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iris-fhir-python-strategy

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Python hooks on IRIS FHIR Repository/Facade

What's new in this version

Initial Release

1. iris-fhir-python-strategy

1.1. Description

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

Image

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

1.2. Installation

1.2.1. Prerequisites

1.2.2. Installation steps

  1. Clone this repository
git clone git@github.com:grongierisc/iris-fhir-python-strategy.git
  1. Build the docker image
docker-compose build
  1. Run the docker image
docker-compose up -d
  1. 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": "ResourceNotSupported",
      "details": {
        "text": "Resource type 'Account' is not supported."
      }
    }
  ]
}
  1. Open get a patient without authentication (you shouldn’t have access to Observation)
GET http://localhost:8089/fhir/r4/Patient/3/$everything
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"
    }
  ]
}
  1. Open get a patient with authentication (you should have access to Observation)
GET http://localhost:8089/fhir/r4/Patient/3/$everything
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.

1.3. 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.

  • WIP

1.4. 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()

1.5. How iris-fhir-python-strategy works

1.5.1. Introduction

First of all, we have to understand how IRIS FHIR Server works.

Every IRIS FHIR Server implements a Strategy.

A Strategy is a set of two classes :

Superclass Subclass Parameters
HS.FHIRServer.API.InteractionsStrategy StrategyKey — Specifies a unique identifier for the InteractionsStrategy.
InteractionsClass — Specifies the name of your Interactions subclass.
HS.FHIRServer.API.RepoManager StrategyClass — Specifies the name of your InteractionsStrategy subclass.
StrategyKey — Specifies a unique identifier for the InteractionsStrategy. Must match the StrategyKey parameter in the InteractionsStrategy subclass.

Both classes are Abstract classes.

  • HS.FHIRServer.API.InteractionsStrategy is an Abstract class that must be implemented to customize the behavior of the FHIR Server.
  • HS.FHIRServer.API.RepoManager is an Abstract class that must be implemented to customize the storage of the FHIR Server.

1.5.2. Remarks

For our example, we will only focus on the HS.FHIRServer.API.InteractionsStrategy class even if the HS.FHIRServer.API.RepoManager class is also implemented and mandatory to customize the FHIR Server.
The HS.FHIRServer.API.RepoManager class is implemented by HS.FHIRServer.Storage.Json.RepoManager class, which is the default implementation of the FHIR Server.

1.5.3. Where to find the code

All source code can be found in the src folder.
The src folder contains the following folders :

  • python : contains the python code
  • cls : contains the ObjectScript code that is used to call the python code

1.5.4. How to implement a Strategy

In this proof of concept, we will only be interested in how to implement a Strategy in Python, not how to implement a RepoManager.

To implement a Strategy you need to create at least two classes :

  • A class that inherits from HS.FHIRServer.API.InteractionsStrategy class
  • A class that inherits from HS.FHIRServer.API.Interactions class

1.5.5. Implementation of InteractionsStrategy

HS.FHIRServer.API.InteractionsStrategy class aim to customize the behavior of the FHIR Server by overriding the following methods :

  • GetMetadataResource : called to get the metadata of the FHIR Server
    • this is the only method we will override in this proof of concept

HS.FHIRServer.API.InteractionsStrategy has also two parameters :

  • StrategyKey : a unique identifier for the InteractionsStrategy
  • InteractionsClass : the name of your Interactions subclass

1.5.6. Implementation of Interactions

HS.FHIRServer.API.Interactions class aim to customize the behavior of the FHIR Server by overriding the following methods :

  • OnBeforeRequest : called before the request is sent to the server
  • OnAfterRequest : called after the request is sent to the server
  • PostProcessRead : called after the read operation is done
  • PostProcessSearch : called after the search operation is done
  • Read : called to read a resource
  • Add : called to add a resource
  • Update : called to update a resource
  • Delete : called to delete a resource
  • and many more…

We implement HS.FHIRServer.API.Interactions class in the src/cls/FHIR/Python/Interactions.cls class.

Click to see the code
Class FHIR.Python.Interactions Extends (HS.FHIRServer.Storage.Json.Interactions, FHIR.Python.Helper)
{

Parameter OAuth2TokenHandlerClass As %String = "FHIR.Python.OAuth2Token";

Method %OnNew(pStrategy As HS.FHIRServer.Storage.Json.InteractionsStrategy) As %Status
{
// %OnNew is called when the object is created.
// The pStrategy parameter is the strategy object that created this object.
// The default implementation does nothing
// Frist set the python path from an env var
set ..PythonPath = $system.Util.GetEnviron("INTERACTION_PATH")
// Then set the python class name from the env var
set ..PythonClassname = $system.Util.GetEnviron("INTERACTION_CLASS")
// Then set the python module name from the env var
set ..PythonModule = $system.Util.GetEnviron("INTERACTION_MODULE")

if (..PythonPath = "") || (..PythonClassname = "") || (..PythonModule = "") {
	//quit ##super(pStrategy)
	set ..PythonPath = "/irisdev/app/src/python/"
	set ..PythonClassname = "CustomInteraction"
	set ..PythonModule = "custom"
}


// Then set the python class
do ..SetPythonPath(..PythonPath)
set ..PythonClass = ##class(FHIR.Python.Interactions).GetPythonInstance(..PythonModule, ..PythonClassname)

quit ##super(pStrategy)

}

Method OnBeforeRequest(
pFHIRService As HS.FHIRServer.API.Service,
pFHIRRequest As HS.FHIRServer.API.Data.Request,
pTimeout As %Integer)
{
// OnBeforeRequest is called before each request is processed.
if $ISOBJECT(..PythonClass) {
set body = ##class(%SYS.Python).None()
if pFHIRRequest.Json '= "" {
set jsonLib = ##class(%SYS.Python).Import("json")
set body = jsonLib.loads(pFHIRRequest.Json.%ToJSON())
}
do ..PythonClass."on_before_request"(pFHIRService, pFHIRRequest, body, pTimeout)
}
}

Method OnAfterRequest(
pFHIRService As HS.FHIRServer.API.Service,
pFHIRRequest As HS.FHIRServer.API.Data.Request,
pFHIRResponse As HS.FHIRServer.API.Data.Response)
{
// OnAfterRequest is called after each request is processed.
if $ISOBJECT(..PythonClass) {
set body = ##class(%SYS.Python).None()
if pFHIRResponse.Json '= "" {
set jsonLib = ##class(%SYS.Python).Import("json")
set body = jsonLib.loads(pFHIRResponse.Json.%ToJSON())
}
do ..PythonClass."on_after_request"(pFHIRService, pFHIRRequest, pFHIRResponse, body)
}
}

Method PostProcessRead(pResourceObject As %DynamicObject) As %Boolean
{
// PostProcessRead is called after a resource is read from the database.
// Return 1 to indicate that the resource should be included in the response.
// Return 0 to indicate that the resource should be excluded from the response.
if $ISOBJECT(..PythonClass) {
if pResourceObject '= "" {
set jsonLib = ##class(%SYS.Python).Import("json")
set body = jsonLib.loads(pResourceObject.%ToJSON())
}
return ..PythonClass."post_process_read"(body)
}
quit 1
}

Method PostProcessSearch(
pRS As HS.FHIRServer.Util.SearchResult,
pResourceType As %String) As %Status
{
// PostProcessSearch is called after a search is performed.
// Return $$$OK to indicate that the search was successful.
// Return an error code to indicate that the search failed.
if $ISOBJECT(..PythonClass) {
return ..PythonClass."post_process_search"(pRS, pResourceType)
}
quit $$$OK
}

Method Read(
pResourceType As %String,
pResourceId As %String,
pVersionId As %String = "") As %DynamicObject
{
return ##super(pResourceType, pResourceId, pVersionId)
}

Method Add(
pResourceObj As %DynamicObject,
pResourceIdToAssign As %String = "",
pHttpMethod = "POST") As %String
{
return ##super(pResourceObj, pResourceIdToAssign, pHttpMethod)
}

/// Returns VersionId for the "deleted" version
Method Delete(
pResourceType As %String,
pResourceId As %String) As %String
{
return ##super(pResourceType, pResourceId)
}

Method Update(pResourceObj As %DynamicObject) As %String
{
return ##super(pResourceObj)
}

}

The FHIR.Python.Interactions class inherits from HS.FHIRServer.Storage.Json.Interactions class and FHIR.Python.Helper class.

The HS.FHIRServer.Storage.Json.Interactions class is the default implementation of the FHIR Server.

The FHIR.Python.Helper class aim to help to call Python code from ObjectScript.

The FHIR.Python.Interactions class overrides the following methods :

  • %OnNew : called when the object is created
    • we use this method to set the python path, python class name and python module name from environment variables
    • if the environment variables are not set, we use default values
    • we also set the python class
    • we call the %OnNew method of the parent class
Method %OnNew(pStrategy As HS.FHIRServer.Storage.Json.InteractionsStrategy) As %Status
{
	// First set the python path from an env var
	set ..PythonPath = $system.Util.GetEnviron("INTERACTION_PATH")
	// Then set the python class name from the env var
	set ..PythonClassname = $system.Util.GetEnviron("INTERACTION_CLASS")
	// Then set the python module name from the env var
	set ..PythonModule = $system.Util.GetEnviron("INTERACTION_MODULE")
if (..PythonPath = "") || (..PythonClassname = "") || (..PythonModule = "") {
	// use default values
	set ..PythonPath = "/irisdev/app/src/python/"
	set ..PythonClassname = "CustomInteraction"
	set ..PythonModule = "custom"
}

// Then set the python class
do ..SetPythonPath(..PythonPath)
set ..PythonClass = ..GetPythonInstance(..PythonModule, ..PythonClassname)

quit ##super(pStrategy)

}

  • OnBeforeRequest : called before the request is sent to the server
    • we call the on_before_request method of the python class
    • we pass the HS.FHIRServer.API.Service object, the HS.FHIRServer.API.Data.Request object, the body of the request and the timeout
Method OnBeforeRequest(
	pFHIRService As HS.FHIRServer.API.Service,
	pFHIRRequest As HS.FHIRServer.API.Data.Request,
	pTimeout As %Integer)
{
	// OnBeforeRequest is called before each request is processed.
	if $ISOBJECT(..PythonClass) {
		set body = ##class(%SYS.Python).None()
		if pFHIRRequest.Json '= "" {
			set jsonLib = ##class(%SYS.Python).Import("json")
			set body = jsonLib.loads(pFHIRRequest.Json.%ToJSON())
		}
		do ..PythonClass."on_before_request"(pFHIRService, pFHIRRequest, body, pTimeout)
	}
}
  • OnAfterRequest : called after the request is sent to the server
    • we call the on_after_request method of the python class
    • we pass the HS.FHIRServer.API.Service object, the HS.FHIRServer.API.Data.Request object, the HS.FHIRServer.API.Data.Response object and the body of the response
Method OnAfterRequest(
	pFHIRService As HS.FHIRServer.API.Service,
	pFHIRRequest As HS.FHIRServer.API.Data.Request,
	pFHIRResponse As HS.FHIRServer.API.Data.Response)
{
	// OnAfterRequest is called after each request is processed.
	if $ISOBJECT(..PythonClass) {
		set body = ##class(%SYS.Python).None()
		if pFHIRResponse.Json '= "" {
			set jsonLib = ##class(%SYS.Python).Import("json")
			set body = jsonLib.loads(pFHIRResponse.Json.%ToJSON())
		}
		do ..PythonClass."on_after_request"(pFHIRService, pFHIRRequest, pFHIRResponse, body)
	}
}
  • And so on…

1.5.7. Interactions in Python

FHIR.Python.Interactions class calls the on_before_request, on_after_request, … methods of the python class.

Here is the abstract python class :

import abc
import iris

class Interaction(object):
metaclass = abc.ABCMeta

@abc.abstractmethod
def on_before_request(self, 
                      fhir_service:'iris.HS.FHIRServer.API.Service',
                      fhir_request:'iris.HS.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.HS.FHIRServer.API.Data.Request',
                     fhir_response:'iris.HS.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
    """

1.5.8. Implementation of the abstract python class

from FhirInteraction import Interaction

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

1.5.9. Too long, do a summary

The FHIR.Python.Interactions class is a wrapper to call the python class.

IRIS abstracts classes are implemented to wrap python abstract classes 🥳.

That help us to keep python code and ObjectScript code separated and for so benefit from the best of both worlds.

Made with
Version
1.0.007 Jul, 2023
Category
Technology Example
Works with
InterSystems IRIS for Health
First published
07 Jul, 2023
Last checked by moderator
22 Sep, 2023Doesn't work