catch up

.github/workflows/fhirbuild.yml

@@ -1,4 +1,4 @@
-# This workflow reuses the openHIE GitHub action for building IGs
+# This workflow reuses the WHO GitHub action for building IGs
 # Change log:
 # v0.1.0
 # 2021-06-18: publish default branches to / , other branches branches/<branch>

.github/workflows/release.yml

@@ -7,7 +7,8 @@ on:
   pull_request:
     branches:
       - release-candidate
-
+  workflow_dispatch:
+
 jobs:
   check:
     runs-on: ubuntu-latest

README.md

@@ -1,21 +1,20 @@
 [![License: CC BY-IGO 3.0](https://licensebuttons.net/l/by-nc/3.0/igo/80x15.png)](https://creativecommons.org/licenses/by/3.0/igo)
-![CI Build](https://img.shields.io/github/actions/workflow/status/worldhealthorganization/smart-immunizations-measles/ghbuild.yml)  
+![CI Build](https://img.shields.io/github/actions/workflow/status/worldhealthorganization/smart-example-immz/ghbuild.yml)  
 
 
-[![QA errors](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fworldhealthorganization.github.io%2Fsmart-immunizations-measles%2Fqa.json&query=%24.errs&logoColor=red&label=QA%20errors&color=yellow)](https://worldhealthorganization.github.io/smart-immunizations-measles/qa.html)
-![QA warnings](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fworldhealthorganization.github.io%2Fsmart-immunizations-measles%2Fqa.json&query=%24.warnings&logoColor=orange&label=QA%20warnings&color=yellow)
-![QA hints](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fworldhealthorganization.github.io%2Fsmart-immunizations-measles%2Fqa.json&query=%24.hints&logoColor=yellow&label=QA%20hints&color=yellow)
+[![QA errors](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fworldhealthorganization.github.io%2Fsmart-example-immz%2Fqa.json&query=%24.errs&logoColor=red&label=QA%20errors&color=yellow)](https://worldhealthorganization.github.io/smart-example-immz/qa.html)
+![QA warnings](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fworldhealthorganization.github.io%2Fsmart-example-immz%2Fqa.json&query=%24.warnings&logoColor=orange&label=QA%20warnings&color=yellow)
+![QA hints](https://img.shields.io/badge/dynamic/json?url=https%3A%2F%2Fworldhealthorganization.github.io%2Fsmart-example-immz%2Fqa.json&query=%24.hints&logoColor=yellow&label=QA%20hints&color=yellow)
 
 
-# WHO SMART GUIDELINES - IMMUNIZATIONS (Measles)
+# WHO SMART GUIDELINES - Example IG 
 
-CI-Build: https://worldhealthorganization.github.io/smart-immunizations-measles/
-
-This Implementation Guide contains the specifications for MEASLES vaccination SMART Guidelines.
+CI-Build: https://worldhealthorganization.github.io/smart-example-immz/
 
+This Implementation Guide is an example IG that follows the L3 SOP. The example is using the Immunizations DAK for the Measles antigen as an example.
 This framework is published under a Creative Commons - IGO [license](LICENSE.md).
 
 ## Changes and feedback
 
 Feedback and issues about this empty framework can be submitted via the [issues](issues) page, and will be incorporated into subsequent releases.
- 
+

_gencontinuous.bat

@@ -0,0 +1,2 @@
+@ECHO OFF
+CALL ./_genonce.bat -watch

_gencontinuous.sh

@@ -0,0 +1,2 @@
+#!/bin/bash
+./_genonce.sh -watch

input/fsh/libraries/FHIRCommon.fsh → _unused/FHIRCommon.fsh

@@ -3,14 +3,14 @@ InstanceOf: Library
 Title: "FHIRCommon"
 Description: "This library defines terminologies and functions commonly used in FHIR-based CQL artifacts"
 Usage: #definition
-* url = "http://smart.who.int/immunizations-measles/Library/FHIRCommon"
+* url = "http://fhir.org/guides/cqf/common/Library/FHIRCommon"
 * extension[+]
-  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * url = "http://hl7.org/fhir/StructureDefinition/cqf-knowledgeCapability"
   * valueCode = #computable
-* version = "0.1.0"
+* version = "4.0.1"
 * name = "FHIRCommon"
 * status = #draft
-* experimental = false
+* experimental = true
 * publisher = "World Health Organization (WHO)"
 * type = $library-type#logic-library
 * content.id = "ig-loader-FHIRCommon.cql"

input/fsh/libraries/FHIRHelpers.fsh → _unused/FHIRHelpers.fsh

@@ -3,14 +3,14 @@ InstanceOf: Library
 Title: "FHIRHelpers"
 Description: "This library defines functions to convert between FHIR data types and CQL system-defined types, as well as functions to support FHIRPath implementation. For more information, the FHIRHelpers wiki page: https://github.com/cqframework/clinical_quality_language/wiki/FHIRHelpers"
 Usage: #definition
-* url = "http://smart.who.int/immunizations-measles/Library/FHIRHelpers"
+* url = "http://fhir.org/guides/cqf/common/Library/FHIRHelpers"
 * extension[+]
-  * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-knowledgeCapability"
+  * url = "http://hl7.org/fhir/StructureDefinition/cqf-knowledgeCapability"
   * valueCode = #computable
-* version = "0.1.0"
+* version = "4.0.1"
 * name = "FHIRHelpers"
 * status = #draft
-* experimental = false
+* experimental = true
 * publisher = "World Health Organization (WHO)"
 * type = $library-type#logic-library
 * content.id = "ig-loader-FHIRHelpers.cql"

ig.ini

@@ -1,5 +1,5 @@
 [IG]
 ig = fsh-generated/resources/ImplementationGuide-smart.who.int.immunizations-measles.json
 
-#template = #local-template
-template = who.fhir.template#current
+template = #local-template
+;template = who.template.root#current

input/_resources/exp-params.json

@@ -0,0 +1,8 @@
+{
+    "resourceType" : "Parameters",
+    "id" : "exp-params",
+    "parameter" : [{
+      "name" : "system-version",
+      "valueUri" : "http://snomed.info/sct|http://snomed.info/sct/900000000000207008"
+    }]
+  }

input/cql/IMMZCommon.cql

@@ -2,238 +2,20 @@ library IMMZCommon
 
 using FHIR version '4.0.1'
 
-include WHOCommon called WCom
-include WHOConcepts called Wcon
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
-include IMMZConcepts called IMMZc
-
-
-code "[#] Births total": '11640-0' from IMMZc."LOINC" display 'Pregnancy outcome'
-code "[#] Births.preterm": '11637-6' from IMMZc."LOINC" display 'Preterm'
-context Patient
-
-//TODO: Check patient is alive
-
-//Get patient immunizations
-define "Get Immunization":
-  [Immunization]
-
-// check vaccine status
-define "Immunization Status":
-  [Immunization] I
-    return I.status
-
-//check Immunization.status for not-done
-define "Immunization Completed":
-  [Immunization] I
-    where I.status in {'completed'}
-
-//check Immunization.status for not-done
-define "Immunization Not Done":
-  [Immunization] I
-    where I.status in {'not-done'}
-
-//how do we handle entered-in-error? It seems like it should be different from not-done in how it should be handled? These should be ignored so we likely don't need to check for them. We should maybe set these to check for statuses like complete, or amended 
-
-//check vaccine status reason - e.g. if vaccine was not given
-define "Immunization StatusReason":
-  [Immunization] I
-    return I.statusReason
-
-//define statusReason Immunizations for when it was not given
-
-//Procedure for vaccine administration
-
-//Get patient observations. Do we need this statement to get all Observations? 
-define "Get Observations":
-  [Observation]
-
-//Check if patient is pregnant
-//not sure if pregnancy is an Observation
-define "Pregnant Observation":
-  [Observation] O
-  //IPS Uses Observation - https://hl7.org/fhir/uv/ips/StructureDefinition-observation-pregnancy-status-uv-ips.html
-    where (O.value as CodeableConcept) in Wcon."Pregnancy Status Pregnant"
-/*
-Need to figure out how to add the OR Condition in case pregnancy is stored in a condition instead of an Observation 
-or [Condition] C
-      where (C.code as CodeableConcept) in Wcon."Pregnancy Status Pregnant"
-*/
-
-/*
-define "Patient Has Active Sickle-cell disease":
-  exists([Condition: code = IMMZc."Sickle-cell Disease Condition"] C
-  where C.clinicalStatus in FC."Active Condition"
-  and C.abatement is null)
-*/
-
-define "Pregnant Condition":
-  [Condition] C
-    where (C.code as CodeableConcept) in Wcon."Pregnancy Status Pregnant" or (C.code as CodeableConcept) ~ IMMZc."Currently Pregnant"
-
-define "Pregnant": 
-  exists
-  ( "Pregnant Observation")
-  or exists ("Pregnant Condition")
-
-//Seronegative. Relevant for Dengue 
-/*
-define "Individual is Seronegative for Dengue":
-  [Observation] O
-    where (O.value as CodeableConcept) in IMMZc.Seronegative
-*/
-
-//Total number of births including abortions, stillbirths and live births.
-define "Patient mother's pregnancy outcome observation":
-  [Observation: code = "[#] Births total"] O
-    return O.value
-
-// Total number of children whose birth occurred through the end of the last day of the 37th week (259th day) 
-// following onset of the last menstrual period
-define "Preterm":
-  [Observation: code = "[#] Births.preterm"] O
-    return O.value
-
-//Observed Preterm birth
-define "Preterm Birth":
-  [Observation] O
-    where (O.value as CodeableConcept) in IMMZc.PretermBirth
-
-//@dataElement Adverse Event:
-define "Adverse Event":
-  from [Immunization] I, [Observation] O
-    where O.id in (I.reaction R return Last(Split(R.detail.reference, '/')))
-    return O
-
-/* 
- * @dataElement Allergy = True
- */
-define "Allergy = True":
-	[AllergyIntolerance] A
-	where 
-	A.clinicalStatus ~ FC."allergy-active"
-	and
-	A.verificationStatus ~ FC."allergy-confirmed"
-
-/* 
- * @dataElement Immunocompromised = True
- */
-define "Immunocompromised = True":
-	exists([Condition] C 
-	where C.code in IMMZc."Immunocompromised"
-	and
-  	C.clinicalStatus in FC."Active Condition"
-	and
-	C.verificationStatus ~ FC."confirmed")
-
-/**
- * @dataElement All Doses Administered to Patient to patient ordered newest to oldest
- */
-define "Doses Administered to Patient":
-  [Immunization] I
-    where I.status = 'completed'
-    sort by date from (occurrence as FHIR.dateTime) desc
-/**
- * Contraindications 
- */
-define "Severely Immunosuppressed Condition":
-  [Condition: IMMZc."Severely immunosuppressed"]
-
-define "History of Anaphylactic Reactions Condition":
-  [Condition: IMMZc."History of anaphylactic reactions"]
-
-define "Severe Allergic Reactions Condition":
-  [Condition: IMMZc."Severe allergic reactions"]
-
-define "Symptomatic HIV Infection Condition":
-  [Condition: IMMZc."Symptomatic HIV infection"]
-
-
-/******************************
- * Test Results
- */
-
-
-define "Patient birth weight observation value":
-[Observation: code in IMMZc."Patient birth weight observation value"] O
-  return O.value as FHIR.Quantity
-
-/** 
- * @dataElement Patient age in years
- */
-define "Current Patient Age In Years":
-  AgeInYearsAt(Today())
-  //Today() - (Patient.birthDate as System.Date)
-
-/** 
- * @dataElement Patient age in weeks
- */
-define "Current Patient Age In Weeks":
-  AgeInWeeksAt(Today())
-
-/** 
- * @dataElement Patient age in months
- */
-define "Current Patient Age In Months":
-  AgeInMonthsAt(Today())
-
-/** 
- * @dataElement Patient biological sex used for deciding vaccine eligibility
- * TODO: "Gender" of patient in FHIR is the administrative gender - or can we expect that this will be biological sex and administrative
- *        gender identity will be captured using the gender identity extension?
- */
-define "Patient Biological Sex":
-  Patient.gender
-
-define "Patient HAART Treatment Start Date":
-  Last([MedicationAdministration] A 
-    where 
-      ExtractMedicationCode(A.medication) in IMMZc."ARV Drugs" 
-      and A.status in { 'active', 'complete' }
-      and ExtractMedicationInitiationDate(A.effective) less than 12 'month' before Today()
-      return ExtractMedicationInitiationDate(A.effective))
-
-define "Patient HAART Treatment Started 6 to 12 Months Ago":
-  "Patient HAART Treatment Start Date" between Now() - 12 months and Now() - 6 months
 
 /**
- * @dataElement The patient has a medication record which indicates that they are receiving ARV
- */
-define "Patient is receiving HAART":
- //exists([MedicationStatement] S where ExtractMedicationCode(S.medication) in IMMZc."ARV Drugs" and S.status = 'active')
- //or 
- exists([MedicationAdministration] A where ExtractMedicationCode(A.medication) in IMMZc."ARV Drugs" and A.status = 'in-progress')
- //union 
- //
-
-/*
-  @dataElement HIV Status observations of the patient most recent first
-*/
-define "HIV Status":
-  [Observation: IMMZc."HIV status"] O
-    where O.status in { 'final', 'amended', 'corrected' }
-      and Coalesce(WCom.ModifierExtension(O, 'who-notDone').value, false) is false
-    return O.value as FHIR.CodeableConcept
-
-/*
-  @dataElement Date and time of last live attenuated vaccine
-*/
-define "Live Attenuated Vaccines":
-  "Doses Administered to Patient" I where I.vaccineCode in IMMZc."Live Attenuated"
-
-define "Date of Latest Live Attenuated Vaccine":
-  First("Live Attenuated Vaccines").occurrence as dateTime
-
-/******************************
- * CQL Helper Functions
+ * @description Fetches a singleton protocol applied from an immunization
+ * @comment The protocol list from the immunization
  */
+define function Only(protocols List<FHIR.Immunization.ProtocolApplied>):
+  singleton from protocols
 
 /**
  * @description Fetches a singleton protocol applied from an immunization
  * @comment The protocol list from the immunization
  */
-define function Only(protocols List<FHIR.Immunization.ProtocolApplied>):
+define fluent function only(protocols List<FHIR.Immunization.ProtocolApplied>):
   singleton from protocols
 
 /**