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Guillaume Rongier · Feb 28, 2022

If you want to discover IRIS for Health with some samples, the best way is to install ZPM (community package manager).
More info here : https://community.intersystems.com/post/install-zpm-one-line

Then, you have access of almost all application in OpenExchange.

Let's have an example with csvgen-ui :
https://openexchange.intersystems.com/package/csvgen-ui

zpm "install csvgen-ui"

In OpenExchange you will find may example about rest API, web app, and so.

Guillaume Rongier · Feb 18, 2022

For now, it's not possible in pure python, because the select namespace is specified by the environment variable IRISNAMESPACE, and environment variable can't be change in the parent process, I have tried by reloading iris module with no success.

To achieve that, for now, as Robert says, you have to create an helper method in objectscript ... :(

Class Embedded.Utils
{

ClassMethod GetNameSpace() As %Status
{

    Return $namespace
}

ClassMethod SetNameSpace(pNameSpace) As %Status
{
    zn pNameSpace
    Return $namespace
}

}

Python :

import iris

print(iris.cls("Embedded.Utils").GetNameSpace())
try:
    print(iris.cls("Security.Users").Exists("SuperUser"))
except RuntimeError:
    print("Wrong NameSpace")

print(iris.cls("Embedded.Utils").SetNameSpace("%SYS"))
try:
    print(iris.cls("Security.Users").Exists("SuperUser"))
except RuntimeError:
    print("Wrong NameSpace")
Guillaume Rongier · Feb 8, 2022

If you are using Ensemble you can use EnsLib.SQL.Snapshot.

This helper class can persist ResutSet in global :

Set rset1 = ##class(%ResultSet).%New()
set sc = rset1.Prepare("Select * FROM Ens_Util.Log")
Set:+sc sc = rset1.Execute()

set snap = ##class(EnsLib.SQL.Snapshot).CreateFromResultSet(rset1)
set glb = snap.%GblRef

zw @glb

glb :

%Ensemble("12@EnsLib.SQL.Snapshot")=21
%Ensemble("12@EnsLib.SQL.Snapshot",1,1)=1
%Ensemble("12@EnsLib.SQL.Snapshot",1,2)=""
%Ensemble("12@EnsLib.SQL.Snapshot",1,3)=445
%Ensemble("12@EnsLib.SQL.Snapshot",1,4)=""
%Ensemble("12@EnsLib.SQL.Snapshot",1,5)=""
%Ensemble("12@EnsLib.SQL.Snapshot",1,6)="Ens.Director"
%Ensemble("12@EnsLib.SQL.Snapshot",1,7)="StartProduction"
%Ensemble("12@EnsLib.SQL.Snapshot",1,8)=""
%Ensemble("12@EnsLib.SQL.Snapshot",1,9)="Production 'Connector.Production' starting..."
%Ensemble("12@EnsLib.SQL.Snapshot",1,10)="2022-02-08 14:29:33.724"
%Ensemble("12@EnsLib.SQL.Snapshot",1,11)=""
%Ensemble("12@EnsLib.SQL.Snapshot",1,12)=4
%Ensemble("12@EnsLib.SQL.Snapshot",2,1)=2
%Ensemble("12@EnsLib.SQL.Snapshot",2,2)="Ens.Actor"
%Ensemble("12@EnsLib.SQL.Snapshot",2,3)=618
%Ensemble("12@EnsLib.SQL.Snapshot",2,4)=""
%Ensemble("12@EnsLib.SQL.Snapshot",2,5)=""
%Ensemble("12@EnsLib.SQL.Snapshot",2,6)="Ens.Job"
%Ensemble("12@EnsLib.SQL.Snapshot",2,7)="Start"
%Ensemble("12@EnsLib.SQL.Snapshot",2,8)=""
%Ensemble("12@EnsLib.SQL.Snapshot",2,9)="ConfigItem 'Ens.Actor' started in job 618"
%Ensemble("12@EnsLib.SQL.Snapshot",2,10)="2022-02-08 14:29:33.978"
%Ensemble("12@EnsLib.SQL.Snapshot",2,11)=""
%Ensemble("12@EnsLib.SQL.Snapshot",2,12)=4
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs")=12
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","configname")=2
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","id")=1
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","job")=3
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","messageid")=4
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","sessionid")=5
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","sourceclass")=6
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","sourcemethod")=7
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","stack")=8
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","text")=9
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","timelogged")=10
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","tracecat")=11
%Ensemble("12@EnsLib.SQL.Snapshot","ColIDs","type")=12
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames")=12
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",1)="ID"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",2)="ConfigName"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",3)="Job"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",4)="MessageId"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",5)="SessionId"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",6)="SourceClass"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",7)="SourceMethod"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",8)="Stack"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",9)="Text"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",10)="TimeLogged"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",11)="TraceCat"
%Ensemble("12@EnsLib.SQL.Snapshot","ColNames",12)="Type"
%Ensemble("12@EnsLib.SQL.Snapshot","ColSizes")=12
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes")=12
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",1)="BIGINT"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",2)="VARCHAR"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",3)="VARCHAR"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",4)="INTEGER"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",5)="INTEGER"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",6)="VARCHAR"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",7)="VARCHAR"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",8)="VARCHAR"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",9)="VARCHAR"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",10)="TIMESTAMP"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",11)="VARCHAR"
%Ensemble("12@EnsLib.SQL.Snapshot","ColTypes",12)="INTEGER"

If you are not using Ensemble, I guess you will have to build this kind of helper class by your self.

Guillaume Rongier · Feb 8, 2022

If you don't want to create new data on the FHIR protocol, you must use the PUT verb with an ID instead of POST.

PUT creates the resource with the specified ID if the ID does not exist, otherwise it replaces the pre-existing data.

POST always creates a new resource with a new ID, that's why the ID is not mandatory when POSTing.

For automatic transformations from HL7/CDA to FHIR, there is the possibility to define the ID for some resources and thus to avoid duplication.

Below is an example of code to transform an HL7 payload to SDA by specifying the ID of the patient in order to avoid duplicating this resource, after that you can transform this SDA to FHIR with no duplication of patient.

/// This is a custom business process that transforms an HL7 message to SDA format (an internal healthcare data format for InterSystems IRIS for Health).
/// To use this class, add a business process with this class to the production and configure the target. The default target will send the SDA to a component
/// that converts the data to FHIR.
/// 
Class FHIRDemo.HL7TransformProcess Extends Ens.BusinessProcess [ ClassType = persistent ]
{

Parameter SETTINGS = "TargetConfigName:Basic:selector?context={Ens.ContextSearch/ProductionItems?targets=1&productionName=@productionId},TransformFile:Basic";

Property TargetConfigName As Ens.DataType.ConfigName [ InitialExpression = "HS.FHIR.DTL.Util.HC.SDA3.FHIR.Process" ];

/// Transforms an HL7 message to SDA, an internal healthcare format for InterSystems IRIS for Health.
Method OnRequest(pRequest As EnsLib.HL7.Message, Output pResponse As Ens.Response) As %Status
{
    set tSC = $$$OK
    try {
        $$$ThrowOnError(##class(HS.Gateway.HL7.HL7ToSDA3).GetSDA(pRequest,.tSDA))
        $$$LOGINFO(tSDA.Read())

        Set tQuickStream = ##class(HS.SDA3.QuickStream).%New()
        $$$ThrowOnError(tQuickStream.CopyFrom(tSDA))

        Set tResponse = ##class(HS.Message.XMLMessage).%New()
        Do tResponse.AdditionalInfo.SetAt(tQuickStream.%Id(),"QuickStreamId")
        Do tResponse.AdditionalInfo.SetAt($P(pRequest.GetValueAt("PID:3:1"),"^"),"PatientResourceId")

        Set tSC = ..SendRequestSync(..TargetConfigName,tResponse,.pResponse)
    } catch ex {
        set tSC = ex.AsStatus()
    }
    quit tSC
}

Storage Default
{
<Data name="HL7TransformProcessDefaultData">
<Subscript>"HL7TransformProcess"</Subscript>
<Value name="1">
<Value>TargetConfigName</Value>
</Value>
</Data>
<DefaultData>HL7TransformProcessDefaultData</DefaultData>
<Type>%Storage.Persistent</Type>
}

}
Guillaume Rongier · Jan 30, 2022

Hi Steve, have a look a this github repo, it has a lot of examples :

Here is what you are looking for call python methods from objectscript and vice versa :

/// embedded python example
Class ObjectScript.Embbeded.Python Extends %SwizzleObject
{

/// HelloWorld with a parameter
ClassMethod HelloWorld(name As %String = "toto") As %Boolean [ Language = python ]
{
    print("Hello",name)
    return True
}

/// Description
Method compare(modèle, chaine) As %Status [ Language = python ]
{
    import re

    # compare la chaîne [chaîne] au modèle [modèle]
    # affichage résultats
    print(f"\nRésultats({chaine},{modèle})")
    match = re.match(modèle, chaine)
    if match:
        print(match.groups())
    else:
        print(f"La chaîne [{chaine}] ne correspond pas au modèle [{modèle}]")
}

/// Description
Method compareObjectScript(modèle, chaine) As %Status
{
    w !,"Résultats("_chaine_","_modèle_")",!
    set matcher=##class(%Regex.Matcher).%New(modèle)                             
    set matcher.Text=chaine
    if matcher.Locate() {
        write matcher.GroupGet(1)
    }
    else {
        w "La chaîne ["_chaine_"] ne correspond pas au modèle ["_modèle_"]"
    }
}

/// Description
Method DemoPyhtonToPython() As %Status [ Language = python ]
{
    # expression régulières en python
    # récupérer les différents champs d'une chaîne
    # le modèle : une suite de chiffres entourée de caractères quelconques
    # on ne veut récupérer que la suite de chiffres
    modèle = r"^.*?(\d+).*?$"

    # on confronte la chaîne au modèle
    self.compare(modèle, "xyz1234abcd")
    self.compare(modèle, "12 34")
    self.compare(modèle, "abcd")
}

Method DemoPyhtonToObjectScript() As %Status [ Language = python ]
{
    # expression régulières en python
    # récupérer les différents champs d'une chaîne
    # le modèle : une suite de chiffres entourée de caractères quelconques
    # on ne veut récupérer que la suite de chiffres
    modèle = r"^.*?(\d+).*?$"

    # on confronte la chaîne au modèle
    self.compareObjectScript(modèle, "xyz1234abcd")
    self.compareObjectScript(modèle, "12 34")
    self.compareObjectScript(modèle, "abcd")
}

/// Description
Method DemoObjectScriptToPython() As %Status
{
    // le modèle - une date au format jj/mm/aa
    set modèle = "^\s*(\d\d)\/(\d\d)\/(\d\d)\s*$"
    do ..compare(modèle, "10/05/97")
    do ..compare(modèle, " 04/04/01 ")
    do ..compare(modèle, "5/1/01")
}

}
/// embedded python example
Class ObjectScript.Embbeded.Python Extends %SwizzleObject
{

/// HelloWorld with a parameter
ClassMethod HelloWorld(name As %String = "toto") As %Boolean [ Language = python ]
{
    print("Hello",name)
    return True
}

/// Description
Method compare(modèle, chaine) As %Status [ Language = python ]
{
    import re

    # compare la chaîne [chaîne] au modèle [modèle]
    # affichage résultats
    print(f"\nRésultats({chaine},{modèle})")
    match = re.match(modèle, chaine)
    if match:
        print(match.groups())
    else:
        print(f"La chaîne [{chaine}] ne correspond pas au modèle [{modèle}]")
}

/// Description
Method compareObjectScript(modèle, chaine) As %Status
{
    w !,"Résultats("_chaine_","_modèle_")",!
    set matcher=##class(%Regex.Matcher).%New(modèle)                             
    set matcher.Text=chaine
    if matcher.Locate() {
        write matcher.GroupGet(1)
    }
    else {
        w "La chaîne ["_chaine_"] ne correspond pas au modèle ["_modèle_"]"
    }
}

/// Description
Method DemoPyhtonToPython() As %Status [ Language = python ]
{
    # expression régulières en python
    # récupérer les différents champs d'une chaîne
    # le modèle : une suite de chiffres entourée de caractères quelconques
    # on ne veut récupérer que la suite de chiffres
    modèle = r"^.*?(\d+).*?$"

    # on confronte la chaîne au modèle
    self.compare(modèle, "xyz1234abcd")
    self.compare(modèle, "12 34")
    self.compare(modèle, "abcd")
}

Method DemoPyhtonToObjectScript() As %Status [ Language = python ]
{
    # expression régulières en python
    # récupérer les différents champs d'une chaîne
    # le modèle : une suite de chiffres entourée de caractères quelconques
    # on ne veut récupérer que la suite de chiffres
    modèle = r"^.*?(\d+).*?$"

    # on confronte la chaîne au modèle
    self.compareObjectScript(modèle, "xyz1234abcd")
    self.compareObjectScript(modèle, "12 34")
    self.compareObjectScript(modèle, "abcd")
}

/// Description
Method DemoObjectScriptToPython() As %Status
{
    // le modèle - une date au format jj/mm/aa
    set modèle = "^\s*(\d\d)\/(\d\d)\/(\d\d)\s*$"
    do ..compare(modèle, "10/05/97")
    do ..compare(modèle, " 04/04/01 ")
    do ..compare(modèle, "5/1/01")
}

}
Guillaume Rongier · Jan 26, 2022

Great article and very useful.

In one of my project, I have almost done the same but instead of using env var, I use an mounted xml file of default settings :

LoadSettings.mac in Interoperability NameSpace

ROUTINE LoadSettings

#Include Ensemble

UseXMLVariables() PUBLIC {

    Try {
        // mounted file of default settings
        set tFileName = "/usr/irissys/conf/DefaultSettings.xml"
        if ##class(%File).Exists(tFileName) {
            do ##class(Ens.Config.DefaultSettings).%Import(tFileName)
            write !,"File : "_tFileName_" loaded the defaultsettings",!
        }
    } Catch e {
        s ^%zStartupError=e.AsStatus()
    }
}

%ZSTART

ROUTINE %ZSTART

#include %occStatus
SYSTEM() PUBLIC {
    /*
        Initial plan to use this as startup configuration.
    */
    Try {
        New $namespace
        Set $namespace ="IRISAPP"

        Do UseXMLVariables^LoadSettings

    } Catch {}
}

/usr/irissys/conf/DefaultSettings.xml

<Export generator="IRIS" version="26" zv="IRIS for UNIX (Ubuntu Server LTS for x86-64 Containers) 2020.4 (Build 521U)" ts="2021-05-10 07:39:07">
<Document name="Ens.Config.DefaultSettings.ESD">
<defaultSettings>
<item production="*" item="FHIR_STU3_Default_Operation" class="*" setting="URL" value="http://fhirserver:52773/fhir/stu3/"><Deployable>true</Deployable></item>
</defaultSettings>
</Document></Export>
Guillaume Rongier · Nov 19, 2021

@Ben Spead

With Embedded Python, code can (and should?) not be stored in the databases and still be executed on the server side with the irispython interpreter.

Here is a GitHub link that demonstrates the use of embedded python with a backend on the Flask micro framework + Iris as a database.

It is true that Embedded python will change a lot of our paradigms, best practices, reflexes.

That's why we, as ObjectScript and IRIS experts, must try to use it as much as possible.

We will have to go out of our comfort zone and it is essential, it is up to us to go towards the python community because the opposite will not happen.

Regarding the [language = python] tag, I'm not saying it's useless. It can be useful in some cases.
I just think that it should not become the norm.

PS: My previous answer is indeed provocative and this is to draw attention to Embedded Python which is not a feature but a major evolution (Révolution ?).