Form-to-FHIR Service

A Java/Apache Camel service for transforming medical forms into structured FHIR data. Apache Camel allows integration of multiple sources including:

Emails with PDF attachments
Message Queues
Restful POST operations
See full list of potential Camel Components

Although the possibilities are endless, the service's initial implementation includes the ability for end-users to email PDF documents to a given email address. The PDF documents will be stored in AWS S3, analyzed using AWS Textract, and ultimately persisted as FHIR data.

Specifically, this service aims to automate the collection of Covid-19 Case Reports in the United States using CDC's Person Under Investigation (PUI) Form. The PUI Form is the standard required by the CDC and adopted by most State Health Departments.

Prerequisites

Java 11 (SdkMan recommended for managing Java installs)
Gradle
Email setup

Email Setup

The service requires a designated email address where PDF documents can be received. A test Gmail account can be configured for the service:

Navigate to Gmail Settings -> Forwarding and POP/IMAP -> IMAP access, then select Enable IMAP
Navigate to Google Account Settings -> Security -> Less secure app access, then toggle to allow less secure apps to connect to the account.

It goes without saying the service and email account will require some additional security configurations to meet HIPAA compliance standards.

Local Setup

Clone the repo. git clone https://github.com/hapifhir/covid-response-app.git
Once you're in the root of cloned repo, change the directory to formtofhirservice
Using gradle wrapper command, build an executable using ./gradlew clean build
Finally, run the service:

java -jar build/libs/formtofhirservice-0.0.1-SNAPSHOT.jar [email protected] --email.password=YOURPASSWORD --email.hostname=imap.gmail.com

FHIR Resources Used

Data from PUI Form is converted into the following FHIR Resources

Todo

Split attachments into individual messages
Write each attachment to S3
For each S3 document asynchronously kickoff Textract, see https://docs.aws.amazon.com/textract/latest/dg/api-async.html
Configure another Consumer endpoint for SNS/SQS,where Textract completion notification are posted
Create Camel Processor for transforming Textract data to FHIR Questionaire/QuestionaireResponse
Use Camel FHIR Component to persist, see https://camel.apache.org/components/latest/fhir-component.html

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