Added references and rationale throughout plan definitions. Added fhi…

…r.cqf.common dependency to remove FHIRCommon and FHIRHelpers libraries

input/cql/IMMZCommon.cql

@@ -11,6 +11,13 @@ include FHIRHelpers version '4.0.1'
 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 fluent function only(protocols List<FHIR.Immunization.ProtocolApplied>):
+  singleton from protocols
+
 /**
  * @description Takes the date choice of a date/string choice (for Immunization date)
  */

input/cql/IMMZElements.cql

@@ -3,7 +3,7 @@ library IMMZElements
 using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
+include fhir.cqf.common.FHIRCommon called FC
 
 include WHOConcepts
 include WHOCommon called WC

input/cql/IMMZEncounterElements.cql

@@ -3,7 +3,6 @@ library IMMZEncounterElements
 using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
 
 include WHOConcepts
 include WHOCommon called WC
@@ -13,7 +12,7 @@ include IMMZConcepts called Concepts
 include IMMZCommon called Common
 include IMMZElements called Elements
 
-parameter AsOf Date default Today()
+parameter Today Date default Today()
 parameter EncounterId String
 
 context Patient
@@ -23,19 +22,19 @@ context Patient
  */
 define "MCV Dose":
   Elements."MCV Dose" MCV
-    where MCV.occurrence.toInterval() on or before AsOf
+    where MCV.occurrence.toInterval() on or before Today
 
 define "MCV Primary Series Dose":
   Elements."MCV Primary Series Dose" MCV
-    where MCV.occurrence.toInterval() on or before AsOf
+    where MCV.occurrence.toInterval() on or before Today
 
 define "MCV Supplementary Dose":
   Elements."MCV Supplementary Dose" MCV
-    where MCV.occurrence.toInterval() on or before AsOf
+    where MCV.occurrence.toInterval() on or before Today
 
 define "MCV Dose 0 Dose":
   Elements."MCV Dose 0 Dose" MCV
-    where MCV.occurrence.toInterval() on or before AsOf
+    where MCV.occurrence.toInterval() on or before Today
 
 /*
  * Contraindications
@@ -55,11 +54,11 @@ define "Currently Pregnant":
 define "Currently Pregnant Observation":
   Elements."Currently Pregnant Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() starts 9 months on or before day of AsOf
+      or O.effective.toInterval() starts 9 months on or before day of Today
 
 define "Currently Pregnant Condition":
   Elements."Currently Pregnant Condition" C
-    where C.prevalenceInterval() includes AsOf
+    where C.prevalenceInterval() includes Today
 
 // TODO: Should this be related to the mother's record?
 //Total number of births including abortions, stillbirths and live births.
@@ -79,7 +78,7 @@ define "Patient Mother's Pregnancy Outcome Observation Value":
 define "Preterm Births Observation":
   Elements."Preterm Births Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() on or before AsOf
+      or O.effective.toInterval() on or before Today
 
 define "Preterm":
   Last(
@@ -92,7 +91,7 @@ define "Preterm":
 define "Preterm Birth":
   Elements."Preterm Birth" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() on or before AsOf
+      or O.effective.toInterval() on or before Today
 
 // TODO: How does/should this relate to the encounter?
 //@dataElement Adverse Event:
@@ -109,7 +108,7 @@ define "Allergy = True":
 
 define "Active Confirmed Allergy":
   Elements."Active Confirmed Allergy" A
-    where A.onset.toInterval() starts on or before AsOf
+    where A.onset.toInterval() starts on or before Today
 
 /* 
  * @dataElement Immunocompromised = True
@@ -119,7 +118,7 @@ define "Immunocompromised = True":
 
 define "Immunocompromised Condition":
   Elements."Immunocompromised Condition" C
-    where C.prevalenceInterval() starts on or before AsOf
+    where C.prevalenceInterval() starts on or before Today
 
 /**
  * @dataElement All Doses Administered to Patient to patient ordered newest to oldest
@@ -137,23 +136,23 @@ define "Severely Immunosuppressed":
 define "Severely Immunosuppressed Observation":
   Elements."Severely Immunosuppressed Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() starts on or before AsOf
+      or O.effective.toInterval() starts on or before Today
 
 define "Severely Immunosuppressed Condition":
   Elements."Severely Immunosuppressed Condition" C
-    where C.prevalenceInterval() starts on or before AsOf
+    where C.prevalenceInterval() starts on or before Today
 
 define "History Of Anaphylactic Reactions":
   exists "History Of Anaphylactic Reactions Condition"
 
 define "History Of Anaphylactic Reactions Observation":
   Elements."History Of Anaphylactic Reactions Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() starts on or before AsOf
+      or O.effective.toInterval() starts on or before Today
 
 define "History Of Anaphylactic Reactions Condition":
   Elements."History Of Anaphylactic Reactions Condition" C
-    where C.prevalenceInterval() starts on or before AsOf
+    where C.prevalenceInterval() starts on or before Today
 
 define "Severe Allergic Reactions":
   exists "Severe Allergic Reactions Observation"
@@ -162,11 +161,11 @@ define "Severe Allergic Reactions":
 define "Severe Allergic Reactions Observation":
   Elements."Severe Allergic Reactions Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() starts on or before AsOf
+      or O.effective.toInterval() starts on or before Today
 
 define "Severe Allergic Reactions Condition":
   Elements."Severe Allergic Reactions Condition" C
-    where C.prevalenceInterval() starts on or before AsOf
+    where C.prevalenceInterval() starts on or before Today
 
 define "Symptomatic HIV Infection":
   exists "Symptomatic HIV Infection Observation"
@@ -175,11 +174,11 @@ define "Symptomatic HIV Infection":
 define "Symptomatic HIV Infection Observation":
   Elements."Symptomatic HIV Infection Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() starts on or before AsOf
+      or O.effective.toInterval() starts on or before Today
 
 define "Symptomatic HIV Infection Condition":
   Elements."Symptomatic HIV Infection Condition" C
-    where C.prevalenceInterval() starts on or before AsOf
+    where C.prevalenceInterval() starts on or before Today
 
 /******************************
  * Test Results
@@ -188,7 +187,7 @@ define "Symptomatic HIV Infection Condition":
 define "Patient Birth Weight Observation":
   Elements."Patient Birth Weight Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() on or before AsOf
+      or O.effective.toInterval() on or before Today
 
 define "Patient Birth Weight Observation Value":
   Last(
@@ -200,19 +199,19 @@ define "Patient Birth Weight Observation Value":
  * @dataElement Patient age in years
  */
 define "Current Patient Age In Years":
-  AgeInYearsAt(AsOf)
+  AgeInYearsAt(Today)
 
 /** 
  * @dataElement Patient age in weeks
  */
 define "Current Patient Age In Weeks":
-  AgeInWeeksAt(AsOf)
+  AgeInWeeksAt(Today)
 
 /** 
  * @dataElement Patient age in months
  */
 define "Current Patient Age In Months":
-  AgeInMonthsAt(AsOf)
+  AgeInMonthsAt(Today)
 
 /** 
  * @dataElement Patient biological sex used for deciding vaccine eligibility
@@ -224,7 +223,7 @@ define "Patient Biological Sex":
 
 define "HAART Medication Administration":
   Elements."HAART Medication Administration" A
-    where A.effective.toInterval() starts less than 12 months before AsOf
+    where A.effective.toInterval() starts less than 12 months before Today
   
 define "Patient HAART Treatment Start Date":
   Last(
@@ -233,7 +232,7 @@ define "Patient HAART Treatment Start Date":
   ).effective.toInterval().low
 
 define "Patient HAART Treatment Started 6 to 12 Months Ago":
-  "Patient HAART Treatment Start Date" between AsOf - 12 months and AsOf - 6 months
+  "Patient HAART Treatment Start Date" between Today - 12 months and Today - 6 months
 
 /**
  * @dataElement The patient has a medication record which indicates that they are receiving ARV
@@ -253,11 +252,11 @@ define "HIV Status":
 define "HIV Status Observation":
   Elements."HIV Status Observation" O
     where O.encounter.references(EncounterId)
-      or O.effective.toInterval() starts on or before AsOf
+      or O.effective.toInterval() starts on or before Today
 
 define "Live vaccine dose":
   Elements."Live vaccine dose" V
-    where V.occurrence.toInterval() starts on or before AsOf
+    where V.occurrence.toInterval() starts on or before Today
 
 /*
   @dataElement Date and time of last live attenuated vaccine
@@ -268,7 +267,7 @@ define "Live Attenuated Vaccines":
 define "Date of Latest Live Attenuated Vaccine":
   Last(
     "Live Attenuated Vaccines" V
-      where V.occurrence.toInterval() starts on or before AsOf
+      where V.occurrence.toInterval() starts on or before Today
       sort by start of occurrence.toInterval()
   ).occurrence as FHIR.dateTime
 

input/cql/IMMZIND08Logic.cql

@@ -28,7 +28,6 @@ For this reason, this measure is modeled as a continuous variable measure where
 using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
 
 include IMMZCommon called Common
 include IMMZConcepts called Concepts

input/cql/IMMZIND12Logic.cql

@@ -16,7 +16,7 @@
  * 
  * References: WHO Immunization facility analysis guide;WHO Handbook on immunization data
  */
-library IMMZIND08Logic
+library IMMZIND12Logic
 
 /*
 NOTE: This is an estimated denominator measure, meaning that all we are contributing from the site perspective is a count
@@ -29,7 +29,6 @@ a measles containing vaccine.
 using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
 
 include IMMZCommon called Common
 include IMMZConcepts called Concepts

input/cql/IMMZIND13Logic.cql

@@ -16,7 +16,7 @@
  * 
  * References: WHO Immunization facility analysis guide;WHO Handbook on immunization data
  */
-library IMMZIND08Logic
+library IMMZIND13Logic
 
 /*
 NOTE: This is an estimated denominator measure, meaning that all we are contributing from the site perspective is a count
@@ -29,8 +29,8 @@ a measles containing vaccine.
 using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
 
+include WHOCommon called WC
 include IMMZCommon called Common
 include IMMZConcepts called Concepts
 include IMMZConfig called Config

input/cql/IMMZIndicatorElements.cql

@@ -7,7 +7,6 @@ library IMMZIndicatorElements
 using FHIR version '4.0.1'
 
 include FHIRHelpers version '4.0.1'
-include FHIRCommon called FC
 
 include WHOConcepts
 include WHOCommon called WC

input/fsh/plandefinitions/IMMZD2DTMeaslesDose0.fsh

@@ -13,6 +13,9 @@ Usage: #definition
 * status = #draft
 * experimental = false
 * publisher = "World Health Organization (WHO)"
+* relatedArtifact[+]
+  * type = #citation
+  * citation = "WHO recommendations for routine immunization - summary tables (March 2023)"
 * action[+]
   * title = "Immunize patient for Measles"
   * condition[+]
@@ -21,7 +24,10 @@ Usage: #definition
       * language = #text/cql-identifier
       * expression = "Measles Routine Immunization Schedule Incomplete"
   * action[+]
-    * title = "No MCV0 Doses Administered"
+    * extension[+]
+      * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-rationale"
+      * valueMarkdown = "Note: The countries should apply the national immunization policy for MCV0 dose and adjust this logic accordingly.<br/>A supplementary dose of MCV (recorded as MCV0) should be considered for infants known to be exposed (i.e. born to an HIV-infected woman) or soon after diagnosis of HIV infection in children older than 6 months who are not receiving HAART and for whom the risk of measles is high, with the aim of providing partial protection until they are revaccinated after immune reconstitution with HAART.<br/>In the following situations, a supplementary dose of MCV should be given to infants from 6 months of age:<br/>* (1) during a measles outbreak as part of intensified service delivery;<br/>* (2) during campaigns in settings where the risk of measles among infants < 9 months of age remains high (e.g. in endemic countries experiencing regular outbreaks);<br/>* (3) for internally displaced populations and refugees, and populations in conflict zones;<br/>* (4) for individual infants at high risk of contracting measles (e.g. contacts of known measles cases or in settings with increased risk of exposure during outbreaks such as day-care facilities);<br/>* (5)for infants travelling to countries experiencing measles outbreaks;<br/>* (6) infants known to be HIV-infected or exposed (i.e. born to an HIV-infected woman).<br/>In areas where there is a high incidence of both HIV infection and measles, an initial dose of MCV may be offered as early as age 6 months (recorded as MCV0). The 2 routine doses of MCV (MCV1 and MCV2) should then be administered to these children according to the national immunization schedule.<br/>As a general rule, live vaccines should be given either simultaneously or at intervals of 4 weeks. An exception to this rule is OPV, which can be given at any time before or after measles vaccination without interference in the response to either vaccine."
+    * title = "Consider MCV0 Dose"
     * condition[+]
       * kind = #applicability
       * expression

input/fsh/plandefinitions/IMMZD2DTMeaslesLT.fsh

@@ -13,6 +13,9 @@ Usage: #definition
 * status = #draft
 * experimental = false
 * publisher = "World Health Organization (WHO)"
+* relatedArtifact[+]
+  * type = #citation
+  * citation = "WHO recommendations for routine immunization - summary tables (March 2023)"
 * action[+]
   * title = "Immunize patient for Measles"
   * condition[+]
@@ -21,7 +24,10 @@ Usage: #definition
       * language = #text/cql-identifier
       * expression = "Measles Routine Immunization Schedule Incomplete"
   * action[+]
-    * title = "No Primary Series Doses Administered"
+    * extension[+]
+      * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-rationale"
+      * valueMarkdown = "In countries with low levels of measles transmission MCV1 may be administered at 12 months of age.<br/>As a general rule, live vaccines should be given either simultaneously or at intervals of 4 weeks. An exception to this rule is OPV, which can be given at any time before or after measles vaccination without interference in the response to either vaccine."
+    * title = "Provide primary series measles vaccination (MCV1)"
     * condition[+]
       * kind = #applicability
       * expression
@@ -53,7 +59,10 @@ Usage: #definition
           * expression = "Client Is Due For MCV1"
       * definitionCanonical = Canonical(IMMZD2DTMeaslesMR)
   * action[+]
-    * title = "Number Of Primary Series Doses Administered = 1"
+    * extension[+]
+      * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-rationale"
+      * valueMarkdown = "In countries with low levels of measles transmission, administration of MCV2 at 15-18 months of age ensures early protection of the individual.<br/>The minimum interval between MCV1 and MCV2 is 4 weeks.<br/>As a general rule, live vaccines should be given either simultaneously or at intervals of 4 weeks. An exception to this rule is OPV, which can be given at any time before or after measles vaccination without interference in the response to either vaccine."
+    * title = "Provide primary series measles vaccination (MCV2)"
     * condition[+]
       * kind = #applicability
       * expression
@@ -85,7 +94,10 @@ Usage: #definition
           * expression = "Client Is Due For MCV2"
       * definitionCanonical = Canonical(IMMZD2DTMeaslesMR)
   * action[+]
-    * title = "Number Of Primary Series Doses Administered = 2"
+    * extension[+]
+      * url = "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-rationale"
+      * valueMarkdown = "An additional dose of MCV should be administered to HIV-infected children receiving HAART following immune reconstitution. If CD4+ T lymphocyte counts are monitored, an additional dose of MCV should be administered when immune reconstitution has been achieved, e.g. when the CD4+ T lymphocyte count reaches 20–25%. Where CD4+ T lymphocyte monitoring is not available, children should receive an additional dose of MCV 6–12 months after initiation of HAART."
+    * title = "Measles primary series is complete."
     * description = "Measles primary series is complete. Two measles primary series doses were administered. Check if a measles supplementary dose is appropriate for the client."
     * condition[+]
       * kind = #applicability