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

/*
 * This file is part of ETL-Processor
 *
 * Copyright (c) 2023       Comprehensive Cancer Center Mainfranken
 * Copyright (c) 2025-2026  Paul-Christian Volkmer, 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 ca.uhn.fhir.context.FhirContext
import dev.dnpm.etl.processor.config.AppConfigProperties
import dev.dnpm.etl.processor.config.GIcsConfigProperties
import dev.dnpm.etl.processor.config.JacksonConfig
import dev.dnpm.etl.processor.consent.MtbFileConsentService
import dev.dnpm.etl.processor.services.ConsentProcessor
import dev.dnpm.etl.processor.services.ConsentProcessorTest
import dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat
import org.hl7.fhir.r4.model.Bundle
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.assertThrows
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.Mock
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.anyValueClass
import org.mockito.kotlin.doAnswer
import org.mockito.kotlin.whenever
import org.springframework.core.io.ClassPathResource
import tools.jackson.databind.json.JsonMapper
import java.time.Instant
import java.util.*

@ExtendWith(MockitoExtension::class)
class ExtensionsTest {
    fun getJsonMapper(): JsonMapper {
        return JacksonConfig().jsonMapper()
    }

    @Nested
    inner class UsingDnpmV2Datamodel {

        val FAKE_MTB_FILE_PATH = "mv64e-mtb-fake-patient.json"
        val CLEAN_PATIENT_ID = "644bae7a-56f6-4ee8-b02f-c532e65af5b1"

        private fun fakeMtbFile(): Mtb {
            val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
            return getJsonMapper().readValue(mtbFile, Mtb::class.java)
        }

        private fun Mtb.serialized(): String {
            return getJsonMapper().writeValueAsString(this)
        }

        @Test
        fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
            doAnswer {
                it.arguments[0]
                "PSEUDO-ID"
            }
                .whenever(pseudonymizeService)
                .patientPseudonym(anyValueClass())

            val mtbFile = fakeMtbFile()
            mtbFile.ensureMetaDataIsInitialized()
            addConsentData(mtbFile)

            mtbFile.pseudonymizeWith(pseudonymizeService)

            assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
            assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
        }

        private fun addConsentData(mtbFile: Mtb) {
            val gIcsConfigProperties = GIcsConfigProperties("", "", "")
            val appConfigProperties = AppConfigProperties(emptyList())

            val bundle = Bundle()
            val dummyConsent = ConsentProcessorTest.getDummyGenomDeConsent()
            dummyConsent.patient.reference = "Patient/$CLEAN_PATIENT_ID"
            bundle.addEntry().resource = dummyConsent

            ConsentProcessor(
                appConfigProperties,
                gIcsConfigProperties,
                JacksonConfig().jsonMapper(),
                FhirContext.forR4(),
                MtbFileConsentService(),
            )
                .embedBroadConsentResources(mtbFile, bundle)
        }

        @Test
        fun shouldNotThrowExceptionOnNullValues(@Mock pseudonymizeService: PseudonymizeService) {
            doAnswer {
                it.arguments[0]
                "PSEUDO-ID"
            }
                .whenever(pseudonymizeService)
                .patientPseudonym(anyValueClass())

            doAnswer { "TESTDOMAIN" }.whenever(pseudonymizeService).prefix()

            val mtbFile =
                Mtb().apply {
                    this.patient =
                        Patient().apply {
                            this.id = "PID"
                            this.birthDate = Date.from(Instant.now())
                            this.gender = GenderCoding().apply { this.code = GenderCodingCode.MALE }
                        }
                    this.episodesOfCare =
                        listOf(
                            MtbEpisodeOfCare().apply {
                                this.id = "1"
                                this.patient = Reference().apply { this.id = "PID" }
                                this.period = PeriodDate().apply { this.start = Date.from(Instant.now()) }
                            }
                        )
                }

            mtbFile.pseudonymizeWith(pseudonymizeService)
            mtbFile.anonymizeContentWith(pseudonymizeService)

            assertThat(mtbFile.episodesOfCare).hasSize(1)
            assertThat(mtbFile.episodesOfCare.map { it.id }).isNotNull
        }

        @Test
        fun shouldNotContainAnyUuidAfterRehashingOfIds(@Mock pseudonymizeService: PseudonymizeService) {
            doAnswer {
                it.arguments[0]
                "PSEUDO-ID"
            }
                .whenever(pseudonymizeService)
                .patientPseudonym(anyValueClass())

            doAnswer { "TESTDOMAIN" }.whenever(pseudonymizeService).prefix()

            val mtbFile = fakeMtbFile()

            /** replace hex values with random long, so our test does not match false positives */
            mtbFile.ngsReports.forEach { report ->
                report.results.simpleVariants.forEach { simpleVariant ->
                    simpleVariant.externalIds.forEach { extIdValue ->
                        extIdValue.value = Math.random().toLong().toString()
                    }
                }
            }
            mtbFile.ngsReports.forEach { report ->
                report.results.rnaFusions.forEach { simpleVariant ->
                    simpleVariant.externalIds.forEach { extIdValue ->
                        extIdValue.value = Math.random().toLong().toString()
                    }
                    simpleVariant.fusionPartner3Prime?.transcriptId?.value = Math.random().toLong().toString()
                    simpleVariant.fusionPartner5Prime?.transcriptId?.value = Math.random().toLong().toString()
                    simpleVariant.externalIds?.forEach { it?.value = Math.random().toLong().toString() }
                }
            }

            mtbFile.pseudonymizeWith(pseudonymizeService)
            mtbFile.anonymizeContentWith(pseudonymizeService)

            val pattern =
                "\"[a-f0-9]{8}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{4}-[a-f0-9]{12}\"".toRegex().toPattern()
            val input = mtbFile.serialized()
            val matcher = pattern.matcher(input)

            assertThrows<IllegalStateException> {
                matcher.find()
                val posSt = "check at pos: " + matcher.start().toString() + ", " + matcher.end()
                println(posSt + " with " + matcher.group())
            }
                .also { assertThat(it.message).isEqualTo("No match found") }
        }
    }

    @Test
    fun shouldUseSameAnonymIdForDiagnosisAndDiagnosisReferences(
        @Mock pseudonymizeService: PseudonymizeService
    ) {

        doAnswer {
            it.arguments[0]
            "PSEUDO-ID"
        }
            .whenever(pseudonymizeService)
            .patientPseudonym(anyValueClass())

        doAnswer { "TESTDOMAIN" }.whenever(pseudonymizeService).prefix()

        val mtbFile =
            Mtb().apply {
                this.patient =
                    Patient().apply {
                        this.id = "PID"
                        this.birthDate = Date.from(Instant.now())
                        this.gender = GenderCoding().apply { this.code = GenderCodingCode.MALE }
                    }
                this.diagnoses = listOf(MtbDiagnosis().apply { this.id = "Diagnosis-1" })
                this.episodesOfCare =
                    listOf(
                        MtbEpisodeOfCare().apply {
                            this.id = "Episode-1"
                            this.diagnoses = listOf(Reference().apply { this.id = "Diagnosis-1" })
                        }
                    )
                this.guidelineTherapies =
                    listOf(
                        MtbSystemicTherapy().apply {
                            this.id = "Systemic-Therapy-1"
                            this.reason = Reference().apply { this.id = "Diagnosis-1" }
                        }
                    )
                this.guidelineProcedures =
                    listOf(
                        OncoProcedure().apply {
                            this.id = "Onco-Procedure-1"
                            this.reason = Reference().apply { this.id = "Diagnosis-1" }
                        }
                    )
                this.specimens =
                    listOf(
                        TumorSpecimen().apply {
                            this.id = "Specimen-1"
                            this.diagnosis = Reference().apply { this.id = "Diagnosis-1" }
                        }
                    )
            }

        mtbFile.pseudonymizeWith(pseudonymizeService)
        mtbFile.anonymizeContentWith(pseudonymizeService)

        assertThat(mtbFile.diagnoses.first().id)
            .isEqualTo(mtbFile.episodesOfCare.first().diagnoses.first().id)
        assertThat(mtbFile.diagnoses.first().id).isEqualTo(mtbFile.guidelineTherapies.first().reason.id)
        assertThat(mtbFile.diagnoses.first().id)
            .isEqualTo(mtbFile.guidelineProcedures.first().reason.id)
        assertThat(mtbFile.diagnoses.first().id).isEqualTo(mtbFile.specimens.first().diagnosis.id)
    }

    @Test
    fun shouldNotThrowAnyExceptionOnMissingMsiId(@Mock pseudonymizeService: PseudonymizeService) {

        doAnswer {
            it.arguments[0]
            "PSEUDO-ID"
        }
            .whenever(pseudonymizeService)
            .patientPseudonym(anyValueClass())

        doAnswer { "TESTDOMAIN" }.whenever(pseudonymizeService).prefix()

        val mtbFile =
            Mtb().apply {
                this.patient =
                    Patient().apply {
                        this.id = "PID"
                        this.birthDate = Date.from(Instant.now())
                        this.gender = GenderCoding().apply { this.code = GenderCodingCode.MALE }
                    }
                this.msiFindings =
                    listOf(
                        null,
                        Msi.builder().id("1").build(),
                        Msi.builder().build(),
                        Msi.builder().specimen(null).build(),
                        Msi.builder().specimen(Reference.builder().build()).build(),
                    )
            }

        mtbFile.pseudonymizeWith(pseudonymizeService)
        mtbFile.anonymizeContentWith(pseudonymizeService)

        assertThat(mtbFile.msiFindings).isNotNull
        assertThat(mtbFile.msiFindings[1])
            .satisfiesAnyOf(
                { assertThat(it.id).isNull() },
                { assertThat(it.id).isEqualTo("TESTDOMAIN44e20a53bbbf9f3ae39626d05df7014dcd77d6098") },
            )
    }
}