Bug#991208: [Debian-med-packaging] Bug#991208: q2-demux: dist missing from q2_demux/_summarize/assets/ directory

[Étienne Mollier]

Control: tag -1 confirmed
Control: tag -1 help

Hi Beatrice,

Thanks for reaching out via reportbug.  I confirm I could
reproduce a similar issue with some test dataset from the
package q2-quality-control:

$ 
QZA_SAMPLE="/usr/lib/python3/dist-packages/q2_quality_control/tests/data/paired-end.qza"
$ qiime demux summarize --i-data "$QZA_SAMPLE" --o-visualization 
demux.qzv
/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:

  [Errno 2] No such file or directory: 
'/usr/lib/python3/dist-packages/q2_demux/_summarize/assets/dist'

Said dist/ directory is not directly part of q2-demux itself,
but, given the content of the Makefile in the source code, is
obtained from "npm install" and "npm run build", which has to
make use of Internet resources.  A quick workaround which "works
for me" is to construct at least an empty directory named:

/usr/lib/python3/dist-packages/q2_demux/_summarize/assets/dist

While this allows the command to produce the demux.qzv, it
misses the appropriate code for running the embedded interactive
quality plot, which one can obtain using the command afterwards:

$ qiime tools view demux.qzv

I could solve this on my local installation, by copying the
resulting minified .js files below the dist/ directory, but
minified javascript is not eligible for being considered as
source code.  I'm not fluent at all with npm to be sure of my
fixes/workarounds yet, so would appreciate if someone with
npm/node experience could have a second look, and maybe advise.

Kind Regards,
-- 
Étienne Mollier 
Fingerprint:  8f91 b227 c7d6 f2b1 948c  8236 793c f67e 8f0d 11da
Sent from /dev/pts/2, please excuse my verbosity.


signature.asc
Description: PGP signature

Bug#991208: q2-demux: dist missing from q2_demux/_summarize/assets/ directory

[Beatrice Torracca]

Package: q2-demux
Version: 2020.11.1-1
Severity: normal

Hi,

I think there is something missing in Debian installation of the demux
plugin for qiime2. Please note that I am at my first steps with qiime
so I apologize if this is me doing something wrong.

When I try to use the qiime demux comand (following one of qiime tutorials) as:

qiime demux summarize --i-data demux.qza --o-visualization demux.qzv

I get this error:

Plugin error from demux:

  [Errno 2] No such file or directory: 
'/usr/lib/python3/dist-packages/q2_demux/_summarize/assets/dist'

and this is the content of the debug log file saved by qiime:

 BEGIN LOG FILE
/usr/lib/python3/dist-packages/seaborn/distributions.py:2557: FutureWarning: 
`distplot` is a deprecated function and will be removed in a future version. 
Please adapt your code to use either `displot` (a figure-level function with 
similar flexibility) or `histplot` (an axes-level function for histograms).
  warnings.warn(msg, FutureWarning)
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/q2cli/commands.py", line 329, in __call__
results = action(**arguments)
  File "", line 2, in summarize
  File "/usr/lib/python3/dist-packages/qiime2/sdk/action.py", line 244, in 
bound_callable
outputs = self._callable_executor_(scope, callable_args,
  File "/usr/lib/python3/dist-packages/qiime2/sdk/action.py", line 452, in 
_callable_executor_
ret_val = self._callable(output_dir=temp_dir, **view_args)
  File "/usr/lib/python3/dist-packages/q2_demux/_summarize/_visualizer.py", 
line 237, in summarize
shutil.copytree(os.path.join(TEMPLATES, 'assets', 'dist'),
  File "/usr/lib/python3.9/shutil.py", line 555, in copytree
with os.scandir(src) as itr:
FileNotFoundError: [Errno 2] No such file or directory: 
'/usr/lib/python3/dist-packages/q2_demux/_summarize/assets/dist'
 END LOG FILE

Thanks a lot for your work of packetization of qiime for Debian!

beatrice



-- System Information:
Debian Release: 11.0
  APT prefers testing-security
  APT policy: (500, 'testing-security'), (500, 'testing'), (100, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 5.10.0-7-amd64 (SMP w/4 CPU threads)
Locale: LANG=it_IT.UTF-8, LC_CTYPE=it_IT.UTF-8 (charmap=UTF-8), LANGUAGE not set
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)
LSM: AppArmor: enabled

Versions of packages q2-demux depends on:
ii  python3 3.9.2-3
ii  python3-ipywidgets  6.0.0-8
ii  python3-numpy   1:1.19.5-1
ii  python3-pandas  1.1.5+dfsg-2
ii  python3-psutil  5.8.0-1
ii  python3-seaborn 0.11.1-1
ii  python3-setuptools  52.0.0-4
ii  python3-skbio   0.5.6-4
ii  python3-yaml5.3.1-4
ii  q2-types2020.11.1-1
ii  q2templates 2020.11.1+dfsg-1
ii  qiime   2020.11.1-1

q2-demux recommends no packages.

q2-demux suggests no packages.

-- no debconf information