From f1d8bbbb6c4789a22fc2bf20a7c1e3bed2539d6f Mon Sep 17 00:00:00 2001
From: Chris Mungall <cjm@berkeleybop.org>
Date: Mon, 1 Jul 2024 19:52:23 -0700
Subject: [PATCH] Update pom.xml

---
 pom.xml | 116 ++++++++++++++++++++++++++++++--------------------------
 1 file changed, 62 insertions(+), 54 deletions(-)

diff --git a/pom.xml b/pom.xml
index 8451818..7343575 100755
--- a/pom.xml
+++ b/pom.xml
@@ -1,69 +1,84 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<!--
-  ~ /*
-  ~  * Copyright © 2014 - 2021 Leipzig University (Database Research Group)
-  ~  *
-  ~  * This program is free software: you can redistribute it and/or modify
-  ~  * it under the terms of the GNU General Public License as published by
-  ~  * the Free Software Foundation, version 3.
-  ~  *
-  ~  * 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
-  ~  * General Public License for more details.
-  ~  *
-  ~  * You should have received a copy of the GNU General Public License
-  ~  * along with this program. If not, see <http://www.gnu.org/licenses/>.
-  ~  */
-  -->
-
 <project xmlns="http://maven.apache.org/POM/4.0.0"
          xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
          xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
     <modelVersion>4.0.0</modelVersion>
-
     <groupId>org.example</groupId>
     <artifactId>ContoDiff</artifactId>
     <version>1.0-SNAPSHOT</version>
+
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>1.8</maven.compiler.source>
+        <maven.compiler.target>1.8</maven.compiler.target>
+    </properties>
+
     <build>
         <plugins>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.8.1</version>
                 <configuration>
-                    <source>8</source>
-                    <target>8</target>
+                    <source>1.8</source>
+                    <target>1.8</target>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-antrun-plugin</artifactId>
+                <version>3.0.0</version>
+                <executions>
+                    <execution>
+                        <id>unpack-gomma-jars</id>
+                        <phase>generate-resources</phase>
+                        <configuration>
+                            <target>
+                                <unzip src="${project.basedir}/lib/enhanced_diff.jar" dest="${project.build.outputDirectory}"/>
+                                <unzip src="${project.basedir}/lib/gomma-kernel.jar" dest="${project.build.outputDirectory}"/>
+                                <unzip src="${project.basedir}/lib/gomma-tools.jar" dest="${project.build.outputDirectory}"/>
+                            </target>
+                        </configuration>
+                        <goals>
+                            <goal>run</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-shade-plugin</artifactId>
+                <version>3.2.4</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>shade</goal>
+                        </goals>
+                        <configuration>
+                            <transformers>
+                                <transformer implementation="org.apache.maven.plugins.shade.resource.ManifestResourceTransformer">
+                                    <mainClass>org.ContoDiffMain</mainClass>
+                                </transformer>
+                            </transformers>
+                            <filters>
+                                <filter>
+                                    <artifact>*:*</artifact>
+                                    <excludes>
+                                        <exclude>META-INF/*.SF</exclude>
+                                        <exclude>META-INF/*.DSA</exclude>
+                                        <exclude>META-INF/*.RSA</exclude>
+                                    </excludes>
+                                </filter>
+                            </filters>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
         </plugins>
     </build>
 
-
     <dependencies>
-        <dependency>
-            <groupId>Gomma</groupId>
-            <artifactId>gomma_enhanced_diff</artifactId>
-            <version>1.0</version>
-            <scope>system</scope>
-            <systemPath>${basedir}/lib/enhanced_diff.jar</systemPath>
-        </dependency>
-        <dependency>
-            <groupId>Gomma</groupId>
-            <artifactId>gomma_kernel</artifactId>
-            <version>1.0</version>
-            <scope>system</scope>
-            <systemPath>${basedir}/lib/gomma-kernel.jar</systemPath>
-        </dependency>
-        <dependency>
-            <groupId>Gomma</groupId>
-            <artifactId>gomma_tools</artifactId>
-            <version>1.0</version>
-            <scope>system</scope>
-            <systemPath>${basedir}/lib/gomma-tools.jar</systemPath>
-        </dependency>
-        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-distribution -->
-
-        <!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
         <dependency>
             <groupId>commons-cli</groupId>
             <artifactId>commons-cli</artifactId>
@@ -74,27 +89,20 @@
             <artifactId>elk-owlapi</artifactId>
             <version>0.4.1</version>
         </dependency>
-        <!-- https://mvnrepository.com/artifact/com.h2database/h2 -->
         <dependency>
             <groupId>com.h2database</groupId>
             <artifactId>h2</artifactId>
             <version>1.4.200</version>
-            <scope>runtime</scope>
         </dependency>
-        <!-- https://mvnrepository.com/artifact/org.apache.logging.log4j/log4j-slf4j-impl -->
         <dependency>
             <groupId>org.apache.logging.log4j</groupId>
             <artifactId>log4j-slf4j-impl</artifactId>
             <version>2.14.1</version>
         </dependency>
-        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-distribution -->
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-distribution</artifactId>
             <version>5.1.17</version>
         </dependency>
-
-
     </dependencies>
-
-</project>
\ No newline at end of file
+</project>