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},