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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?
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