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Add legends to show Disease and Chemical as Annotation#54

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Leolty wants to merge 38 commits intomasterfrom
53_add_legend
Open

Add legends to show Disease and Chemical as Annotation#54
Leolty wants to merge 38 commits intomasterfrom
53_add_legend

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@Leolty
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@Leolty Leolty commented Jul 21, 2022

This PR fixes #53.

Description of changes

This PR makes the following 4 main changes:

  1. add new ontology Disease and Chemical ( as annotation)
  2. add a new processor to label Disease and Chemical NER
  3. add the test file to test the processor
  4. add a example where you can use streamlit as search engine to link to Stave, and show Disease and Chemical annotations

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codecov bot commented Jul 22, 2022

Codecov Report

❌ Patch coverage is 90.10989% with 9 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.04%. Comparing base (867b854) to head (a8494cf).
⚠️ Report is 201 commits behind head on master.

Files with missing lines Patch % Lines
fortex/health/processors/ner_label_processor.py 83.63% 9 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master      #54      +/-   ##
==========================================
+ Coverage   84.17%   85.04%   +0.87%     
==========================================
  Files           9       10       +1     
  Lines         512      602      +90     
==========================================
+ Hits          431      512      +81     
- Misses         81       90       +9     

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@@ -0,0 +1,57 @@
'''
this file defines search functions for searching data in elasticsearch.
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Any specific reason why we aren't using LastUtteranceSearcher processor to search through elastic search and return the links for documents?

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Here is what I think:

We create a search engine by streamlit, and I think it is a simple and easy way to wrap the search into method and when the user clicks "Query", this method is called directly to query and then displayed the results on the interface

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I feel its just redundant if we already have this functionality implemented in our processors and we still write another method to achieve the same thing, but it could be simpler and hence could be used for just the demo. You should confirm this with hector once. @hunterhector

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Update the legends in Stave to show Disease, Medical, etc.

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