ApiError not defined. Listing of environment/dependencies is needed.

[ilibarra]

Dear remap-cisreg team.

I have gotten two issues using the default repo. Due to the repo not listing dependencies explicitly, it seems that these occur sequentially in a de novo environment with the latest python version.

Upon reversion to 3.1. I have found that:

• chardet raises an error due to chardet.detect not found if version is 4.0.0. chardet has to be version 3.0.4 for it to work successfully.
• I get ApiError when using Python 3.10.4 after the encoding is processed (see below).

python remap-pipeline/2.scripts/utils/python3/extract_info/extract_info_download_v3_1.py -wd . -f 1.metadata/EXAMPLE_hsap_TF.tsv
Traceback (most recent call last):
  File "remap-pipeline/2.scripts/utils/python3/extract_info/extract_info_download_v3_1.py", line 465, in <module>
    raise ApiError('GET /tasks/ {}'.format( ena_resp.status_code))
NameError: name 'ApiError' is not defined. Did you mean: 'TypeError'?

I strongly suggest an requirements.txt and/or environment.yml file describing the lib versions needed. Happy to provide more details if required.

Thank you

[benoitballester]

Hi @ilibarra ,

Thanks for your interest in our pipeline, and sorry about the issue/

Let me discuss this with @fayrouzhammal and see where/what could be the error.
We will get back to you asap to fix this.
If you happen to use our pipeline, please cite the latest ReMap paper.

Best,
Ben