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Lucas0TLucas0T
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Increase Redaction Code Coverage
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4 files changed

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‎src/test/java/de/medizininformatikinitiative/torch/RedactionTest.java‎

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@@ -23,6 +23,7 @@
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import static de.medizininformatikinitiative.torch.util.FhirUtil.createAbsentReasonExtension;
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import static org.assertj.core.api.Assertions.assertThat;
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import static org.assertj.core.api.Assertions.assertThatThrownBy;
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public class RedactionTest {
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@@ -82,6 +83,38 @@ void testReferenceComplexType(String resource) throws IOException {
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assertThat(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(tgt)).isEqualTo(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(expected));
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}
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@Test
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public void mismatchProfileWithAssignedProfile() {
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org.hl7.fhir.r4.model.Condition src = new org.hl7.fhir.r4.model.Condition();
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Meta meta = new Meta();
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meta.setProfile(List.of(new CanonicalType(MEDICATION)));
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src.setMeta(meta);
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ExtractionRedactionWrapper wrapper = new ExtractionRedactionWrapper(src, Set.of(DIAGNOSIS), Map.of(), Set.of());
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assertThatThrownBy(() -> integrationTestSetup.redaction().redact(wrapper)).isInstanceOf(RuntimeException.class)
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.hasMessage("Resource is missing required profiles: []");
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}
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@Test
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public void unknownProfile() {
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org.hl7.fhir.r4.model.Condition src = new org.hl7.fhir.r4.model.Condition();
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Meta meta = new Meta();
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meta.setProfile(List.of(new CanonicalType("UnknownProfile")));
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src.setMeta(meta);
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ExtractionRedactionWrapper wrapper = new ExtractionRedactionWrapper(src, Set.of("UnknownProfile"), Map.of(), Set.of());
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assertThatThrownBy(() -> integrationTestSetup.redaction().redact(wrapper)).isInstanceOf(RuntimeException.class)
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.hasMessage("Trying to handle unknown profiles: [UnknownProfile]");
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}
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@Test
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public void metaMissing() {
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org.hl7.fhir.r4.model.Condition src = new org.hl7.fhir.r4.model.Condition();
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ExtractionRedactionWrapper wrapper = new ExtractionRedactionWrapper(src, Set.of(DIAGNOSIS), Map.of(), Set.of());
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assertThatThrownBy(() -> integrationTestSetup.redaction().redact(wrapper)).isInstanceOf(RuntimeException.class);
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}
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@Test
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public void unknownSlice() throws IOException {
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DomainResource expected = integrationTestSetup.readResource(EXPECTED_OUTPUT_DIR + "unknownSlice.json");
@@ -100,6 +133,35 @@ public void unknownSlice() throws IOException {
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assertThat(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(tgt)).isEqualTo(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(expected));
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}
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@ParameterizedTest
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@ValueSource(strings = {"DiagnosisWithExtensionAtCodeWithUnknownField.json"})
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void notHandlingUnknownElementID(String resource) throws IOException {
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DomainResource src = integrationTestSetup.readResource(INPUT_CONDITION_DIR + resource);
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DomainResource expected = integrationTestSetup.readResource(EXPECTED_OUTPUT_DIR + resource);
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ExtractionRedactionWrapper wrapper = new ExtractionRedactionWrapper(src, Set.of(DIAGNOSIS), Map.of("Condition.subject", Set.of("Patient/12345", "Patient/123"), "Condition.encounter", Set.of("Encounter/12345")), Set.of());
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DomainResource tgt = (DomainResource) integrationTestSetup.redaction().redact(wrapper);
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assertThat(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(tgt)).isEqualTo(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(expected));
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}
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@Test
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public void emptyValues() throws IOException {
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DomainResource expected = integrationTestSetup.readResource(EXPECTED_OUTPUT_DIR + "EmptyValues.json");
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org.hl7.fhir.r4.model.Condition src = new org.hl7.fhir.r4.model.Condition();
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Meta meta = new Meta();
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meta.setProfile(List.of(new CanonicalType(DIAGNOSIS)));
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src.setMeta(meta);
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ExtractionRedactionWrapper wrapper = new ExtractionRedactionWrapper(src, Set.of(DIAGNOSIS), Map.of(), Set.of());
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DomainResource tgt = (DomainResource) integrationTestSetup.redaction().redact(wrapper);
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assertThat(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(tgt)).isEqualTo(fhirContext.newJsonParser().setPrettyPrint(true).encodeResourceToString(expected));
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}
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@ParameterizedTest
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@ValueSource(strings = {"DiagnosisUnknownPrimitiveExtension.json", "DiagnosisWithExtensionAtCode.json", "DiagnosisUnknownComplexExtension.json"})
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void removeUnknownPrimitiveAndComplexExtension(String resource) throws IOException {

‎src/test/resources/InputResources/Condition/DiagnosisWithExtensionAtCodeWithUnknownField.json‎

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{
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"resourceType": "Condition",
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"id": "mii-exa-diagnose-mehrfachkodierung-primaercode",
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"meta": {
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"profile": [
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"https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
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"extension": [
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{
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"url": "http://fhir.de/StructureDefinition/seitenlokalisation",
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"valueCoding": {
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"code": "L",
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"system": "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_SEITENLOKALISATION",
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"display": "links"
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}
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},
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{
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"url": "http://fhir.de/StructureDefinition/icd-10-gm-mehrfachcodierungs-kennzeichen",
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"valueCoding": {
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"code": "†",
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"system": "http://fhir.de/CodeSystem/icd-10-gm-mehrfachcodierungs-kennzeichen"
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}
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}
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],
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"code": "A54.4",
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"version": "2020",
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"display": "Gonokokkeninfektion des Muskel-Skelett-Systems"
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},
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{
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"system": "http://fhir.de/CodeSystem/bfarm/alpha-id",
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"code": "I97525",
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"version": "2020",
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"display": "Bursitis gonorrhoica"
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}
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]
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},
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"clinicalStatus": {
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"coding": [
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{
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"code": "active",
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"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
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"extension": [
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{
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"url": "http://fhir.de/StructureDefinition/seitenlokalisation",
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"valueCoding": {
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"code": "L",
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"system": "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_SEITENLOKALISATION",
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"display": "links"
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}
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}
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]
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}
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]
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},
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"verificationStatus": {
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"coding": [
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{
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"code": "confirmed",
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"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status"
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}
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]
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},
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"subject": {
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"reference": "Patient/12345"
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},
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"encounter": {
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"reference": "Encounter/12345"
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},
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"onsetPeriod": {
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"start": "2019-09-26T12:45:00+01:00",
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"end": "2020-03-25T13:00:00+01:00"
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},
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"recordedDate": "2020-01-05T12:53:00+01:00"
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}

‎src/test/resources/RedactTest/expectedOutput/DiagnosisWithExtensionAtCodeWithUnknownField.json‎

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{
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"resourceType": "Condition",
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"id": "mii-exa-diagnose-mehrfachkodierung-primaercode",
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"meta": {
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"profile": [
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"https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose"
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]
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},
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"code": {
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"coding": [
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{
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"system": "http://fhir.de/CodeSystem/bfarm/icd-10-gm",
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"extension": [
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{
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"url": "http://fhir.de/StructureDefinition/seitenlokalisation",
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"valueCoding": {
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"code": "L",
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"system": "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_SEITENLOKALISATION",
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"display": "links"
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}
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},
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{
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"url": "http://fhir.de/StructureDefinition/icd-10-gm-mehrfachcodierungs-kennzeichen",
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"valueCoding": {
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"code": "†",
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"system": "http://fhir.de/CodeSystem/icd-10-gm-mehrfachcodierungs-kennzeichen"
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}
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}
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],
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"code": "A54.4",
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"version": "2020",
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"display": "Gonokokkeninfektion des Muskel-Skelett-Systems"
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},
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{
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"system": "http://fhir.de/CodeSystem/bfarm/alpha-id",
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"code": "I97525",
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"version": "2020",
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"display": "Bursitis gonorrhoica"
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}
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]
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},
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"clinicalStatus": {
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"coding": [
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{
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"code": "active",
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"system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
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"extension": [
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{
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"url": "http://fhir.de/StructureDefinition/seitenlokalisation",
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"valueCoding": {
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"code": "L",
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"system": "https://fhir.kbv.de/CodeSystem/KBV_CS_SFHIR_ICD_SEITENLOKALISATION",
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"display": "links"
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}
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}
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]
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}
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]
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},
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"verificationStatus": {
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"coding": [
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{
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"code": "confirmed",
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"system": "http://terminology.hl7.org/CodeSystem/condition-ver-status"
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}
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]
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},
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"subject": {
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"reference": "Patient/12345"
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},
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"encounter": {
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"reference": "Encounter/12345"
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},
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"onsetPeriod": {
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"start": "2019-09-26T12:45:00+01:00",
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"end": "2020-03-25T13:00:00+01:00"
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},
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"recordedDate": "2020-01-05T12:53:00+01:00"
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}

‎src/test/resources/RedactTest/expectedOutput/EmptyValues.json‎

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{
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"resourceType": "Condition",
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"meta": {
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"profile": [
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"https://www.medizininformatik-initiative.de/fhir/core/modul-diagnose/StructureDefinition/Diagnose"
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]
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},
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"code": {
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"extension": [
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{
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"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
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"valueCode": "masked"
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}
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]
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},
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"subject": {
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"extension": [
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{
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"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
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"valueCode": "masked"
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}
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]
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},
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"_recordedDate": {
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"extension": [
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{
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"url": "http://hl7.org/fhir/StructureDefinition/data-absent-reason",
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"valueCode": "masked"
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}
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]
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}
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}

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