From 5e18a272bec3f45ee41d967747bac1e2ecc53b46 Mon Sep 17 00:00:00 2001
From: JUEST4 <juest4@pitt.edu>
Date: Thu, 12 Mar 2026 13:11:57 -0400
Subject: [PATCH] restored the jar with dependencies and runnable jar parts of
 the build.  tested with corretto 25

---
 pom.xml | 44 ++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 42 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 8c77b75..fd294be 100644
--- a/pom.xml
+++ b/pom.xml
@@ -339,8 +339,8 @@
                 <artifactId>maven-compiler-plugin</artifactId>
                 <version>3.13.0</version>
                 <configuration>
-                    <source>25</source>
-                    <target>25</target>
+                    <source>22</source>
+                    <target>22</target>
                 </configuration>
             </plugin>
             <plugin>
@@ -372,11 +372,51 @@
                 <configuration>
                     <archive>
                         <manifest>
+                            <mainClass>edu.pitt.dbmi.causal.cmd.CausalCmdApplication</mainClass>
                             <addClasspath>true</addClasspath>
                         </manifest>
                     </archive>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-assembly-plugin</artifactId>
+                <version>3.4.2</version>
+                <executions>
+                    <execution>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                        <configuration>
+                            <archive>
+                                <manifest>
+                                    <mainClass>edu.pitt.dbmi.causal.cmd.CausalCmdApplication</mainClass>
+                                    <addDefaultImplementationEntries>true</addDefaultImplementationEntries>
+                                </manifest>
+                            </archive>
+                            <descriptorRefs>
+                                <descriptorRef>jar-with-dependencies</descriptorRef>
+                            </descriptorRefs>
+                        </configuration>
+                    </execution>
+                    <execution>
+                        <id>dist</id>
+                        <phase>package</phase>
+                        <goals>
+                            <goal>single</goal>
+                        </goals>
+                        <configuration>
+                            <filters>
+                                <filter>src/assembly/filter.properties</filter>
+                            </filters>
+                            <descriptors>
+                                <descriptor>src/assembly/distribution.xml</descriptor>
+                            </descriptors>
+                        </configuration>
+                    </execution>
+                </executions>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-javadoc-plugin</artifactId>