Instructions

Development

Run a Local Server

In order to develop the implementation guide, do the following steps:

Clone the repository https://github.com/HealthSamurai/ig-ae

git clone https://github.com/HealthSamurai/ig-ae.git

browse to the ig-ae folder

cd ig-ae

Install modules

npm install

Init submodules

git submodule init

Update submodules

git submodule update

Run a local server on the 8891 port (or specify another port if needed)

./igpop.sh dev -p 8891

Navigate to the http://localhost:8891 to see results of editing

Console output:

$ ./igpop.sh dev -p 8891
Dev... (dev -p 8891)
Run server on http://localhost: 8891

Project Structure and Configuration

Project structure

Update the ig.yaml file in the project root folder:

id: prefix for your FHIR resources
title: title displayed on the home page of your IG site
url: base URL for your profiles (StructureDefinition.url and fixedUri)
description: your IG general description
fhir: FHIR version (current value is 4.0.0)

ig.yaml

You will need to stop and start server to apply ig.yaml changes

Edit Profiles and ValueSets

When you are running profiles locally, you can edit them directly on the site:

Editing

Generate Structure Definitions

Click the Package link to generate a package of FHIR StructureDefinitions and ValueSets
The package will be downloaded as a zip-archive
Unzip the archive
Browse the folder
The folder will contain FHIR StructureDefinitions and ValueSets

Package

Validate Generated Structure Definitions

Having that you downloaded and unzipped the archive with generated structure definitions, you can validate them against the base FHIR specification and your IG.
Download the official FHIR validator — a Java jar file that can be used to validate resources (download page). (See the Validator documentation)
Say, you've extracted files to the adverse-event-profile folder. Then, you will run the following command from the parent folder.
Remove the package.json file from the adverse-event-profile folder
Run the validator:

java -jar validator_cli.jar -version 4.0.1 adverse-event-profile/* -ig adverse-event-profile/ -recurse

See more Using the FHIR Validator.

Validate Resources against AZ Profiles

Validate against an IG as a FHIR Package .tgz file's URL

You can specify an IG .tgz file to validate against in the command:

java -jar validator_cli.jar -version 4.0.1 path/to/resource -ig https://github.com/HealthSamurai/ig-ae/raw/master/package/az-ig-package.tgz -profile profile/StructureDefinition/url

Example 1:

java -jar validator_cli.jar -version 4.0.1 resourcesToValidate/adverseEventSample.json -ig https://github.com/HealthSamurai/ig-ae/raw/master/package/az-ig-package.tgz -profile https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent

Example 2:

java -jar validator_cli.jar -version 4.0.1 "docs/for review/fixed/New Adverse Event FHIR payload.json" -ig https://github.com/HealthSamurai/ig-ae/raw/master/package/az-ig-package.tgz -profile https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent

Example 3 (fast):

java -jar validator_cli.jar -version 4.0.1 "docs/for review/fixed/New Adverse Event FHIR payload.json" -tx n/a

Example 4:

java -jar validator_cli.jar -version 4.0.1 "docs/for review/fixed/New Adverse Event FHIR payload.json" -ig https://github.com/HealthSamurai/ig-ae/raw/master/package/az-ig-package.tgz -tx n/a

Validate against an IG as a FHIR Package .tgz local file

You can specify an IG .tgz local file to validate against in the command:

java -jar validator_cli.jar -version 4.0.1 path/to/resource.json -ig D:/path/to/az-ig-package.tgz -profile profile/canonical/url

Example:

java -jar validator_cli.jar -version 4.0.1 resourcesToValidate/adverseEventSample.json -ig D:/Work/Healthsamurai/az-fhir-profiles/az-ig-package.tgz -profile https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent

Validate against an IG as a local folder

You can download an IG files and validate resources against it with the recurse parameter:

java -jar validator_cli.jar -version 4.0.1 path/to/resource -ig path/to/ig/folder/ -recurse -profile profile/canonical/url

Example:

java -jar validator_cli.jar -version 4.0.1 resourcesToValidate/adverseEventSample.json -ig adverse-event-profile/ -recurse -profile https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent

Validate a resource with meta element

You can specify profiles to validate against in the resource's meta element:

"meta": {
    "profile": ["https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent"]
  }

Then, you can run the following command without specifying the profile parameter:

java -jar validator_cli.jar -version 4.0.1 path/to/resource -ig https://github.com/HealthSamurai/ig-ae/raw/master/package/az-ig-package.tgz

Example:

java -jar validator_cli.jar -version 4.0.1 resourcesToValidate/adverseEventSample.json -ig https://github.com/HealthSamurai/ig-ae/raw/master/package/az-ig-package.tgz

Validation without a terminology server

Sometimes a terminology server is unavailable. You can set the following parameter to validate without a terminology server.

-tx n/a

Example:

Validate against a FHIR Package published to FHIR Registry

Sample FHIR Package

java -jar validator_cli.jar -version 4.0.1 resourcesToValidate/adverseEventSample.json -ig hl7.fhir.us.patient-reported-outcomes

Validate against an IG files by their URLs

java -jar validator_cli.jar -version 4.0.1 resourcesToValidate/adverseEventSample.json -profile https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-AZEmployeeReporter.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-lateReason.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-localReference.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-positiveDechallenge.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-positiveRechallenge.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-programNumber.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-rechallenge.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-reporterType.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-sourceType.json -ig https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent-surveyStatus.json -ig https://healthsamurai.github.io/ig-ae/ValueSet/astrazeneca.fhir.ig.ae-survey-status.json -ig https://healthsamurai.github.io/ig-ae/ValueSet/astrazeneca.fhir.ig.ae-intelligent-source.json

Validating a single resource in a bundle

To validate a particular resource in the bundle against a given profile:

-bundle {entry rule} {profile url}

This invokes the nominated profile (by canonical URL) on any entry in any bundle validated that meets the entry rule. The entry rule is either a Resource name, a integer index, or both:

Patient - validate any patient against the nominated profile
1 - validate the 1th resource (actually the second - index is 0 based) against the nominated profile
Patient:0 - validate the first patient resource against the nominated profile

Example:

java -jar validator_cli.jar path/to/bundle.json -version 4.0.1 -ig https://github.com/HealthSamurai/ig-ae/raw/master/package/az-ig-package.tgz -bundle Patient:0 https://healthsamurai.github.io/ig-ae/StructureDefinition/astrazeneca.fhir.ig.ae-AdverseEvent

Create new profile

See the IGPOP spec.

AstraZeneca FHIR IG