From b2a046ab5a08a83e0c5011cff17e1b2e56704deb Mon Sep 17 00:00:00 2001
From: Nils Hoffmann <3309580+nilshoffmann@users.noreply.github.com>
Date: Wed, 24 Jul 2024 09:23:04 +0200
Subject: [PATCH] Fixed test expectations

---
 pom.xml                                       | 18 +++++-----
 .../src/main/resources/logback-test.xml       | 36 +++++++++++++++++++
 .../ExampleFilesValidationTestIT.java         |  2 +-
 3 files changed, 46 insertions(+), 10 deletions(-)
 create mode 100644 validation/src/main/resources/logback-test.xml

diff --git a/pom.xml b/pom.xml
index ef53008a..82248151 100644
--- a/pom.xml
+++ b/pom.xml
@@ -549,7 +549,7 @@
         <!--<maven.compiler.target>1.8</maven.compiler.target>-->
         <java.version>17</java.version>
         <maven.compiler.release>${java.version}</maven.compiler.release>
-        <lombok.version>1.18.24</lombok.version>
+        <lombok.version>1.18.34</lombok.version>
         <junit.version>4.13.2</junit.version>
         <hamcrest.version>2.2</hamcrest.version>
         <javax.validation.version>2.0.1.Final</javax.validation.version>
@@ -558,20 +558,20 @@
         <junit.platform.version>1.0.3</junit.platform.version>
         <swagger.version>1.6.14</swagger.version>
         <jersey.version>2.37</jersey.version>
-        <jackson.version>2.14.1</jackson.version>
-        <jackson.databind.version>2.14.1</jackson.databind.version>
-        <jackson.core.version>2.14.1</jackson.core.version>
+        <jackson.version>2.15.4</jackson.version>
+        <jackson.databind.version>2.15.4</jackson.databind.version>
+        <jackson.core.version>2.15.4</jackson.core.version>
         <jodatime.version>2.12.7</jodatime.version>
         <hibernate.validator.version>6.2.5.Final</hibernate.validator.version>
-        <slf4j.version>2.0.6</slf4j.version>
-        <commons-cli.version>1.5.0</commons-cli.version>
+        <slf4j.version>2.0.12</slf4j.version>
+        <commons-cli.version>1.6.0</commons-cli.version>
         <javax.el.version>3.0.1-b12</javax.el.version>
         <migbase.version>2.2</migbase.version>
         <swagger2markup.version>1.3.7</swagger2markup.version>
         <maven-plugin-version>1.0.0</maven-plugin-version>
-        <jacoco.version>0.8.10</jacoco.version>
+        <jacoco.version>0.8.11</jacoco.version>
         <mockito.version>3.12.4</mockito.version><!--2.19.0-->
-        <olsclient.version>2.11</olsclient.version>
+        <olsclient.version>2.13</olsclient.version>
         <jxpath.version>1.3</jxpath.version>
         <spring.version>5.3.30</spring.version>
         <logback.version>1.4.5</logback.version>
@@ -584,7 +584,7 @@
         <javax.annotation-api.version>1.3.2</javax.annotation-api.version>
         <assembly.dir>${project.artifactId}</assembly.dir>
         <javax.activation-api.version>1.2.0</javax.activation-api.version>
-        <jib.plugin.version>2.8.0</jib.plugin.version>
+        <jib.plugin.version>3.4.0</jib.plugin.version>
         <docker.service.prefix>jmztabm</docker.service.prefix>
         <docker.image.prefix>lifs</docker.image.prefix>
         <docker.base.image>azul/zulu-openjdk-alpine</docker.base.image>
diff --git a/validation/src/main/resources/logback-test.xml b/validation/src/main/resources/logback-test.xml
new file mode 100644
index 00000000..237cdd2f
--- /dev/null
+++ b/validation/src/main/resources/logback-test.xml
@@ -0,0 +1,36 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+Copyright 2024 Center For Biotechnology, Bielefeld University, Bielefeld, Germany.
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+     http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
+-->
+
+<configuration debug="false" scan="true">
+
+  <appender name="STDOUT" target="System.out" class="ch.qos.logback.core.ConsoleAppender">
+    <encoder>
+      <pattern>%d{HH:mm:ss.SSS} [%thread] %-5level %logger{36} -%kvp- %msg%n</pattern>
+    </encoder>
+    <filter class="ch.qos.logback.classic.filter.ThresholdFilter">
+      <level>DEBUG</level>
+    </filter>
+  </appender>
+
+  <logger name="org.lifstools" level="DEBUG"/>
+
+  <root level="INFO">
+    <appender-ref ref="STDOUT" />
+  </root>
+
+</configuration>
+
diff --git a/validation/src/test/java/org/lifstools/mztab2/validation/ExampleFilesValidationTestIT.java b/validation/src/test/java/org/lifstools/mztab2/validation/ExampleFilesValidationTestIT.java
index 0525a750..1c400ba1 100644
--- a/validation/src/test/java/org/lifstools/mztab2/validation/ExampleFilesValidationTestIT.java
+++ b/validation/src/test/java/org/lifstools/mztab2/validation/ExampleFilesValidationTestIT.java
@@ -94,7 +94,7 @@ public class ExampleFilesValidationTestIT {
         name = "{index}: semantic validation of ''{0}'' on level ''{1}'' expecting ''{2}'' structural/logical errors and ''{3}'' cross check/semantic errors.")
     public static Collection<Object[]> data() {
         return Arrays.asList(new Object[][]{
-            {XCMS_EXAMPLE, MZTabErrorType.Level.Info, 1, 0},
+            {XCMS_EXAMPLE, MZTabErrorType.Level.Info, 1, 21},
             {LIPIDOMICS_EXAMPLE, MZTabErrorType.Level.Info,
                 0, 8},
             {MTBLS263, MZTabErrorType.Level.Info, 0, 15},