is to package the files for release anyways, I don't think that this issue is of too much concern, as all of the files will be at the mtime of the release. 03/26/11 14:50 umhameld
    With getbirch-614c2ba, the timestamps of files (ie. their original dates and times of the last modification) are not preserved. Rather, as tiles are untarred, they get the time and date at which they are written.

    This may just be an artifact of reverting to an older version of getbirch, for the stable snapshot?
    03/17/11 18:44 B_Fristensky
    This seems to be fixed, reopen it if it is still an issue 03/15/11 22:15 umhameld
    The reason why extract seemed so slow was probably the verbosity. It is very expensive to write to the console and to a file. I have ditched the prints in favor of the progress bar. On albacore, the extraction now takes minutes.

    Using a clever wrapper around extractall, the permission issue is fixed too.

    I am leaving this bug open pending verification.
    03/11/11 21:56 umhameld
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    Ticket change history
    Field Old value Date By
    status_id Open 08/11/11 19:09 umhameld
    close_date 03/15/11 22:16 08/11/11 19:09 umhameld
    priority 6 03/26/11 14:50 umhameld
    status_id Closed 03/17/11 18:44 B_Fristensky
    priority 1 03/17/11 18:44 B_Fristensky
    status_id Open 03/15/11 22:16 umhameld
    close_date 12/31/69 19:00 03/15/11 22:16 umhameld
    priority 5 03/11/11 22:00 umhameld
    resolution_id Not Resolved 03/11/11 21:56 umhameld
    status_id Pending 03/11/11 14:33 B_Fristensky
    assigned_to unset 03/11/11 14:33 B_Fristensky
    resolution_id Unset 03/11/11 14:33 B_Fristensky


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