feat: Participation at genomeDE §64e will trigger creation of a transaction number

README.md

@@ -28,8 +28,13 @@ Konfigurationsparameter
 
 Zusätzlich zur Patienten Identifier Pseudonymisierung müssen Vorgangsummern generiert werden, die
 jede Übertragung eindeutig identifizieren aber gleichzeitig dem Patienten zugeordnet werden können.
-Dies lässt sich durch weitere Pseudonyme abbilden, allerdings werden pro Originalwert mehrere Pseudonyme benötigt. 
+Dies lässt sich durch weitere Pseudonyme abbilden, allerdings werden pro Originalwert mehrere
-Zu diesem Zweck muss in gPas eine **Multi-Pseudonym-Domäne** konfiguriert werden (siehe auch *APP_PSEUDONYMIZE_GPAS_CCDN*).
+Pseudonyme benötigt.
+Zu diesem Zweck muss in gPas eine **Multi-Pseudonym-Domäne** konfiguriert werden (siehe auch
+*APP_PSEUDONYMIZE_GPAS_CCDN*).
+
+**WICHTIG:** Deaktivierte Pseudonymisierung ist nur für Tests nutzbar. Vorgangsummern sind zufällig
+und werden anschließend verworfen.
 
 ### Datenübermittlung über HTTP/REST
 
@@ -110,7 +115,8 @@ Wurde die Verwendung von gPAS konfiguriert, so sind weitere Angaben zu konfiguri
 * `APP_PSEUDONYMIZE_GPAS_TARGET`: gPas Domänenname für Patienten ID
 * `APP_PSEUDONYMIZE_GPAS_USERNAME`: gPas Basic-Auth Benutzername
 * `APP_PSEUDONYMIZE_GPAS_PASSWORD`: gPas Basic-Auth Passwort
-* `APP_PSEUDONYMIZE_GPAS_CCDN`: gPas Multi-Pseudonym-Domäne für genomDE Vorgangsnummern (Clinical data node)
+* `APP_PSEUDONYMIZE_GPAS_GENOM_DE_DOMAIN`: gPas Multi-Pseudonym-Domäne für genomDE Vorgangsnummern (
+  Clinical data node)
 
 ### Anmeldung mit einem Passwort
 

build.gradle.kts

@@ -90,6 +90,7 @@ dependencies {
     implementation("org.webjars:webjars-locator:${versions["webjars-locator"]}")
     implementation("org.webjars.npm:echarts:${versions["echarts"]}")
     implementation("org.webjars.npm:htmx.org:${versions["htmx.org"]}")
+    implementation ("org.apache.commons:commons-math3:3.6.1")
 
     runtimeOnly("org.mariadb.jdbc:mariadb-java-client")
     runtimeOnly("org.postgresql:postgresql")

src/integrationTest/kotlin/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGeneratorTest.kt

@@ -48,7 +48,7 @@ class GpasPseudonymGeneratorTest {
         val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(1)).build()
         val gPasConfigProperties = GPasConfigProperties(
             "https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate",
-            "test",
+            "test", "test2",
             null,
             null
         )
@@ -64,7 +64,13 @@ class GpasPseudonymGeneratorTest {
             method(HttpMethod.POST)
             requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
         }.andRespond {
-            withStatus(HttpStatus.OK).body(getDummyResponseBody("1234", "test", "test1234ABCDEF567890"))
+            withStatus(HttpStatus.OK).body(
+                getDummyResponseBody(
+                    "1234",
+                    "test",
+                    "test1234ABCDEF567890"
+                )
+            )
                 .createResponse(it)
         }
 
@@ -90,7 +96,10 @@ class GpasPseudonymGeneratorTest {
             requestTo("https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
         }.andRespond {
             withStatus(HttpStatus.FOUND)
-                .header(HttpHeaders.LOCATION, "https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate")
+                .header(
+                    HttpHeaders.LOCATION,
+                    "https://localhost/ttp-fhir/fhir/gpas/\$pseudonymizeAllowCreate"
+                )
                 .createResponse(it)
         }
 

src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java

@@ -23,4 +23,6 @@ public interface Generator {
 
     String generate(String id);
 
+    String generateGenomDeTan(String id);
+
 }

src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java

@@ -38,30 +38,41 @@ public class GpasPseudonymGenerator implements Generator {
 
     private final static FhirContext r4Context = FhirContext.forR4();
     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 genomDeDomain;
+    private final @NotNull String psnTargetDomain;
 
-    public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate, RestTemplate restTemplate) {
+    public GpasPseudonymGenerator(GPasConfigProperties gpasCfg, RetryTemplate retryTemplate,
+        RestTemplate restTemplate) {
         this.retryTemplate = retryTemplate;
         this.restTemplate = restTemplate;
         this.gPasUrl = gpasCfg.getUri();
         this.psnTargetDomain = gpasCfg.getTarget();
+        this.genomDeDomain = gpasCfg.getGenomDeDomain();
         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);
+        return generate(id, psnTargetDomain);
+    }
+
+    @Override
+    public String generateGenomDeTan(String id) {
+        return generate(id, genomDeDomain);
+    }
+
+    protected String generate(String id, String targetDomain) {
+        var gPasRequestBody = getGpasRequestBody(id, targetDomain);
         var responseEntity = getGpasPseudonym(gPasRequestBody);
         var gPasPseudonymResult = (Parameters) r4Context.newJsonParser()
-                .parseResource(responseEntity.getBody());
+            .parseResource(responseEntity.getBody());
 
         return unwrapPseudonym(gPasPseudonymResult);
     }
@@ -75,9 +86,9 @@ public class GpasPseudonymGenerator implements Generator {
         }
 
         final var identifier = (Identifier) parameters.get().getPart().stream()
-                .filter(a -> a.getName().equals("pseudonym"))
+            .filter(a -> a.getName().equals("pseudonym"))
-                .findFirst()
+            .findFirst()
-                .orElseGet(ParametersParameterComponent::new).getValue();
+            .orElseGet(ParametersParameterComponent::new).getValue();
 
         // pseudonym
         return sanitizeValue(identifier.getValue());
@@ -106,8 +117,8 @@ public class GpasPseudonymGenerator implements Generator {
 
         try {
             responseEntity = retryTemplate.execute(
-                    ctx -> restTemplate.exchange(gPasUrl, HttpMethod.POST, requestEntity,
+                ctx -> restTemplate.exchange(gPasUrl, HttpMethod.POST, requestEntity,
-                            String.class));
+                    String.class));
 
             if (responseEntity.getStatusCode().is2xxSuccessful()) {
                 log.debug("API request succeeded. Response: {}", responseEntity.getStatusCode());
@@ -119,16 +130,16 @@ public class GpasPseudonymGenerator implements Generator {
             return responseEntity;
         } catch (Exception unexpected) {
             throw new PseudonymRequestFailed(
-                    "API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
+                "API request due unexpected error unsuccessful gPas unsuccessful.", unexpected);
         }
     }
 
-    protected String getGpasRequestBody(String id) {
+    protected String getGpasRequestBody(String id, String targetDomain) {
         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));
+            .setValue(new StringType().setValue(id));
         final IParser iParser = r4Context.newJsonParser();
         return iParser.encodeResourceToString(requestParameters);
     }

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

@@ -48,6 +48,7 @@ data class PseudonymizeConfigProperties(
 data class GPasConfigProperties(
     val uri: String?,
     val target: String = "etl-processor",
+    val genomDeDomain: String = "ccdn",
     val username: String?,
     val password: String?,
 ) {

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt

@@ -21,6 +21,7 @@ package dev.dnpm.etl.processor.pseudonym
 
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
+import org.apache.commons.math3.random.RandomDataGenerator
 
 
 class AnonymizingGenerator : Generator {
@@ -31,4 +32,9 @@ class AnonymizingGenerator : Generator {
             .lowercase()
     }
 
+    override fun generateGenomDeTan(id: String?): String? {
+        val randomDataGenerator = RandomDataGenerator()
+        return randomDataGenerator.nextSecureHexString(64).lowercase()
+    }
+
 }

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt

@@ -35,6 +35,10 @@ class PseudonymizeService(
         }
     }
 
+    fun genomDeTan(patientId: PatientId): String {
+        return generator.generateGenomDeTan(patientId.value)
+    }
+
     fun prefix(): String {
         return configProperties.prefix
     }

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt

@@ -317,3 +317,8 @@ infix fun Mtb.anonymizeContentWith(pseudonymizeService: PseudonymizeService) {
 
     // TODO all other properties
 }
+
+infix fun Mtb.addGenomDeTan(pseudonymizeService: PseudonymizeService)
+{
+    this.metadata.transferTan = pseudonymizeService.genomDeTan(PatientId(this.patient.id))
+}

src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt

@@ -29,8 +29,11 @@ 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
@@ -68,6 +71,13 @@ class RequestProcessor(
 
     fun processMtbFile(mtbFile: Mtb, requestId: RequestId) {
         val pid = PatientId(mtbFile.patient.id)
+        val isModelProjectConsented = mtbFile.metadata?.modelProjectConsent?.provisions?.any { p ->
+            p.purpose == ModelProjectConsentPurpose.SEQUENCING
+                    && p.type == ConsentProvision.PERMIT
+        } == true
+        if (isModelProjectConsented) {
+            mtbFile addGenomDeTan pseudonymizeService
+        }
         mtbFile pseudonymizeWith pseudonymizeService
         mtbFile anonymizeContentWith pseudonymizeService
         val request = DnpmV2MtbFileRequest(requestId, transformationService.transform(mtbFile))
@@ -120,11 +130,14 @@ class RequestProcessor(
 
         val lastMtbFileRequestForPatient =
             requestService.lastMtbFileRequestForPatientPseudonym(patientPseudonym)
-        val isLastRequestDeletion = requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
+        val isLastRequestDeletion =
+            requestService.isLastRequestWithKnownStatusDeletion(patientPseudonym)
 
         return null != lastMtbFileRequestForPatient
                 && !isLastRequestDeletion
-                && lastMtbFileRequestForPatient.fingerprint == fingerprint(pseudonymizedMtbFileRequest)
+                && lastMtbFileRequestForPatient.fingerprint == fingerprint(
+            pseudonymizedMtbFileRequest
+        )
     }
 
     fun processDeletion(patientId: PatientId) {

src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt

@@ -207,7 +207,7 @@ class ExtensionsTest {
     inner class UsingDnpmV2Datamodel {
 
         val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
-        val CLEAN_PATIENT_ID = "aca5a971-28be-4089-8128-0036a4fe6f1a"
+        val CLEAN_PATIENT_ID = "644bae7a-56f6-4ee8-b02f-c532e65af5b1"
 
         private fun fakeMtbFile(): Mtb {
             val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream

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

@@ -72,7 +72,7 @@ class PseudonymizeServiceTest {
 
     @Test
     fun sanitizeFileName(@Mock generator: GpasPseudonymGenerator) {
-        val result= GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
+        val result = GpasPseudonymGenerator.sanitizeValue("l://a\\bs;1*2?3>")
 
         assertThat(result).isEqualTo("l___a_bs_1_2_3_")
     }
@@ -90,4 +90,10 @@ class PseudonymizeServiceTest {
         assertThat(mtbFile.patient.id).isEqualTo("UNKNOWN_123")
     }
 
+    @Test
+    fun shouldReturnDifferentValues() {
+        val ag = AnonymizingGenerator()
+        val tan = ag.generateGenomDeTan("12345")
+        assertThat(tan).hasSize(64)
+    }
 }