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intersystems-ru / fhir-terminology-service

Implementation of FHIR Terminology Service specification (https://www.hl7.org/fhir/R4/terminology-service.html) to expose arbitrary persistent classes as FHIR value sets and code systems. Runs on InterSystems IRIS for Health 2020+.

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fhir-terminology-service

Implementation of FHIR Terminology Service specification (https://www.hl7.org/fhir/R4/terminology-service.html) to expose arbitrary persistent classes as FHIR value sets and code systems. Runs on InterSystems IRIS for Health 2020+.

Installation

  1. Clone/git pull the repo into any local directory, e.g.:

    $ git clone https://github.com/intersystems-ru/fhir-terminology-service.git

  2. Install IRIS for Health 2020.1 or newer.

  3. Open IRIS terminal and set up a new "foundation" namespace, e.g.:

    USER> zn "HSLIB"
HSLIB> do ##class(HS.Util.Installer.Foundation).Install("terminology")

  4. Import classes into the namespace, e.g.:

    HSLIB> zn "terminology"
TERMINOLOGY> do $System.OBJ.ImportDir("/tmp/fhir-terminology-service/", "*.cls", "ckbud", .err, 1)

    There is going to be one "class not found" exception if IRIS version is prior to 2020.4. It is safe to just ignore that error.

  5. Create InteractionsStrategy class for your FHIR Terminology Service endpoint, or skip this step and use Sample.iscru.fhir.fts.SimpleStrategy.

    If you choose to create a new InteractionsStrategy class, then do the following:

    1. subclass iscru.fhir.fts.FTSStrategy,
    2. override StrategyKey class parameter,
    3. implement getCodeTablePackage(), getCodePropertyName() and getDisplayPropertyName() methods, e.g.: 
      Parameter StrategyKey = "<full name of the new class>";

ClassMethod getCodeTablePackage(shortClassName As %String, resourceType As %String, url As %String) As %String
{
  quit "<name of the package that all code table classes belong to>"
}

ClassMethod getCodePropertyName(className As %String) As %String
{
  quit "<name of the 'code' property, i.e. the property that will be mapped to CodeSystem.concept.code element>"
}

ClassMethod getDisplayPropertyName(className As %String) As %String
{
  quit "<name of the 'display' property, i.e. the property that will be mapped to CodeSystem.concept.display element>"
}
    • Refer to Sample.iscru.fhir.fts.SimpleStrategy as an example of a custom InteractionsStrategy class.
    • Additionally implement listCodeTableClasses() method to enable returning a list of all available code systems (or value sets) in response to a search request without url parameter.
    • Override isExcludedProperty() method if any code table class property should not show up in the corresponding CodeSystem resource.

  6. This step is only applicable to 2020.4 or newer versions of InterSystems IRIS.

    Create RepoManager class for your FHIR Terminology Service endpoint (or skip this step if you are using Sample.iscru.fhir.fts.SimpleStrategy):

    1. subclass HS.FHIRServer.Storage.Json.RepoManager system class,
    2. override StrategyClass and StrategyKey class parameters as follows: 
       Parameter StrategyClass = "<full name of your InteractionsStrategy class>";
 Parameter StrategyKey = "<value of StrategyKey parameter of your InteractionsStrategy class>";

  7. Depending on the version of InterSystems IRIS for Health, either create a custom FHIR metadata set (2020.1-2020.3), or import FHIR metadata package (2020.4+) with custom search parameters. This step is a workaround needed for $expand and $validate-code operations to support HTTP GET requests.

    6.1. This step is only applicable to 2020.1-2020.3 versions of InterSystems IRIS for Health (see section 6.2 below for 2020.4+).

    1. Create terminology directory within <installation directory>/dev/fhir/fhir-metadata and copy dummy-search-parameters.json file there.

      The file contains definitions of additional search parameters for ValueSet and CodeSystem resources. Those fake search parameters correspond to input parameters of $expand and $validate-code operations.

    2. Create custom FHIR metadata set based on R4 set with additional search parameters defined in <installation directory>/dev/fhir/fhir-metadata/terminology/dummy-search-parameters.json.

      In the example below the new metadata set is named HL7v40terminology and the directory containing search parameters definition file is C:\InterSystems\IRISHealth20202\dev\fhir\fhir-metadata\terminology:

      TERMINOLOGY>do ##class(HS.FHIRServer.ConsoleSetup).Setup()
What do you want to do?
  0)  Quit
  1)  Create a FHIRServer Endpoint
  2)  Display a FHIRServer Endpoint Configuration
  3)  Configure a FHIRServer Endpoint
  4)  Delete a FHIRServer Endpoint
  5)  Update the CapabilityStatement Resource
  6)  Migrate Data from pre-2020.1
  7)  Re-index FHIRServer Storage
  8)  Create a custom metadata set
  9)  Update a custom metadata set
  10) Delete a custom metadata set
Choose your Option[1] (0-10): 8
 
Choose a base FHIR Metadata Configuration to extend
  1) HL7v30 (Base HL7 Metadata for FHIR STU3 (3.0.1))
  2) HL7v40 (Base HL7 Metadata for FHIR R4 (4.0.1))
Choose the Metadata Set[1] (1-2): 2
Enter a name for the metadata set without spaces or punctuation[-]: HL7v40terminology
Enter a description for the metadata set[-]: FHIR R4 metadata plus dummy search parameters
Enter a directory which contains the custom metadata[-]: C:\InterSystems\IRISHealth20202\dev\fhir\fhir-metadata\terminology
You are about to create metadata set 'HL7v40terminology'. Proceed?[no] (y/n): yes
...

    6.2. This step is only applicable to 2020.4 or newer versions of InterSystems IRIS for Health.

    Import FHIR metadata package from package directory either using the Management Portal or the interactive utility:

    TERMINOLOGY>do ##class(HS.FHIRServer.ConsoleSetup).Setup()
What do you want to do?
  0)  Quit
  1)  Create a FHIRServer Endpoint
  2)  Add a profile package to an endpoint
  3)  Display a FHIRServer Endpoint Configuration
  4)  Configure a FHIRServer Endpoint
  5)  Decommission a FHIRServer Endpoint
  6)  Delete a FHIRServer Endpoint
  7)  Update the CapabilityStatement Resource
  8)  Index new SearchParameters for an Endpoint
  9)  Upload a FHIR metadata package
  10) Delete a FHIR metadata package
Choose your Option[1] (0-10): 9
The following packages are installed:
[core] hl7.fhir.r3.core@3.0.2: Definitions (API, structures and terminologies) for the R3 version of the FHIR standard
[core] hl7.fhir.r4.core@4.0.1: Definitions (API, structures and terminologies) for the R4 version of the FHIR standard
[custom for 4.0.1] hl7.fhir.us.core@3.1.0:
Enter the path to a directory containing one or more metadata packages (or return to exit)[-]: /tmp/fhir-terminology-service/src/fhir-search-parameters/package
Found packages:
  fhir.dummy-search-params@1
Proceed?[yes] (y/n): yes
Saving fhir.dummy-search-params@1
Load Resources: fhir.dummy-search-params@1

  8. Create a new FHIR endpoint based on your custom InteractionsStrategy class (or on Sample.iscru.fhir.fts.SimpleStrategy). Depending on the version of InterSystems IRIS for Health, either add imported metadata package to the endpoint (2020.4+), or use new metadata set when creating the endpoint (2020.1-2020.3). Note that in 2020.4+ you can create the endpoint using Management Portal.

    TERMINOLOGY>do ##class(HS.FHIRServer.ConsoleSetup).Setup()
What do you want to do?
  0)  Quit
  1)  Create a FHIRServer Endpoint
  2)  Add a profile package to an endpoint
  3)  Display a FHIRServer Endpoint Configuration
  4)  Configure a FHIRServer Endpoint
  5)  Decommission a FHIRServer Endpoint
  6)  Delete a FHIRServer Endpoint
  7)  Update the CapabilityStatement Resource
  8)  Index new SearchParameters for an Endpoint
  9)  Upload a FHIR metadata package
  10) Delete a FHIR metadata package
Choose your Option[9] (0-10): 1
  1) Json (All Resources stored in a single table as Json text)
  2) Sample.iscru.fhir.fts.SimpleStrategy (All Resources stored in a single table as Json text)
Choose the Storage Strategy[1] (1-2): 2
  1) hl7.fhir.r3.core version 3.0.2 (Definitions (API, structures and terminologies) for the R3 version of the FHIR standard)
  2) hl7.fhir.r4.core version 4.0.1 (Definitions (API, structures and terminologies) for the R4 version of the FHIR standard)
Choose the FHIR version for this endpoint[1] (1-2): 2
The following profile packages are available:
  1) fhir.dummy-search-params version 1 ()
  2) hl7.fhir.us.core version 3.1.0 ()
Enter any package numbers (separated by a comma) or press enter to skip[] (1-2): 1
...

  9. Next, configure the new endpoint: just change DebugMode to 4 leaving default values for everything else:

    What do you want to do?
  0)  Quit
  1)  Create a FHIRServer Endpoint
  2)  Add a profile package to an endpoint
  3)  Display a FHIRServer Endpoint Configuration
  4)  Configure a FHIRServer Endpoint
  5)  Decommission a FHIRServer Endpoint
  6)  Delete a FHIRServer Endpoint
  7)  Update the CapabilityStatement Resource
  8)  Index new SearchParameters for an Endpoint
  9)  Upload a FHIR metadata package
  10) Delete a FHIR metadata package
Choose your Option[4] (0-10): 4
 
Which Endpoint do you want to configure?
  1) /csp/healthshare/terminology/fhir/r4 [enabled] (for Strategy 'Sample.iscru.fhir.fts.SimpleStrategy' and Metadata Set 'hl7.fhir.r4.core@4.0.1,fhir.dummy-search-params@1')
Choose the Endpoint[1] (1-1): 1
Endpoint enabled[yes] (y/n): yes
 
-- Edit CSP Application Configuration --
OAuthClientName[-]:
ServiceConfigName[-]:
 
-- Edit FHIRService Configuration --
RequiredResource[-]:
FHIRSessionTimeout[300]: 300
DefaultSearchPageSize[100]: 100
MaxSearchPageSize[100]: 100
MaxSearchResults[1000]: 1000
MaxConditionalDeleteResults[3]: 3
DefaultPreferHandling[lenient]: lenient
DebugMode[0]: 4
				FHIRVersion: 4.0.1
  InteractionsStrategyClass: Sample.iscru.fhir.fts.SimpleStrategy
		   RequiredResource:
		 FHIRSessionTimeout: 300
	  DefaultSearchPageSize: 100
		  MaxSearchPageSize: 100
		   MaxSearchResults: 1000
MaxConditionalDeleteResults: 3
	  DefaultPreferHandling: lenient
				  DebugMode: 4
Save Changes? (y/n): yes
Changes have been saved

  10. Import fhir-terminology-service.postman_collection.json file into Postman, adjust url variable defined for the collection and test the service against Sample.iscru.fhir.fts.model.CodeTable or your own code table classes (depending on whether you've created a custom InteractionsStrategy class). In the latter case, you will need to modify request parameters accordingly.

Supported FHIR Interactions

Currently read and search-type interactions are supported for ValueSet and CodeSystem resources. The only supported search parameter for both resources is url.

Supported operations: $lookup and $validate-code on CodeSystem, $expand and $validate-code on ValueSet. Both HTTP GET and HTTP POST methods are supported for all operations.

The table below lists some of the possible HTTP GET requests against Sample.iscru.fhir.fts.model.CodeTable class.

URI (to be prepended with
http://<server>:<port><web app path>)		 Description
/metadata Get endpoint's Capability Statement resource.
/CodeSystem/Sample.iscru.fhir.fts.model.CodeTable Read CodeSystem resource corresponding to Sample.iscru.fhir.fts.model.CodeTable class.
/ValueSet/Sample.iscru.fhir.fts.model.CodeTable Read ValueSet resource corresponding to Sample.iscru.fhir.fts.model.CodeTable class.
/CodeSystem?url=urn:CodeSystem:CodeTable Search CodeSystem resource by url.
/CodeSystem Output all avaliable CodeSystem resources.
/ValueSet?url=urn:ValueSet:CodeTable Search ValueSet resource by url.
/ValueSet Output all avaliable ValueSet resources.
/CodeSystem/$lookup?system=urn:CodeSystem:CodeTable&code=TEST Given system and code, get all the details about the concept.
/ValueSet/$expand?url=urn:ValueSet:CodeTable Expand the ValueSet.
/CodeSystem/Sample.iscru.fhir.fts.model.CodeTable/$validate-code?code=TEST Validate that a code is in the code system.

About

Implementation of FHIR Terminology Service specification (https://www.hl7.org/fhir/R4/terminology-service.html) to expose arbitrary persistent classes as FHIR value sets and code systems. Runs on InterSystems IRIS for Health 2020+.

fhirintersystemsintersystems-irisintersystems-iris-for-healthobjectscriptterminology

License:MIT License

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