119 add transaction (#124)

9 files changed, 132 insertions, 21 deletions

diff --git a/src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java b/src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java
index e1938ba..8d0d0c1 100644
--- a/src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java
+++ b/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);
+
 }
diff --git a/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java b/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java
index a22100b..6a2b947 100644
--- a/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java
+++ b/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java
@@ -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);
+    }
+
+    @Override
+    public String generateGenomDeTan(String id) {
+        return generate(id, PsnDomainType.MULTI_PSN_DOMAIN);
+    }
 
-        return unwrapPseudonym(gPasPseudonymResult);
+    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();
diff --git a/src/main/java/dev/dnpm/etl/processor/pseudonym/PsnDomainType.java b/src/main/java/dev/dnpm/etl/processor/pseudonym/PsnDomainType.java
new file mode 100644
index 0000000..a0fbc93
--- /dev/null
+++ b/src/main/java/dev/dnpm/etl/processor/pseudonym/PsnDomainType.java
@@ -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
+}
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
index a2ea032..207785e 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
@@ -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?,
 ) {
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt
index c03db12..0537cbb 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt
@@ -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) }
+
+    }
+
 }
\ No newline at end of file
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
index e80f6ec..96225a9 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
+++ b/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
     }
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
index 77f3399..50d5b20 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
@@ -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))
+}
\ No newline at end of file
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
index 3841641..11aff57 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/ConsentProcessor.kt
@@ -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.
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
index bb226c0..f2e8390 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
@@ -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(