Do not append custom prefix to gPAS pseudonym

3 files changed, 62 insertions, 38 deletions

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 1a79850..ab8ce2f 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt
@@ -19,7 +19,6 @@
 
 package dev.dnpm.etl.processor.pseudonym
 
-import de.ukw.ccc.bwhc.dto.MtbFile
 import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties
 
 class PseudonymizeService(
@@ -27,38 +26,11 @@ class PseudonymizeService(
     private val configProperties: PseudonymizeConfigProperties
 ) {
 
-    fun pseudonymize(mtbFile: MtbFile): MtbFile {
-        val patientPseudonym = patientPseudonym(mtbFile.patient.id)
-
-        mtbFile.episode.patient = patientPseudonym
-        mtbFile.carePlans.forEach { it.patient = patientPseudonym }
-        mtbFile.patient.id = patientPseudonym
-        mtbFile.claims.forEach { it.patient = patientPseudonym }
-        mtbFile.consent.patient = patientPseudonym
-        mtbFile.claimResponses.forEach { it.patient = patientPseudonym }
-        mtbFile.diagnoses.forEach { it.patient = patientPseudonym }
-        mtbFile.ecogStatus.forEach { it.patient = patientPseudonym }
-        mtbFile.familyMemberDiagnoses.forEach { it.patient = patientPseudonym }
-        mtbFile.geneticCounsellingRequests.forEach { it.patient = patientPseudonym }
-        mtbFile.histologyReevaluationRequests.forEach { it.patient = patientPseudonym }
-        mtbFile.histologyReports.forEach { it.patient = patientPseudonym }
-        mtbFile.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
-        mtbFile.molecularPathologyFindings.forEach { it.patient = patientPseudonym }
-        mtbFile.molecularTherapies.forEach { it.history.forEach { it.patient = patientPseudonym } }
-        mtbFile.ngsReports.forEach { it.patient = patientPseudonym }
-        mtbFile.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
-        mtbFile.rebiopsyRequests.forEach { it.patient = patientPseudonym }
-        mtbFile.recommendations.forEach { it.patient = patientPseudonym }
-        mtbFile.recommendations.forEach { it.patient = patientPseudonym }
-        mtbFile.responses.forEach { it.patient = patientPseudonym }
-        mtbFile.specimens.forEach { it.patient = patientPseudonym }
-        mtbFile.specimens.forEach { it.patient = patientPseudonym }
-
-        return mtbFile
-    }
-
     fun patientPseudonym(patientId: String): String {
-        return "${configProperties.prefix}_${generator.generate(patientId)}"
+        return when (generator) {
+            is GpasPseudonymGenerator -> generator.generate(patientId)
+            else -> "${configProperties.prefix}_${generator.generate(patientId)}"
+        }
     }
 
 }
\ No newline at end of file
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
new file mode 100644
index 0000000..580785d
--- /dev/null
+++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt
@@ -0,0 +1,50 @@
+/*
+ * This file is part of ETL-Processor
+ *
+ * Copyright (c) 2023  Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published
+ * by the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package dev.dnpm.etl.processor.pseudonym
+
+import de.ukw.ccc.bwhc.dto.MtbFile
+
+infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
+    val patientPseudonym = pseudonymizeService.patientPseudonym(this.patient.id)
+
+    this.episode.patient = patientPseudonym
+    this.carePlans.forEach { it.patient = patientPseudonym }
+    this.patient.id = patientPseudonym
+    this.claims.forEach { it.patient = patientPseudonym }
+    this.consent.patient = patientPseudonym
+    this.claimResponses.forEach { it.patient = patientPseudonym }
+    this.diagnoses.forEach { it.patient = patientPseudonym }
+    this.ecogStatus.forEach { it.patient = patientPseudonym }
+    this.familyMemberDiagnoses.forEach { it.patient = patientPseudonym }
+    this.geneticCounsellingRequests.forEach { it.patient = patientPseudonym }
+    this.histologyReevaluationRequests.forEach { it.patient = patientPseudonym }
+    this.histologyReports.forEach { it.patient = patientPseudonym }
+    this.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
+    this.molecularPathologyFindings.forEach { it.patient = patientPseudonym }
+    this.molecularTherapies.forEach { it.history.forEach { it.patient = patientPseudonym } }
+    this.ngsReports.forEach { it.patient = patientPseudonym }
+    this.previousGuidelineTherapies.forEach { it.patient = patientPseudonym }
+    this.rebiopsyRequests.forEach { it.patient = patientPseudonym }
+    this.recommendations.forEach { it.patient = patientPseudonym }
+    this.recommendations.forEach { it.patient = patientPseudonym }
+    this.responses.forEach { it.patient = patientPseudonym }
+    this.specimens.forEach { it.patient = patientPseudonym }
+    this.specimens.forEach { it.patient = patientPseudonym }
+}
\ No newline at end of file
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 936c1bf..6465e82 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
@@ -27,6 +27,7 @@ import dev.dnpm.etl.processor.monitoring.RequestStatus
 import dev.dnpm.etl.processor.monitoring.RequestType
 import dev.dnpm.etl.processor.output.MtbFileSender
 import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
+import dev.dnpm.etl.processor.pseudonym.pseudonymizeWith
 import org.apache.commons.codec.binary.Base32
 import org.apache.commons.codec.digest.DigestUtils
 import org.slf4j.LoggerFactory
@@ -47,12 +48,13 @@ class RequestProcessor(
 
     fun processMtbFile(mtbFile: MtbFile) {
         val pid = mtbFile.patient.id
-        val pseudonymized = pseudonymizeService.pseudonymize(mtbFile)
 
-        if (isDuplication(pseudonymized)) {
+        mtbFile pseudonymizeWith pseudonymizeService
+
+        if (isDuplication(mtbFile)) {
             requestService.save(
                 Request(
-                    patientId = pseudonymized.patient.id,
+                    patientId = mtbFile.patient.id,
                     pid = pid,
                     fingerprint = fingerprint(mtbFile),
                     status = RequestStatus.DUPLICATION,
@@ -64,19 +66,19 @@ class RequestProcessor(
             return
         }
 
-        val request = MtbFileSender.MtbFileRequest(UUID.randomUUID().toString(), pseudonymized)
+        val request = MtbFileSender.MtbFileRequest(UUID.randomUUID().toString(), mtbFile)
 
         val responseStatus = sender.send(request)
         if (responseStatus.status == MtbFileSender.ResponseStatus.SUCCESS || responseStatus.status == MtbFileSender.ResponseStatus.WARNING) {
             logger.info(
                 "Sent file for Patient '{}' using '{}'",
-                pseudonymized.patient.id,
+                mtbFile.patient.id,
                 sender.javaClass.simpleName
             )
         } else {
             logger.error(
                 "Error sending file for Patient '{}' using '{}'",
-                pseudonymized.patient.id,
+                mtbFile.patient.id,
                 sender.javaClass.simpleName
             )
         }