Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Add two new covid_symptom GPT tasks #337

Merged
merged 1 commit into from
Aug 9, 2024
Merged

Add two new covid_symptom GPT tasks #337

merged 1 commit into from
Aug 9, 2024

Conversation

mikix
Copy link
Contributor

@mikix mikix commented Aug 9, 2024

  • covid_symptom__nlp_results_gpt35
  • covid_symptom__nlp_results_gpt4

Both call out to Azure ChatGPT and detects COVID symptoms in clinical notes, with the same cohort selection as the other covid_symptom tasks (ED notes).

You will need to set the following two environment variables to use them:

  • AZURE_OPENAI_API_KEY
  • AZURE_OPENAI_ENDPOINT

These tasks will also need to be added to your AWS config (see the new template) and the Crawler run to detect their schemas.

The Library covid study has not yet been updated to consume the tables yet, but will be.

Checklist

  • Consider if documentation (like in docs/) needs to be updated
  • Consider if tests should be added

Copy link

github-actions bot commented Aug 9, 2024

☂️ Python Coverage

current status: ✅

Overall Coverage

Lines Covered Coverage Threshold Status
3369 3290 98% 97% 🟢

New Files

No new covered files...

Modified Files

File Coverage Status
cumulus_etl/etl/studies/covid_symptom/init.py 100% 🟢
cumulus_etl/etl/studies/covid_symptom/covid_ctakes.py 100% 🟢
cumulus_etl/etl/studies/covid_symptom/covid_tasks.py 100% 🟢
cumulus_etl/etl/studies/hftest/hf_tasks.py 100% 🟢
cumulus_etl/etl/tasks/task_factory.py 100% 🟢
cumulus_etl/nlp/init.py 100% 🟢
cumulus_etl/nlp/utils.py 100% 🟢
TOTAL 100% 🟢

updated for commit: 8978f1c by action🐍

- covid_symptom__nlp_results_gpt35
- covid_symptom__nlp_results_gpt4

Both call out to Azure ChatGPT and detects COVID symptoms in clinical
notes, with the same cohort selection as the other covid_symptom
tasks (ED notes).

You will need to set the following two environment variables to use
them:
- AZURE_OPENAI_API_KEY
- AZURE_OPENAI_ENDPOINT

These tasks will also need to be added to your AWS config (see the new
template) and the Crawler run to detect their schemas.

The Library covid study has not yet been updated to consume the tables
yet, but will be.
@mikix mikix merged commit 6f18af2 into main Aug 9, 2024
3 checks passed
@mikix mikix deleted the mikix/gpt branch August 9, 2024 18:32
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants