Merge branch 'master' into add-docker-build

# Conflicts:
#	README.md
#	build.gradle.kts

4 files changed, 332 insertions, 0 deletions

diff --git a/src/integrationTest/kotlin/dev/dnpm/etl/processor/AbstractTestcontainerTest.kt b/src/integrationTest/kotlin/dev/dnpm/etl/processor/AbstractTestcontainerTest.kt
new file mode 100644
index 0000000..13b57d0
--- /dev/null
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/AbstractTestcontainerTest.kt
@@ -0,0 +1,51 @@
+/*
+ * 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 <https://www.gnu.org/licenses/>.
+ */
+
+package dev.dnpm.etl.processor
+
+import org.springframework.test.context.DynamicPropertyRegistry
+import org.springframework.test.context.DynamicPropertySource
+import org.testcontainers.containers.PostgreSQLContainer
+import org.testcontainers.junit.jupiter.Container
+
+abstract class AbstractTestcontainerTest {
+
+    companion object {
+        @Container
+        val dbContainer = CustomPostgreSQLContainer("postgres:10-alpine")
+            .withDatabaseName("test")
+            .withUsername("test")
+            .withPassword("test") ?: throw RuntimeException("Failed to create testcontainer!")
+
+        @DynamicPropertySource
+        @JvmStatic
+        fun registerDynamicProperties(registry: DynamicPropertyRegistry) {
+            registry.add("spring.datasource.url", dbContainer::getJdbcUrl)
+            registry.add("spring.datasource.username", dbContainer::getUsername)
+            registry.add("spring.datasource.password", dbContainer::getPassword)
+        }
+    }
+
+}
+
+class CustomPostgreSQLContainer(dockerImageName: String) : PostgreSQLContainer<CustomPostgreSQLContainer>(dockerImageName) {
+    override fun stop() {
+        // Keep Testcontainer alive until JVM destroys it
+    }
+}
\ No newline at end of file
diff --git a/src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt b/src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt
new file mode 100644
index 0000000..c5a20bb
--- /dev/null
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/EtlProcessorApplicationTests.kt
@@ -0,0 +1,45 @@
+/*
+ * 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 <https://www.gnu.org/licenses/>.
+ */
+
+package dev.dnpm.etl.processor
+
+import dev.dnpm.etl.processor.output.MtbFileSender
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.extension.ExtendWith
+import org.springframework.beans.factory.annotation.Autowired
+import org.springframework.boot.test.context.SpringBootTest
+import org.springframework.boot.test.mock.mockito.MockBean
+import org.springframework.context.ApplicationContext
+import org.springframework.test.context.junit.jupiter.SpringExtension
+import org.testcontainers.junit.jupiter.Testcontainers
+
+@Testcontainers
+@ExtendWith(SpringExtension::class)
+@SpringBootTest
+@MockBean(MtbFileSender::class)
+class EtlProcessorApplicationTests : AbstractTestcontainerTest() {
+
+    @Test
+    fun contextLoadsIfMtbFileSenderConfigured(@Autowired context: ApplicationContext) {
+        // Simply check bean configuration
+        assertThat(context).isNotNull
+    }
+
+}
diff --git a/src/integrationTest/kotlin/dev/dnpm/etl/processor/config/AppConfigurationTest.kt b/src/integrationTest/kotlin/dev/dnpm/etl/processor/config/AppConfigurationTest.kt
new file mode 100644
index 0000000..8bdaa60
--- /dev/null
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/config/AppConfigurationTest.kt
@@ -0,0 +1,102 @@
+/*
+ * 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 <https://www.gnu.org/licenses/>.
+ */
+
+package dev.dnpm.etl.processor.config
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import dev.dnpm.etl.processor.monitoring.RequestRepository
+import dev.dnpm.etl.processor.output.KafkaMtbFileSender
+import dev.dnpm.etl.processor.output.RestMtbFileSender
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.Nested
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.assertThrows
+import org.springframework.beans.factory.NoSuchBeanDefinitionException
+import org.springframework.boot.autoconfigure.kafka.KafkaAutoConfiguration
+import org.springframework.boot.test.context.SpringBootTest
+import org.springframework.boot.test.mock.mockito.MockBean
+import org.springframework.boot.test.mock.mockito.MockBeans
+import org.springframework.context.ApplicationContext
+import org.springframework.test.context.ContextConfiguration
+import org.springframework.test.context.TestPropertySource
+
+@SpringBootTest
+@ContextConfiguration(classes = [KafkaAutoConfiguration::class, AppKafkaConfiguration::class, AppRestConfiguration::class])
+class AppConfigurationTest {
+
+    @Nested
+    @TestPropertySource(
+        properties = [
+            "app.rest.uri=http://localhost:9000"
+        ]
+    )
+    inner class AppConfigurationRestTest(private val context: ApplicationContext) {
+
+        @Test
+        fun shouldUseRestMtbFileSenderNotKafkaMtbFileSender() {
+            assertThat(context.getBean(RestMtbFileSender::class.java)).isNotNull
+            assertThrows<NoSuchBeanDefinitionException> { context.getBean(KafkaMtbFileSender::class.java) }
+        }
+
+    }
+
+    @Nested
+    @TestPropertySource(
+        properties = [
+            "app.kafka.servers=localhost:9092",
+            "app.kafka.topic=test",
+            "app.kafka.response-topic=test-response",
+            "app.kafka.group-id=test"
+        ]
+    )
+    @MockBeans(value = [
+        MockBean(ObjectMapper::class),
+        MockBean(RequestRepository::class)
+    ])
+    inner class AppConfigurationKafkaTest(private val context: ApplicationContext) {
+
+        @Test
+        fun shouldUseKafkaMtbFileSenderNotRestMtbFileSender() {
+            assertThrows<NoSuchBeanDefinitionException> { context.getBean(RestMtbFileSender::class.java) }
+            assertThat(context.getBean(KafkaMtbFileSender::class.java)).isNotNull
+        }
+
+    }
+
+    @Nested
+    @TestPropertySource(
+        properties = [
+            "app.rest.uri=http://localhost:9000",
+            "app.kafka.servers=localhost:9092",
+            "app.kafka.topic=test",
+            "app.kafka.response-topic=test-response",
+            "app.kafka.group-id=test"
+        ]
+    )
+    inner class AppConfigurationRestInPrecedenceTest(private val context: ApplicationContext) {
+
+        @Test
+        fun shouldUseRestMtbFileSenderNotKafkaMtbFileSender() {
+            assertThat(context.getBean(RestMtbFileSender::class.java)).isNotNull
+            assertThrows<NoSuchBeanDefinitionException> { context.getBean(KafkaMtbFileSender::class.java) }
+        }
+
+    }
+
+}
\ No newline at end of file
diff --git a/src/integrationTest/kotlin/dev/dnpm/etl/processor/services/RequestServiceIntegrationTest.kt b/src/integrationTest/kotlin/dev/dnpm/etl/processor/services/RequestServiceIntegrationTest.kt
new file mode 100644
index 0000000..ff85296
--- /dev/null
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/services/RequestServiceIntegrationTest.kt
@@ -0,0 +1,134 @@
+/*
+ * 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 <https://www.gnu.org/licenses/>.
+ */
+
+package dev.dnpm.etl.processor.services
+
+import dev.dnpm.etl.processor.AbstractTestcontainerTest
+import dev.dnpm.etl.processor.monitoring.Request
+import dev.dnpm.etl.processor.monitoring.RequestRepository
+import dev.dnpm.etl.processor.monitoring.RequestStatus
+import dev.dnpm.etl.processor.monitoring.RequestType
+import dev.dnpm.etl.processor.output.MtbFileSender
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.BeforeEach
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.extension.ExtendWith
+import org.springframework.beans.factory.annotation.Autowired
+import org.springframework.boot.test.context.SpringBootTest
+import org.springframework.boot.test.mock.mockito.MockBean
+import org.springframework.test.context.junit.jupiter.SpringExtension
+import org.springframework.transaction.annotation.Transactional
+import org.testcontainers.junit.jupiter.Testcontainers
+import java.time.Instant
+import java.util.*
+
+@Testcontainers
+@ExtendWith(SpringExtension::class)
+@SpringBootTest
+@Transactional
+@MockBean(MtbFileSender::class)
+class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
+
+    private lateinit var requestRepository: RequestRepository
+
+    private lateinit var requestService: RequestService
+
+    @BeforeEach
+    fun setup(
+        @Autowired requestRepository: RequestRepository
+    ) {
+        this.requestRepository = requestRepository
+        this.requestService = RequestService(requestRepository)
+    }
+
+    @Test
+    fun shouldResultInEmptyRequestList() {
+        val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
+
+        assertThat(actual).isEmpty()
+    }
+
+    private fun setupTestData() {
+        // Prepare DB
+        this.requestRepository.saveAll(
+            listOf(
+                Request(
+                    uuid = UUID.randomUUID().toString(),
+                    patientId = "TEST_12345678901",
+                    pid = "P1",
+                    fingerprint = "0123456789abcdef1",
+                    type = RequestType.MTB_FILE,
+                    status = RequestStatus.SUCCESS,
+                    processedAt = Instant.parse("2023-07-07T02:00:00Z")
+                ),
+                // Should be ignored - wrong patient ID -->
+                Request(
+                    uuid = UUID.randomUUID().toString(),
+                    patientId = "TEST_12345678902",
+                    pid = "P2",
+                    fingerprint = "0123456789abcdef2",
+                    type = RequestType.MTB_FILE,
+                    status = RequestStatus.WARNING,
+                    processedAt = Instant.parse("2023-08-08T00:00:00Z")
+                ),
+                // <--
+                Request(
+                    uuid = UUID.randomUUID().toString(),
+                    patientId = "TEST_12345678901",
+                    pid = "P2",
+                    fingerprint = "0123456789abcdee1",
+                    type = RequestType.DELETE,
+                    status = RequestStatus.SUCCESS,
+                    processedAt = Instant.parse("2023-08-08T02:00:00Z")
+                )
+            )
+        )
+    }
+
+    @Test
+    fun shouldResultInSortedRequestList() {
+        setupTestData()
+
+        val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
+
+        assertThat(actual).hasSize(2)
+        assertThat(actual[0].fingerprint).isEqualTo("0123456789abcdee1")
+        assertThat(actual[1].fingerprint).isEqualTo("0123456789abcdef1")
+    }
+
+    @Test
+    fun shouldReturnDeleteRequestAsLastRequest() {
+        setupTestData()
+
+        val actual = requestService.isLastRequestWithKnownStatusDeletion("TEST_12345678901")
+
+        assertThat(actual).isTrue()
+    }
+
+    @Test
+    fun shouldReturnLastMtbFileRequest() {
+        setupTestData()
+
+        val actual = requestService.lastMtbFileRequestForPatientPseudonym("TEST_12345678901")
+
+        assertThat(actual).isNotNull
+        assertThat(actual?.fingerprint).isEqualTo("0123456789abcdef1")
+    }
+
+}
\ No newline at end of file