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Article Guillaume Rongier · Jul 7, 2023 8m read

Iris FHIR Python Strategy

#InterSystems IRIS for Health #FHIR #Python

Description

With InterSystems IRIS FHIR Server you can build a Strategy to customize the behavior of the server (see documentation for more details).

This repository contains a Python Strategy that can be used as a starting point to build your own Strategy in python.

This demo strategy provides the following features:

Update the capability statement to remove the Account resource
Simulate a consent management system to allow or not access to the Observation resource
- If the User has sufficient rights, the Observation resource is returned
- Otherwise, the Observation resource is not returned

Installation

Prerequisites

Installation steps

Clone this repository

git clone git@github.com:grongierisc/iris-fhir-python-strategy.git

Build the docker image

docker-compose build

Run the docker image

docker-compose up -d

Open the FHIR server in your browser

GET http://localhost:8083/fhir/r4/metadata
Accept: application/json+fhir

The Account resource should not be present in the Capability Statement.

GET http://localhost:8083/fhir/r4/Account
Accept: application/json+fhir

returns :

{
  "resourceType": "OperationOutcome",
  "issue": [
    {
      "severity": "error",
      "code": "not-supported",
      "diagnostics": "<HSFHIRErr>ResourceNotSupported",
      "details": {
        "text": "Resource type 'Account' is not supported."
      }
    }
  ]
}

Open get a patient without authentication (you shouldn't have access to Observation)

GET http://localhost:8083/fhir/r4/Observation?patient=178
Content-Type: application/json+fhir
Accept: application/json+fhir

returns :

{
  "resourceType": "Bundle",
  "id": "feaa09c0-1cb7-11ee-b77a-0242c0a88002",
  "type": "searchset",
  "timestamp": "2023-07-07T11:07:49Z",
  "total": 0,
  "link": [
    {
      "relation": "self",
      "url": "http://localhost:8083/fhir/r4/Observation?patient=178"
    }
  ]
}

Open get a patient with authentication (you should have access to Observation)

GET http://localhost:8083/fhir/r4/Observation?patient=178
Content-Type: application/json+fhir
Accept: application/json+fhir
Authorization: Basic U3VwZXJVc2VyOlNZUw==

returns :

{
  "resourceType": "Bundle",
  "id": "953a1b06-1cb7-11ee-b77b-0242c0a88002",
  "type": "searchset",
  "timestamp": "2023-07-07T11:08:04Z",
  "total": 100,
  "link": [
    {
      "relation": "self",
      "url": "http://localhost:8083/fhir/r4/Observation?patient=178"
    }
  ],
  "entry": [
    {
      "fullUrl": "http://localhost:8083/fhir/r4/Observation/277",
      "resource": {
        "resourceType": "Observation",
        "id": "277",
        "status": "final",
        "category": [
          ...
        ],
      }
    },
    ...
  ]
}

More details on a next section about Consent.

Consent

The consent management system is simulated by the consent method in the CustomInteraction class in the custom module.

The consent method returns True if the user has sufficient rights to access the resource, False otherwise.

    def consent(self, resource_type, user, roles):
        #Example consent logic - only allow users with the role '%All' to see
        #Observation resources.
        if resource_type == 'Observation':
            if '%All' in roles:
                return True
            else:
                return False
        else:
            return True

The consent function is part of the CustomInteraction.

The CustomInteraction class is an implementation of the Interaction class.

The Interaction class is an Abstract class that must be implemented by the Strategy. It part of the FhirInteraction module.

class Interaction(object):
    __metaclass__ = abc.ABCMeta

    @abc.abstractmethod
    def on_before_request(self, 
                          fhir_service:'iris.HS.FHIRServer.API.Service',
                          fhir_request:'iris.FHIRServer.API.Data.Request',
                          body:dict,
                          timeout:int):
        """
        on_before_request is called before the request is sent to the server.
        param fhir_service: the fhir service object iris.HS.FHIRServer.API.Service
        param fhir_request: the fhir request object iris.FHIRServer.API.Data.Request
        param timeout: the timeout in seconds
        return: None
        """
        

    @abc.abstractmethod
    def on_after_request(self,
                         fhir_service:'iris.HS.FHIRServer.API.Service',
                         fhir_request:'iris.FHIRServer.API.Data.Request',
                         fhir_response:'iris.FHIRServer.API.Data.Response',
                         body:dict):
        """
        on_after_request is called after the request is sent to the server.
        param fhir_service: the fhir service object iris.HS.FHIRServer.API.Service
        param fhir_request: the fhir request object iris.FHIRServer.API.Data.Request
        param fhir_response: the fhir response object iris.FHIRServer.API.Data.Response
        return: None
        """
        

    @abc.abstractmethod
    def post_process_read(self,
                          fhir_object:dict) -> bool:
        """
        post_process_read is called after the read operation is done.
        param fhir_object: the fhir object
        return: True the resource should be returned to the client, False otherwise
        """
        

    @abc.abstractmethod
    def post_process_search(self,
                            rs:'iris.HS.FHIRServer.Util.SearchResult',
                            resource_type:str):
        """
        post_process_search is called after the search operation is done.
        param rs: the search result iris.HS.FHIRServer.Util.SearchResult
        param resource_type: the resource type
        return: None
        """

The CustomInteraction class is an implementation of the Interaction class.

class CustomInteraction(Interaction):

    def on_before_request(self, fhir_service, fhir_request, body, timeout):
        #Extract the user and roles for this request
        #so consent can be evaluated.
        self.requesting_user = fhir_request.Username
        self.requesting_roles = fhir_request.Roles

    def on_after_request(self, fhir_service, fhir_request, fhir_response, body):
        #Clear the user and roles between requests.
        self.requesting_user = ""
        self.requesting_roles = ""

    def post_process_read(self, fhir_object):
        #Evaluate consent based on the resource and user/roles.
        #Returning 0 indicates this resource shouldn't be displayed - a 404 Not Found
        #will be returned to the user.
        return self.consent(fhir_object['resourceType'],
                        self.requesting_user,
                        self.requesting_roles)

    def post_process_search(self, rs, resource_type):
        #Iterate through each resource in the search set and evaluate
        #consent based on the resource and user/roles.
        #Each row marked as deleted and saved will be excluded from the Bundle.
        rs._SetIterator(0)
        while rs._Next():
            if not self.consent(rs.ResourceType,
                            self.requesting_user,
                            self.requesting_roles):
                #Mark the row as deleted and save it.
                rs.MarkAsDeleted()
                rs._SaveRow()

    def consent(self, resource_type, user, roles):
        #Example consent logic - only allow users with the role '%All' to see
        #Observation resources.
        if resource_type == 'Observation':
            if '%All' in roles:
                return True
            else:
                return False
        else:
            return True

You can modify the custom module to implement your own consent logic.

All modifications to the custom module will be directly reflected in the FHIR Server.

Other behaviors can be implemented by overriding the Interaction classes.

Custom CapabilityStatement

IRIS FHIR Server provides a default CapabilityStatement based on the Implementation Guide guiven at installation time.

More information how to customize the CapabilityStatement can be found at FHIR CapabilityStatement.

For this example, the Implementation Guide is raw FHIR R4.

To customize the CapabilityStatement, you can modify the custom module.

The CustomStrategy class is an implementation of the Strategy class.

The Strategy class is an Abstract class that must be implemented by the Strategy. It part of the FhirInteraction module.

class Strategy(object):
    __metaclass__ = abc.ABCMeta

    @abc.abstractmethod
    def on_get_capability_statement(self,capability_statement:dict)-> dict:
        """
        on_after_get_capability_statement is called after the capability statement is retrieved.
        param capability_statement: the capability statement
        return: None
        """

The on_get_capability_statement method is called after the CapabilityStatement is generated.

The CustomStrategy class is an implementation of the Strategy class.

class CustomStrategy(Strategy):
    
    def on_get_capability_statement(self, capability_statement):
        # Example : del resources Account
        capability_statement['rest'][0]['resource'] = [resource for resource in capability_statement['rest'][0]['resource'] if resource['type'] != 'Account']
        return capability_statement

You can modify the custom module to implement your own Custom CapabilityStatement.

To apply the changes, you need to update the fhir server configuration.

cd /irisdev/app/src/python
/usr/irissys/bin/irispython
>>> import custom
>>> custom.set_capability_statement()

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