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/*
* This file is part of ETL-Processor
*
* Copyright (c) 2023 Comprehensive Cancer Center Mainfranken
* Copyright (c) 2023-2026 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
import dev.dnpm.etl.processor.monitoring.RequestRepository
import dev.dnpm.etl.processor.monitoring.RequestStatus
import dev.dnpm.etl.processor.output.DnpmV2MtbFileRequest
import dev.dnpm.etl.processor.output.MtbFileSender
import dev.pcvolkmer.mv64e.mtb.*
import org.assertj.core.api.Assertions.assertThat
import org.junit.jupiter.api.BeforeEach
import org.junit.jupiter.api.Nested
import org.junit.jupiter.api.Test
import org.junit.jupiter.api.extension.ExtendWith
import org.mockito.kotlin.*
import org.springframework.beans.factory.annotation.Autowired
import org.springframework.boot.webmvc.test.autoconfigure.AutoConfigureMockMvc
import org.springframework.boot.test.context.SpringBootTest
import org.springframework.context.ApplicationContext
import org.springframework.http.MediaType
import org.springframework.security.test.web.servlet.request.SecurityMockMvcRequestPostProcessors.user
import org.springframework.test.context.TestPropertySource
import org.springframework.test.context.bean.override.mockito.MockitoBean
import org.springframework.test.context.junit.jupiter.SpringExtension
import org.springframework.test.web.servlet.MockMvc
import org.springframework.test.web.servlet.post
import org.testcontainers.junit.jupiter.Testcontainers
import tools.jackson.databind.json.JsonMapper
@Testcontainers
@ExtendWith(SpringExtension::class)
@SpringBootTest
@MockitoBean(types = [MtbFileSender::class])
@TestPropertySource(
properties =
[
"app.rest.uri=http://example.com",
"app.pseudonymize.generator=buildin",
"app.consent.service=none",
]
)
class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
@Test
fun contextLoadsIfMtbFileSenderConfigured(@Autowired context: ApplicationContext) {
// Simply check bean configuration
assertThat(context).isNotNull
}
@Nested
@SpringBootTest(webEnvironment = SpringBootTest.WebEnvironment.MOCK)
@AutoConfigureMockMvc
@TestPropertySource(
properties =
[
"app.security.admin-user=admin",
"app.security.admin-password={noop}very-secret",
"app.pseudonymize.generator=buildin",
"app.consent.service=none",
"app.transformations[0].path=diagnoses[*].code.version",
"app.transformations[0].from=2013",
"app.transformations[0].to=2014",
]
)
inner class TransformationTest {
@MockitoBean private lateinit var mtbFileSender: MtbFileSender
private lateinit var mockMvc: MockMvc
private lateinit var jsonMapper: JsonMapper
@BeforeEach
fun setup(
@Autowired mockMvc: MockMvc,
@Autowired jsonMapper: JsonMapper,
@Autowired requestRepository: RequestRepository
) {
this.mockMvc = mockMvc
this.jsonMapper = jsonMapper
requestRepository.deleteAll()
}
@Test
fun mtbFileIsTransformed() {
doAnswer { MtbFileSender.Response(RequestStatus.SUCCESS) }
.whenever(mtbFileSender)
.send(any<DnpmV2MtbFileRequest>())
val mtbFile =
Mtb.builder()
.patient(Patient.builder().id("TEST_12345678").build())
.metadata(
MvhMetadata.builder()
.modelProjectConsent(
ModelProjectConsent.builder()
.provisions(
listOf(
Provision.builder()
.type(ConsentProvision.PERMIT)
.purpose(ModelProjectConsentPurpose.SEQUENCING)
.build()
)
)
.build()
)
.build()
)
.diagnoses(
listOf(
MtbDiagnosis.builder()
.id("1234")
.patient(Reference.builder().id("TEST_12345678").build())
.code(Coding.builder().code("F79.9").version("2013").build())
.build(),
)
)
.build()
mockMvc
.post("/mtbfile") {
content = jsonMapper.writeValueAsString(mtbFile)
contentType = MediaType.APPLICATION_JSON
with(user("admin").roles("ADMIN"))
}
.andExpect { status { isAccepted() } }
val captor = argumentCaptor<DnpmV2MtbFileRequest>()
verify(mtbFileSender).send(captor.capture())
assertThat(captor.firstValue.content.diagnoses).hasSize(1).allMatch { diagnosis ->
diagnosis.code.version == "2014"
}
}
}
}
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