Add an example to incorporate remote clinical pipeline and stave#43
Add an example to incorporate remote clinical pipeline and stave#43Leolty wants to merge 22 commits intoasyml:masterfrom
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hunterhector
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A few comments, but overall, if this example is runnable it is fine with me. We can improve in the future.
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Could we leave these two issues metioned in the conversations in the future? I am not familiar with the ontology generation yet so it may take much time. |
Actually, it might be important to understand the following items since they are the key for understanding our visualization:
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Got it. Actually, I understand how the ontologies related to stave. I didn't understand what you meant at first, I thought it was about writing python code to automatically generate ontologies. So I think what you want me to do is to omit most of the ontologies that were already written, write only the extra ones we added here, and then use the generate ontology function to merge them? |
Yeah I think you got the idea, basically we don’t need to repeat the ontology spec here again, and be able to comtrol the ontology should help you demo |
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This PR fixes #42.
Description of changes
This PR is totally based on what has been done by Piyush, here is the reference: https://github.com/Piyush13y/forte/tree/745_clinical_pipeline_stave
The changes include:
clinical_processing_pipeline.py, and add an argument to supportPlainTextReader(). In case users may not have the mimic iii datasets, they can just use the sample data in thesample_data/notes.txtfor the function test.README.md, according to the errors or obstacles I encountered when I set up the connection between the pipeline and stave.Bugs encountered
Initially, the version of Elasticsearch I downloaded is 8.2.2, and I failed the setup of this according to the tutorials. ( Many unsolvable bugs). When I change the version to 7.12.2 (given in
README.md), everything works perfectly fine.