Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Bug when running python run.py transform #2

Open
Hannah-Doerpholz opened this issue May 4, 2023 · 0 comments
Open

Bug when running python run.py transform #2

Hannah-Doerpholz opened this issue May 4, 2023 · 0 comments

Comments

@Hannah-Doerpholz
Copy link

While following your Readme I ran into an error at the step python run.py transform.
It looks like there is a file missing from the downloaded raw data: eol_trait_ids.txt. Indeed, when I looked in data/raw/ there was no such file, also not in the EOLTraitbank zip archive. My terminal output is the following:

Parsing data/raw/go-basic.json
Parsing data/raw/taxslim.json
Parsing data/raw/to.json
Parsing data/raw/po.json
Traceback (most recent call last):
  File "run.py", line 165, in <module>
    cli()
  File "/home/hannah/anaconda3/envs/genophenoenvo/lib/python3.8/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/home/hannah/anaconda3/envs/genophenoenvo/lib/python3.8/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/home/hannah/anaconda3/envs/genophenoenvo/lib/python3.8/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/hannah/anaconda3/envs/genophenoenvo/lib/python3.8/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/hannah/anaconda3/envs/genophenoenvo/lib/python3.8/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "run.py", line 64, in transform
    kg_transform(*args, **kwargs)
  File "/home/hannah/Apps/knowledge-graph/eco_kg/transform.py", line 51, in transform
    t.

Since python stops running it might be possible that there are more files missing as well further along this step. Perhaps you can help resolve this issue?

@Hannah-Doerpholz Hannah-Doerpholz changed the title But when running python run.py transform Bug when running python run.py transform May 30, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant