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Upgrade some library because the old versions have security vulnerabi…
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…lities.
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@fcyu
fcyu committed Dec 22, 2021
1 parent f01c6d7 commit 90d97ac
Showing 1 changed file with 5 additions and 48 deletions.
53 changes: 5 additions & 48 deletions pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -41,12 +41,12 @@
<dependency>
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
<version>1.2.3</version>
<version>1.2.8</version>
</dependency>
<dependency>
<groupId>junit</groupId>
<artifactId>junit</artifactId>
<version>4.12</version>
<version>4.13.2</version>
<scope>test</scope>
</dependency>
<dependency>
Expand All @@ -57,12 +57,12 @@
<dependency>
<groupId>com.google.guava</groupId>
<artifactId>guava</artifactId>
<version>26.0-jre</version>
<version>31.0.1-jre</version>
</dependency>
<dependency>
<groupId>org.xerial</groupId>
<artifactId>sqlite-jdbc</artifactId>
<version>3.25.2</version>
<version>3.36.0.2</version>
</dependency>
<dependency>
<groupId>hk.ust.bioinformatics</groupId>
Expand All @@ -76,7 +76,7 @@
<repository>
<id>pst-release</id>
<name>EBI Nexus Repository</name>
<url>http://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
<url>https://www.ebi.ac.uk/Tools/maven/repos/content/repositories/pst-release</url>
</repository>
</repositories>

Expand Down Expand Up @@ -105,49 +105,6 @@
</execution>
</executions>
</plugin>
<plugin>
<groupId>com.github.wvengen</groupId>
<artifactId>proguard-maven-plugin</artifactId>
<version>2.0.14</version>
<executions>
<execution>
<phase>package</phase>
<goals><goal>proguard</goal></goals>
</execution>
</executions>
<configuration>
<injar>${project.build.finalName}-jar-with-dependencies.jar</injar>
<outjar>${project.build.finalName}-publish.jar</outjar>
<outputDirectory>${project.build.directory}</outputDirectory>
<proguardInclude>${basedir}/proguard.conf</proguardInclude>
<proguardVersion>6.0.3</proguardVersion>
<libs>
<lib>${java.home}/lib/rt.jar</lib>
<lib>${java.home}/lib/jce.jar</lib>
</libs>
<options>
<option>-keep class !proteomics.**,!ProteomicsLibrary.** { *; }</option>
<option>-keepclasseswithmembers public class * { public static void main(java.lang.String[]); }</option>
<option>-keepattributes *Annotation*,Signature,InnerClasses,EnclosingMethod</option>
<option>-keepclasseswithmembernames,includedescriptorclasses class * { native &lt;methods&gt;; } </option>
<option>-optimizationpasses 3</option>
<option>-overloadaggressively</option>
<option>-repackageclasses</option>
<option>-allowaccessmodification</option>
<option>-dontwarn ch.qos.logback.**,com.sun.**,afu.org.checkerframework.checker.**,org.bytedeco.javacpp.**,org.checkerframework.checker.**,org.slf4j.**</option>
<option>-dontnote **</option>
<option>-adaptresourcefilenames **.xml,**.fasta,**.def</option>
</options>
</configuration>
<dependencies>
<dependency>
<groupId>net.sf.proguard</groupId>
<artifactId>proguard-base</artifactId>
<version>6.0.3</version>
<scope>runtime</scope>
</dependency>
</dependencies>
</plugin>
</plugins>
</build>
</project>

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