Bump version

This uses fake MTBFile JSON as described here:
https://ibmi-intra.cs.uni-tuebingen.de/display/ZPM/bwHC+REST+API

build.gradle.kts

@@ -4,14 +4,14 @@ import org.springframework.boot.gradle.tasks.bundling.BootBuildImage
 
 plugins {
     war
-    id("org.springframework.boot") version "3.1.6"
+    id("org.springframework.boot") version "3.2.0"
     id("io.spring.dependency-management") version "1.1.4"
     kotlin("jvm") version "1.9.21"
     kotlin("plugin.spring") version "1.9.21"
 }
 
 group = "de.ukw.ccc"
-version = "0.2.0-SNAPSHOT"
+version = "0.3.0"
 
 var versions = mapOf(
     "bwhc-dto-java" to "0.2.0",

src/main/kotlin/dev/dnpm/etl/processor/monitoring/ReportService.kt

@@ -34,7 +34,10 @@ class ReportService(
             return listOf()
         }
         return try {
-            objectMapper.readValue(dataQualityReport, DataQualityReport::class.java).issues
+            objectMapper
+                .readValue(dataQualityReport, DataQualityReport::class.java)
+                .issues
+                .sortedBy { it.severity }
         } catch (e: Exception) {
             val otherIssue =
                 Issue(Severity.ERROR, "Not parsable data quality report '$dataQualityReport'")
@@ -56,5 +59,6 @@ class ReportService(
     enum class Severity(@JsonValue val value: String) {
         ERROR("error"),
         WARNING("warning"),
+        INFO("info")
     }
 }

src/main/kotlin/dev/dnpm/etl/processor/pseudonym/extensions.kt

@@ -35,7 +35,10 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     this.familyMemberDiagnoses.forEach { it.patient = patientPseudonym }
     this.geneticCounsellingRequests.forEach { it.patient = patientPseudonym }
     this.histologyReevaluationRequests.forEach { it.patient = patientPseudonym }
-    this.histologyReports.forEach { it.patient = patientPseudonym }
+    this.histologyReports.forEach {
+        it.patient = patientPseudonym
+        it.tumorMorphology.patient = patientPseudonym
+    }
     this.lastGuidelineTherapies.forEach { it.patient = patientPseudonym }
     this.molecularPathologyFindings.forEach { it.patient = patientPseudonym }
     this.molecularTherapies.forEach { molecularTherapy -> molecularTherapy.history.forEach { it.patient = patientPseudonym } }
@@ -45,6 +48,6 @@ infix fun MtbFile.pseudonymizeWith(pseudonymizeService: PseudonymizeService) {
     this.recommendations.forEach { it.patient = patientPseudonym }
     this.recommendations.forEach { it.patient = patientPseudonym }
     this.responses.forEach { it.patient = patientPseudonym }
-    this.specimens.forEach { it.patient = patientPseudonym }
+    this.studyInclusionRequests.forEach { it.patient = patientPseudonym }
     this.specimens.forEach { it.patient = patientPseudonym }
 }

src/main/resources/static/style.css

@@ -1,6 +1,9 @@
 :root {
     --table-border: rgba(96, 96, 96, 1);
 
+    --bg-blue: rgb(0, 74, 157);
+    --bg-blue-op: rgba(0, 74, 157, .35);
+
     --bg-green: rgb(0, 128, 0);
     --bg-green-op: rgba(0, 128, 0, .35);
 
@@ -181,6 +184,15 @@ td {
     font-family: monospace;
 }
 
+td.bg-blue, th.bg-blue {
+    background: var(--bg-blue);
+    color: white;
+}
+
+tr:has(td.bg-blue) {
+    background: var(--bg-blue-op);
+}
+
 td.bg-green, th.bg-green {
     background: var(--bg-green);
     color: white;

src/main/resources/templates/report.html

@@ -45,6 +45,7 @@
             </thead>
             <tbody>
             <tr th:each="issue : ${issues}">
+                <td th:if="${issue.severity.value == 'info'}" class="bg-blue"><small>[[ ${issue.severity} ]]</small></td>
                 <td th:if="${issue.severity.value == 'warning'}" class="bg-yellow"><small>[[ ${issue.severity} ]]</small></td>
                 <td th:if="${issue.severity.value == 'error'}" class="bg-red"><small>[[ ${issue.severity} ]]</small></td>
                 <td>[[ ${issue.message} ]]</td>

src/test/kotlin/dev/dnpm/etl/processor/pseudonym/ExtensionsTest.kt

@@ -0,0 +1,64 @@
+/*
+ * 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.pseudonym
+
+import com.fasterxml.jackson.databind.ObjectMapper
+import de.ukw.ccc.bwhc.dto.MtbFile
+import org.assertj.core.api.Assertions.assertThat
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.extension.ExtendWith
+import org.mockito.ArgumentMatchers
+import org.mockito.Mock
+import org.mockito.junit.jupiter.MockitoExtension
+import org.mockito.kotlin.doAnswer
+import org.mockito.kotlin.whenever
+import org.springframework.core.io.ClassPathResource
+
+const val FAKE_MTB_FILE_PATH = "fake_MTBFile.json"
+const val CLEAN_PATIENT_ID = "5dad2f0b-49c6-47d8-a952-7b9e9e0f7549"
+
+@ExtendWith(MockitoExtension::class)
+class ExtensionsTest {
+
+    private fun fakeMtbFile(): MtbFile {
+        val mtbFile = ClassPathResource(FAKE_MTB_FILE_PATH).inputStream
+        return ObjectMapper().readValue(mtbFile, MtbFile::class.java)
+    }
+
+    private fun MtbFile.serialized(): String {
+        return ObjectMapper().writeValueAsString(this)
+    }
+
+    @Test
+    fun shouldNotContainCleanPatientId(@Mock pseudonymizeService: PseudonymizeService) {
+        doAnswer {
+            it.arguments[0]
+            "PSEUDO-ID"
+        }.whenever(pseudonymizeService).patientPseudonym(ArgumentMatchers.anyString())
+
+        val mtbFile = fakeMtbFile()
+
+        mtbFile.pseudonymizeWith(pseudonymizeService)
+
+        assertThat(mtbFile.patient.id).isEqualTo("PSEUDO-ID")
+        assertThat(mtbFile.serialized()).doesNotContain(CLEAN_PATIENT_ID)
+    }
+
+}

src/test/kotlin/dev/dnpm/etl/processor/services/ReportServiceTest.kt

@@ -41,6 +41,7 @@ class ReportServiceTest {
             {
                 "patient": "4711",
                 "issues": [
+                    { "severity": "info", "message": "Info Message" },
                     { "severity": "warning", "message": "Warning Message" },
                     { "severity": "error", "message": "Error Message" }
                 ]
@@ -49,11 +50,13 @@ class ReportServiceTest {
 
         val actual = this.reportService.deserialize(json)
 
-        assertThat(actual).hasSize(2)
-        assertThat(actual[0].severity).isEqualTo(ReportService.Severity.WARNING)
-        assertThat(actual[0].message).isEqualTo("Warning Message")
-        assertThat(actual[1].severity).isEqualTo(ReportService.Severity.ERROR)
-        assertThat(actual[1].message).isEqualTo("Error Message")
+        assertThat(actual).hasSize(3)
+        assertThat(actual[0].severity).isEqualTo(ReportService.Severity.ERROR)
+        assertThat(actual[0].message).isEqualTo("Error Message")
+        assertThat(actual[1].severity).isEqualTo(ReportService.Severity.WARNING)
+        assertThat(actual[1].message).isEqualTo("Warning Message")
+        assertThat(actual[2].severity).isEqualTo(ReportService.Severity.INFO)
+        assertThat(actual[2].message).isEqualTo("Info Message")
     }
 
     @Test