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Support FHIR R6 #2928

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8dc65c8
Extract Bundle Link Creation into a Function
alexanderkiel Aug 26, 2025
0d44c2d
Support FHIR R6
alexanderkiel Aug 19, 2025
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2 changes: 2 additions & 0 deletions .github/distributed-test/docker-compose.yml
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Expand Up @@ -110,6 +110,7 @@ services:
environment:
JAVA_TOOL_OPTIONS: "-Xmx2g"
STORAGE: "distributed"
FHIR_VERSION: "6.0.0-ballot3"
DB_KAFKA_BOOTSTRAP_SERVERS: "kafka:9092"
DB_KAFKA_MAX_REQUEST_SIZE: "10485760"
DB_KAFKA_SECURITY_PROTOCOL: "SSL"
Expand Down Expand Up @@ -144,6 +145,7 @@ services:
environment:
JAVA_TOOL_OPTIONS: "-Xmx2g"
STORAGE: "distributed"
FHIR_VERSION: "6.0.0-ballot3"
DB_KAFKA_BOOTSTRAP_SERVERS: "kafka:9092"
DB_KAFKA_MAX_REQUEST_SIZE: "10485760"
DB_KAFKA_SECURITY_PROTOCOL: "SSL"
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2 changes: 1 addition & 1 deletion .github/scripts/check-capability-statement-terminology-service.sh
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Expand Up @@ -10,7 +10,7 @@ test "status" "$(echo "$CAPABILITY_STATEMENT" | jq -r .status)" "active"
test "kind" "$(echo "$CAPABILITY_STATEMENT" | jq -r .kind)" "instance"
test "software name" "$(echo "$CAPABILITY_STATEMENT" | jq -r .software.name)" "Blaze"
test "URL" "$(echo "$CAPABILITY_STATEMENT" | jq -r .implementation.url)" "http://localhost:8080/fhir"
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "4.0.1"
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "6.0.0-ballot3"
test "format" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.format | join(",")')" "application/fhir+json,application/fhir+xml"

test "Operation CodeSystem \$validate-code Definition" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "CodeSystem") .operation[] | select(.name == "validate-code") | .definition')" "http://hl7.org/fhir/OperationDefinition/CodeSystem-validate-code"
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2 changes: 1 addition & 1 deletion .github/scripts/check-capability-statement.sh
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Expand Up @@ -10,7 +10,7 @@ test "status" "$(echo "$CAPABILITY_STATEMENT" | jq -r .status)" "active"
test "kind" "$(echo "$CAPABILITY_STATEMENT" | jq -r .kind)" "instance"
test "software name" "$(echo "$CAPABILITY_STATEMENT" | jq -r .software.name)" "Blaze"
test "URL" "$(echo "$CAPABILITY_STATEMENT" | jq -r .implementation.url)" "http://localhost:8080/fhir"
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "4.0.1"
test "FHIR version" "$(echo "$CAPABILITY_STATEMENT" | jq -r .fhirVersion)" "6.0.0-ballot3"
test "format" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.format | join(",")')" "application/fhir+json,application/fhir+xml"

test "Patient Profile" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Patient") .profile')" "http://hl7.org/fhir/StructureDefinition/Patient"
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4 changes: 0 additions & 4 deletions .github/scripts/check-frontend.sh
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Expand Up @@ -58,7 +58,3 @@ CONTENT_TYPE_HEADER=$(echo "$HEADERS" | grep -iv 'X-Content-Type-Options' | grep

test "status code" "$STATUS_CODE" "200"
test "Content-Type header" "$CONTENT_TYPE_HEADER" "application/fhir+xml;charset=utf-8"

echo "check Encounter supported profile..."
CAPABILITY_STATEMENT=$(curl -sL --cacert "$CA_CERT_BLAZE" --oauth2-bearer "$ACCESS_TOKEN" -H 'Accept: application/fhir+json' "$BASE/metadata")
test "Encounter Supported Profile" "$(echo "$CAPABILITY_STATEMENT" | jq -r '.rest[0].resource[] | select(.type == "Encounter") .supportedProfile[0]')" "https://www.medizininformatik-initiative.de/fhir/core/modul-fall/StructureDefinition/KontaktGesundheitseinrichtung|2025.0.0"
20 changes: 1 addition & 19 deletions .github/scripts/check-resource-totals-after-patient-purge.sh
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Expand Up @@ -6,30 +6,12 @@ SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
BASE="http://localhost:8080/fhir"
ACTUAL_TOTALS="$(curl -sH 'Accept: application/fhir+json' "$BASE/\$totals" | jq -r '.parameter[] | [.name, .valueUnsignedInt] | @csv')"
EXPECTED_TOTALS="$(cat <<END
"AllergyIntolerance",2
"CarePlan",33
"CareTeam",33
"Claim",1053
"Condition",157
"Device",28
"DiagnosticReport",1113
"DocumentReference",407
"Encounter",407
"ExplanationOfBenefit",407
"Immunization",104
"Location",194
"Medication",326
"MedicationAdministration",26
"MedicationRequest",646
"Observation",6944
"Organization",194
"Patient",8
"Practitioner",195
"PractitionerRole",195
"Procedure",307
"Provenance",8
"StructureDefinition",185
"SupplyDelivery",571
"StructureDefinition",204
END
)"

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5 changes: 1 addition & 4 deletions .github/scripts/check-resource-totals.sh
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Expand Up @@ -11,16 +11,13 @@ EXPECTED_TOTALS="$(cat <<END
"CareTeam",540
"Claim",9856
"Condition",1597
"Device",28
"DiagnosticReport",8229
"DocumentReference",4769
"Encounter",4769
"ExplanationOfBenefit",4769
"ImagingStudy",145
"Immunization",1616
"Location",194
"Medication",326
"MedicationAdministration",326
"MedicationRequest",5087
"Observation",42929
"Organization",194
Expand All @@ -29,7 +26,7 @@ EXPECTED_TOTALS="$(cat <<END
"PractitionerRole",195
"Procedure",3608
"Provenance",120
"StructureDefinition",185
"StructureDefinition",204
"SupplyDelivery",1886
END
)"
Expand Down
2 changes: 1 addition & 1 deletion .github/scripts/graph.sh
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Expand Up @@ -14,7 +14,7 @@ BUNDLE=$(curl -sH 'Accept: application/fhir+json' "$BASE/Patient/$PATIENT_ID/\$g
ACTUAL_SIZE=$(echo "$BUNDLE" | jq -r .total)
IDS="$(echo "$BUNDLE" | jq -r '.entry[].resource.id')"

test "size" "$ACTUAL_SIZE" "195"
test "size" "$ACTUAL_SIZE" "150"

test "no duplicates" "$(echo "$IDS" | sort -u | wc -l | xargs)" "$(echo "$IDS" | wc -l | xargs)"

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250 changes: 46 additions & 204 deletions .github/scripts/graph/GraphDefinition-patient-observation-encounter.json
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@@ -1,242 +1,84 @@
{
"resourceType": "GraphDefinition",
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.start",
"valueId": "patient"
},
"url": "patient-observation-encounter",
"name": "patient-observation-encounter",
"status": "active",
"start": "patient",
"node": [
{
"extension": [
{
"url": "nodeId",
"valueId": "patient"
},
{
"url": "type",
"valueCode": "Patient"
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
"nodeId": "patient",
"type": "Patient"
},
{
"extension": [
{
"url": "nodeId",
"valueId": "viral-sinusitis"
},
{
"url": "type",
"valueCode": "Condition"
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
"nodeId": "viral-sinusitis",
"type": "Condition"
},
{
"extension": [
{
"url": "nodeId",
"valueId": "cisplatin-reason"
},
{
"url": "type",
"valueCode": "Condition"
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
"nodeId": "cisplatin-reason",
"type": "Condition"
},
{
"extension": [
{
"url": "nodeId",
"valueId": "leukocytes"
},
{
"url": "type",
"valueCode": "Observation"
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
"nodeId": "leukocytes",
"type": "Observation"
},
{
"extension": [
{
"url": "nodeId",
"valueId": "erythrocytes"
},
{
"url": "type",
"valueCode": "Observation"
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
"nodeId": "erythrocytes",
"type": "Observation"
},
{
"extension": [
{
"url": "nodeId",
"valueId": "cisplatin"
},
{
"url": "type",
"valueCode": "MedicationAdministration"
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
"nodeId": "cisplatin",
"type": "MedicationAdministration"
},
{
"extension": [
{
"url": "nodeId",
"valueId": "encounter"
},
{
"url": "type",
"valueCode": "Encounter"
}
],
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.node"
"nodeId": "encounter",
"type": "Encounter"
}
],
"url": "patient-observation-encounter",
"name": "patient-observation-encounter",
"status": "active",
"_start": {
"extension": [
{
"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
"valueCode": "unsupported"
}
]
},
"link": [
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "patient"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "viral-sinusitis"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
"valueString": "patient={ref}&code=http://snomed.info/sct|444814009"
}
]
"sourceId": "patient",
"targetId": "viral-sinusitis",
"params": "patient={ref}&code=http://snomed.info/sct|444814009"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "patient"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "leukocytes"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
"valueString": "patient={ref}&code=http://loinc.org|6690-2"
}
]
"sourceId": "patient",
"targetId": "leukocytes",
"params": "patient={ref}&code=http://loinc.org|6690-2"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "patient"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "erythrocytes"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
"valueString": "patient={ref}&code=http://loinc.org|789-8"
}
]
"sourceId": "patient",
"targetId": "erythrocytes",
"params": "patient={ref}&code=http://loinc.org|789-8"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "patient"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "cisplatin"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.params",
"valueString": "patient={ref}&code=http://www.nlm.nih.gov/research/umls/rxnorm|1736854"
}
]
"sourceId": "patient",
"targetId": "cisplatin",
"params": "patient={ref}&code=http://www.nlm.nih.gov/research/umls/rxnorm|1736854"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "viral-sinusitis"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "encounter"
}
],
"path": "encounter"
"sourceId": "viral-sinusitis",
"path": "encounter",
"targetId": "encounter"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "leukocytes"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "encounter"
}
],
"path": "encounter"
"sourceId": "leukocytes",
"path": "encounter",
"targetId": "encounter"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "erythrocytes"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "encounter"
}
],
"path": "encounter"
"sourceId": "erythrocytes",
"path": "encounter",
"targetId": "encounter"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "cisplatin"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "encounter"
}
],
"path": "context"
"sourceId": "cisplatin",
"path": "context",
"targetId": "encounter"
},
{
"extension": [
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.sourceId",
"valueId": "cisplatin"
},
{
"url": "http://hl7.org/fhir/5.0/StructureDefinition/extension-GraphDefinition.link.targetId",
"valueId": "cisplatin-reason"
}
],
"path": "reason"
"sourceId": "cisplatin",
"path": "reason",
"targetId": "cisplatin-reason"
}
]
}
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