Validation Support for Resources

.github/scripts/validation-patient.sh

@@ -0,0 +1,150 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+. "$SCRIPT_DIR/util.sh"
+
+patient-valid-no-profile() {
+cat <<END
+{
+  "resourceType": "Patient"
+}
+END
+}
+
+patient-invalid-with-profile() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "meta": {
+    "profile": "http://example.org/url-114730"
+  }
+}
+END
+}
+
+patient-valid-with-profile() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "active": true,
+  "meta": {
+    "profile": "http://example.org/url-114730"
+  }
+}
+END
+}
+
+patient-valid-with-profile-as-bundle() {
+cat <<END
+{
+  "resourceType": "Patient",
+  "active": true,
+  "meta": {
+    "profile": "http://example.org/url-114730"
+  }
+}
+END
+}
+
+bundle-valid-patient-with-profile() {
+cat <<END
+{ 
+  "resourceType": "Bundle",
+  "type": "transaction",
+  "entry": [
+    {
+      "resource": $(patient-valid-with-profile),
+      "request": {
+        "method": "POST",
+        "url": "/Patient"
+      }
+    }
+  ]
+}
+END
+}
+
+structure-definition-patient() {
+cat <<END
+{
+    "resourceType": "StructureDefinition",
+    "name": "Patient-profile-1",
+    "status": "active",
+    "kind": "resource",
+    "abstract": false,
+    "url": "http://example.org/url-114730",
+    "type": "Patient",
+    "baseDefinition": "http://hl7.org/fhir/StructureDefinition/Patient",
+    "derivation": "constraint",
+    "differential": {
+        "element": [
+            {
+                "id": "patient-active-rule",
+                "path": "Patient.active",
+                "mustSupport": true,
+                "min": 1
+            }
+        ]
+    }
+}
+END
+}
+
+BASE="http://localhost:8080/fhir"
+
+echo "1: testing before Patient profile created"
+
+echo "testing valid patient without profile"
+RESULT_NO_PROFILE=$(patient-valid-no-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/Patient")
+test "resource type" "$(echo "$RESULT_NO_PROFILE" | jq -r .resourceType)" "Patient"
+
+echo "testing invalid patient with profile"
+RESULT_INVALID_WITH_PROFILE=$(patient-invalid-with-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/Patient")
+test "resource type" "$(echo "$RESULT_INVALID_WITH_PROFILE" | jq -r .resourceType)" "OperationOutcome"
+test "issue diagnostics" "$(echo "$RESULT_INVALID_WITH_PROFILE" | jq -r .issue[0].diagnostics)" "Profile reference 'http://example.org/url-114730' has not been checked because it could not be found"
+
+echo "testing valid patient with profile"
+RESULT_VALID_WITH_PROFILE=$(patient-valid-with-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/Patient")
+test "resource type" "$(echo "$RESULT_VALID_WITH_PROFILE" | jq -r .resourceType)" "OperationOutcome"
+test "issue diagnostics" "$(echo "$RESULT_VALID_WITH_PROFILE" | jq -r .issue[0].diagnostics)" "Profile reference 'http://example.org/url-114730' has not been checked because it could not be found"
+
+echo "testing valid patient with profile as bundle"
+RESULT_BUNDLE_VALID_WITH_PROFILE=$(bundle-valid-patient-with-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE")
+test "resource type" "$(echo "$RESULT_VALID_WITH_PROFILE" | jq -r .resourceType)" "OperationOutcome"
+test "issue diagnostics" "$(echo "$RESULT_VALID_WITH_PROFILE" | jq -r .issue[0].diagnostics)" "Profile reference 'http://example.org/url-114730' has not been checked because it could not be found"
+
+echo "2: creating the patient profile"
+RESULT_STRUCTURE_DEFINITION=$(structure-definition-patient | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/StructureDefinition")
+test "resource type" "$(echo "$RESULT_STRUCTURE_DEFINITION" | jq -r .resourceType)" "StructureDefinition"
+STRUCTURE_DEFINITION_ID=$(echo "$RESULT_STRUCTURE_DEFINITION" | jq -r .id)
+
+sleep 1
+echo "3: testing after Patient profile created"
+echo "testing valid patient without profile"
+RESULT_NO_PROFILE=$(patient-valid-no-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/Patient")
+test "resource type" "$(echo "$RESULT_NO_PROFILE" | jq -r .resourceType)" "Patient"
+
+echo "testing invalid patient with profile"
+RESULT_INVALID_WITH_PROFILE=$(patient-invalid-with-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/Patient")
+test "resource type" "$(echo "$RESULT_INVALID_WITH_PROFILE" | jq -r .resourceType)" "OperationOutcome"
+test "issue diagnostics" "$(echo "$RESULT_INVALID_WITH_PROFILE" | jq -r .issue[0].diagnostics)" "Patient.active: minimum required = 1, but only found 0 (from http://example.org/url-114730)"
+
+echo "testing valid patient with profile"
+RESULT_VALID_WITH_PROFILE=$(patient-valid-with-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/Patient")
+test "resource type" "$(echo "$RESULT_VALID_WITH_PROFILE" | jq -r .resourceType)" "Patient"
+
+echo "testing valid patient with profile as bundle"
+RESULT_BUNDLE_VALID_WITH_PROFILE=$(bundle-valid-patient-with-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE")
+echo "$RESULT_BUNDLE_VALID_WITH_PROFILE"
+test "resource type" "$(echo "$RESULT_BUNDLE_VALID_WITH_PROFILE" | jq -r .resourceType)" "Bundle"
+test "response status" "$(echo "$RESULT_BUNDLE_VALID_WITH_PROFILE" | jq -r .entry[0].response.status)" "201"
+
+sleep 1
+echo "4: deleting Patient profile and testing invalid again"
+RESULT_STRUCTURE_DEFINITION_DELETE=$(structure-definition-patient | curl -s -X DELETE -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/StructureDefinition/$STRUCTURE_DEFINITION_ID")
+test "delete response is empty" "$RESULT_STRUCTURE_DEFINITION_DELETE" ""
+
+echo "testing invalid patient with profile"
+RESULT_INVALID_WITH_PROFILE=$(patient-invalid-with-profile | curl -s -H 'Accept: application/fhir+json' -H "Content-Type: application/fhir+json" -d @- "$BASE/Patient")
+test "resource type" "$(echo "$RESULT_INVALID_WITH_PROFILE" | jq -r .resourceType)" "OperationOutcome"
+test "issue diagnostics" "$(echo "$RESULT_INVALID_WITH_PROFILE" | jq -r .issue[0].diagnostics)" "Profile reference 'http://example.org/url-114730' has not been checked because it could not be found"

.github/test-data/Makefile

@@ -8,8 +8,20 @@ kds-testdata-2024.0.1/tx: kds-testdata-2024.0.1
 	mkdir kds-testdata-2024.0.1/tx
 	cp kds-testdata-2024.0.1/resources/Bundle-mii-exa-test-data-bundle.json kds-testdata-2024.0.1/tx
 
+kds-testdata-2025.0.0.zip:
+	wget -q https://github.com/medizininformatik-initiative/mii-testdata/releases/download/v2025.0.0-dev.7/kds-testdata-2025.0.0-20251021-124316.zip
+
+kds-testdata-2025.0.0: kds-testdata-2025.0.0.zip
+	unzip kds-testdata-2025.0.0-20251021-124316.zip
+
+kds-testdata-2025.0.0/tx: kds-testdata-2025.0.0
+	mkdir kds-testdata-2025.0.0/tx
+	cp kds-testdata-2025.0.0-20251021-124316/resources/Bundle-mii-exa-test-data-bundle-pat-1.json kds-testdata-2025.0.0/tx
+
 clean:
 	rm -rf kds-testdata-2024.0.1
 	rm kds-testdata-2024.0.1.zip
+	rm -rf kds-testdata-2025.0.0
+	rm kds-testdata-2025.0.0-20251021-124316.zip
 
 .PHONY: clean

.github/validation/.gitignore

@@ -0,0 +1 @@
+node_modules

.github/validation/package.json

@@ -0,0 +1,27 @@
+{
+  "dependencies": {
+    "de.basisprofil.r4": "^1.5.4",
+    "de.einwilligungsmanagement": "^2.0.1",
+    "de.gematik.isik-basismodul": "^4.0.3",
+    "de.medizininformatikinitiative.kerndatensatz.bildgebung": "^2026.0.0-ballot",
+    "de.medizininformatikinitiative.kerndatensatz.biobank": "^2026.0.0-ballot1",
+    "de.medizininformatikinitiative.kerndatensatz.consent": "^2025.0.4",
+    "de.medizininformatikinitiative.kerndatensatz.diagnose": "^2025.0.1",
+    "de.medizininformatikinitiative.kerndatensatz.fall": "^2025.0.1",
+    "de.medizininformatikinitiative.kerndatensatz.icu": "^2025.0.4",
+    "de.medizininformatikinitiative.kerndatensatz.laborbefund": "^2025.0.2",
+    "de.medizininformatikinitiative.kerndatensatz.medikation": "^2025.0.0",
+    "de.medizininformatikinitiative.kerndatensatz.meta": "^2025.0.3",
+    "de.medizininformatikinitiative.kerndatensatz.mikrobiologie": "^2025.0.1",
+    "de.medizininformatikinitiative.kerndatensatz.molgen": "^2026.0.0-ballot.2",
+    "de.medizininformatikinitiative.kerndatensatz.patho": "^2026.0.0-ballot",
+    "de.medizininformatikinitiative.kerndatensatz.person": "^2025.0.1",
+    "de.medizininformatikinitiative.kerndatensatz.prozedur": "^2025.0.1",
+    "de.medizininformatikinitiative.kerndatensatz.studie": "^2026.0.0-ballot",
+    "eu.miabis.r4": "^0.2.0",
+    "hl7.fhir.r4b.core": "^4.3.0",
+    "hl7.fhir.uv.extensions": "^5.3.0-ballot-tc1",
+    "hl7.fhir.uv.genomics-reporting": "^3.0.0",
+    "hl7.terminology.r5": "^6.5.0"
+  }
+}

.github/validation/upload-definition.sh

@@ -0,0 +1,15 @@
+#!/bin/bash -e
+
+FILENAME=$1
+BASE="http://localhost:8080/fhir"
+
+RESOURCE_TYPE="$(jq -r .resourceType "$FILENAME")"
+if [[ "$RESOURCE_TYPE" =~ ValueSet|CodeSystem|StructureDefinition ]]; then
+  URL="$(jq -r .url "$FILENAME")"
+  if [[ "$URL" =~ http://unitsofmeasure.org|http://snomed.info/sct|http://loinc.org|urn:ietf:bcp:13 ]]; then
+    echo "Skip creating the code system or value set $URL which is internal in Blaze"
+  else
+    echo "Upload $FILENAME"
+    curl -sf -H "Content-Type: application/fhir+json" -H "Prefer: return=minimal" -d @"$FILENAME" "$BASE/$RESOURCE_TYPE"
+  fi
+fi

.github/validation/upload-definitions-from-dir.sh

@@ -0,0 +1,8 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+DIR="$1"
+
+# Upload Resources
+find "$DIR" -name "*.json" -and -not -name "package.json" -and -not -name ".package-lock.json" -and -not -name ".index.json" -print0 |\
+ xargs -0 -P 4 -I {} "$SCRIPT_DIR/upload-definition.sh" {}

.github/validation/upload-testdata-from-dir.sh

@@ -0,0 +1,7 @@
+#!/bin/bash -e
+
+SCRIPT_DIR="$(dirname "$(readlink -f "$0")")"
+DIR="$1"
+
+find "$DIR" -name "*.json" -and -not -name "Bundle*.json" -and -not -name "package.json" -and -not -name ".package-lock.json" -and -not -name ".index.json" -print0 |\
+ xargs -0 -I {} "$SCRIPT_DIR/upload-testdata.sh" {}