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Fix unit test to run local PRs + fix tutorial #850

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hakunanatasha
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@hakunanatasha hakunanatasha commented Jan 3, 2023

Enables unit testing of local scripts with --test_local flag; borrows the test_bigbio_hub.py script. I tested this by making a copy of scitail as test_scitail in the biodatasets folder, and

To replicate:

  • copy the scitail folder in bigbio/biodatasets as cp -r bigbio/biodatasets/scitail bigbio/biodatasets/test_scitail.
  • change the name of scitail.py in this folder as test_scitail.py
  • add bigbiohub.py into this new test_scitail folder
  • in the main directory, run python -m tests.test_bigbio_hub test_scitail --test_local

Note- the contributions guide makes a reference to the templates folder that has 2 scripts; bigbiohub and a template file that can be used to fill-in-the-blanks. To avoid a deprecated script, maybe we should automate that for every new update, bigbiohub is either copied into the template folder OR I can just change the tutorial to reflect it's actual "default" location of bigbio/hub/bigbiohub.py

TODO: on 2023/01/03 I'm going to add one more small change that also tests whether the METADATA is in the acceptable set of values to ensure standardization!

@galtay

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galtay commented Jan 3, 2023

  • copy the scitail folder in bigbio/biodatasets as cp -r bigbio/biodatasets/scitail bigbio/biodatasets/test_scitail.

I thought we are trying to test the data loader scripts in this directory? https://github.com/bigscience-workshop/biomedical/tree/main/bigbio/hub/hub_repos

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Superceded by #856

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