[WIP] Switch to Internal Resource Identifier in the Index

.github/distributed-test/docker-compose.yml

@@ -1,4 +1,3 @@
-version: '3.7'
 services:
   zookeeper:
     image: "docker.io/bitnami/zookeeper:3"
@@ -65,7 +64,7 @@ services:
       HEAP_NEWSIZE: "100M"
 
   blaze-1:
-    image: "ghcr.io/samply/blaze:sha-${GITHUB_SHA}"
+    image: "blaze:latest"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx512m"
       STORAGE: "distributed"
@@ -92,9 +91,10 @@ services:
     - kafka-topic-creator
     - cassandra-1
     - cassandra-2
+    restart: unless-stopped
 
   blaze-2:
-    image: "ghcr.io/samply/blaze:sha-${GITHUB_SHA}"
+    image: "blaze:latest"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx512m"
       STORAGE: "distributed"
@@ -121,6 +121,7 @@ services:
     - kafka-topic-creator
     - cassandra-1
     - cassandra-2
+    restart: unless-stopped
 
   ingress:
     image: "haproxy:2.3"

.github/doc-copy-data-test/docker-compose.override.yml

@@ -0,0 +1,6 @@
+services:
+  src:
+    image: "blaze:latest"
+
+  dst:
+    image: "blaze:latest"

.github/openid-auth-test/docker-compose.yml

@@ -1,4 +1,3 @@
-version: '3.7'
 services:
   keycloak:
     image: "jboss/keycloak:15.0.2"
@@ -12,7 +11,7 @@ services:
     - "${GITHUB_WORKSPACE}/.github/openid-auth-test/realm.json:/tmp/realm.json"
 
   blaze:
-    image: "ghcr.io/samply/blaze:sha-${GITHUB_SHA}"
+    image: "blaze:latest"
     environment:
       JAVA_TOOL_OPTIONS: "-Xmx2g"
       OPENID_PROVIDER_URL: "http://keycloak:8080/auth/realms/blaze"

.github/scripts/batch-metadata.sh

@@ -0,0 +1,57 @@
+#!/bin/bash -e
+
+#
+# This script fetches the CapabilityStatement through a batch request.
+#
+
+BASE="http://localhost:8080/fhir"
+
+bundle() {
+cat <<END
+{
+  "resourceType": "Bundle",
+  "type": "batch",
+  "entry": [
+    {
+      "request": {
+        "method": "GET",
+        "url": "metadata"
+      }
+    }
+  ]
+}
+END
+}
+RESULT=$(curl -sH "Content-Type: application/fhir+json" -d "$(bundle)" "$BASE")
+
+RESOURCE_TYPE="$(echo "$RESULT" | jq -r .resourceType)"
+if [ "$RESOURCE_TYPE" = "Bundle" ]; then
+  echo "OK: the resource type is Bundle"
+else
+  echo "Fail: the resource type is $RESOURCE_TYPE, expected Bundle"
+  exit 1
+fi
+
+BUNDLE_TYPE="$(echo "$RESULT" | jq -r .type)"
+if [ "$BUNDLE_TYPE" = "batch-response" ]; then
+  echo "OK: the bundle type is batch-response"
+else
+  echo "Fail: the bundle type is $BUNDLE_TYPE, expected batch-response"
+  exit 1
+fi
+
+RESPONSE_STATUS="$(echo "$RESULT" | jq -r .entry[].response.status)"
+if [ "$RESPONSE_STATUS" = "200" ]; then
+  echo "OK: the response status is 200"
+else
+  echo "Fail: the response status is $RESPONSE_STATUS, expected 200"
+  exit 1
+fi
+
+RESPONSE_RESOURCE_TYPE="$(echo "$RESULT" | jq -r .entry[].resource.resourceType)"
+if [ "$RESPONSE_RESOURCE_TYPE" = "CapabilityStatement" ]; then
+  echo "OK: resource type is CapabilityStatement"
+else
+  echo "Fail: resource type was $RESPONSE_RESOURCE_TYPE but should be CapabilityStatement"
+  exit 1
+fi

.github/scripts/batch.sh

@@ -55,6 +55,6 @@ RESPONSE_PATIENT_ID="$(echo "$RESULT" | jq -r .entry[].resource.id)"
 if [ "$RESPONSE_PATIENT_ID" = "$PATIENT_ID" ]; then
   echo "OK: patient id's match"
 else
-  echo "Fail: response patient id was $RESPONSE_PATIENT_ID but should be $RESPONSE_PATIENT_ID"
+  echo "Fail: response patient id was $RESPONSE_PATIENT_ID but should be $PATIENT_ID"
   exit 1
 fi

.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/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