cBioPortal Case Summarizer

Uses OpenAI to create a summary for a patient

Development

To set up the development environment, install the development dependencies:

poetry install

Run:

poetry run summarize-case --model gpt-4o --openai-api-key YOUR_OPENAPI_KEY data/data_clinical_patient.txt data/data_clinical_sample.txt data/data_mutations.txt data/data_timeline_specimen.txt data/data_timeline_status.txt  data/data_timeline_surgery.txt data/data_timeline_treatment.txt data/nihms-569639.pdf > export/P04.json

Currently only generates data for one case

Upload exported files

Currently manual upload via surge.sh (Ino's account):

cd export && surge .

TODO

• Use cBioPortal datahub directly (rather than files downloaded per case)
• Add Deployment Preview for frontend