From 6621f7ff749a4f412efc43d3ce81871f7385f10c Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Thu, 19 Dec 2024 12:49:29 -0500
Subject: [PATCH 01/14] Add JaCoCo

---
 pom.xml | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/pom.xml b/pom.xml
index d71d7ea5..0605624b 100644
--- a/pom.xml
+++ b/pom.xml
@@ -107,6 +107,49 @@
         <artifactId>maven-dependency-plugin</artifactId>
         <version>${maven-dependency-plugin.version}</version>
       </plugin>
+
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <version>0.8.12</version>
+        <executions>
+          <execution>
+            <id>prepare-agent</id>
+            <goals>
+              <goal>prepare-agent</goal>
+            </goals>
+          </execution>
+          <execution>
+            <id>report</id>
+            <phase>verify</phase>
+            <goals>
+              <goal>report</goal>
+            </goals>
+          </execution>
+          <execution>
+            <id>check</id>
+            <phase>verify</phase>
+            <goals>
+              <goal>check</goal>
+            </goals>
+            <configuration>
+              <rules>
+                <rule>
+                  <element>BUNDLE</element>
+                  <limits>
+                    <limit>
+                      <counter>LINE</counter>
+                      <value>COVEREDRATIO</value>
+                      <minimum>0.65</minimum>
+                    </limit>
+                  </limits>
+                </rule>
+              </rules>
+            </configuration>
+          </execution>
+        </executions>
+      </plugin>
+
     </plugins>
   </build>
 </project>

From 3f373363c538281d318e3bfe61fefcc59f8760cd Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Thu, 19 Dec 2024 13:13:40 -0500
Subject: [PATCH 02/14] Modify coverage to 0.45

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 0605624b..89b7cdd2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -140,7 +140,7 @@
                     <limit>
                       <counter>LINE</counter>
                       <value>COVEREDRATIO</value>
-                      <minimum>0.65</minimum>
+                      <minimum>0.45</minimum>
                     </limit>
                   </limits>
                 </rule>

From e6b1ad23947fc8e93cd0900a30458f6a39f6968d Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Thu, 19 Dec 2024 17:25:44 -0500
Subject: [PATCH 03/14] Remove tests from the coverage

---
 pom.xml | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 89b7cdd2..3eaf19b0 100644
--- a/pom.xml
+++ b/pom.xml
@@ -140,11 +140,14 @@
                     <limit>
                       <counter>LINE</counter>
                       <value>COVEREDRATIO</value>
-                      <minimum>0.45</minimum>
+                      <minimum>0.15</minimum>
                     </limit>
                   </limits>
                 </rule>
               </rules>
+              <excludes>
+                <exclude>**/test/**</exclude>
+              </excludes>
             </configuration>
           </execution>
         </executions>

From 513ef267993296b71defec530511e44707a1d57a Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Fri, 20 Dec 2024 14:15:19 -0500
Subject: [PATCH 04/14] Remove tests from the coverage

---
 pom.xml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/pom.xml b/pom.xml
index 3eaf19b0..b29a9026 100644
--- a/pom.xml
+++ b/pom.xml
@@ -145,9 +145,6 @@
                   </limits>
                 </rule>
               </rules>
-              <excludes>
-                <exclude>**/test/**</exclude>
-              </excludes>
             </configuration>
           </execution>
         </executions>

From ca31748e00b1910af5bf3e1576031530504fa2f1 Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Fri, 20 Dec 2024 14:17:11 -0500
Subject: [PATCH 05/14] Add artifact version

---
 pom.xml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index b29a9026..1dd74723 100644
--- a/pom.xml
+++ b/pom.xml
@@ -72,6 +72,7 @@
 
   <properties>
     <maven-dependency-plugin.version>3.8.1</maven-dependency-plugin.version>
+    <jacoco-maven-plugin.version>0.8.12</jacoco-maven-plugin.version>
   </properties>
 
   <dependencyManagement>
@@ -111,7 +112,7 @@
       <plugin>
         <groupId>org.jacoco</groupId>
         <artifactId>jacoco-maven-plugin</artifactId>
-        <version>0.8.12</version>
+        <version>${jacoco-maven-plugin.version}</version>
         <executions>
           <execution>
             <id>prepare-agent</id>

From 6d8a73bc15cce7d2ad9a737aaeac3819f8e442fc Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Fri, 20 Dec 2024 15:14:17 -0500
Subject: [PATCH 06/14] Remove coverage ratio limit

---
 pom.xml | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/pom.xml b/pom.xml
index 1dd74723..bcb1f720 100644
--- a/pom.xml
+++ b/pom.xml
@@ -133,20 +133,6 @@
             <goals>
               <goal>check</goal>
             </goals>
-            <configuration>
-              <rules>
-                <rule>
-                  <element>BUNDLE</element>
-                  <limits>
-                    <limit>
-                      <counter>LINE</counter>
-                      <value>COVEREDRATIO</value>
-                      <minimum>0.15</minimum>
-                    </limit>
-                  </limits>
-                </rule>
-              </rules>
-            </configuration>
           </execution>
         </executions>
       </plugin>

From 17b0dd6ff0dffe7c03acc37ef625e12da62d7f80 Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Fri, 20 Dec 2024 15:17:24 -0500
Subject: [PATCH 07/14] Remove coverage ratio limit

---
 pom.xml | 7 -------
 1 file changed, 7 deletions(-)

diff --git a/pom.xml b/pom.xml
index bcb1f720..a3a01e89 100644
--- a/pom.xml
+++ b/pom.xml
@@ -127,13 +127,6 @@
               <goal>report</goal>
             </goals>
           </execution>
-          <execution>
-            <id>check</id>
-            <phase>verify</phase>
-            <goals>
-              <goal>check</goal>
-            </goals>
-          </execution>
         </executions>
       </plugin>
 

From d615eda6cc7bf340ce9dfcd2d5c3cb00f444ef2c Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Fri, 20 Dec 2024 16:53:21 -0500
Subject: [PATCH 08/14] Add full JaCoCo aggregate report

---
 pom.xml | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/pom.xml b/pom.xml
index a3a01e89..f89a4ae2 100644
--- a/pom.xml
+++ b/pom.xml
@@ -127,6 +127,13 @@
               <goal>report</goal>
             </goals>
           </execution>
+          <execution>
+            <id>report-aggregate</id>
+            <phase>verify</phase>
+            <goals>
+              <goal>report-aggregate</goal>
+            </goals>
+          </execution>
         </executions>
       </plugin>
 

From ce93ce94057648f701173816fb2f8c26eb172621 Mon Sep 17 00:00:00 2001
From: tsande16 <tsande16@jhu.edu>
Date: Fri, 3 Jan 2025 16:38:30 -0500
Subject: [PATCH 09/14] Refactor for aggregate report

---
 jacoco-aggregate-report/pom.xml   | 39 +++++++++++++++++++++++++++++++
 pass-data-client/pom.xml          | 15 ++++++++++++
 pass-deposit-services/pom.xml     | 14 +++++++++++
 pass-grant-loader/pom.xml         | 14 +++++++++++
 pass-journal-loader/pom.xml       | 15 ++++++++++++
 pass-nihms-loader/pom.xml         | 15 ++++++++++++
 pass-notification-service/pom.xml | 15 ++++++++++++
 pom.xml                           | 19 +++------------
 8 files changed, 130 insertions(+), 16 deletions(-)
 create mode 100644 jacoco-aggregate-report/pom.xml

diff --git a/jacoco-aggregate-report/pom.xml b/jacoco-aggregate-report/pom.xml
new file mode 100644
index 00000000..f148df9d
--- /dev/null
+++ b/jacoco-aggregate-report/pom.xml
@@ -0,0 +1,39 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<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>
+    <parent>
+        <groupId>org.eclipse.pass</groupId>
+        <artifactId>pass-support</artifactId>
+        <version>1.14.0-SNAPSHOT</version>
+    </parent>
+
+    <artifactId>jacoco-aggregate-report</artifactId>
+
+    <properties>
+        <maven.compiler.source>17</maven.compiler.source>
+        <maven.compiler.target>17</maven.compiler.target>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    </properties>
+
+    <build>
+        <plugins>
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>${jacoco-maven-plugin.version}</version>
+                <executions>
+                    <execution>
+                        <id>report-aggregate</id>
+                        <phase>verify</phase>
+                        <goals>
+                            <goal>report-aggregate</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+        </plugins>
+    </build>
+
+</project>
\ No newline at end of file
diff --git a/pass-data-client/pom.xml b/pass-data-client/pom.xml
index bb470248..9f259925 100644
--- a/pass-data-client/pom.xml
+++ b/pass-data-client/pom.xml
@@ -182,6 +182,21 @@
         <groupId>org.cyclonedx</groupId>
         <artifactId>cyclonedx-maven-plugin</artifactId>
       </plugin>
+
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <version>${jacoco-maven-plugin.version}</version>
+        <executions>
+          <execution>
+            <id>prepare-agent</id>
+            <goals>
+              <goal>prepare-agent</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+
     </plugins>
   </build>
 </project>
diff --git a/pass-deposit-services/pom.xml b/pass-deposit-services/pom.xml
index 06fb1df4..25a8ebe1 100644
--- a/pass-deposit-services/pom.xml
+++ b/pass-deposit-services/pom.xml
@@ -400,6 +400,20 @@
         <version>3.4.0</version>
       </plugin>
 
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <version>${jacoco-maven-plugin.version}</version>
+        <executions>
+          <execution>
+            <id>prepare-agent</id>
+            <goals>
+              <goal>prepare-agent</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+
     </plugins>
   </build>
 </project>
diff --git a/pass-grant-loader/pom.xml b/pass-grant-loader/pom.xml
index 9b4f6077..771189fd 100644
--- a/pass-grant-loader/pom.xml
+++ b/pass-grant-loader/pom.xml
@@ -296,6 +296,20 @@
           <artifactId>cyclonedx-maven-plugin</artifactId>
         </plugin>
 
+        <plugin>
+          <groupId>org.jacoco</groupId>
+          <artifactId>jacoco-maven-plugin</artifactId>
+          <version>${jacoco-maven-plugin.version}</version>
+          <executions>
+            <execution>
+              <id>prepare-agent</id>
+              <goals>
+                <goal>prepare-agent</goal>
+              </goals>
+            </execution>
+          </executions>
+        </plugin>
+
       </plugins>
   </build>
 </project>
diff --git a/pass-journal-loader/pom.xml b/pass-journal-loader/pom.xml
index 476abe39..6872f8e7 100644
--- a/pass-journal-loader/pom.xml
+++ b/pass-journal-loader/pom.xml
@@ -141,6 +141,21 @@
           <artifactId>maven-help-plugin</artifactId>
           <version>3.4.0</version>
         </plugin>
+
+        <plugin>
+          <groupId>org.jacoco</groupId>
+          <artifactId>jacoco-maven-plugin</artifactId>
+          <version>${jacoco-maven-plugin.version}</version>
+          <executions>
+            <execution>
+              <id>prepare-agent</id>
+              <goals>
+                <goal>prepare-agent</goal>
+              </goals>
+            </execution>
+          </executions>
+        </plugin>
+
       </plugins>
 
   </build>
diff --git a/pass-nihms-loader/pom.xml b/pass-nihms-loader/pom.xml
index 96cd061e..3504c611 100644
--- a/pass-nihms-loader/pom.xml
+++ b/pass-nihms-loader/pom.xml
@@ -178,6 +178,21 @@
                 <artifactId>maven-help-plugin</artifactId>
                 <version>3.4.0</version>
             </plugin>
+
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>${jacoco-maven-plugin.version}</version>
+                <executions>
+                    <execution>
+                        <id>prepare-agent</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
         </plugins>
     </build>
 
diff --git a/pass-notification-service/pom.xml b/pass-notification-service/pom.xml
index 6fcdbe57..b163e559 100644
--- a/pass-notification-service/pom.xml
+++ b/pass-notification-service/pom.xml
@@ -355,6 +355,21 @@
                 <groupId>org.cyclonedx</groupId>
                 <artifactId>cyclonedx-maven-plugin</artifactId>
             </plugin>
+
+            <plugin>
+                <groupId>org.jacoco</groupId>
+                <artifactId>jacoco-maven-plugin</artifactId>
+                <version>${jacoco-maven-plugin.version}</version>
+                <executions>
+                    <execution>
+                        <id>prepare-agent</id>
+                        <goals>
+                            <goal>prepare-agent</goal>
+                        </goals>
+                    </execution>
+                </executions>
+            </plugin>
+
         </plugins>
     </build>
 </project>
diff --git a/pom.xml b/pom.xml
index f89a4ae2..f21024bd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -56,11 +56,12 @@
 
   <modules>
     <module>pass-data-client</module>
-    <module>pass-journal-loader</module>
+    <module>pass-deposit-services</module>
     <module>pass-grant-loader</module>
+    <module>pass-journal-loader</module>
     <module>pass-nihms-loader</module>
     <module>pass-notification-service</module>
-    <module>pass-deposit-services</module>
+    <module>jacoco-aggregate-report</module>
   </modules>
 
   <scm>
@@ -120,20 +121,6 @@
               <goal>prepare-agent</goal>
             </goals>
           </execution>
-          <execution>
-            <id>report</id>
-            <phase>verify</phase>
-            <goals>
-              <goal>report</goal>
-            </goals>
-          </execution>
-          <execution>
-            <id>report-aggregate</id>
-            <phase>verify</phase>
-            <goals>
-              <goal>report-aggregate</goal>
-            </goals>
-          </execution>
         </executions>
       </plugin>
 

From 37075274b57a6293faf5652fa333545494cda330 Mon Sep 17 00:00:00 2001
From: tsande16 <tsande16@jhu.edu>
Date: Mon, 6 Jan 2025 14:22:50 -0500
Subject: [PATCH 10/14] Add submodules dependencies

---
 jacoco-aggregate-report/pom.xml | 58 +++++++++++++++++++++++++++++++++
 1 file changed, 58 insertions(+)

diff --git a/jacoco-aggregate-report/pom.xml b/jacoco-aggregate-report/pom.xml
index f148df9d..29f32960 100644
--- a/jacoco-aggregate-report/pom.xml
+++ b/jacoco-aggregate-report/pom.xml
@@ -17,6 +17,64 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     </properties>
 
+    <dependencies>
+        <dependency>
+            <groupId>org.eclipse.pass</groupId>
+            <artifactId>pass-data-client</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass.deposit</groupId>
+            <artifactId>deposit-core</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass.deposit</groupId>
+            <artifactId>deposit-cri</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass.deposit</groupId>
+            <artifactId>deposit-model</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass.deposit</groupId>
+            <artifactId>deposit-util</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass</groupId>
+            <artifactId>pass-grant-loader</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass</groupId>
+            <artifactId>pass-journal-loader-nih</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass</groupId>
+            <artifactId>nihms-data-harvest</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass</groupId>
+            <artifactId>nihms-data-transform-load</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass</groupId>
+            <artifactId>nihms-etl-model</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+        <dependency>
+            <groupId>org.eclipse.pass</groupId>
+            <artifactId>pass-notification-service</artifactId>
+            <version>${project.version}</version>
+        </dependency>
+    </dependencies>
+
     <build>
         <plugins>
             <plugin>

From 237b6dd876bbc5f82b17223ca5dd425a66bea7b7 Mon Sep 17 00:00:00 2001
From: tsande16 <tsande16@jhu.edu>
Date: Tue, 7 Jan 2025 10:23:30 -0500
Subject: [PATCH 11/14] Remove compile version

---
 jacoco-aggregate-report/pom.xml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/jacoco-aggregate-report/pom.xml b/jacoco-aggregate-report/pom.xml
index 29f32960..a82c2e29 100644
--- a/jacoco-aggregate-report/pom.xml
+++ b/jacoco-aggregate-report/pom.xml
@@ -12,9 +12,6 @@
     <artifactId>jacoco-aggregate-report</artifactId>
 
     <properties>
-        <maven.compiler.source>17</maven.compiler.source>
-        <maven.compiler.target>17</maven.compiler.target>
-        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     </properties>
 
     <dependencies>

From ed83d7e29271019d5afb19ba983ca0a10e1c0883 Mon Sep 17 00:00:00 2001
From: tsande16 <tsande16@jhu.edu>
Date: Mon, 13 Jan 2025 17:21:20 -0500
Subject: [PATCH 12/14] Refactor to use pluginManagement

---
 pass-data-client/pom.xml          | 14 ------------
 pass-deposit-services/pom.xml     | 14 ------------
 pass-grant-loader/pom.xml         | 14 ------------
 pass-journal-loader/pom.xml       | 14 ------------
 pass-nihms-loader/pom.xml         | 14 ------------
 pass-notification-service/pom.xml | 13 -----------
 pom.xml                           | 38 +++++++++++++++++++------------
 7 files changed, 24 insertions(+), 97 deletions(-)

diff --git a/pass-data-client/pom.xml b/pass-data-client/pom.xml
index 9f259925..92dbd1ee 100644
--- a/pass-data-client/pom.xml
+++ b/pass-data-client/pom.xml
@@ -183,20 +183,6 @@
         <artifactId>cyclonedx-maven-plugin</artifactId>
       </plugin>
 
-      <plugin>
-        <groupId>org.jacoco</groupId>
-        <artifactId>jacoco-maven-plugin</artifactId>
-        <version>${jacoco-maven-plugin.version}</version>
-        <executions>
-          <execution>
-            <id>prepare-agent</id>
-            <goals>
-              <goal>prepare-agent</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
-
     </plugins>
   </build>
 </project>
diff --git a/pass-deposit-services/pom.xml b/pass-deposit-services/pom.xml
index 25a8ebe1..06fb1df4 100644
--- a/pass-deposit-services/pom.xml
+++ b/pass-deposit-services/pom.xml
@@ -400,20 +400,6 @@
         <version>3.4.0</version>
       </plugin>
 
-      <plugin>
-        <groupId>org.jacoco</groupId>
-        <artifactId>jacoco-maven-plugin</artifactId>
-        <version>${jacoco-maven-plugin.version}</version>
-        <executions>
-          <execution>
-            <id>prepare-agent</id>
-            <goals>
-              <goal>prepare-agent</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
-
     </plugins>
   </build>
 </project>
diff --git a/pass-grant-loader/pom.xml b/pass-grant-loader/pom.xml
index 771189fd..9b4f6077 100644
--- a/pass-grant-loader/pom.xml
+++ b/pass-grant-loader/pom.xml
@@ -296,20 +296,6 @@
           <artifactId>cyclonedx-maven-plugin</artifactId>
         </plugin>
 
-        <plugin>
-          <groupId>org.jacoco</groupId>
-          <artifactId>jacoco-maven-plugin</artifactId>
-          <version>${jacoco-maven-plugin.version}</version>
-          <executions>
-            <execution>
-              <id>prepare-agent</id>
-              <goals>
-                <goal>prepare-agent</goal>
-              </goals>
-            </execution>
-          </executions>
-        </plugin>
-
       </plugins>
   </build>
 </project>
diff --git a/pass-journal-loader/pom.xml b/pass-journal-loader/pom.xml
index 6872f8e7..d205797f 100644
--- a/pass-journal-loader/pom.xml
+++ b/pass-journal-loader/pom.xml
@@ -142,20 +142,6 @@
           <version>3.4.0</version>
         </plugin>
 
-        <plugin>
-          <groupId>org.jacoco</groupId>
-          <artifactId>jacoco-maven-plugin</artifactId>
-          <version>${jacoco-maven-plugin.version}</version>
-          <executions>
-            <execution>
-              <id>prepare-agent</id>
-              <goals>
-                <goal>prepare-agent</goal>
-              </goals>
-            </execution>
-          </executions>
-        </plugin>
-
       </plugins>
 
   </build>
diff --git a/pass-nihms-loader/pom.xml b/pass-nihms-loader/pom.xml
index 3504c611..ec360380 100644
--- a/pass-nihms-loader/pom.xml
+++ b/pass-nihms-loader/pom.xml
@@ -179,20 +179,6 @@
                 <version>3.4.0</version>
             </plugin>
 
-            <plugin>
-                <groupId>org.jacoco</groupId>
-                <artifactId>jacoco-maven-plugin</artifactId>
-                <version>${jacoco-maven-plugin.version}</version>
-                <executions>
-                    <execution>
-                        <id>prepare-agent</id>
-                        <goals>
-                            <goal>prepare-agent</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
-
         </plugins>
     </build>
 
diff --git a/pass-notification-service/pom.xml b/pass-notification-service/pom.xml
index b163e559..47d43a4f 100644
--- a/pass-notification-service/pom.xml
+++ b/pass-notification-service/pom.xml
@@ -356,19 +356,6 @@
                 <artifactId>cyclonedx-maven-plugin</artifactId>
             </plugin>
 
-            <plugin>
-                <groupId>org.jacoco</groupId>
-                <artifactId>jacoco-maven-plugin</artifactId>
-                <version>${jacoco-maven-plugin.version}</version>
-                <executions>
-                    <execution>
-                        <id>prepare-agent</id>
-                        <goals>
-                            <goal>prepare-agent</goal>
-                        </goals>
-                    </execution>
-                </executions>
-            </plugin>
 
         </plugins>
     </build>
diff --git a/pom.xml b/pom.xml
index f21024bd..f1f886f7 100644
--- a/pom.xml
+++ b/pom.xml
@@ -93,7 +93,31 @@
   </repositories>
 
   <build>
+    <pluginManagement>
+      <plugins>
+        <plugin>
+          <groupId>org.jacoco</groupId>
+          <artifactId>jacoco-maven-plugin</artifactId>
+          <version>${jacoco-maven-plugin.version}</version>
+        </plugin>
+      </plugins>
+    </pluginManagement>
+
     <plugins>
+
+      <plugin>
+        <groupId>org.jacoco</groupId>
+        <artifactId>jacoco-maven-plugin</artifactId>
+        <executions>
+          <execution>
+            <id>prepare-agent</id>
+            <goals>
+              <goal>prepare-agent</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-source-plugin</artifactId>
@@ -110,20 +134,6 @@
         <version>${maven-dependency-plugin.version}</version>
       </plugin>
 
-      <plugin>
-        <groupId>org.jacoco</groupId>
-        <artifactId>jacoco-maven-plugin</artifactId>
-        <version>${jacoco-maven-plugin.version}</version>
-        <executions>
-          <execution>
-            <id>prepare-agent</id>
-            <goals>
-              <goal>prepare-agent</goal>
-            </goals>
-          </execution>
-        </executions>
-      </plugin>
-
     </plugins>
   </build>
 </project>

From 54710e09095fa76774513e02be553981be248d8d Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Wed, 15 Jan 2025 18:43:42 -0500
Subject: [PATCH 13/14] Revert back to pluginManagement and plugin

- Revert back to using the pluginManagement and the agent in the plugin
- Remove extra line feeds at closing tags
- Remove jacoco plugin version in the aggregateReport
---
 jacoco-aggregate-report/pom.xml                     | 1 -
 pass-data-client/pom.xml                            | 1 -
 pass-deposit-services/pom.xml                       | 1 -
 pass-grant-loader/pom.xml                           | 1 -
 pass-journal-loader/pass-journal-loader-nih/pom.xml | 1 -
 pass-journal-loader/pom.xml                         | 3 ---
 pass-nihms-loader/pom.xml                           | 2 --
 pass-notification-service/pom.xml                   | 2 --
 pom.xml                                             | 2 --
 9 files changed, 14 deletions(-)

diff --git a/jacoco-aggregate-report/pom.xml b/jacoco-aggregate-report/pom.xml
index a82c2e29..8d9bef29 100644
--- a/jacoco-aggregate-report/pom.xml
+++ b/jacoco-aggregate-report/pom.xml
@@ -77,7 +77,6 @@
             <plugin>
                 <groupId>org.jacoco</groupId>
                 <artifactId>jacoco-maven-plugin</artifactId>
-                <version>${jacoco-maven-plugin.version}</version>
                 <executions>
                     <execution>
                         <id>report-aggregate</id>
diff --git a/pass-data-client/pom.xml b/pass-data-client/pom.xml
index 92dbd1ee..bb470248 100644
--- a/pass-data-client/pom.xml
+++ b/pass-data-client/pom.xml
@@ -182,7 +182,6 @@
         <groupId>org.cyclonedx</groupId>
         <artifactId>cyclonedx-maven-plugin</artifactId>
       </plugin>
-
     </plugins>
   </build>
 </project>
diff --git a/pass-deposit-services/pom.xml b/pass-deposit-services/pom.xml
index 06fb1df4..9202928b 100644
--- a/pass-deposit-services/pom.xml
+++ b/pass-deposit-services/pom.xml
@@ -399,7 +399,6 @@
         <artifactId>maven-help-plugin</artifactId>
         <version>3.4.0</version>
       </plugin>
-
     </plugins>
   </build>
 </project>
diff --git a/pass-grant-loader/pom.xml b/pass-grant-loader/pom.xml
index 9b4f6077..f8abd8d5 100644
--- a/pass-grant-loader/pom.xml
+++ b/pass-grant-loader/pom.xml
@@ -295,7 +295,6 @@
           <groupId>org.cyclonedx</groupId>
           <artifactId>cyclonedx-maven-plugin</artifactId>
         </plugin>
-
       </plugins>
   </build>
 </project>
diff --git a/pass-journal-loader/pass-journal-loader-nih/pom.xml b/pass-journal-loader/pass-journal-loader-nih/pom.xml
index 846d3b12..78d6f02f 100644
--- a/pass-journal-loader/pass-journal-loader-nih/pom.xml
+++ b/pass-journal-loader/pass-journal-loader-nih/pom.xml
@@ -151,7 +151,6 @@
         <groupId>org.cyclonedx</groupId>
         <artifactId>cyclonedx-maven-plugin</artifactId>
       </plugin>
-
     </plugins>
   </build>
 </project>
diff --git a/pass-journal-loader/pom.xml b/pass-journal-loader/pom.xml
index d205797f..c122ed66 100644
--- a/pass-journal-loader/pom.xml
+++ b/pass-journal-loader/pom.xml
@@ -141,9 +141,6 @@
           <artifactId>maven-help-plugin</artifactId>
           <version>3.4.0</version>
         </plugin>
-
       </plugins>
-
   </build>
-
 </project>
diff --git a/pass-nihms-loader/pom.xml b/pass-nihms-loader/pom.xml
index ec360380..42b0fc8a 100644
--- a/pass-nihms-loader/pom.xml
+++ b/pass-nihms-loader/pom.xml
@@ -178,8 +178,6 @@
                 <artifactId>maven-help-plugin</artifactId>
                 <version>3.4.0</version>
             </plugin>
-
         </plugins>
     </build>
-
 </project>
\ No newline at end of file
diff --git a/pass-notification-service/pom.xml b/pass-notification-service/pom.xml
index 47d43a4f..6fcdbe57 100644
--- a/pass-notification-service/pom.xml
+++ b/pass-notification-service/pom.xml
@@ -355,8 +355,6 @@
                 <groupId>org.cyclonedx</groupId>
                 <artifactId>cyclonedx-maven-plugin</artifactId>
             </plugin>
-
-
         </plugins>
     </build>
 </project>
diff --git a/pom.xml b/pom.xml
index f1f886f7..6d7e03e4 100644
--- a/pom.xml
+++ b/pom.xml
@@ -104,7 +104,6 @@
     </pluginManagement>
 
     <plugins>
-
       <plugin>
         <groupId>org.jacoco</groupId>
         <artifactId>jacoco-maven-plugin</artifactId>
@@ -133,7 +132,6 @@
         <artifactId>maven-dependency-plugin</artifactId>
         <version>${maven-dependency-plugin.version}</version>
       </plugin>
-
     </plugins>
   </build>
 </project>

From 8d3e812696ce2081d53ace92ab4615373a65cc71 Mon Sep 17 00:00:00 2001
From: Timothy Sanders <tsande16@jhu.edu>
Date: Thu, 16 Jan 2025 07:40:59 -0500
Subject: [PATCH 14/14] Revert back to pluginManagement and plugin

- Revert back to using the pluginManagement and the agent in the plugin
- Remove extra line feeds at closing tags
- Remove jacoco plugin version in the aggregateReport
---
 pom.xml | 11 +----------
 1 file changed, 1 insertion(+), 10 deletions(-)

diff --git a/pom.xml b/pom.xml
index 6d7e03e4..b5954cbf 100644
--- a/pom.xml
+++ b/pom.xml
@@ -93,20 +93,11 @@
   </repositories>
 
   <build>
-    <pluginManagement>
-      <plugins>
-        <plugin>
-          <groupId>org.jacoco</groupId>
-          <artifactId>jacoco-maven-plugin</artifactId>
-          <version>${jacoco-maven-plugin.version}</version>
-        </plugin>
-      </plugins>
-    </pluginManagement>
-
     <plugins>
       <plugin>
         <groupId>org.jacoco</groupId>
         <artifactId>jacoco-maven-plugin</artifactId>
+        <version>${jacoco-maven-plugin.version}</version>
         <executions>
           <execution>
             <id>prepare-agent</id>