AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

[marcbennedbaek]

Hi!
I am trying to run sierra-local, but I get an error when I try to run with the example given I get an error message:

The installation completed with no errors and I am able to see options for running the program.

I am running this with Python 3.10.9 on Ubuntu 20.04.06 LTS. I looked at a closed issue with a similar error, but there are differences, so it seems the error I encount is different from the one that is closed.

Not sure if it is just me doing something wrong or have misunderstood some directions.

Thanks!
Best regards,
Marc

[ArtPoon]

Looks like we left a deprecated function in there
https://docs.python.org/3.8/library/xml.etree.elementtree.html#xml.etree.ElementTree.Element.getchildren
Most of our testing was back in the pre-3.9 era. I'll have a look.

[ArtPoon]

Looks like I patched this problem a couple of years ago:
0310f13

Can you update sierralocal to the current version?

[marcbennedbaek]

Thank you for the response!

I tried to reinstall again, but got the older version again. When I cloned from my browser instead of a terminal and installed from that repository I got the most recent version.

And now it works!

[ArtPoon]

Glad you were able to resolve the problem. Strange that pulling from the repository in your terminal did not retrieve the latest version.

[CEJ-R]

Hi there @ArtPoon!
So I'm re-opening this again, as I'm seeing the same issue as the person above:

sierralocal indata/my_input.fa
searching path /my/dir/Code/sierra-local/env/envs/sierra_local_250114/lib/python3.10/site-packages/sierralocal/data/HIVDB*.xml
searching path /my/dir/Code/sierra-local/env/envs/sierra_local_250114/lib/python3.10/site-packages/sierralocal/data/apobec*.tsv
HIVdb version 8.8
Traceback (most recent call last):
  File "/my/dir/Code/sierra-local/env/envs/sierra_local_250114/bin/sierralocal", line 11, in <module>
    exit_code = main.main()
  File "/my/dir/Code/sierra-local/env/envs/sierra_local_250114/lib/python3.10/site-packages/sierralocal/main.py", line 178, in main
    count, time_elapsed = sierralocal(args.fasta, args.outfile, xml=args.xml, tsv=args.tsv,
  File "/my/dir/Code/sierra-local/env/envs/sierra_local_250114/lib/python3.10/site-packages/sierralocal/main.py", line 108, in sierralocal
    writer = JSONWriter(algorithm)
  File "/my/dir/Code/sierra-local/env/envs/sierra_local_250114/lib/python3.10/site-packages/sierralocal/jsonwriter.py", line 19, in __init__
    self.definitions = self.algorithm.parse_definitions(self.algorithm.root)
  File "/my/dir/Code/sierra-local/env/envs/sierra_local_250114/lib/python3.10/site-packages/sierralocal/hivdb.py", line 128, in parse_definitions
    element_list = list(map(lambda x: xml.tostring(x).strip().decode("utf-8"), root.getchildren()))
AttributeError: 'xml.etree.ElementTree.Element' object has no attribute 'getchildren'

This after installing the proper version (or so I think?) through pip:
pip install sierralocal==0.2.1

I see that the latest one on git is 0.4, but the most recent in pip is 0.2.1. Is the pip-version out of date, then?

Thanks in advance for any help!

[ArtPoon]

Sounds like the pip version is way out of date, we are at 0.4. Can you do an install directly from the GitHub repo? In the meantime I will look into updating the pip version.

[CEJ-R]

Thanks for your quick reply, and it would be great if the pip-version is updated!

Installing through the repo: would this have to be done in this way, where it installs to /usr/local/lib. For "reasons" (working in a shared cluster) I need this to be installed in a conda/mamba env, or something similar.

[ArtPoon]

Why not run python3 setup.py install --user if you don't have sudo?
Alternatively, you could make a virtual env within your home directory and install there:

cd ~
python3 -m venv venv
source venv/bin/activate
which python  # should return /home/<username>/venv/bin/python3
cd <to git clone dir>
python setup.py install

[ArtPoon]

@WilliamZekaiWang can you please look into integrating pip updating into GitHub workflow?