From 05149bac0b60423cda3865e3119ce87b9e8cba62 Mon Sep 17 00:00:00 2001 From: Paul-Christian Volkmer Date: Mon, 24 Jul 2023 18:50:12 +0200 Subject: Initial commit --- .../dnpm/etl/processor/pseudonym/Generator.java | 26 +++++++ .../pseudonym/GpasPseudonymGenerator.java | 41 +++++++++++ .../dnpm/etl/processor/EtlProcessorApplication.kt | 31 ++++++++ .../dev/dnpm/etl/processor/ServletInitializer.kt | 31 ++++++++ .../etl/processor/config/AppConfigProperties.kt | 77 ++++++++++++++++++++ .../dnpm/etl/processor/config/AppConfiguration.kt | 82 ++++++++++++++++++++++ .../etl/processor/output/KafkaMtbFileSender.kt | 46 ++++++++++++ .../dev/dnpm/etl/processor/output/MtbFileSender.kt | 28 ++++++++ .../dnpm/etl/processor/output/RestMtbFileSender.kt | 62 ++++++++++++++++ .../processor/pseudonym/AnonymizingGenerator.kt | 34 +++++++++ .../etl/processor/pseudonym/PseudonymizeService.kt | 60 ++++++++++++++++ .../dnpm/etl/processor/web/MtbFileController.kt | 52 ++++++++++++++ src/main/resources/application.yml | 5 ++ 13 files changed, 575 insertions(+) create mode 100644 src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java create mode 100644 src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/EtlProcessorApplication.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/ServletInitializer.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/output/MtbFileSender.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt create mode 100644 src/main/kotlin/dev/dnpm/etl/processor/web/MtbFileController.kt create mode 100644 src/main/resources/application.yml (limited to 'src') diff --git a/src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java b/src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java new file mode 100644 index 0000000..e1938ba --- /dev/null +++ b/src/main/java/dev/dnpm/etl/processor/pseudonym/Generator.java @@ -0,0 +1,26 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.pseudonym; + +public interface Generator { + + String generate(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 new file mode 100644 index 0000000..98f4ba6 --- /dev/null +++ b/src/main/java/dev/dnpm/etl/processor/pseudonym/GpasPseudonymGenerator.java @@ -0,0 +1,41 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.pseudonym; + +import java.net.URI; + +public class GpasPseudonymGenerator implements Generator { + + private final URI uri; + + private final String target; + + public GpasPseudonymGenerator(URI uri, String target) { + this.uri = uri; + this.target = target; + } + + @Override + public String generate(String id) { + // TODO Implement this + return "?"; + } + +} diff --git a/src/main/kotlin/dev/dnpm/etl/processor/EtlProcessorApplication.kt b/src/main/kotlin/dev/dnpm/etl/processor/EtlProcessorApplication.kt new file mode 100644 index 0000000..0c4ab68 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/EtlProcessorApplication.kt @@ -0,0 +1,31 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor + +import org.springframework.boot.autoconfigure.SpringBootApplication +import org.springframework.boot.runApplication + +@SpringBootApplication +class EtlProcessorApplication + +fun main(args: Array) { + runApplication(*args) +} + diff --git a/src/main/kotlin/dev/dnpm/etl/processor/ServletInitializer.kt b/src/main/kotlin/dev/dnpm/etl/processor/ServletInitializer.kt new file mode 100644 index 0000000..2618b09 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/ServletInitializer.kt @@ -0,0 +1,31 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor + +import org.springframework.boot.builder.SpringApplicationBuilder +import org.springframework.boot.web.servlet.support.SpringBootServletInitializer + +class ServletInitializer : SpringBootServletInitializer() { + + override fun configure(application: SpringApplicationBuilder): SpringApplicationBuilder { + return application.sources(EtlProcessorApplication::class.java) + } + +} diff --git a/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt new file mode 100644 index 0000000..1575c39 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfigProperties.kt @@ -0,0 +1,77 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.config + +import org.springframework.boot.context.properties.ConfigurationProperties +import java.net.URI +import java.net.URL + +@ConfigurationProperties(AppConfigProperties.NAME) +data class AppConfigProperties( + var bwhc_uri: String?, + var pseudonymizer: Pseudonymizer = Pseudonymizer.BUILDIN +) { + companion object { + const val NAME = "app" + } +} + +@ConfigurationProperties(PseudonymizeConfigProperties.NAME) +data class PseudonymizeConfigProperties( + val prefix: String = "UNKNOWN", +) { + companion object { + const val NAME = "app.pseudonymize" + } +} + +@ConfigurationProperties(GPasConfigProperties.NAME) +data class GPasConfigProperties( + val uri: String?, + val target: String = "etl-processor" +) { + companion object { + const val NAME = "app.pseudonymize.gpas" + } +} + +@ConfigurationProperties(RestTargetProperties.NAME) +data class RestTargetProperties( + val uri: String?, +) { + companion object { + const val NAME = "app.rest" + } +} + +@ConfigurationProperties(KafkaTargetProperties.NAME) +data class KafkaTargetProperties( + val topic: String = "etl-processor", + val servers: String = "" +) { + companion object { + const val NAME = "app.kafka" + } +} + +enum class Pseudonymizer { + BUILDIN, + GPAS +} \ 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 new file mode 100644 index 0000000..ed3be5d --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt @@ -0,0 +1,82 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.config + +import com.fasterxml.jackson.databind.ObjectMapper +import dev.dnpm.etl.processor.output.KafkaMtbFileSender +import dev.dnpm.etl.processor.output.MtbFileSender +import dev.dnpm.etl.processor.output.RestMtbFileSender +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 org.springframework.boot.autoconfigure.condition.ConditionalOnProperty +import org.springframework.boot.context.properties.EnableConfigurationProperties +import org.springframework.context.annotation.Bean +import org.springframework.context.annotation.Configuration +import org.springframework.kafka.core.KafkaTemplate +import java.net.URI + +@Configuration +@EnableConfigurationProperties( + value = [ + AppConfigProperties::class, + PseudonymizeConfigProperties::class, + GPasConfigProperties::class, + RestTargetProperties::class, + KafkaTargetProperties::class + ] +) +class AppConfiguration { + + @ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "GPAS") + @Bean + fun gpasPseudonymGenerator(configProperties: GPasConfigProperties): Generator { + return GpasPseudonymGenerator(URI.create(configProperties.uri!!), configProperties.target) + } + + @ConditionalOnProperty(value = ["app.pseudonymizer"], havingValue = "BUILDIN", matchIfMissing = true) + @Bean + fun buildinPseudonymGenerator(): Generator { + return AnonymizingGenerator() + } + + @Bean + fun pseudonymizeService(generator: Generator, pseudonymizeConfigProperties: PseudonymizeConfigProperties): PseudonymizeService { + return PseudonymizeService(generator, pseudonymizeConfigProperties) + } + + @ConditionalOnProperty(value = ["app.rest.uri"]) + @Bean + fun restMtbFileSender(restTargetProperties: RestTargetProperties): MtbFileSender { + return RestMtbFileSender(restTargetProperties) + } + + @ConditionalOnProperty(value = ["app.kafka.topic", "app.kafka.servers"]) + @Bean + fun kafkaMtbFileSender( + kafkaTemplate: KafkaTemplate, + objectMapper: ObjectMapper + ): MtbFileSender { + return KafkaMtbFileSender(kafkaTemplate, objectMapper) + } + +} + diff --git a/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt b/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt new file mode 100644 index 0000000..0983e35 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/output/KafkaMtbFileSender.kt @@ -0,0 +1,46 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.output + +import com.fasterxml.jackson.databind.ObjectMapper +import de.ukw.ccc.bwhc.dto.MtbFile +import dev.dnpm.etl.processor.config.KafkaTargetProperties +import org.slf4j.LoggerFactory +import org.springframework.kafka.core.KafkaTemplate + +class KafkaMtbFileSender( + private val kafkaTemplate: KafkaTemplate, + private val objectMapper: ObjectMapper +) : MtbFileSender { + + private val logger = LoggerFactory.getLogger(KafkaMtbFileSender::class.java) + + override fun send(mtbFile: MtbFile): Boolean { + return try { + kafkaTemplate.sendDefault(objectMapper.writeValueAsString(mtbFile)) + logger.debug("Sent file via KafkaMtbFileSender") + true + } catch (e: Exception) { + logger.error("An error occured sending to kafka", e) + false + } + } + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/dnpm/etl/processor/output/MtbFileSender.kt b/src/main/kotlin/dev/dnpm/etl/processor/output/MtbFileSender.kt new file mode 100644 index 0000000..f8279db --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/output/MtbFileSender.kt @@ -0,0 +1,28 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.output + +import de.ukw.ccc.bwhc.dto.MtbFile + +interface MtbFileSender { + + fun send(mtbFile: MtbFile): Boolean + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt b/src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt new file mode 100644 index 0000000..018c7d6 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/output/RestMtbFileSender.kt @@ -0,0 +1,62 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.output + +import de.ukw.ccc.bwhc.dto.MtbFile +import dev.dnpm.etl.processor.config.RestTargetProperties +import org.slf4j.LoggerFactory +import org.springframework.http.HttpEntity +import org.springframework.http.HttpHeaders +import org.springframework.http.MediaType +import org.springframework.web.client.RestClientException +import org.springframework.web.client.RestTemplate + +class RestMtbFileSender(private val restTargetProperties: RestTargetProperties) : MtbFileSender { + + private val logger = LoggerFactory.getLogger(RestMtbFileSender::class.java) + + private val restTemplate = RestTemplate() + + override fun send(mtbFile: MtbFile): Boolean { + try { + val headers = HttpHeaders() + headers.contentType = MediaType.APPLICATION_JSON + val entityReq = HttpEntity(mtbFile, headers) + val response = restTemplate.postForEntity( + restTargetProperties.uri!!, + entityReq, + String::class.java + ) + if (!response.statusCode.is2xxSuccessful) { + logger.warn("Error sending to remote system: {}", response.body) + return false + } + logger.debug("Sent file via RestMtbFileSender") + return true + } catch (e: IllegalArgumentException) { + logger.error("Not a valid URI to export to: '{}'", restTargetProperties.uri!!) + } catch (e: RestClientException) { + logger.info(restTargetProperties.uri!!.toString()) + logger.error("Cannot send data to remote system", e) + } + return false + } + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt new file mode 100644 index 0000000..c03db12 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/AnonymizingGenerator.kt @@ -0,0 +1,34 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.pseudonym + +import org.apache.commons.codec.binary.Base32 +import org.apache.commons.codec.digest.DigestUtils + + +class AnonymizingGenerator : Generator { + + override fun generate(id: String): String { + return Base32().encodeAsString(DigestUtils.sha256(id)) + .substring(0..41) + .lowercase() + } + +} \ 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 new file mode 100644 index 0000000..364e296 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/pseudonym/PseudonymizeService.kt @@ -0,0 +1,60 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.pseudonym + +import de.ukw.ccc.bwhc.dto.MtbFile +import dev.dnpm.etl.processor.config.PseudonymizeConfigProperties + +class PseudonymizeService( + private val generator: Generator, + private val configProperties: PseudonymizeConfigProperties +) { + + fun pseudonymize(mtbFile: MtbFile): MtbFile { + val patientPseudonym = "${configProperties.prefix}_${generator.generate(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 + } + +} \ No newline at end of file diff --git a/src/main/kotlin/dev/dnpm/etl/processor/web/MtbFileController.kt b/src/main/kotlin/dev/dnpm/etl/processor/web/MtbFileController.kt new file mode 100644 index 0000000..900b8c8 --- /dev/null +++ b/src/main/kotlin/dev/dnpm/etl/processor/web/MtbFileController.kt @@ -0,0 +1,52 @@ +/* + * 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 . + */ + +package dev.dnpm.etl.processor.web + +import de.ukw.ccc.bwhc.dto.MtbFile +import dev.dnpm.etl.processor.output.MtbFileSender +import dev.dnpm.etl.processor.output.RestMtbFileSender +import dev.dnpm.etl.processor.pseudonym.PseudonymizeService +import org.slf4j.LoggerFactory +import org.springframework.web.bind.annotation.PostMapping +import org.springframework.web.bind.annotation.RequestBody +import org.springframework.web.bind.annotation.RestController + +@RestController +class MtbFileController( + private val pseudonymizeService: PseudonymizeService, + private val senders: List +) { + + private val logger = LoggerFactory.getLogger(MtbFileController::class.java) + + @PostMapping(path = ["/mtbfile"]) + fun mtbFile(@RequestBody mtbFile: MtbFile) { + val pseudonymized = pseudonymizeService.pseudonymize(mtbFile) + senders.forEach { + val success = it.send(pseudonymized) + if (success) { + logger.info("Sent file for Patient '{}' using '{}'", pseudonymized.patient.id, it.javaClass.simpleName) + } else { + logger.error("Error sending file for Patient '{}' using '{}'", pseudonymized.patient.id, it.javaClass.simpleName) + } + } + } + +} \ No newline at end of file diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml new file mode 100644 index 0000000..da543bd --- /dev/null +++ b/src/main/resources/application.yml @@ -0,0 +1,5 @@ +spring: + kafka: + bootstrap-servers: ${app.kafka.servers} + template: + default-topic: ${app.kafka.topic} \ No newline at end of file -- cgit v1.2.3