Merge pull request #13 from CCC-MF/issue_12

Transformation of MTBFile data based on rules

4 files changed, 108 insertions, 3 deletions

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 06e730b..6b85603 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt
@@ -24,7 +24,8 @@ import org.springframework.boot.context.properties.ConfigurationProperties
 @ConfigurationProperties(AppConfigProperties.NAME)
 data class AppConfigProperties(
     var bwhcUri: String?,
-    var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN
+    var generator: PseudonymGenerator = PseudonymGenerator.BUILDIN,
+    var transformations: List<TransformationProperties> = listOf()
 ) {
     companion object {
         const val NAME = "app"
@@ -78,4 +79,10 @@ data class KafkaTargetProperties(
 enum class PseudonymGenerator {
     BUILDIN,
     GPAS
-}
\ No newline at end of file
+}
+
+data class TransformationProperties(
+    val path: String,
+    val from: String,
+    val to: String
+)
\ No newline at end of file
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
index 6b15fc0..c8e86fb 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
@@ -25,6 +25,9 @@ import dev.dnpm.etl.processor.pseudonym.AnonymizingGenerator
 import dev.dnpm.etl.processor.pseudonym.Generator
 import dev.dnpm.etl.processor.pseudonym.GpasPseudonymGenerator
 import dev.dnpm.etl.processor.pseudonym.PseudonymizeService
+import dev.dnpm.etl.processor.services.Transformation
+import dev.dnpm.etl.processor.services.TransformationService
+import org.slf4j.LoggerFactory
 import org.springframework.boot.autoconfigure.condition.ConditionalOnProperty
 import org.springframework.boot.context.properties.EnableConfigurationProperties
 import org.springframework.context.annotation.Bean
@@ -41,6 +44,8 @@ import reactor.core.publisher.Sinks
 )
 class AppConfiguration {
 
+    private val logger = LoggerFactory.getLogger(AppConfiguration::class.java)
+
     @ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS")
     @Bean
     fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator {
@@ -71,5 +76,16 @@ class AppConfiguration {
         return Sinks.many().multicast().directBestEffort()
     }
 
+    @Bean
+    fun transformationService(
+        objectMapper: ObjectMapper,
+        configProperties: AppConfigProperties
+    ): TransformationService {
+        logger.info("Apply ${configProperties.transformations.size} transformation rules")
+        return TransformationService(objectMapper, configProperties.transformations.map {
+            Transformation.of(it.path) from it.from to it.to
+        })
+    }
+
 }
 
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 3cd912c..fd9a3f5 100644
--- a/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
@@ -38,6 +38,7 @@ import java.util.*
 @Service
 class RequestProcessor(
     private val pseudonymizeService: PseudonymizeService,
+    private val transformationService: TransformationService,
     private val sender: MtbFileSender,
     private val requestService: RequestService,
     private val objectMapper: ObjectMapper,
@@ -50,7 +51,7 @@ class RequestProcessor(
 
         mtbFile pseudonymizeWith pseudonymizeService
 
-        val request = MtbFileSender.MtbFileRequest(requestId, mtbFile)
+        val request = MtbFileSender.MtbFileRequest(requestId, transformationService.transform(mtbFile))
 
         requestService.save(
             Request(
diff --git a/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt b/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
new file mode 100644
index 0000000..26de550
--- /dev/null
+++ b/src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
@@ -0,0 +1,81 @@
+/*
+ * 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.services
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import com.jayway.jsonpath.JsonPath
+import com.jayway.jsonpath.PathNotFoundException
+import de.ukw.ccc.bwhc.dto.MtbFile
+
+class TransformationService(private val objectMapper: ObjectMapper, private val transformations: List<Transformation>) {
+    fun transform(mtbFile: MtbFile): MtbFile {
+        var json = objectMapper.writeValueAsString(mtbFile)
+
+        transformations.forEach { transformation ->
+            val jsonPath = JsonPath.parse(json)
+
+            try {
+                val before = transformation.path.substringBeforeLast(".")
+                val last = transformation.path.substringAfterLast(".")
+
+                val existingValue = if (transformation.existingValue is Number) transformation.existingValue else transformation.existingValue.toString()
+                val newValue = if (transformation.newValue is Number) transformation.newValue else transformation.newValue.toString()
+
+                jsonPath.set("$.$before.[?]$last", newValue, {
+                    it.item(HashMap::class.java)[last] == existingValue
+                })
+            } catch (e: PathNotFoundException) {
+                // Ignore
+            }
+
+            json = jsonPath.jsonString()
+        }
+
+        return objectMapper.readValue(json, MtbFile::class.java)
+    }
+
+}
+
+class Transformation private constructor(internal val path: String) {
+
+    lateinit var existingValue: Any
+        private set
+    lateinit var newValue: Any
+        private set
+
+    infix fun from(value: Any): Transformation {
+        this.existingValue = value
+        return this
+    }
+
+    infix fun to(value: Any): Transformation {
+        this.newValue = value
+        return this
+    }
+
+    companion object {
+
+        fun of(path: String): Transformation {
+            return Transformation(path)
+        }
+
+    }
+
+}