From f94dc0b6654a1b9f0fca4029277218abfe5253b7 Mon Sep 17 00:00:00 2001
From: Richard Stanley <2528387+citizenrich@users.noreply.github.com>
Date: Mon, 10 Jul 2023 11:51:05 -0400
Subject: [PATCH] fix build errors, update load script

---
 input/cql/Debug.cql       |  6 +++++
 input/fsh/measure.fsh     | 52 ++++++++++++++++++++++++++++-----------
 input/fsh/terminology.fsh |  1 +
 input/fsh/test-ciel0.fsh  |  6 ++++-
 test/scripts/_runload.sh  | 27 ++++++++++----------
 5 files changed, 63 insertions(+), 29 deletions(-)

diff --git a/input/cql/Debug.cql b/input/cql/Debug.cql
index 74d668289..06b969348 100644
--- a/input/cql/Debug.cql
+++ b/input/cql/Debug.cql
@@ -12,6 +12,12 @@ parameter "Measurement Period" Interval<DateTime> default Interval[@1990-01-01T,
 context Patient
 
 
+
+define "Exists Patient":
+  exists ["Patient"] P
+
+
+
 define "Deceased":
   Patient.deceased is not null 
   and (Patient.deceased is true or Patient.deceased before end of "Measurement Period")
diff --git a/input/fsh/measure.fsh b/input/fsh/measure.fsh
index 1256fbe84..769f060c5 100644
--- a/input/fsh/measure.fsh
+++ b/input/fsh/measure.fsh
@@ -93,19 +93,41 @@ Description: "MERTXCURR"
 * insert common-numonly
 
 
-Instance: MERDebug
-InstanceOf: Measure
-Title: "MERDebug"
-Description: "MERDebug"
-* id = "MERDebug"
-* insert meas-common
-* name = "MERDebug"
-* title = "MERDebug"
-* description = "MERDebug"
-* url = "https://path-global-health.github.io/MERindicators/Measure/MERDebug"
-* identifier[0].value = "MERDebug"
-// only numerator
-* scoring = $measure-scoring#cohort
-* library[+] = Canonical(Debug)
-* insert common-numonly
+// Not using for now, will try evaluate library:
+// https://build.fhir.org/ig/HL7/cqf-recommendations/OperationDefinition-cpg-library-evaluate.html
+
+// Instance: MERDebug
+// InstanceOf: Measure
+// Title: "MERDebug"
+// Description: "MERDebug"
+// * id = "MERDebug"
+// * insert meas-common
+// * name = "MERDebug"
+// * title = "MERDebug"
+// * description = "MERDebug"
+// * url = "https://path-global-health.github.io/MERindicators/Measure/MERDebug"
+// * identifier[0].value = "MERDebug"
+// // only numerator
+// * scoring = $measure-scoring#cohort
+// * library[+] = Canonical(Debug)
+// * group[+]
+//   * code = $OpenHIE#cohort "cohort"
+//   * population[+]
+//     * description = "Initial Population"
+//     * code = $measure-population#initial-population
+//     * criteria.language = #text/cql
+//     * criteria.expression = "Initial Population"
+//   * population[+]
+//     * description = "Numerator-Exclusion"
+//     * code = $measure-population#numerator-exclusion
+//     * criteria.language = #text/cql
+//     * criteria.expression = "Numerator-Exclusion"
+//   * population[+]
+//     * description = "Numerator"
+//     * code = $measure-population#numerator
+//     * criteria.language = #text/cql
+//     * criteria.expression = "Numerator"
+  // * stratifier[+]
+  //   * criteria.language = #text/cql
+  //   * criteria.expression = "Stratifier"
 
diff --git a/input/fsh/terminology.fsh b/input/fsh/terminology.fsh
index 148bc961d..463924797 100644
--- a/input/fsh/terminology.fsh
+++ b/input/fsh/terminology.fsh
@@ -42,6 +42,7 @@ Description: "Columbia International eHealth Laboratory (CIEL)"
 * #1434 "Currently pregnant" // boolean
 * #138405 "Human immunodeficiency virus (HIV) disease" // coded
 * #160119 "CURRENTLY TAKING ARV" // q&a
+* #116128 "Malaria" // For tests from OMRS IG
 // WIP
 * #86663 "Zidovudine"
 * #74807 "Didanosine"
diff --git a/input/fsh/test-ciel0.fsh b/input/fsh/test-ciel0.fsh
index 0d86d1899..5fa09eb49 100644
--- a/input/fsh/test-ciel0.fsh
+++ b/input/fsh/test-ciel0.fsh
@@ -8,7 +8,11 @@ Description: "PatientCIEL"
 * gender = #female
 * birthDate = "1985-01-01"
 * identifier.use = #official
-* identifier.extension[OMRSPatientIdentifierLocationExtension].valueReference = Reference(LocationCIEL)
+// * identifier.extension[OMRSPatientIdentifierLocationExtension].url = "http://fhir.openmrs.org/ext/patient/identifier#location"
+// * identifier.extension[OMRSPatientIdentifierLocationExtension].valueReference = Reference(LocationCIEL)
+// have to fix the openmrs ig patient.identififer.extension.url until its fixed in that ig
+* identifier.extension.url = "http://fhir.openmrs.org/ext/patient/identifier#location"
+* identifier.extension.valueReference = Reference(LocationCIEL)
   * type = "Location"
   * display = "Inpatient Ward"
 * identifier.type = http://terminology.hl7.org/CodeSystem/v2-0203#MR
diff --git a/test/scripts/_runload.sh b/test/scripts/_runload.sh
index 9f577fba3..d3b958698 100755
--- a/test/scripts/_runload.sh
+++ b/test/scripts/_runload.sh
@@ -14,20 +14,21 @@ export FHIR="http://localhost:8080/fhir"
 # export FHIR="http://ryzen.local:8080/fhir"
 
 export HEADER="Content-Type: application/fhir+json"
-export output="../../../output"
-export OUTPUT="@../../../output"
+export output="../../output"
+export OUTPUT="@../../output"
+export SCRIPTS="../test/scripts"
 
-function confirmation {
-    printf '\nDo you wish to continue (y/n)? '
-    read answer
+# function confirmation {
+#     printf '\nDo you wish to continue (y/n)? '
+#     read answer
 
-    if [ "$answer" != "${answer#[Yy]}" ] ;then 
-        echo ""
-    else
-        echo ""
-        exit
-    fi
-}
+#     if [ "$answer" != "${answer#[Yy]}" ] ;then 
+#         echo ""
+#     else
+#         echo ""
+#         exit
+#     fi
+# }
 
 function Loader() {
     cd ${output}
@@ -38,7 +39,7 @@ function Loader() {
         curl -s -X PUT -H "$HEADER" --data @${FILE} $FHIR/$1/${EYED} | jq .
 
     done
-    cd ../input/tests/server
+    cd ${SCRIPTS}
 }
 
 # on some servers this isn't needed, but it is included here