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Code Issues Releases Activity

119 add transaction (#124)

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This commit is contained in:
jlidke
2025-07-23 22:11:47 +02:00
committed by GitHub
parent 199511e567
commit dfc9de78ce
12 changed files with 172 additions and 38 deletions
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6
src/integrationTest/kotlin/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGeneratorTest.kt
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@@ -43,14 +43,14 @@ class GpasPseudonymGeneratorTest {
private lateinit var mockRestServiceServer: MockRestServiceServer
private lateinit var generator: GpasPseudonymGenerator
private lateinit var restTemplate: RestTemplate
private var appFhirConfig: AppFhirConfig = AppFhirConfig()
private var appFhirConfig: AppFhirConfig = AppFhirConfig()
@BeforeEach
fun setup() {
val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
val gPasConfigProperties = GPasConfigProperties(
"https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
"test",
"https://localhost:9990/ttp-fhir/fhir/gpas",
"test", "test2",
null,
null
)

2
src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java
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@@ -23,4 +23,6 @@ public interface Generator {
String generate(String id);
String generateGenomDeTan(String id);
}

93
src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java
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@@ -23,7 +23,11 @@ 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;
import org.hl7.fhir.r4.model.Identifier;
import org.hl7.fhir.r4.model.Parameters;
import org.hl7.fhir.r4.model.Parameters.ParametersParameterComponent;
@@ -42,38 +46,67 @@ public class GpasPseudonymGenerator implements Generator {
private final FhirContext r4Context;
private final String gPasUrl;
private final String psnTargetDomain;
private final HttpHeaders httpHeader;
private final RetryTemplate retryTemplate;
private final Logger log = LoggerFactory.getLogger(GpasPseudonymGenerator.class);
private final RestTemplate restTemplate;
private final @NotNull String genomDeTanDomain;
private final @NotNull String pidPsnDomain;
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) {
this.retryTemplate = retryTemplate;
this.restTemplate = restTemplate;
this.gPasUrl = gpasCfg.getUri();
this.psnTargetDomain = gpasCfg.getTarget();
this.pidPsnDomain = gpasCfg.getPatientDomain();
this.genomDeTanDomain = gpasCfg.getGenomDeTanDomain();
this.r4Context = appFhirConfig.fhirContext();
httpHeader = getHttpHeaders(gpasCfg.getUsername(), gpasCfg.getPassword());
log.debug(String.format("%s has been initialized", this.getClass().getName()));
log.debug("{} has been initialized", this.getClass().getName());
}
@Override
public String generate(String id) {
var gPasRequestBody = getGpasRequestBody(id);
var responseEntity = getGpasPseudonym(gPasRequestBody);
var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
return generate(id, PsnDomainType.SINGLE_PSN_DOMAIN);
}
return unwrapPseudonym(gPasPseudonymResult);
@Override
public String generateGenomDeTan(String id) {
return generate(id, PsnDomainType.MULTI_PSN_DOMAIN);
}
protected String generate(String id, PsnDomainType domainType) {
switch (domainType) {
case SINGLE_PSN_DOMAIN -> {
final var requestBody = createSinglePsnRequestBody(id, pidPsnDomain);
final var responseEntity = getGpasPseudonym(requestBody, createOrGetPsn);
final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
return unwrapPseudonym(gPasPseudonymResult, SINGLE_PSN_PART_NAME);
}
case MULTI_PSN_DOMAIN -> {
final var requestBody = createMultiPsnRequestBody(id, genomDeTanDomain);
final var responseEntity = getGpasPseudonym(requestBody, createMultiDomainPsn);
final var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
.parseResource(responseEntity.getBody());
return unwrapPseudonym(gPasPseudonymResult, MULTI_PSN_PART_NAME);
}
}
throw new NotImplementedException(
"give domain type '%s' is unexpected and is currently not supported!".formatted(
domainType));
}
@NotNull
public static String unwrapPseudonym(Parameters gPasPseudonymResult) {
public static String unwrapPseudonym(Parameters gPasPseudonymResult, String targetPartName) {
final var parameters = gPasPseudonymResult.getParameter().stream().findFirst();
if (parameters.isEmpty()) {
@@ -81,7 +114,7 @@ public class GpasPseudonymGenerator implements Generator {
}
final var identifier = (Identifier) parameters.get().getPart().stream()
.filter(a -> a.getName().equals("pseudonym"))
.filter(a -> a.getName().equals(targetPartName))
.findFirst()
.orElseGet(ParametersParameterComponent::new).getValue();
@@ -104,13 +137,14 @@ public class GpasPseudonymGenerator implements Generator {
}
@NotNull
protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody) {
protected ResponseEntity<String> getGpasPseudonym(String gPasRequestBody, String apiEndpoint) {
HttpEntity<String> requestEntity = new HttpEntity<>(gPasRequestBody, this.httpHeader);
try {
var targetUrl = buildRequestUrl(apiEndpoint);
ResponseEntity<String> responseEntity = retryTemplate.execute(
ctx -> restTemplate.exchange(gPasUrl, HttpMethod.POST, requestEntity,
ctx -> restTemplate.exchange(targetUrl, HttpMethod.POST, requestEntity,
String.class));
if (responseEntity.getStatusCode().is2xxSuccessful()) {
log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
@@ -139,16 +173,43 @@ public class GpasPseudonymGenerator implements Generator {
}
protected String getGpasRequestBody(String id) {
var requestParameters = new Parameters();
protected URI buildRequestUrl(String apiEndpoint) throws URISyntaxException {
var gPasUrl1 = gPasUrl;
if (gPasUrl.lastIndexOf("/") == gPasUrl.length() - 1) {
gPasUrl1 = gPasUrl.substring(0, gPasUrl.length() - 1);
}
var urlBuilder = new URIBuilder(new URI(gPasUrl1)).appendPath(apiEndpoint);
return urlBuilder.build();
}
protected String createSinglePsnRequestBody(String id, String targetDomain) {
final var requestParameters = new Parameters();
requestParameters.addParameter().setName("target")
.setValue(new StringType().setValue(psnTargetDomain));
.setValue(new StringType().setValue(targetDomain));
requestParameters.addParameter().setName("original")
.setValue(new StringType().setValue(id));
final IParser iParser = r4Context.newJsonParser();
return iParser.encodeResourceToString(requestParameters);
}
protected String createMultiPsnRequestBody(String id, String targetDomain) {
final var param = new Parameters();
ParametersParameterComponent targetParam = param.addParameter().setName("original");
targetParam.addPart(
new ParametersParameterComponent().setName("target")
.setValue(new StringType(targetDomain)));
targetParam.addPart(
new ParametersParameterComponent().setName("value").setValue(new StringType(id)));
targetParam
.addPart(new ParametersParameterComponent().setName("count").setValue(
new StringType("1")));
final IParser iParser = r4Context.newJsonParser();
return iParser.encodeResourceToString(param);
}
@NotNull
protected HttpHeaders getHttpHeaders(String gPasUserName, String gPasPassword) {
var headers = new HttpHeaders();

12
src/main/java/dev/dnpm/etl/processor/pseudonym/PsnDomainType.java Normal file
View File

@@ -0,0 +1,12 @@
package dev.dnpm.etl.processor.pseudonym;
public enum PsnDomainType {
/**
* one pseudonym per original value
*/
SINGLE_PSN_DOMAIN,
/**
* multiple pseudonymes for one original value
*/
MULTI_PSN_DOMAIN
}

3
src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
View File

@@ -48,7 +48,8 @@ data class PseudonymizeConfigProperties(
@ConfigurationProperties(GPasConfigProperties.NAME)
data class GPasConfigProperties(
val uri: String?,
val target: String = "etl-processor",
val patientDomain: String = "etl-processor",
val genomDeTanDomain: String = "ccdn",
val username: String?,
val password: String?,
) {

15
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt
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@@ -21,9 +21,12 @@ package dev.dnpm.etl.processor.pseudonym
import org.apache.commons.codec.binary.Base32
import org.apache.commons.codec.digest.DigestUtils
import java.security.SecureRandom
class AnonymizingGenerator : Generator {
companion object fun getSecureRandom() : SecureRandom {
return SecureRandom()
}
override fun generate(id: String): String {
return Base32().encodeAsString(DigestUtils.sha256(id))
@@ -31,4 +34,14 @@ class AnonymizingGenerator : Generator {
.lowercase()
}
@OptIn(ExperimentalStdlibApi::class)
override fun generateGenomDeTan(id: String?): String {
val bytes = ByteArray(64 / 2)
getSecureRandom().nextBytes(bytes)
return bytes.joinToString("") { "%02x".format(it) }
}
}

4
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
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@@ -35,6 +35,10 @@ class PseudonymizeService(
}
}
fun genomDeTan(patientId: PatientId): String {
return generator.generateGenomDeTan(patientId.value)
}
fun prefix(): String {
return configProperties.prefix
}

5
src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
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@@ -349,3 +349,8 @@ fun Mtb.ensureMetaDataIsInitialized() {
this.metadata.modelProjectConsent.provisions.toMutableList()
}
}
infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService)
{
this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
}

2
src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
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@@ -38,7 +38,7 @@ class ConsentProcessor(
/**
* In case an instance of {@link ICheckConsent} is active, consent will be embedded and checked.
*
* Logik:
* Logic:
* * <c>true</c> IF consent check is disabled.
* * <c>true</c> IF broad consent (BC) has been given.
* * <c>true</c> BC has been asked AND declined but genomDe consent has been consented.

17
src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
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@@ -30,8 +30,11 @@ import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.monitoring.RequestType
import dev.dnpm.etl.processor.output.*
import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
import dev.dnpm.etl.processor.pseudonym.addGenomDeTan
import dev.dnpm.etl.processor.pseudonym.anonymizeContentWith
import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
import dev.pcvolkmer.mv64e.mtb.ConsentProvision
import dev.pcvolkmer.mv64e.mtb.ModelProjectConsentPurpose
import dev.pcvolkmer.mv64e.mtb.Mtb
import org.apache.commons.codec.binary.Base32
import org.apache.commons.codec.digest.DigestUtils
@@ -76,9 +79,12 @@ class RequestProcessor(
fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
val pid = PatientId(extractPatientIdentifier(mtbFile))
val isConsentOk = consentProcessor != null &&
consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
val isConsentOk =
consentProcessor != null && consentProcessor.consentGatedCheckAndTryEmbedding(mtbFile) || consentProcessor == null
if (isConsentOk) {
if (isGenomDeConsented(mtbFile)) {
mtbFile addGenomDeTan pseudonymizeService
}
mtbFile pseudonymizeWith pseudonymizeService
mtbFile anonymizeContentWith pseudonymizeService
val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
@@ -93,6 +99,13 @@ class RequestProcessor(
}
}
private fun isGenomDeConsented(mtbFile: Mtb): Boolean {
val isModelProjectConsented = mtbFile.metadata?.modelProjectConsent?.provisions?.any { p ->
p.purpose == ModelProjectConsentPurpose.SEQUENCING && p.type == ConsentProvision.PERMIT
} == true
return isModelProjectConsented
}
private fun <T> saveAndSend(request: MtbFileRequest<T>, pid: PatientId) {
requestService.save(
Request(

16
src/test/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeServiceTest.kt
View File

@@ -71,8 +71,8 @@ class PseudonymizeServiceTest {
}
@Test
fun sanitizeFileName(@Mock generator: GpasPseudonymGenerator) {
val result= GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
fun sanitizeFileName() {
val result = GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
assertThat(result).isEqualTo("l___a_bs_1_2_3_")
}
@@ -90,4 +90,16 @@ class PseudonymizeServiceTest {
assertThat(mtbFile.patient.id).isEqualTo("UNKNOWN_123")
}
@Test
fun shouldReturnDifferentValues() {
val ag = AnonymizingGenerator()
val tans = HashSet<String>()
(1..1000).forEach { i ->
val tan = ag.generateGenomDeTan("12345")
assertThat(tan).hasSize(64)
assertThat(tans.add(tan)).`as`("never the same result!").isTrue
}
}
}