Merge pull request #869 from samply/release-v0.18.5

Release v0.18.5

.github/scripts/chaining-without-referential-integrity.sh

@@ -0,0 +1,15 @@
+#!/bin/bash -e
+
+BASE="http://localhost:8080/fhir"
+
+curl -sXPUT -d '{"resourceType": "Observation", "id": "0", "subject": {"reference": "Patient/0"}}' -H 'Content-Type: application/fhir+json' "$BASE/Observation/0" > /dev/null
+curl -sXPUT -d '{"resourceType" : "Patient", "id": "0", "gender": "male"}' -H 'Content-Type: application/fhir+json' "$BASE/Patient/0" > /dev/null
+
+RESULT="$(curl -sH 'Prefer: handling=strict' -H 'Accept: application/fhir+json' "$BASE/Observation?patient.gender=male&_summary=count" | jq -r '.total')"
+
+if [ "$RESULT" = "1" ]; then
+  echo "Success: chaining works"
+else
+  echo "Fail: chaining doesn't work"
+  exit 1
+fi

.github/scripts/check-capability-statement.sh

@@ -1,10 +1,8 @@
 #!/bin/bash -e
 
-SOFTWARE_NAME=$(curl -s http://localhost:8080/fhir/metadata | jq -r .software.name)
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
 
-if [ "Blaze" = "$SOFTWARE_NAME" ]; then
-  echo "Success"
-else
-  echo "Fail"
-  exit 1
-fi
+BASE="http://localhost:8080/fhir"
+
+test "software name" "$(curl -s "$BASE/metadata" | jq -r .software.name)" "Blaze"

.github/scripts/check-total-number-of-resources.sh

@@ -1,10 +1,6 @@
 #!/bin/bash -e
 
-TOTAL=$(curl -s http://localhost:8080/fhir | jq -r .total)
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
 
-if [ "$1" = "$TOTAL" ]; then
-  echo "Success"
-else
-  echo "Fail: total number of resources was $TOTAL but should be $1"
-  exit 1
-fi
+test "total number of resources" "$(curl -s http://localhost:8080/fhir | jq -r .total)" "$1"

.github/scripts/conditional-create.sh

@@ -34,7 +34,7 @@ STATUS=$(curl -sH "Content-Type: application/fhir+json" \
   -d "$(bundle)" "$BASE" | jq -r '.entry[].response.status')
 
 if [ "$STATUS" = "201" ]; then
-  echo "OK: first atempt created the Organization"
+  echo "OK: first attempt created the Organization"
 else
   echo "Fail: status was ${STATUS} but should be 201"
   exit 1
@@ -44,7 +44,7 @@ STATUS=$(curl -sH "Content-Type: application/fhir+json" \
   -d "$(bundle)" "$BASE" | jq -r '.entry[].response.status')
 
 if [ "$STATUS" = "200" ]; then
-  echo "OK: second atempt returned the already created Organization"
+  echo "OK: second attempt returned the already created Organization"
 else
   echo "Fail: status was ${STATUS} but should be 200"
   exit 1

.github/scripts/conditional-update-if-none-match.sh

@@ -0,0 +1,22 @@
+#!/bin/bash -e
+
+#
+# This script first creates a patient and expects the conditional update with
+# If-None-Match=* to fail afterwards.
+#
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+BASE="http://localhost:8080/fhir"
+PATIENT_ID=$(curl -sH "Content-Type: application/fhir+json" \
+  -d '{"resourceType": "Patient"}' "$BASE/Patient" | jq -r .id)
+
+PATIENT="{\"resourceType\": \"Patient\", \"id\": \"$PATIENT_ID\"}"
+RESULT=$(curl -sXPUT -H "Content-Type: application/fhir+json" -H "If-None-Match: *" \
+  -d "$PATIENT" "$BASE/Patient/$PATIENT_ID")
+
+test "resource type" "$(echo "$RESULT" | jq -r .resourceType)" "OperationOutcome"
+test "severity" "$(echo "$RESULT" | jq -r .issue[0].severity)" "error"
+test "code" "$(echo "$RESULT" | jq -r .issue[0].code)" "conflict"
+test "diagnostics" "$(echo "$RESULT" | jq -r .issue[0].diagnostics)" "Resource \`Patient/$PATIENT_ID\` already exists."

.github/scripts/cql/q1.yml

@@ -0,0 +1,5 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q1.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation

.github/scripts/cql/q14.yml

@@ -0,0 +1,5 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q14.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation

.github/scripts/cql/q15.yml

@@ -0,0 +1,5 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q15.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation

.github/scripts/cql/q17.yml

@@ -0,0 +1,5 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q17.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation

.github/scripts/cql/q19-stratifier-ageclass.csv

@@ -0,0 +1,11 @@
+"0",7
+"10",15
+"100",3
+"20",13
+"30",10
+"40",13
+"50",19
+"60",15
+"70",16
+"80",2
+"90",7

.github/scripts/cql/q19-stratifier-ageclass.yml

@@ -0,0 +1,8 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q19-stratifier-ageclass.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation
+  stratifier:
+  - code: ageclass
+    expression: AgeClass

.github/scripts/cql/q2.yml

@@ -0,0 +1,5 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q2.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation

.github/scripts/cql/q20-stratifier-city.csv

@@ -0,0 +1,68 @@
+"Abington",1
+"Acton",1
+"Acushnet",1
+"Adams",1
+"Amherst",1
+"Arlington",1
+"Attleboro",2
+"Auburn",1
+"Barnstable",2
+"Billerica",1
+"Boston",8
+"Boxborough",1
+"Brimfield",1
+"Brockton",1
+"Cambridge",1
+"Charlton",1
+"Chelsea",2
+"Concord",1
+"Dracut",2
+"East Douglas",7
+"East Sandwich",1
+"Easton",3
+"Everett",1
+"Fall River",1
+"Foxborough",1
+"Framingham",1
+"Grafton",1
+"Greenfield",1
+"Hampden",1
+"Harvard",1
+"Haverhill",1
+"Hingham",1
+"Hudson",1
+"Lancaster",1
+"Lawrence",1
+"Lexington",3
+"Ludlow",2
+"Marlborough",3
+"Medford",2
+"Methuen",1
+"Milford",1
+"Nantucket",1
+"New Bedford",1
+"Newton",4
+"North Andover",1
+"Norwood",3
+"Peabody",1
+"Plymouth",3
+"Pocasset",1
+"Quincy",1
+"Rehoboth",3
+"Sandwich",3
+"Shrewsbury",1
+"Somerville",3
+"Springfield",3
+"Stoughton",1
+"Swampscott",1
+"Taunton",3
+"Topsfield",1
+"Upton",1
+"Walpole",1
+"Waltham",2
+"Watertown",1
+"Weymouth",1
+"Williamstown",1
+"Winchendon",1
+"Winchester",1
+"Worcester",10

.github/scripts/cql/q20-stratifier-city.yml

@@ -0,0 +1,8 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q20-stratifier-city.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation
+  stratifier:
+  - code: city
+    expression: City

.github/scripts/cql/q21-stratifier-city-of-only-women.csv

@@ -0,0 +1,41 @@
+"Acton",1
+"Acushnet",1
+"Adams",1
+"Amherst",1
+"Auburn",1
+"Barnstable",1
+"Billerica",1
+"Boston",5
+"Boxborough",1
+"Chelsea",1
+"Concord",1
+"East Douglas",7
+"Easton",3
+"Everett",1
+"Fall River",1
+"Foxborough",1
+"Framingham",1
+"Greenfield",1
+"Hampden",1
+"Harvard",1
+"Haverhill",1
+"Hingham",1
+"Hudson",1
+"Lancaster",1
+"Marlborough",1
+"New Bedford",1
+"Newton",1
+"Norwood",1
+"Peabody",1
+"Plymouth",2
+"Pocasset",1
+"Quincy",1
+"Rehoboth",3
+"Springfield",3
+"Stoughton",1
+"Taunton",2
+"Upton",1
+"Watertown",1
+"Winchendon",1
+"Winchester",1
+"Worcester",6

.github/scripts/cql/q21-stratifier-city-of-only-women.yml

@@ -0,0 +1,8 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q21-stratifier-city-of-only-women.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation
+  stratifier:
+  - code: city
+    expression: City

.github/scripts/cql/q26-stratifier-bmi.csv

@@ -0,0 +1,23 @@
+"15",4
+"16",5
+"17",4
+"18",2
+"19",2
+"20",3
+"21",4
+"22",5
+"23",3
+"24",3
+"25",3
+"26",3
+"27",11
+"28",22
+"29",26
+"30",8
+"31",5
+"32",1
+"35",1
+"39",2
+"40",1
+"41",1
+"null",1

.github/scripts/cql/q26-stratifier-bmi.yml

@@ -0,0 +1,8 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q26-stratifier-bmi.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation
+  stratifier:
+  - code: bmi
+    expression: Bmi

.github/scripts/cql/q27-stratifier-calculated-bmi.csv

@@ -0,0 +1,74 @@
+"15.0",1
+"15.6",1
+"15.7",1
+"16.1",1
+"16.2",1
+"16.7",1
+"16.9",2
+"17.0",1
+"17.7",1
+"17.8",1
+"17.9",1
+"18.3",1
+"18.8",1
+"19.3",1
+"19.4",1
+"19.8",1
+"19.9",1
+"21.2",2
+"21.4",1
+"21.9",1
+"22.6",1
+"22.7",1
+"23.1",1
+"23.2",2
+"23.8",1
+"24.1",1
+"24.3",1
+"24.7",1
+"24.9",1
+"25.4",2
+"25.8",1
+"26.2",1
+"26.3",1
+"26.4",1
+"26.5",1
+"27.2",2
+"27.3",2
+"27.4",6
+"27.5",4
+"27.6",3
+"27.7",2
+"27.8",8
+"27.9",3
+"28.0",2
+"28.1",1
+"28.2",3
+"28.4",1
+"28.5",1
+"28.6",1
+"28.7",1
+"28.8",2
+"29.0",2
+"29.1",1
+"29.7",2
+"29.8",1
+"29.9",1
+"30.0",1
+"30.1",2
+"30.2",5
+"30.3",5
+"30.4",3
+"30.5",4
+"30.6",1
+"30.8",1
+"30.9",1
+"31.5",1
+"31.7",1
+"34.1",1
+"34.2",1
+"35.8",1
+"38.5",1
+"38.6",1
+"40.1",1
+"41.4",1

.github/scripts/cql/q27-stratifier-calculated-bmi.yml

@@ -0,0 +1,8 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q27-stratifier-calculated-bmi.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation
+  stratifier:
+  - code: bmi
+    expression: Bmi

.github/scripts/cql/q32-stratifier-underweight.csv

@@ -0,0 +1 @@
+"false",120

.github/scripts/cql/q32-stratifier-underweight.yml

@@ -0,0 +1,8 @@
+library: modules/operation-measure-evaluate-measure/test/blaze/fhir/operation/evaluate_measure/q32-stratifier-underweight.cql
+group:
+- type: Patient
+  population:
+  - expression: InInitialPopulation
+  stratifier:
+  - code: underweight
+    expression: Underweight