[BioRuby] Installing & testing BioRuby on Windows

[Peter Cock]

On Fri, Nov 25, 2011 at 4:50 AM, Naohisa Goto
<ngoto at gen-info.osaka-u.ac.jp> wrote:
> Hi Peter,
>
> I think the failure may be due to the setting of permission for the file
> or the folder.

Yes, you are right :)

> Please look at the permisson for the file
> C:\repositories\bioruby\Test\data\command\echoarg2.bat
>
> By using explorer, right click the file and see "Property" -- "Security"
> and see details. Please confirm if the ACL "Traverse Folder/Execute File"
> is allowed and is not denyed.
> http://www.microsoft.com/resources/documentation/windows/xp/all/proddocs/en-us/acl_special_permissions.mspx?mfr=true

I see the following table, with two columns of tick boxes:

Permissions for XXX: Allow? Deny?
Full Control: Neither ticked
Modify: Neither ticked
Read and Execute: Neither ticked
Read: Allow ticked
Write: Allow ticked for me, not everyone or administrators
Special Permissions: Greyed out

Via the advanced settings button, it seems allow permissions are not inherited.

> The file permission can also be viewed by using cacls command
> on Windows.  Please show the output of the command.
> C:\> cacls C:\repositories\bioruby\Test\data\command\echoarg2.bat
>
> If the special ACL "FILE_EXECUTE" is shown as "DENY", its execution is
> denyed and thus the tests failed.
>

I've had to edit the line wrapping because otherwise it was unreadable,
but there is no mention of FILE_EXECUTE at all.

C:\repositories\bioruby>cacls
C:\repositories\bioruby\Test\data\command\echoarg2.bat
C:\repositories\bioruby\Test\data\command\echoarg2.bat XXX:(special access:)
        STANDARD_RIGHTS_ALL
        DELETE
        READ_CONTROL
        WRITE_DAC
        WRITE_OWNER
        SYNCHRONIZE
        STANDARD_RIGHTS_REQUIRED
        FILE_GENERIC_READ
        FILE_GENERIC_WRITE
        FILE_READ_DATA
        FILE_WRITE_DATA
        FILE_APPEND_DATA
        FILE_READ_EA
        FILE_WRITE_EA
        FILE_READ_ATTRIBUTES
        FILE_WRITE_ATTRIBUTES

     BUILTIN\Administrators:(special access:)
        READ_CONTROL
        SYNCHRONIZE
        FILE_GENERIC_READ
        FILE_READ_DATA
        FILE_READ_EA
        FILE_READ_ATTRIBUTES

     Everyone:(special access:)
        READ_CONTROL
        SYNCHRONIZE
        FILE_GENERIC_READ
        FILE_READ_DATA
        FILE_READ_EA
        FILE_READ_ATTRIBUTES

C:\repositories\bioruby>

Via the cygwin's ls command the execute permission is not set for
echoarg2.bat or echoarg2.sh

The following seems to fix it, and the tests then pass on my machine:

https://github.com/peterjc/bioruby/commit/f33abf9bbd90c3c1e320f06447fdb54ffd094c5d
https://github.com/bioruby/bioruby/pull/42

If you can commit that (or something similar), we can set this machine
up as a buildslave :)

Regards,

Peter