PFB - Githubissues

ACED-IDP / data_model

Schema and synthetic data

2 stars 1 forks source link

PFB #12

Closed bwalsh closed 1 year ago

bwalsh commented 1 year ago

This PR:

Ensure DocumentReference for DICOM files
Matches patients by condition to ResearchStudy
Data wrangles missing entities Practitioner, Location, Organizations
Normalizes resource references
Creates PFB
Visualizes resulting data model

jordan2lee commented 1 year ago

after running python3 scripts/pfb.py | sh there are many missing entities (example below) - I assume this is because we are using synthetic data and these requirements by the schema will be updated specific to ACED project (once we have the data)? @bwalsh

entities -> AllergyIntolerance -> links -> patient -> id
  field required (type=value_error.missing)

jordan2lee commented 1 year ago

creating figures with visualize.sh expects pfb/ dir - this needs to be updated to create pfb dir or remove the renaming step

mv: rename pfb/research_study_*.png to docs/research_study_*.png: No such file or directory