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Code Issues Releases Activity

Issue #12: Transform MTBFile objects by using transformation rules

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This commit is contained in:
Paul-Christian Volkmer 2023-10-05 12:09:56 +02:00
parent 2824951e5e
commit 4196664060
5 changed files with 41 additions and 22 deletions
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10
src/main/kotlin/dev/dnpm/etl/processor/config/AppConfiguration.kt
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@ -26,6 +26,7 @@ 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.springframework.boot.autoconfigure.condition.ConditionalOnProperty
import org.springframework.boot.context.properties.EnableConfigurationProperties
import org.springframework.context.annotation.Bean
@ -73,10 +74,13 @@ class AppConfiguration {
}
@Bean
fun transformations(configProperties: AppConfigProperties): List<Transformation> {
return configProperties.transformations.map {
fun transformationService(
objectMapper: ObjectMapper,
configProperties: AppConfigProperties
): TransformationService {
return TransformationService(objectMapper, configProperties.transformations.map {
Transformation.of(it.path) from it.from to it.to
}
})
}
}

3
src/main/kotlin/dev/dnpm/etl/processor/services/RequestProcessor.kt
View File

@ -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(

4
src/main/kotlin/dev/dnpm/etl/processor/services/TransformationService.kt
View File

@ -24,8 +24,8 @@ import com.jayway.jsonpath.JsonPath
import com.jayway.jsonpath.PathNotFoundException
import de.ukw.ccc.bwhc.dto.MtbFile
class TransformationService(private val objectMapper: ObjectMapper) {
fun transform(mtbFile: MtbFile, vararg transformations: Transformation): 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 ->

21
src/test/kotlin/dev/dnpm/etl/processor/services/RequestProcessorTest.kt
View File

@ -37,6 +37,7 @@ import org.mockito.Mockito.*
import org.mockito.junit.jupiter.MockitoExtension
import org.mockito.kotlin.any
import org.mockito.kotlin.argumentCaptor
import org.mockito.kotlin.whenever
import org.springframework.context.ApplicationEventPublisher
import java.time.Instant
import java.util.*
@ -46,6 +47,7 @@ import java.util.*
class RequestProcessorTest {
private lateinit var pseudonymizeService: PseudonymizeService
private lateinit var transformationService: TransformationService
private lateinit var sender: MtbFileSender
private lateinit var requestService: RequestService
private lateinit var applicationEventPublisher: ApplicationEventPublisher
@ -55,11 +57,13 @@ class RequestProcessorTest {
@BeforeEach
fun setup(
@Mock pseudonymizeService: PseudonymizeService,
@Mock transformationService: TransformationService,
@Mock sender: RestMtbFileSender,
@Mock requestService: RequestService,
@Mock applicationEventPublisher: ApplicationEventPublisher
) {
this.pseudonymizeService = pseudonymizeService
this.transformationService = transformationService
this.sender = sender
this.requestService = requestService
this.applicationEventPublisher = applicationEventPublisher
@ -68,6 +72,7 @@ class RequestProcessorTest {
requestProcessor = RequestProcessor(
pseudonymizeService,
transformationService,
sender,
requestService,
objectMapper,
@ -98,6 +103,10 @@ class RequestProcessorTest {
it.arguments[0] as String
}.`when`(pseudonymizeService).patientPseudonym(any())
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any())
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
@ -153,6 +162,10 @@ class RequestProcessorTest {
it.arguments[0] as String
}.`when`(pseudonymizeService).patientPseudonym(any())
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any())
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
@ -212,6 +225,10 @@ class RequestProcessorTest {
it.arguments[0] as String
}.`when`(pseudonymizeService).patientPseudonym(any())
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any())
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()
@ -271,6 +288,10 @@ class RequestProcessorTest {
it.arguments[0] as String
}.`when`(pseudonymizeService).patientPseudonym(any())
doAnswer {
it.arguments[0]
}.whenever(transformationService).transform(any())
val mtbFile = MtbFile.builder()
.withPatient(
Patient.builder()

25
src/test/kotlin/dev/dnpm/etl/processor/services/TransformationServiceTest.kt
View File

@ -34,15 +34,16 @@ class TransformationServiceTest {
@BeforeEach
fun setup() {
this.service = TransformationService(ObjectMapper())
this.service = TransformationService(
ObjectMapper(), listOf(
Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED,
Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
)
)
}
@Test
fun shouldTransformMtbFile() {
val transformations = arrayOf(
Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
)
val mtbFile = MtbFile.builder().withDiagnoses(
listOf(
Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
@ -51,7 +52,7 @@ class TransformationServiceTest {
)
).build()
val actual = this.service.transform(mtbFile, *transformations)
val actual = this.service.transform(mtbFile)
assertThat(actual).isNotNull
assertThat(actual.diagnoses[0].icd10.version).isEqualTo("2014")
@ -59,10 +60,6 @@ class TransformationServiceTest {
@Test
fun shouldOnlyTransformGivenValues() {
val transformations = arrayOf(
Transformation.of("diagnoses[*].icd10.version") from "2013" to "2014",
)
val mtbFile = MtbFile.builder().withDiagnoses(
listOf(
Diagnosis.builder().withId("1234").withIcd10(Icd10("F79.9").also {
@ -74,7 +71,7 @@ class TransformationServiceTest {
)
).build()
val actual = this.service.transform(mtbFile, *transformations)
val actual = this.service.transform(mtbFile)
assertThat(actual).isNotNull
assertThat(actual.diagnoses[0].icd10.code).isEqualTo("F79.9")
@ -85,15 +82,11 @@ class TransformationServiceTest {
@Test
fun shouldTransformMtbFileWithConsentEnum() {
val transformations = arrayOf(
Transformation.of("consent.status") from Consent.Status.ACTIVE to Consent.Status.REJECTED,
)
val mtbFile = MtbFile.builder().withConsent(
Consent("123", "456", Consent.Status.ACTIVE)
).build()
val actual = this.service.transform(mtbFile, *transformations)
val actual = this.service.transform(mtbFile)
assertThat(actual.consent).isNotNull
assertThat(actual.consent.status).isEqualTo(Consent.Status.REJECTED)