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mirror of https://github.com/pcvolkmer/mv64e-etl-processor synced 2025-09-13 17:02:52 +00:00

1 Commits

Author SHA1 Message Date
328bf019af chore: bump version 2025-09-03 22:17:48 +02:00
8 changed files with 214 additions and 264 deletions

View File

@@ -7,22 +7,22 @@ plugins {
war
id("org.springframework.boot") version "3.5.5"
id("io.spring.dependency-management") version "1.1.7"
kotlin("jvm") version "2.2.10"
kotlin("plugin.spring") version "2.2.10"
kotlin("jvm") version "1.9.25"
kotlin("plugin.spring") version "1.9.25"
jacoco
}
group = "dev.dnpm"
version = "0.12.0-SNAPSHOT"
version = "0.11.1"
var versions = mapOf(
"mtb-dto" to "0.1.0-SNAPSHOT",
"hapi-fhir" to "8.4.0",
"mockito-kotlin" to "6.0.0",
"archunit" to "1.4.1",
"hapi-fhir" to "7.6.1",
"mockito-kotlin" to "5.4.0",
"archunit" to "1.3.0",
// Webjars
"webjars-locator" to "0.52",
"echarts" to "6.0.0",
"echarts" to "5.4.3",
"htmx.org" to "1.9.12"
)

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@@ -39,14 +39,12 @@ public class GicsConsentService implements IConsentService {
private final RestTemplate restTemplate;
private final FhirContext fhirContext;
private final GIcsConfigProperties gIcsConfigProperties;
private final String BROAD_CONSENT_PROFILE_URI = "https://www.medizininformatik-initiative.de/fhir/modul-consent/StructureDefinition/mii-pr-consent-einwilligung";
private final String BROAD_CONSENT_POLICY = "urn:oid:2.16.840.1.113883.3.1937.777.24.2.1791";
public GicsConsentService(
GIcsConfigProperties gIcsConfigProperties,
RetryTemplate retryTemplate,
RestTemplate restTemplate,
AppFhirConfig appFhirConfig
GIcsConfigProperties gIcsConfigProperties,
RetryTemplate retryTemplate,
RestTemplate restTemplate,
AppFhirConfig appFhirConfig
) {
this.retryTemplate = retryTemplate;
this.restTemplate = restTemplate;
@@ -56,34 +54,34 @@ public class GicsConsentService implements IConsentService {
}
protected Parameters getFhirRequestParameters(
String personIdentifierValue
String personIdentifierValue
) {
var result = new Parameters();
result.addParameter(
new ParametersParameterComponent()
.setName("personIdentifier")
.setValue(
new Identifier()
.setValue(personIdentifierValue)
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
)
new ParametersParameterComponent()
.setName("personIdentifier")
.setValue(
new Identifier()
.setValue(personIdentifierValue)
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
)
);
result.addParameter(
new ParametersParameterComponent()
.setName("domain")
.setValue(
new StringType()
.setValue(this.gIcsConfigProperties.getBroadConsentDomainName())
)
new ParametersParameterComponent()
.setName("domain")
.setValue(
new StringType()
.setValue(this.gIcsConfigProperties.getBroadConsentDomainName())
)
);
result.addParameter(
new ParametersParameterComponent()
.setName("policy")
.setValue(
new Coding()
.setCode(this.gIcsConfigProperties.getBroadConsentPolicyCode())
.setSystem(this.gIcsConfigProperties.getBroadConsentPolicySystem())
)
new ParametersParameterComponent()
.setName("policy")
.setValue(
new Coding()
.setCode(this.gIcsConfigProperties.getBroadConsentPolicyCode())
.setSystem(this.gIcsConfigProperties.getBroadConsentPolicySystem())
)
);
/*
@@ -91,10 +89,10 @@ public class GicsConsentService implements IConsentService {
* 'ignoreVersionNumber'.
*/
result.addParameter(
new ParametersParameterComponent()
.setName("version")
.setValue(new StringType().setValue("1.1")
)
new ParametersParameterComponent()
.setName("version")
.setValue(new StringType().setValue("1.1")
)
);
/* add config parameter with:
@@ -103,17 +101,17 @@ public class GicsConsentService implements IConsentService {
* unknownStateIsConsideredAsDecline -> true
*/
var config = new ParametersParameterComponent()
.setName("config")
.addPart(
new ParametersParameterComponent()
.setName("ignoreVersionNumber")
.setValue(new BooleanType().setValue(true))
)
.addPart(
new ParametersParameterComponent()
.setName("unknownStateIsConsideredAsDecline")
.setValue(new BooleanType().setValue(false))
);
.setName("config")
.addPart(
new ParametersParameterComponent()
.setName("ignoreVersionNumber")
.setValue(new BooleanType().setValue(true))
)
.addPart(
new ParametersParameterComponent()
.setName("unknownStateIsConsideredAsDecline")
.setValue(new BooleanType().setValue(false))
);
result.addParameter(config);
@@ -132,8 +130,8 @@ public class GicsConsentService implements IConsentService {
headers.setContentType(MediaType.APPLICATION_XML);
if (
StringUtils.isBlank(this.gIcsConfigProperties.getUsername())
|| StringUtils.isBlank(this.gIcsConfigProperties.getPassword())
StringUtils.isBlank(this.gIcsConfigProperties.getUsername())
|| StringUtils.isBlank(this.gIcsConfigProperties.getPassword())
) {
return headers;
}
@@ -147,28 +145,28 @@ public class GicsConsentService implements IConsentService {
HttpEntity<String> requestEntity = new HttpEntity<>(parameterAsXml, this.headersWithHttpBasicAuth());
try {
var responseEntity = retryTemplate.execute(
ctx -> restTemplate.exchange(endpointUri(endpoint), HttpMethod.POST, requestEntity, String.class)
ctx -> restTemplate.exchange(endpointUri(endpoint), HttpMethod.POST, requestEntity, String.class)
);
if (responseEntity.getStatusCode().is2xxSuccessful()) {
return responseEntity.getBody();
} else {
var msg = String.format(
"Trusted party system reached but request failed! code: '%s' response: '%s'",
responseEntity.getStatusCode(), responseEntity.getBody());
"Trusted party system reached but request failed! code: '%s' response: '%s'",
responseEntity.getStatusCode(), responseEntity.getBody());
log.error(msg);
return null;
}
} catch (RestClientException e) {
var msg = String.format("Get consents status request failed reason: '%s",
e.getMessage());
e.getMessage());
log.error(msg);
return null;
} catch (TerminatedRetryException terminatedRetryException) {
var msg = String.format(
"Get consents status process has been terminated. termination reason: '%s",
terminatedRetryException.getMessage());
"Get consents status process has been terminated. termination reason: '%s",
terminatedRetryException.getMessage());
log.error(msg);
return null;
}
@@ -177,45 +175,45 @@ public class GicsConsentService implements IConsentService {
@Override
public TtpConsentStatus getTtpBroadConsentStatus(String personIdentifierValue) {
var consentStatusResponse = callGicsApi(
getFhirRequestParameters(personIdentifierValue),
GicsConsentService.IS_CONSENTED_ENDPOINT
getFhirRequestParameters(personIdentifierValue),
GicsConsentService.IS_CONSENTED_ENDPOINT
);
return evaluateConsentResponse(consentStatusResponse);
}
protected Bundle currentConsentForPersonAndTemplate(
String personIdentifierValue,
ConsentDomain consentDomain,
Date requestDate
String personIdentifierValue,
ConsentDomain consentDomain,
Date requestDate
) {
var requestParameter = buildRequestParameterCurrentPolicyStatesForPerson(
personIdentifierValue,
requestDate,
consentDomain
personIdentifierValue,
requestDate,
consentDomain
);
var consentDataSerialized = callGicsApi(requestParameter,
GicsConsentService.IS_POLICY_STATES_FOR_PERSON_ENDPOINT);
GicsConsentService.IS_POLICY_STATES_FOR_PERSON_ENDPOINT);
if (consentDataSerialized == null) {
// error occurred - should not process further!
throw new IllegalStateException(
"consent data request failed - stopping processing! - try again or fix other problems first.");
"consent data request failed - stopping processing! - try again or fix other problems first.");
}
var iBaseResource = fhirContext.newJsonParser()
.parseResource(consentDataSerialized);
.parseResource(consentDataSerialized);
if (iBaseResource instanceof OperationOutcome) {
// log error - very likely a configuration error
String errorMessage =
"Consent request failed! Check outcome:\n " + consentDataSerialized;
"Consent request failed! Check outcome:\n " + consentDataSerialized;
log.error(errorMessage);
throw new IllegalStateException(errorMessage);
} else if (iBaseResource instanceof Bundle bundle) {
return bundle;
} else {
String errorMessage = "Consent request failed! Unexpected response received! -> "
+ consentDataSerialized;
+ consentDataSerialized;
log.error(errorMessage);
throw new IllegalStateException(errorMessage);
}
@@ -230,43 +228,43 @@ public class GicsConsentService implements IConsentService {
}
protected Parameters buildRequestParameterCurrentPolicyStatesForPerson(
String personIdentifierValue,
Date requestDate,
ConsentDomain consentDomain
String personIdentifierValue,
Date requestDate,
ConsentDomain consentDomain
) {
var requestParameter = new Parameters();
requestParameter.addParameter(
new ParametersParameterComponent()
.setName("personIdentifier")
.setValue(
new Identifier()
.setValue(personIdentifierValue)
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
)
new ParametersParameterComponent()
.setName("personIdentifier")
.setValue(
new Identifier()
.setValue(personIdentifierValue)
.setSystem(this.gIcsConfigProperties.getPersonIdentifierSystem())
)
);
requestParameter.addParameter(
new ParametersParameterComponent()
.setName("domain")
.setValue(new StringType().setValue(getConsentDomainName(consentDomain)))
new ParametersParameterComponent()
.setName("domain")
.setValue(new StringType().setValue(getConsentDomainName(consentDomain)))
);
Parameters nestedConfigParameters = new Parameters();
nestedConfigParameters
.addParameter(
new ParametersParameterComponent()
.setName("idMatchingType")
.setValue(new Coding()
.setSystem("https://ths-greifswald.de/fhir/CodeSystem/gics/IdMatchingType")
.setCode("AT_LEAST_ONE")
)
)
.addParameter("ignoreVersionNumber", false)
.addParameter("unknownStateIsConsideredAsDecline", false)
.addParameter("requestDate", new DateType().setValue(requestDate));
.addParameter(
new ParametersParameterComponent()
.setName("idMatchingType")
.setValue(new Coding()
.setSystem("https://ths-greifswald.de/fhir/CodeSystem/gics/IdMatchingType")
.setCode("AT_LEAST_ONE")
)
)
.addParameter("ignoreVersionNumber", false)
.addParameter("unknownStateIsConsideredAsDecline", false)
.addParameter("requestDate", new DateType().setValue(requestDate));
requestParameter.addParameter(
new ParametersParameterComponent().setName("config").addPart().setResource(nestedConfigParameters)
new ParametersParameterComponent().setName("config").addPart().setResource(nestedConfigParameters)
);
return requestParameter;
@@ -293,7 +291,7 @@ public class GicsConsentService implements IConsentService {
}
} else if (response instanceof OperationOutcome outcome) {
log.error("failed to get consent status from ttp. probably configuration error. "
+ "outcome: '{}'", fhirContext.newJsonParser().encodeToString(outcome));
+ "outcome: '{}'", fhirContext.newJsonParser().encodeToString(outcome));
}
} catch (DataFormatException dfe) {
@@ -304,36 +302,6 @@ public class GicsConsentService implements IConsentService {
@Override
public Bundle getConsent(String patientId, Date requestDate, ConsentDomain consentDomain) {
Bundle gIcsResultBundle = currentConsentForPersonAndTemplate(patientId, consentDomain, requestDate);
if (ConsentDomain.BROAD_CONSENT == consentDomain) {
return convertGicsResultToMiiBroadConsent(gIcsResultBundle);
}
return gIcsResultBundle;
}
protected Bundle convertGicsResultToMiiBroadConsent(Bundle gIcsResultBundle) {
if (gIcsResultBundle == null
|| gIcsResultBundle.getEntry().isEmpty()
|| !(gIcsResultBundle.getEntry().getFirst().getResource() instanceof Consent))
return gIcsResultBundle;
Bundle.BundleEntryComponent bundleEntryComponent = gIcsResultBundle.getEntry().getFirst();
var consentAsOne = (Consent) bundleEntryComponent.getResource();
if (consentAsOne.getPolicy().stream().noneMatch(p -> p.getUri().equals(BROAD_CONSENT_POLICY))) {
consentAsOne.addPolicy(new Consent.ConsentPolicyComponent().setUri(BROAD_CONSENT_POLICY));
}
if (consentAsOne.getMeta().getProfile().stream().noneMatch(p -> p.getValue().equals(BROAD_CONSENT_PROFILE_URI))) {
consentAsOne.getMeta().addProfile(BROAD_CONSENT_PROFILE_URI);
}
consentAsOne.setPolicyRule(null);
gIcsResultBundle.getEntry().stream().skip(1).forEach(c -> consentAsOne.getProvision().addProvision(((Consent) c.getResource()).getProvision().getProvisionFirstRep()));
gIcsResultBundle.getEntry().clear();
gIcsResultBundle.addEntry(bundleEntryComponent);
return gIcsResultBundle;
return currentConsentForPersonAndTemplate(patientId, consentDomain, requestDate);
}
}

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@@ -23,6 +23,8 @@ import ca.uhn.fhir.context.FhirContext;
import ca.uhn.fhir.parser.IParser;
import dev.dnpm.etl.processor.config.AppFhirConfig;
import dev.dnpm.etl.processor.config.GPasConfigProperties;
import java.net.URI;
import java.net.URISyntaxException;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.lang3.StringUtils;
import org.apache.hc.core5.net.URIBuilder;
@@ -37,11 +39,9 @@ import org.springframework.http.*;
import org.springframework.retry.support.RetryTemplate;
import org.springframework.web.client.HttpClientErrorException.BadRequest;
import org.springframework.web.client.HttpClientErrorException.Unauthorized;
import org.springframework.web.client.RestClientException;
import org.springframework.web.client.RestTemplate;
import java.net.URI;
import java.net.URISyntaxException;
public class GpasPseudonymGenerator implements Generator {
private final FhirContext r4Context;
@@ -52,10 +52,10 @@ public class GpasPseudonymGenerator implements Generator {
private final RestTemplate restTemplate;
private final @NotNull String genomDeTanDomain;
private final @NotNull String pidPsnDomain;
protected static final String CREATE_OR_GET_PSN = "$pseudonymizeAllowCreate";
protected static final String CREATE_MULTI_DOMAIN_PSN = "$pseudonymize-secondary";
private static final String SINGLE_PSN_PART_NAME = "pseudonym";
private static final String MULTI_PSN_PART_NAME = "value";
protected final static String createOrGetPsn = "$pseudonymizeAllowCreate";
protected final static String createMultiDomainPsn = "$pseudonymize-secondary";
private final static String SINGLE_PSN_PART_NAME = "pseudonym";
private final static String MULTI_PSN_PART_NAME = "value";
public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
RestTemplate restTemplate, AppFhirConfig appFhirConfig) {
@@ -85,7 +85,7 @@ public class GpasPseudonymGenerator implements Generator {
switch (domainType) {
case SINGLE_PSN_DOMAIN -> {
final var requestBody = createSinglePsnRequestBody(id, pidPsnDomain);
final var responseEntity = getGpasPseudonym(requestBody, CREATE_OR_GET_PSN);
final var responseEntity = getGpasPseudonym(requestBody, createOrGetPsn);
final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
@@ -93,7 +93,7 @@ public class GpasPseudonymGenerator implements Generator {
}
case MULTI_PSN_DOMAIN -> {
final var requestBody = createMultiPsnRequestBody(id, genomDeTanDomain);
final var responseEntity = getGpasPseudonym(requestBody, CREATE_MULTI_DOMAIN_PSN);
final var responseEntity = getGpasPseudonym(requestBody, createMultiDomainPsn);
final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
@@ -150,22 +150,23 @@ public class GpasPseudonymGenerator implements Generator {
log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
return responseEntity;
}
} catch (BadRequest e) {
String msg = "gPas or request configuration is incorrect. Please check both."
+ e.getMessage();
log.error(msg);
throw new PseudonymRequestFailed(msg, e);
} catch (Unauthorized e) {
var msg = "gPas access credentials are invalid check your configuration. msg: '%s"
.formatted(e.getMessage());
log.error(msg);
throw new PseudonymRequestFailed(msg, e);
}
catch (Exception unexpected) {
} catch (RestClientException rce) {
if (rce instanceof BadRequest) {
String msg = "gPas or request configuration is incorrect. Please check both."
+ rce.getMessage();
log.debug(
msg);
throw new PseudonymRequestFailed(msg, rce);
}
if (rce instanceof Unauthorized) {
var msg = "gPas access credentials are invalid check your configuration. msg: '%s".formatted(
rce.getMessage());
log.error(msg);
throw new PseudonymRequestFailed(msg, rce);
}
} catch (Exception unexpected) {
throw new PseudonymRequestFailed(
"API request due unexpected error unsuccessful gPas unsuccessful.",
unexpected
);
"API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
}
throw new PseudonymRequestFailed(
"API request due unexpected error unsuccessful gPas unsuccessful.");

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@@ -30,7 +30,6 @@ import org.springframework.data.relational.core.mapping.Table
import org.springframework.data.repository.CrudRepository
import org.springframework.data.repository.PagingAndSortingRepository
import java.time.Instant
import java.time.temporal.ChronoUnit
import java.util.*
@Table("request")
@@ -66,12 +65,6 @@ data class Request(
processedAt: Instant
) :
this(null, uuid, patientPseudonym, pid, fingerprint, type, status, processedAt)
fun isPendingUnknown(): Boolean {
return this.status == RequestStatus.UNKNOWN && this.processedAt.isBefore(
Instant.now().minus(10, ChronoUnit.MINUTES)
)
}
}
@JvmRecord
@@ -97,23 +90,19 @@ interface RequestRepository : CrudRepository<Request, Long>, PagingAndSortingRep
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'MTB_FILE' GROUP BY status ORDER BY status, count DESC;")
fun countStates(): List<CountedState>
@Query(
"SELECT count(*) AS count, status FROM (" +
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
"WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
)
@Query("SELECT count(*) AS count, status FROM (" +
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
"WHERE type = 'MTB_FILE' AND status NOT IN ('DUPLICATION') " +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
fun findPatientUniqueStates(): List<CountedState>
@Query("SELECT count(*) AS count, status FROM request WHERE type = 'DELETE' GROUP BY status ORDER BY status, count DESC;")
fun countDeleteStates(): List<CountedState>
@Query(
"SELECT count(*) AS count, status FROM (" +
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
"WHERE type = 'DELETE'" +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;"
)
@Query("SELECT count(*) AS count, status FROM (" +
"SELECT status, rank() OVER (PARTITION BY patient_pseudonym ORDER BY processed_at DESC) AS rank FROM request " +
"WHERE type = 'DELETE'" +
") rank WHERE rank = 1 GROUP BY status ORDER BY status, count DESC;")
fun findPatientUniqueDeleteStates(): List<CountedState>
}
}

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@@ -137,7 +137,15 @@ class ConsentProcessor(
}
val provisionComponent: ProvisionComponent = provisions.first()
val provisionCode = getProvisionCode(provisionComponent)
var provisionCode: String? = null
if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
val codableConcept: CodeableConcept = provisionComponent.code.first()
if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
provisionCode = codableConcept.coding.first().code
}
}
if (provisionCode != null) {
try {
val modelProjectConsentPurpose =
@@ -169,17 +177,6 @@ class ConsentProcessor(
}
}
private fun getProvisionCode(provisionComponent: ProvisionComponent): String? {
var provisionCode: String? = null
if (provisionComponent.code != null && provisionComponent.code.isNotEmpty()) {
val codableConcept: CodeableConcept = provisionComponent.code.first()
if (codableConcept.coding != null && codableConcept.coding.isNotEmpty()) {
provisionCode = codableConcept.coding.first().code
}
}
return provisionCode
}
private fun setGenomDeSubmissionType(mtbFile: Mtb) {
if (appConfigProperties.genomDeTestSubmission) {
mtbFile.metadata.type = MvhSubmissionType.TEST
@@ -241,9 +238,9 @@ class ConsentProcessor(
consent.provision.provision.filter { subProvision ->
isRequestDateInRange(requestDate, subProvision.period)
// search coding entries of current provision for code and system
subProvision.code.map { c -> c.coding }.flatten().any { code ->
subProvision.code.map { c -> c.coding }.flatten().firstOrNull { code ->
targetCode.equals(code.code) && targetSystem.equals(code.system)
}
} != null
}.map { subProvision ->
subProvision
}
@@ -260,11 +257,11 @@ class ConsentProcessor(
researchAllowedPolicySystem: String?,
policyRules: Collection<Coding>
): Boolean {
return policyRules.any { code ->
return policyRules.find { code ->
researchAllowedPolicySystem.equals(code.getSystem()) && (researchAllowedPolicyOid.equals(
code.getCode()
))
}
} != null
}
fun isRequestDateInRange(requestDate: Date?, provPeriod: Period): Boolean {

View File

@@ -52,8 +52,7 @@
<td th:if="${request.status.value.contains('success')}" class="bg-green"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('warning')}" class="bg-yellow"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value.contains('error')}" class="bg-red"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'unknown' and not request.isPendingUnknown()}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'unknown' and request.isPendingUnknown()}" class="bg-yellow"><small>⏰ [[ ${request.status} ]] ⏰</small></td>
<td th:if="${request.status.value == 'unknown'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'duplication'}" class="bg-gray"><small>[[ ${request.status} ]]</small></td>
<td th:if="${request.status.value == 'no-consent'}" class="bg-blue"><small>[[ ${request.status} ]]</small></td>
<td th:style="${request.type.value == 'delete'} ? 'color: red;'"><small>[[ ${request.type} ]]</small></td>

View File

@@ -24,15 +24,14 @@ import java.time.Instant;
import java.util.Date;
import static org.assertj.core.api.Assertions.assertThat;
import static org.assertj.core.api.Assertions.fail;
import static org.springframework.test.web.client.match.MockRestRequestMatchers.requestTo;
import static org.springframework.test.web.client.response.MockRestResponseCreators.withServerError;
import static org.springframework.test.web.client.response.MockRestResponseCreators.withSuccess;
@ContextConfiguration(classes = {AppConfiguration.class, ObjectMapper.class})
@TestPropertySource(properties = {
"app.consent.service=gics",
"app.consent.gics.uri=http://localhost:8090/ttp-fhir/fhir/gics"
"app.consent.service=gics",
"app.consent.gics.uri=http://localhost:8090/ttp-fhir/fhir/gics"
})
@RestClientTest
class GicsConsentServiceTest {
@@ -47,8 +46,8 @@ class GicsConsentServiceTest {
@BeforeEach
void setUp(
@Autowired AppFhirConfig appFhirConfig,
@Autowired GIcsConfigProperties gIcsConfigProperties
@Autowired AppFhirConfig appFhirConfig,
@Autowired GIcsConfigProperties gIcsConfigProperties
) {
this.appFhirConfig = appFhirConfig;
this.gIcsConfigProperties = gIcsConfigProperties;
@@ -57,33 +56,33 @@ class GicsConsentServiceTest {
this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate);
this.gicsConsentService = new GicsConsentService(
this.gIcsConfigProperties,
RetryTemplate.builder().maxAttempts(1).build(),
restTemplate,
this.appFhirConfig
this.gIcsConfigProperties,
RetryTemplate.builder().maxAttempts(1).build(),
restTemplate,
this.appFhirConfig
);
}
@Test
void shouldReturnTtpBroadConsentStatus() {
final Parameters consentedResponse = new Parameters()
.addParameter(
new ParametersParameterComponent()
.setName("consented")
.setValue(new BooleanType().setValue(true))
);
.addParameter(
new ParametersParameterComponent()
.setName("consented")
.setValue(new BooleanType().setValue(true))
);
mockRestServiceServer
.expect(
requestTo(
"http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT)
.expect(
requestTo(
"http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT)
)
.andRespond(
withSuccess(
appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(consentedResponse),
MediaType.APPLICATION_JSON
)
.andRespond(
withSuccess(
appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(consentedResponse),
MediaType.APPLICATION_JSON
)
);
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.BROAD_CONSENT_GIVEN);
@@ -92,22 +91,22 @@ class GicsConsentServiceTest {
@Test
void shouldReturnRevokedConsent() {
final Parameters revokedResponse = new Parameters()
.addParameter(
new ParametersParameterComponent()
.setName("consented")
.setValue(new BooleanType().setValue(false))
);
.addParameter(
new ParametersParameterComponent()
.setName("consented")
.setValue(new BooleanType().setValue(false))
);
mockRestServiceServer
.expect(
requestTo(
"http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT)
)
.andRespond(
withSuccess(
appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(revokedResponse),
MediaType.APPLICATION_JSON)
);
.expect(
requestTo(
"http://localhost:8090/ttp-fhir/fhir/gics" + GicsConsentService.IS_CONSENTED_ENDPOINT)
)
.andRespond(
withSuccess(
appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(revokedResponse),
MediaType.APPLICATION_JSON)
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.BROAD_CONSENT_MISSING_OR_REJECTED);
@@ -117,23 +116,23 @@ class GicsConsentServiceTest {
@Test
void shouldReturnInvalidParameterResponse() {
final OperationOutcome responseWithErrorOutcome = new OperationOutcome()
.addIssue(
new OperationOutcomeIssueComponent()
.setSeverity(IssueSeverity.ERROR)
.setCode(IssueType.PROCESSING)
.setDiagnostics("Invalid policy parameter...")
);
.addIssue(
new OperationOutcomeIssueComponent()
.setSeverity(IssueSeverity.ERROR)
.setCode(IssueType.PROCESSING)
.setDiagnostics("Invalid policy parameter...")
);
mockRestServiceServer
.expect(
requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)
.expect(
requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)
)
.andRespond(
withSuccess(
appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(responseWithErrorOutcome),
MediaType.APPLICATION_JSON
)
.andRespond(
withSuccess(
appFhirConfig.fhirContext().newJsonParser().encodeResourceToString(responseWithErrorOutcome),
MediaType.APPLICATION_JSON
)
);
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.FAILED_TO_ASK);
@@ -142,12 +141,12 @@ class GicsConsentServiceTest {
@Test
void shouldReturnRequestError() {
mockRestServiceServer
.expect(
requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)
)
.andRespond(
withServerError()
);
.expect(
requestTo(GICS_BASE_URI + GicsConsentService.IS_CONSENTED_ENDPOINT)
)
.andRespond(
withServerError()
);
var consentStatus = gicsConsentService.getTtpBroadConsentStatus("123456");
assertThat(consentStatus).isEqualTo(TtpConsentStatus.FAILED_TO_ASK);
@@ -157,29 +156,26 @@ class GicsConsentServiceTest {
void buildRequestParameterCurrentPolicyStatesForPersonTest() {
String pid = "12345678";
var result = gicsConsentService
.buildRequestParameterCurrentPolicyStatesForPerson(
pid,
Date.from(Instant.now()),
ConsentDomain.MODELLVORHABEN_64E
);
.buildRequestParameterCurrentPolicyStatesForPerson(
pid,
Date.from(Instant.now()),
ConsentDomain.MODELLVORHABEN_64E
);
assertThat(result.getParameter())
.as("should contain 3 parameter resources")
.hasSize(3);
.as("should contain 3 parameter resources")
.hasSize(3);
assertThat(((StringType) result.getParameter("domain").getValue()).getValue())
.isEqualTo(
gIcsConfigProperties.getGenomDeConsentDomainName()
);
.isEqualTo(
gIcsConfigProperties.getGenomDeConsentDomainName()
);
assertThat(((Identifier) result.getParameter("personIdentifier").getValue()).getValue())
.isEqualTo(
pid
);
.isEqualTo(
pid
);
}
@Test
public void convertGicsResultToMiiBroadConsent() {
fail("todo: implement Test gicsConsentService.convertGicsResultToMiiBroadConsent");
}
}

View File

@@ -80,7 +80,7 @@ class ConsentProcessorTest {
val checkResult = consentProcessor.consentGatedCheckAndTryEmbedding(inputMtb)
assertThat(checkResult).isTrue
assertThat(inputMtb.metadata.researchConsents).isNotEmpty
assertThat(inputMtb.metadata.researchConsents).hasSize(26)
}
companion object {