Dev Days

Let's Build a Synthetic Dataset

In a classroom setting, the instructor will walk you through the process of using, configuring, and customizing Synthea^TM – an open-source synthetic patient generator – to create a patient and provider cohort and all the FHIR DSTU2, STU3, or R4 resources you need for your next software development, testing or integration event…

Prerequisites

• Git
  • https://git-scm.com/downloads
• Java JDK 8, 11, 12
  • https://adoptopenjdk.net
• Microsoft Azure azcopy Utility (Optional for this Tutorial)
  • Windows (zip)
  • Linux (tar)
  • MacOS (zip)

Clone and Build the Repository

git clone https://github.com/synthetichealth/synthea.git
cd synthea
./gradlew test

Estimate 5-10 minutes

Browse the Diseases

Browse the diseases in the Module Builder

The instructor will make a change to the CHF module. Follow along.

Download the JSON, and overwrite your current module with the changes.

cp ~/Downloads/congestive_heart_failure.json ./src/main/resources/modules/congestive_heart_failure.json
./run_synthea -p 10

When finished, undo the changes:

git checkout -- src

Run Synthea

./run_synthea –s 0

Look at the FHIR record in ./output/fhir

Configuring Properties

Examine the configurable properties in the synthea.properties file.

POST our patient record to a server

Make sure you adjust the path in the command below to match your path and FHIR file name.

curl http://hapi.fhir.org/baseR4 --data-binary "@/Users/Path/synthea/output/fhir/Brigitte394_Jaskolski867_f45fe01f-de94-4587-97f0-4cbd39f775c5.json" -H "Content-Type: application/fhir+json" 

Generate a lot of data

Choose the State you want. Feel free to also specify a city. States or cities with spaces in the name need to be quoted.

./run_synthea -p 10000 Washington

Estimate 5-10 minutes and 5-10 GB storage

POST all the data to a server

Do not do this step for the tutorial today. Skip due to time constraints...

cd output/fhir/
for file in *; do curl --write-out '.' http://hapi.fhir.org/baseR4 --data-binary "@$file" -H "Content-Type: application/fhir+json" > /dev/null; done;

Estimate: a long time... too long.

Upload all the data to Microsoft Azure

Zip your ./output/fhir folder into fhir_{p}_{state}_{city}.zip.

Get the azcopy utility to upload your data to Microsoft Azure:

• Windows (zip)
• Linux (tar)
• MacOS (zip)

Unpack the download to use the azcopy executable -- no installation should be required.

Copy your file to our Azure storage:

azcopy cp "output/fhir_{p}_{state}_{town}.zip" "https://syntheadevdays2019.blob.core.windows.net/synthea/?sv=2018-03-28&ss=bfqt&srt=sco&sp=rwdlacup&se=2019-06-22T04:32:42Z&st=2019-06-10T20:32:42Z&spr=https&sig=7mG96EHAJ1jIVlShwxxui5g74%2F%2F6enrCXjCx%2BteM0k0%3D" --recursive=true

List all the data files:

azcopy list https://syntheadevdays2019.blob.core.windows.net/synthea

Download a particular data {file}:

azcopy cp https://syntheadevdays2019.blob.core.windows.net/synthea/{file} .

Thank you!

Have a great #FHIRDevDays