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Add PubAnnotation test #3

Merged
merged 10 commits into from
Dec 6, 2022
Merged

Add PubAnnotation test #3

merged 10 commits into from
Dec 6, 2022

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gaurav
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@gaurav gaurav commented Jul 25, 2022

This PR adds a test that, given a list of either PubMed or PubMedCentral IDs, will:

  1. Download the text and annotations for that document from PubAnnotation.org.
  2. Run the text against Nemo-Serve.
  3. Run annotations against SAPBERT, which is written into a separate track, so that both the Nemo-Serve output and the SAPBERT output can be compared.
  4. Test that we get back a non-zero number of annotations from Nemo-Serve.

It also includes the produced annotations in the PubAnnotator format, which can be viewed in a PubAnnotator editor such as https://textae.pubannotation.org/editor.html?mode=edit.

@gaurav gaurav changed the base branch from add-integration-tests to main November 22, 2022 06:33
@gaurav gaurav marked this pull request as ready for review November 22, 2022 07:05
The only thing that has changed is the scores, which are new.
@gaurav gaurav merged commit edc3559 into main Dec 6, 2022
@gaurav gaurav deleted the extend-integration-tests branch December 8, 2022 22:07
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3 participants