[Debian-med-packaging] Bug#994459: libjs-jquery removed symlinked files

[Étienne Mollier]

Control: tag -1 moreinfo

Greetings chrysn,

On Thu, 16 Sep 2021 11:15:31 +0200 chrysn <chrysn at fsfe.org> wrote:
> Running qiime like this produces an error:
> 
> | $ qiime demux summarize --i-data test.qza --o-visualization test.qzv
> | /usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py:36: UserWarning: h5py is running against HDF5 1.10.7 when it was built against 1.10.6, this may cause problems
> |   _warn(("h5py is running against HDF5 {0} when it was built against {1}, "
> | /usr/lib/python3/dist-packages/skbio/util/_testing.py:15: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
> |   import pandas.util.testing as pdt
> | Plugin error from demux:
> |
> |   [('/usr/lib/python3/dist-packages/q2templates/templates/assets/js/jquery.min.js', '/tmp/qiime2-temp-worx3rub/q2templateassets/js/jquery.min.js', "[Errno 2] No such file or directory: '/usr/lib/python3/dist-packages/q2templates/templates/assets/js/jquery.min.js'")]
> 
> The critical part is the absence of
> /usr/lib/python3/dist-packages/q2templates/templates/assets/js/jquery.min.js,
> which is a broken symlink.

Thanks for the reproducer!  I'm afraid I didn't get to reproduce
the problem on my end though:

	$ qiime demux summarize \
		--i-data /usr/lib/python3/dist-packages/q2_quality_control/tests/data/single-end.qza  \
		--o-visualization test.qzv
	/usr/lib/python3/dist-packages/h5py/_debian_h5py_serial/__init__.py:36: UserWarning: h5py is running against HDF5 1.10.7 when it was built against 1.10.6, this may cause problems
	  _warn(("h5py is running against HDF5 {0} when it was built against {1}, "
	/usr/lib/python3/dist-packages/skbio/util/_testing.py:15: FutureWarning: pandas.util.testing is deprecated. Use the functions in the public API at pandas.testing instead.
	  import pandas.util.testing as pdt
	Saved Visualization to: test.qzv

But it is possible I didn't look at the right thing: different
.qza files raise different behaviors.  If things are still wrong
on your end I would be happy to have a copy of your test data,
to make sure I have a reliable reproducer.

> My `apt-file find` opined that libjs-jquery would have that file, but
> since 3.5.1+dfsg+~3.5.5-4 these are not present any more.

Ah, thanks for indicating the libjs-query you used!  Apparently,
if I read #977960 [1] properly, the libjs-jquery package
suffered from symlinks interlacing in the past few package
uploads.  I believe the issue should now be solved with
libjs-jquery version 3.5.1+dfsg+~3.5.5-7.

[1]: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=977960

Please, could you let us know if the problem still appears on
your end with this newer version?

Thank you for your report!
Have a nice day,  :)
-- 
Étienne Mollier <emollier at emlwks999.eu>
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/9, please excuse my verbosity.
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