refactor: add types for patient id and pseudonym

2025-09-13 17:02:52 +00:00 · 2024-07-15 10:27:51 +02:00
parent c949ec07e5
commit c8f6e6efc8
25 changed files with 216 additions and 180 deletions
--- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/helpers.kt
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/helpers.kt
@@ -0,0 +1,30 @@
+/*
+ * This file is part of ETL-Processor
+ *
+ * Copyright (c) 2024  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.mockito.ArgumentMatchers
+
+@Suppress("UNCHECKED_CAST")
+inline fun <reified T> anyValueClass(): T {
+    val unboxedClass = T::class.java.declaredFields.first().type
+    return ArgumentMatchers.any(unboxedClass as Class<T>)
+        ?: T::class.java.getDeclaredMethod("box-impl", unboxedClass)
+            .invoke(null, null) as T
+}
--- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/input/MtbFileRestControllerTest.kt
@@ -21,6 +21,7 @@ package dev.dnpm.etl.processor.input

 import com.fasterxml.jackson.databind.ObjectMapper
 import de.ukw.ccc.bwhc.dto.*
+import dev.dnpm.etl.processor.anyValueClass
 import dev.dnpm.etl.processor.config.AppSecurityConfiguration
 import dev.dnpm.etl.processor.security.TokenRepository
 import dev.dnpm.etl.processor.security.UserRoleRepository
@@ -29,7 +30,6 @@ 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.ArgumentMatchers.anyString
 import org.mockito.junit.jupiter.MockitoExtension
 import org.mockito.kotlin.any
 import org.mockito.kotlin.never
@@ -141,7 +141,7 @@ class MtbFileRestControllerTest {
            status { isAccepted() }
        }

-        verify(requestProcessor, times(1)).processDeletion(anyString())
+        verify(requestProcessor, times(1)).processDeletion(anyValueClass())
    }

    @Test
@@ -152,7 +152,7 @@ class MtbFileRestControllerTest {
            status { isUnauthorized() }
        }

-        verify(requestProcessor, never()).processDeletion(anyString())
+        verify(requestProcessor, never()).processDeletion(anyValueClass())
    }

    @Nested
--- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/monitoring/RequestRepositoryTest.kt
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/monitoring/RequestRepositoryTest.kt
@@ -19,10 +19,8 @@

 package dev.dnpm.etl.processor.monitoring

-import dev.dnpm.etl.processor.AbstractTestcontainerTest
-import dev.dnpm.etl.processor.Fingerprint
+import dev.dnpm.etl.processor.*
 import dev.dnpm.etl.processor.output.MtbFileSender
-import dev.dnpm.etl.processor.randomRequestId
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.extension.ExtendWith
@@ -63,8 +61,8 @@ class RequestRepositoryTest : AbstractTestcontainerTest() {
    fun shouldSaveRequest() {
        val request = Request(
            randomRequestId(),
-            "TEST_12345678901",
-            "P1",
+            PatientPseudonym("TEST_12345678901"),
+            PatientId("P1"),
            Fingerprint("0123456789abcdef1"),
            RequestType.MTB_FILE,
            RequestStatus.WARNING,
--- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/services/RequestServiceIntegrationTest.kt
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/services/RequestServiceIntegrationTest.kt
@@ -19,14 +19,12 @@

 package dev.dnpm.etl.processor.services

-import dev.dnpm.etl.processor.AbstractTestcontainerTest
-import dev.dnpm.etl.processor.Fingerprint
+import dev.dnpm.etl.processor.*
 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 dev.dnpm.etl.processor.randomRequestId
 import org.assertj.core.api.Assertions.assertThat
 import org.junit.jupiter.api.BeforeEach
 import org.junit.jupiter.api.Test
@@ -67,7 +65,7 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {

    @Test
    fun shouldResultInEmptyRequestList() {
-        val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
+        val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)

        assertThat(actual).isEmpty()
    }
@@ -78,8 +76,8 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
            listOf(
                Request(
                    randomRequestId(),
-                    "TEST_12345678901",
-                    "P1",
+                    PatientPseudonym("TEST_12345678901"),
+                    PatientId("P1"),
                    Fingerprint("0123456789abcdef1"),
                    RequestType.MTB_FILE,
                    RequestStatus.SUCCESS,
@@ -88,8 +86,8 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
                // Should be ignored - wrong patient ID -->
                Request(
                    randomRequestId(),
-                    "TEST_12345678902",
-                    "P2",
+                    PatientPseudonym("TEST_12345678902"),
+                    PatientId("P2"),
                    Fingerprint("0123456789abcdef2"),
                    RequestType.MTB_FILE,
                    RequestStatus.WARNING,
@@ -98,8 +96,8 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
                // <--
                Request(
                    randomRequestId(),
-                    "TEST_12345678901",
-                    "P2",
+                    PatientPseudonym("TEST_12345678901"),
+                    PatientId("P2"),
                    Fingerprint("0123456789abcdee1"),
                    RequestType.DELETE,
                    RequestStatus.SUCCESS,
@@ -113,7 +111,7 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
    fun shouldResultInSortedRequestList() {
        setupTestData()

-        val actual = requestService.allRequestsByPatientPseudonym("TEST_12345678901")
+        val actual = requestService.allRequestsByPatientPseudonym(TEST_PATIENT_PSEUDONYM)

        assertThat(actual).hasSize(2)
        assertThat(actual[0].fingerprint).isEqualTo(Fingerprint("0123456789abcdee1"))
@@ -124,7 +122,7 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
    fun shouldReturnDeleteRequestAsLastRequest() {
        setupTestData()

-        val actual = requestService.isLastRequestWithKnownStatusDeletion("TEST_12345678901")
+        val actual = requestService.isLastRequestWithKnownStatusDeletion(TEST_PATIENT_PSEUDONYM)

        assertThat(actual).isTrue()
    }
@@ -133,10 +131,14 @@ class RequestServiceIntegrationTest : AbstractTestcontainerTest() {
    fun shouldReturnLastMtbFileRequest() {
        setupTestData()

-        val actual = requestService.lastMtbFileRequestForPatientPseudonym("TEST_12345678901")
+        val actual = requestService.lastMtbFileRequestForPatientPseudonym(TEST_PATIENT_PSEUDONYM)

        assertThat(actual).isNotNull
        assertThat(actual?.fingerprint).isEqualTo(Fingerprint("0123456789abcdef1"))
    }

+    companion object {
+        val TEST_PATIENT_PSEUDONYM = PatientPseudonym("TEST_12345678901")
+    }
+
 }
--- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/web/HomeControllerTest.kt
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/web/HomeControllerTest.kt
@@ -21,15 +21,13 @@ package dev.dnpm.etl.processor.web

 import com.gargoylesoftware.htmlunit.WebClient
 import com.gargoylesoftware.htmlunit.html.HtmlPage
-import dev.dnpm.etl.processor.Fingerprint
-import dev.dnpm.etl.processor.NotFoundException
+import dev.dnpm.etl.processor.*
 import dev.dnpm.etl.processor.config.AppConfiguration
 import dev.dnpm.etl.processor.config.AppSecurityConfiguration
 import dev.dnpm.etl.processor.monitoring.Report
 import dev.dnpm.etl.processor.monitoring.Request
 import dev.dnpm.etl.processor.monitoring.RequestStatus
 import dev.dnpm.etl.processor.monitoring.RequestType
-import dev.dnpm.etl.processor.randomRequestId
 import dev.dnpm.etl.processor.services.RequestService
 import org.assertj.core.api.Assertions.assertThat
 import org.junit.jupiter.api.BeforeEach
@@ -37,8 +35,6 @@ 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.ArgumentMatchers
-import org.mockito.ArgumentMatchers.anyString
 import org.mockito.junit.jupiter.MockitoExtension
 import org.mockito.kotlin.any
 import org.mockito.kotlin.whenever
@@ -83,13 +79,6 @@ class HomeControllerTest {
    private lateinit var mockMvc: MockMvc
    private lateinit var webClient: WebClient

-    inline fun <reified T> anyValueClass(): T {
-        val unboxedClass = T::class.java.declaredFields.first().type
-        return ArgumentMatchers.any(unboxedClass as Class<T>)
-            ?: T::class.java.getDeclaredMethod("box-impl", unboxedClass)
-                .invoke(null, null) as T
-    }
-
    @BeforeEach
    fun setup(
        @Autowired mockMvc: MockMvc,
@@ -129,8 +118,8 @@ class HomeControllerTest {
                        Request(
                            2L,
                            randomRequestId(),
-                            "PSEUDO1",
-                            "PATIENT1",
+                            PatientPseudonym("PSEUDO1"),
+                            PatientId("PATIENT1"),
                            Fingerprint("ashdkasdh"),
                            RequestType.MTB_FILE,
                            RequestStatus.SUCCESS
@@ -138,8 +127,8 @@ class HomeControllerTest {
                        Request(
                            1L,
                            randomRequestId(),
-                            "PSEUDO1",
-                            "PATIENT1",
+                            PatientPseudonym("PSEUDO1"),
+                            PatientId("PATIENT1"),
                            Fingerprint("asdasdasd"),
                            RequestType.MTB_FILE,
                            RequestStatus.ERROR
@@ -163,8 +152,8 @@ class HomeControllerTest {
                    Request(
                        2L,
                        requestId,
-                        "PSEUDO1",
-                        "PATIENT1",
+                        PatientPseudonym("PSEUDO1"),
+                        PatientId("PATIENT1"),
                        Fingerprint("ashdkasdh"),
                        RequestType.MTB_FILE,
                        RequestStatus.SUCCESS,
@@ -182,14 +171,14 @@ class HomeControllerTest {
        @Test
        @WithMockUser(username = "admin", roles = ["ADMIN"])
        fun testShouldShowPatientDetails() {
-            whenever(requestService.findRequestByPatientId(anyString(), any<Pageable>())).thenReturn(
+            whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(
                PageImpl(
                    listOf(
                        Request(
                            2L,
                            randomRequestId(),
-                            "PSEUDO1",
-                            "PATIENT1",
+                            PatientPseudonym("PSEUDO1"),
+                            PatientId("PATIENT1"),
                            Fingerprint("ashdkasdh"),
                            RequestType.MTB_FILE,
                            RequestStatus.SUCCESS
@@ -197,8 +186,8 @@ class HomeControllerTest {
                        Request(
                            1L,
                            randomRequestId(),
-                            "PSEUDO1",
-                            "PATIENT1",
+                            PatientPseudonym("PSEUDO1"),
+                            PatientId("PATIENT1"),
                            Fingerprint("asdasdasd"),
                            RequestType.MTB_FILE,
                            RequestStatus.ERROR
@@ -254,7 +243,7 @@ class HomeControllerTest {
        @Test
        @WithMockUser(username = "admin", roles = ["ADMIN"])
        fun testShouldShowEmptyPatientDetails() {
-            whenever(requestService.findRequestByPatientId(anyString(), any<Pageable>())).thenReturn(Page.empty())
+            whenever(requestService.findRequestByPatientId(anyValueClass(), any<Pageable>())).thenReturn(Page.empty())

            val page = webClient.getPage<HtmlPage>("http://localhost/patient/PSEUDO1")
            assertThat(page.querySelectorAll("tbody tr")).isEmpty()
--- a/src/integrationTest/kotlin/dev/dnpm/etl/processor/web/StatisticsRestControllerTest.kt
+++ b/src/integrationTest/kotlin/dev/dnpm/etl/processor/web/StatisticsRestControllerTest.kt
@@ -20,6 +20,8 @@
 package dev.dnpm.etl.processor.web

 import dev.dnpm.etl.processor.Fingerprint
+import dev.dnpm.etl.processor.PatientId
+import dev.dnpm.etl.processor.PatientPseudonym
 import dev.dnpm.etl.processor.config.AppConfiguration
 import dev.dnpm.etl.processor.config.AppSecurityConfiguration
 import dev.dnpm.etl.processor.monitoring.CountedState
@@ -188,8 +190,8 @@ class StatisticsRestControllerTest {
                    Request(
                        1,
                        randomRequestId(),
-                        "TEST_12345678901",
-                        "P1",
+                        PatientPseudonym("TEST_12345678901"),
+                        PatientId("P1"),
                        Fingerprint("0123456789abcdef1"),
                        RequestType.MTB_FILE,
                        RequestStatus.SUCCESS,
@@ -198,8 +200,8 @@ class StatisticsRestControllerTest {
                    Request(
                        2,
                        randomRequestId(),
-                        "TEST_12345678902",
-                        "P2",
+                        PatientPseudonym("TEST_12345678902"),
+                        PatientId("P2"),
                        Fingerprint("0123456789abcdef2"),
                        RequestType.MTB_FILE,
                        RequestStatus.WARNING,
@@ -208,8 +210,8 @@ class StatisticsRestControllerTest {
                    Request(
                        3,
                        randomRequestId(),
-                        "TEST_12345678901",
-                        "P2",
+                        PatientPseudonym("TEST_12345678901"),
+                        PatientId("P2"),
                        Fingerprint("0123456789abcdee1"),
                        RequestType.DELETE,
                        RequestStatus.ERROR,
@@ -218,8 +220,8 @@ class StatisticsRestControllerTest {
                    Request(
                        4,
                        randomRequestId(),
-                        "TEST_12345678902",
-                        "P2",
+                        PatientPseudonym("TEST_12345678902"),
+                        PatientId("P2"),
                        Fingerprint("0123456789abcdef2"),
                        RequestType.MTB_FILE,
                        RequestStatus.DUPLICATION,
@@ -228,8 +230,8 @@ class StatisticsRestControllerTest {
                    Request(
                        5,
                        randomRequestId(),
-                        "TEST_12345678902",
-                        "P2",
+                        PatientPseudonym("TEST_12345678902"),
+                        PatientId("P2"),
                        Fingerprint("0123456789abcdef2"),
                        RequestType.DELETE,
                        RequestStatus.UNKNOWN,