mirror of
https://github.com/pcvolkmer/mv64e-etl-processor
synced 2025-09-14 01:12:51 +00:00
feat: use issue severity to create status (#90)
This commit is contained in:
GitHub
@@ -19,14 +19,18 @@
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package dev.dnpm.etl.processor.output
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import com.fasterxml.jackson.databind.ObjectMapper
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import com.fasterxml.jackson.module.kotlin.KotlinModule
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import de.ukw.ccc.bwhc.dto.*
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import dev.dnpm.etl.processor.PatientPseudonym
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import dev.dnpm.etl.processor.RequestId
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import dev.dnpm.etl.processor.config.RestTargetProperties
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import dev.dnpm.etl.processor.monitoring.ReportService
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import org.assertj.core.api.Assertions.assertThat
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import org.junit.jupiter.api.BeforeEach
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import org.junit.jupiter.params.ParameterizedTest
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import org.junit.jupiter.params.provider.Arguments
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import org.junit.jupiter.params.provider.MethodSource
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import org.springframework.http.HttpMethod
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import org.springframework.http.HttpStatus
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@@ -45,6 +49,8 @@ class RestBwhcMtbFileSenderTest {
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private lateinit var restMtbFileSender: RestMtbFileSender
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private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
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@BeforeEach
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fun setup() {
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val restTemplate = RestTemplate()
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@@ -53,7 +59,8 @@ class RestBwhcMtbFileSenderTest {
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this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
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this.restMtbFileSender = RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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this.restMtbFileSender =
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RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
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}
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@ParameterizedTest
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@@ -94,7 +101,8 @@ class RestBwhcMtbFileSenderTest {
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val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
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this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
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this.restMtbFileSender = RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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this.restMtbFileSender =
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RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
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val expectedCount = when (requestWithResponse.httpStatus) {
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// OK - No Retry
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@@ -123,7 +131,8 @@ class RestBwhcMtbFileSenderTest {
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val retryTemplate = RetryTemplateBuilder().customPolicy(SimpleRetryPolicy(3)).build()
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this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
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this.restMtbFileSender = RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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this.restMtbFileSender =
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RestBwhcMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
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val expectedCount = when (requestWithResponse.httpStatus) {
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// OK - No Retry
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@@ -154,24 +163,6 @@ class RestBwhcMtbFileSenderTest {
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val TEST_REQUEST_ID = RequestId("TestId")
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val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
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private val warningBody = """
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{
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"patient_id": "PID",
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"issues": [
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{ "severity": "warning", "message": "Something is not right" }
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]
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}
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""".trimIndent()
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private val errorBody = """
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{
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"patient_id": "PID",
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"issues": [
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{ "severity": "error", "message": "Something is very bad" }
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]
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}
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""".trimIndent()
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val mtbFile: MtbFile = MtbFile.builder()
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.withPatient(
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Patient.builder()
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@@ -205,21 +196,34 @@ class RestBwhcMtbFileSenderTest {
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@JvmStatic
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fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
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return setOf(
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RequestWithResponse(HttpStatus.OK, "{}", MtbFileSender.Response(RequestStatus.SUCCESS, "{}")),
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RequestWithResponse(
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HttpStatus.OK,
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responseBodyWithMaxSeverity(ReportService.Severity.INFO),
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MtbFileSender.Response(
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RequestStatus.SUCCESS,
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responseBodyWithMaxSeverity(ReportService.Severity.INFO)
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)
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),
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RequestWithResponse(
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HttpStatus.CREATED,
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warningBody,
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MtbFileSender.Response(RequestStatus.WARNING, warningBody)
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responseBodyWithMaxSeverity(ReportService.Severity.WARNING),
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MtbFileSender.Response(
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RequestStatus.WARNING,
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responseBodyWithMaxSeverity(ReportService.Severity.WARNING)
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)
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),
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RequestWithResponse(
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HttpStatus.BAD_REQUEST,
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ERROR_RESPONSE_BODY,
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MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
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responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
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MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
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),
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RequestWithResponse(
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HttpStatus.UNPROCESSABLE_ENTITY,
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errorBody,
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MtbFileSender.Response(RequestStatus.ERROR, errorBody)
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responseBodyWithMaxSeverity(ReportService.Severity.FATAL),
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MtbFileSender.Response(
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RequestStatus.ERROR,
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responseBodyWithMaxSeverity(ReportService.Severity.FATAL)
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)
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),
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// Some more errors not mentioned in documentation
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RequestWithResponse(
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@@ -256,6 +260,52 @@ class RestBwhcMtbFileSenderTest {
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)
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)
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}
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fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String {
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return when (severity) {
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ReportService.Severity.INFO -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" }
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]
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}
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"""
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ReportService.Severity.WARNING -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" },
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{ "severity": "warning", "message": "Warning Message" }
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]
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}
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"""
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ReportService.Severity.ERROR -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" },
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{ "severity": "warning", "message": "Warning Message" },
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{ "severity": "error", "message": "Error Message" }
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]
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}
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"""
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ReportService.Severity.FATAL -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" },
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{ "severity": "warning", "message": "Warning Message" },
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{ "severity": "error", "message": "Error Message" },
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{ "severity": "fatal", "message": "Fatal Message" }
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]
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}
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"""
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}
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}
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}
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@@ -19,13 +19,17 @@
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package dev.dnpm.etl.processor.output
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import com.fasterxml.jackson.databind.ObjectMapper
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import com.fasterxml.jackson.module.kotlin.KotlinModule
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import de.ukw.ccc.bwhc.dto.*
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import dev.dnpm.etl.processor.PatientPseudonym
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import dev.dnpm.etl.processor.RequestId
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import dev.dnpm.etl.processor.config.AppConfigProperties
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import dev.dnpm.etl.processor.config.AppConfiguration
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import dev.dnpm.etl.processor.config.RestTargetProperties
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import dev.dnpm.etl.processor.monitoring.ReportService
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import dev.dnpm.etl.processor.output.RestBwhcMtbFileSenderTest.Companion
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import org.assertj.core.api.Assertions.assertThat
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import org.junit.jupiter.api.BeforeEach
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import org.junit.jupiter.params.ParameterizedTest
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@@ -48,6 +52,8 @@ class RestDipMtbFileSenderTest {
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private lateinit var restMtbFileSender: RestMtbFileSender
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private var reportService = ReportService(ObjectMapper().registerModule(KotlinModule.Builder().build()))
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@BeforeEach
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fun setup() {
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val restTemplate = RestTemplate()
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@@ -56,7 +62,7 @@ class RestDipMtbFileSenderTest {
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this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
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this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
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}
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@ParameterizedTest
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@@ -98,11 +104,14 @@ class RestDipMtbFileSenderTest {
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retryTemplate.setBackOffPolicy(NoBackOffPolicy())
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this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
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this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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this.restMtbFileSender =
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RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
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val expectedCount = when (requestWithResponse.httpStatus) {
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// OK - No Retry
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HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(1)
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HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
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1
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)
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// Request failed - Retry max 3 times
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else -> ExpectedCount.max(3)
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}
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@@ -128,11 +137,14 @@ class RestDipMtbFileSenderTest {
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retryTemplate.setBackOffPolicy(NoBackOffPolicy())
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this.mockRestServiceServer = MockRestServiceServer.createServer(restTemplate)
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this.restMtbFileSender = RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate)
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this.restMtbFileSender =
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RestDipMtbFileSender(restTemplate, restTargetProperties, retryTemplate, reportService)
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val expectedCount = when (requestWithResponse.httpStatus) {
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// OK - No Retry
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HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(1)
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HttpStatus.OK, HttpStatus.CREATED, HttpStatus.UNPROCESSABLE_ENTITY, HttpStatus.BAD_REQUEST -> ExpectedCount.max(
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1
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)
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// Request failed - Retry max 3 times
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else -> ExpectedCount.max(3)
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}
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@@ -159,24 +171,6 @@ class RestDipMtbFileSenderTest {
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val TEST_REQUEST_ID = RequestId("TestId")
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val TEST_PATIENT_PSEUDONYM = PatientPseudonym("PID")
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private val warningBody = """
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{
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"patient_id": "PID",
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"issues": [
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{ "severity": "warning", "message": "Something is not right" }
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]
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}
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""".trimIndent()
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private val errorBody = """
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{
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"patient_id": "PID",
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"issues": [
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{ "severity": "error", "message": "Something is very bad" }
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]
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}
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""".trimIndent()
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val mtbFile: MtbFile = MtbFile.builder()
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.withPatient(
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Patient.builder()
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@@ -210,21 +204,28 @@ class RestDipMtbFileSenderTest {
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@JvmStatic
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fun mtbFileRequestWithResponseSource(): Set<RequestWithResponse> {
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return setOf(
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RequestWithResponse(HttpStatus.OK, "{}", MtbFileSender.Response(RequestStatus.SUCCESS, "{}")),
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RequestWithResponse(
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HttpStatus.OK,
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responseBodyWithMaxSeverity(ReportService.Severity.INFO),
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MtbFileSender.Response(
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RequestStatus.SUCCESS,
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responseBodyWithMaxSeverity(ReportService.Severity.INFO)
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)
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),
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RequestWithResponse(
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HttpStatus.CREATED,
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warningBody,
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MtbFileSender.Response(RequestStatus.WARNING, warningBody)
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responseBodyWithMaxSeverity(ReportService.Severity.WARNING),
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MtbFileSender.Response(RequestStatus.WARNING, responseBodyWithMaxSeverity(ReportService.Severity.WARNING))
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),
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RequestWithResponse(
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HttpStatus.BAD_REQUEST,
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ERROR_RESPONSE_BODY,
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MtbFileSender.Response(RequestStatus.ERROR, ERROR_RESPONSE_BODY)
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responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
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MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
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),
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RequestWithResponse(
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HttpStatus.UNPROCESSABLE_ENTITY,
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errorBody,
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MtbFileSender.Response(RequestStatus.ERROR, errorBody)
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responseBodyWithMaxSeverity(ReportService.Severity.ERROR),
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MtbFileSender.Response(RequestStatus.ERROR, responseBodyWithMaxSeverity(ReportService.Severity.ERROR))
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),
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// Some more errors not mentioned in documentation
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RequestWithResponse(
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@@ -261,6 +262,52 @@ class RestDipMtbFileSenderTest {
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)
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)
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}
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fun responseBodyWithMaxSeverity(severity: ReportService.Severity): String {
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return when (severity) {
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ReportService.Severity.INFO -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" }
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]
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}
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"""
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ReportService.Severity.WARNING -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" },
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{ "severity": "warning", "message": "Warning Message" }
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]
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}
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"""
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ReportService.Severity.ERROR -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" },
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{ "severity": "warning", "message": "Warning Message" },
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{ "severity": "error", "message": "Error Message" }
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]
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}
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"""
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ReportService.Severity.FATAL -> """
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{
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"patient": "PID",
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"issues": [
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{ "severity": "info", "message": "Info Message" },
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{ "severity": "warning", "message": "Warning Message" },
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{ "severity": "error", "message": "Error Message" },
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{ "severity": "fatal", "message": "Fatal Message" }
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]
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}
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"""
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}
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}
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}
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@@ -1,7 +1,7 @@
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/*
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* This file is part of ETL-Processor
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*
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* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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* Copyright (c) 2025 Comprehensive Cancer Center Mainfranken, Datenintegrationszentrum Philipps-Universität Marburg and Contributors
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*
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU Affero General Public License as published
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@@ -22,9 +22,14 @@ package dev.dnpm.etl.processor.services
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import com.fasterxml.jackson.databind.ObjectMapper
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import com.fasterxml.jackson.module.kotlin.KotlinModule
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import dev.dnpm.etl.processor.monitoring.ReportService
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import dev.dnpm.etl.processor.monitoring.RequestStatus
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import dev.dnpm.etl.processor.monitoring.asRequestStatus
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import org.assertj.core.api.Assertions.assertThat
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import org.junit.jupiter.api.BeforeEach
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import org.junit.jupiter.api.Test
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import org.junit.jupiter.params.ParameterizedTest
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import org.junit.jupiter.params.provider.Arguments
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import org.junit.jupiter.params.provider.MethodSource
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class ReportServiceTest {
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@@ -60,6 +65,15 @@ class ReportServiceTest {
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assertThat(actual[2].message).isEqualTo("Warning Message")
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assertThat(actual[3].severity).isEqualTo(ReportService.Severity.INFO)
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assertThat(actual[3].message).isEqualTo("Info Message")
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assertThat(actual.asRequestStatus()).isEqualTo(RequestStatus.ERROR)
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}
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|
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@ParameterizedTest
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@MethodSource("testData")
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fun shouldParseDataQualityReport(json: String, requestStatus: RequestStatus) {
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val actual = this.reportService.deserialize(json)
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assertThat(actual.asRequestStatus()).isEqualTo(requestStatus)
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}
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@Test
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@@ -73,4 +87,75 @@ class ReportServiceTest {
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assertThat(actual[0].message).isEqualTo("Not parsable data quality report '$invalidResponse'")
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}
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|
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companion object {
|
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|
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@JvmStatic
|
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fun testData(): Set<Arguments> {
|
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return setOf(
|
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Arguments.of(
|
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"""
|
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{
|
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"patient": "4711",
|
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"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" },
|
||||
{ "severity": "fatal", "message": "Fatal Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.ERROR
|
||||
),
|
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Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
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"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" },
|
||||
{ "severity": "error", "message": "Error Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.ERROR
|
||||
),
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "error", "message": "Error Message" }
|
||||
{ "severity": "info", "message": "Info Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.ERROR
|
||||
),
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" },
|
||||
{ "severity": "warning", "message": "Warning Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.WARNING
|
||||
),
|
||||
Arguments.of(
|
||||
"""
|
||||
{
|
||||
"patient": "4711",
|
||||
"issues": [
|
||||
{ "severity": "info", "message": "Info Message" }
|
||||
]
|
||||
}
|
||||
""".trimIndent(),
|
||||
RequestStatus.SUCCESS
|
||||
)
|
||||
)
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
Reference in New Issue
Block a user