Renaming URL

Renaming URL

To rename the URL across all of the MIMIC FHIR files use sed:

Linux: find . -type f -exec sed -i 's/mimic.mit.edu\/fhir/mimic.mit.edu\/fhir\/mimic/g' {} + Mac: find . -type f -exec sed -i '' s/mimic.mit.edu\/fhir/mimic.mit.edu\/fhir\/mimic/g {} +

• find . -type f {} +: grabs all the files in the base directory '.'
• sed
  • -i replaces in place
  • /g replaces all instances in a file (default is only replace first)
  • You need to escape the special charters with a backslash (ie / needs to be \/)\

Apply this to both the mimic-fhir and mimic-profiles repos

Steps to regenerate a valid demo

1. Regenerate mimic_fhir schema with create_fhir_tables.sql

• psql -d mimic_demo -f create_fhir_tables.sql

2. Update terminology

• Need to create terminology for everything, so run create_fhir_terminology.sql on full mimic db
  • psql -d mimic -f create_fhir_terminology.sql
• py_mimic_fhir terminology --version=2.0 ***
  • Need to update .env to point DBNAME_MIMIC='mimic'
  • Run source.env

3. Generate updated IG from mimic-profiles

• ./_genonce.sh

4. Create a new FHIR Store

• To avoid conflicts in the resources/profiles it's suggested to create a new FHIR Store
• gcloud healthcare fhir-stores create $GOOGLE_DATASTORE --dataset=$GOOGLE_DATASET --version=R4 --enable-update-create
  • GOOGLE_DATASTORE=
  • GOOGLE_DATASET=mimic-iv-on-fhir-dataset

5. Update IG on Google Healthcare API

• Follow the Import Implementation Guide walkthrough
• Remember to CURL to update the IG, update IG name to include the new url

6. Validate/populate mimic-fhir FHIR Store

• make sure .env file in mimic-fhir repo updated with
  • DBNAME_MIMIC='mimic_demo'
  • FHIR_VALIDATOR='GCP'
  • Run source .env
• Using Google Healthcare API: py_mimic_fhir validate --num_patients=100 --init
  • need the init flag to post the medication, locations, and organization resources (only need to load once)