Release/0008 (#173)

* [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * Sync new Release/0008 with Master (#168) * [ALS-5422] Add persistence.xml to visualization resource (#161) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. * [ALS-0000] Fix aggregate resource - Very confused as to how this was working before * [ALS-5422] Add persistence.xml to visualization resource (#161) (#162) (#163) The visualization resource is failing to start due to an error injecting persistence unit into CDI managed bean. It is unable to find a persistence unit named ''. --------- Co-authored-by: Luke Sikina <[email protected]> * [ALS-5061] Remove HSAPIResource (#166) [ALS-5061] Remove HSAPIResource (#166) * [ALS-3978] Update version handling in multiple pom.xml files (#167) * [ALS-3978] Update version handling in multiple pom.xml files This commit removes hardcoded versions of dependencies from individual pom.xml files and introduces them into the root pom.xml's properties section. This centralizes the control of dependency versions to prevent inconsistencies and makes future updates more straightforward. This change covers several libraries including Guava, JUnit Jupiter, Mockito, and others. * Update library versions and clean up pom.xml Upgraded dependencies including Jackson, Guava, JUnit, Hibernate, HttpClient, and Commons-IO. Also, improved the management of versions via property variables and cleaned up inconsistent formatting. Removed an unnecessary comment related to Mockito version compatibility. * Remove specific version references in pom.xml files The changes encompass the removal of explicit version references in the project's pom.xml files. By relying on property variables, this maintenance update enhances dependency management flexibility. Specific version comments also have been removed to eliminate clutter and improve overall file readability. * Update pom.xml to use property variables for versions The changes primarily involve updating the pom.xml file to use property variables instead of hardcoding the version numbers. This is a better approach as it improves the flexibility in managing dependencies. This change also results in cleaner and more readable code by removing unnecessary explicit version references. * Downgrade Spring version in pom.xml The Spring version has been downgraded in the pom.xml file from 6.1.1 to 5.3.31. This is due to java version requirement of 17+ for 6.x --------- Co-authored-by: Luke Sikina <[email protected]>
hms-dbmi · Dec 21, 2023 · c484815 · c484815
1 parent 9514f91
commit c484815
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Showing 20 changed files with 120 additions and 1,187 deletions.
diff --git a/pic-sure-api-data/pom.xml b/pic-sure-api-data/pom.xml
@@ -40,7 +40,6 @@
 		<dependency>
 			<groupId>io.swagger.core.v3</groupId>
 			<artifactId>swagger-annotations</artifactId>
-			<version>2.2.8</version>
 		</dependency>
 	</dependencies>
 </project>
diff --git a/pic-sure-api-war/pom.xml b/pic-sure-api-war/pom.xml
@@ -32,7 +32,6 @@
 		<dependency>
 			<groupId>com.github.tomakehurst</groupId>
 			<artifactId>wiremock-jre8</artifactId>
-			<version>2.27.2</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -69,7 +68,6 @@
 		<dependency>
 			<groupId>org.apache.cxf</groupId>
 			<artifactId>cxf-rt-frontend-jaxrs</artifactId>
-			<version>3.4.1</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>

diff --git a/pic-sure-api-wildfly/pom.xml b/pic-sure-api-wildfly/pom.xml
@@ -35,12 +35,6 @@
             <classifier>classes</classifier>
             <version>${project.version}</version>
         </dependency>
-		<dependency>
-			<groupId>edu.harvard.hms.dbmi.avillach</groupId>
-			<artifactId>pic-sure-hsapi-resource</artifactId>
-			<classifier>classes</classifier>
-			<version>${project.version}</version>
-		</dependency>
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 			<artifactId>pic-sure-resource-api</artifactId>

diff --git a/pic-sure-api-wildfly/src/test/java/edu/harvard/dbmi/avillach/HSAPIResourceIT.java b/pic-sure-api-wildfly/src/test/java/edu/harvard/dbmi/avillach/HSAPIResourceIT.java
diff --git a/pic-sure-initializer/pom.xml b/pic-sure-initializer/pom.xml
@@ -7,16 +7,12 @@
 		<groupId>edu.harvard.hms.dbmi.avillach</groupId>
 		<version>2.0.0-SNAPSHOT</version>
 	</parent>
-
 	<artifactId>pic-sure-initializer</artifactId>
-
 	<name>pic-sure-initializer</name>
-
 	<dependencies>
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.7</version>
 		</dependency>
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.avillach</groupId>
@@ -26,19 +22,16 @@
 		<dependency>
 			<groupId>junit</groupId>
 			<artifactId>junit</artifactId>
-			<version>4.11</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpclient</artifactId>
-			<version>4.5.13</version>
 			<scope>compile</scope>
 		</dependency>
 		<dependency>
 			<groupId>commons-cli</groupId>
 			<artifactId>commons-cli</artifactId>
-			<version>1.4</version>
 		</dependency>
 	</dependencies>
 

diff --git a/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/pom.xml b/pic-sure-resources/pic-sure-aggregate-data-sharing-resource/pom.xml
@@ -40,7 +40,6 @@
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
-            <version>4.5.13</version>
         </dependency>
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
@@ -53,12 +52,10 @@
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.7</version>
 		</dependency>
 		<dependency>
 			<groupId>org.jboss.resteasy</groupId>
 			<artifactId>resteasy-jaxb-provider</artifactId>
-			<version>3.0.8.Final</version>
 		</dependency>
 		<dependency>
 			<groupId>edu.harvard.hms.dbmi.avillach</groupId>
@@ -68,7 +65,6 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-lang3</artifactId>
-			<version>3.7</version>
 		</dependency>
 		<dependency>
 			<groupId>org.hibernate.javax.persistence</groupId>

diff --git a/pic-sure-resources/pic-sure-ga4gh-dos/pom.xml b/pic-sure-resources/pic-sure-ga4gh-dos/pom.xml
@@ -31,7 +31,6 @@
 		<dependency>
 			<groupId>org.apache.httpcomponents</groupId>
 			<artifactId>httpclient</artifactId>
-			<version>4.5.13</version>
 		</dependency>
 		<dependency>
 			<groupId>com.fasterxml.jackson.core</groupId>
@@ -40,12 +39,10 @@
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.7</version>
 		</dependency>
 		<dependency>
 			<groupId>org.jboss.resteasy</groupId>
 			<artifactId>resteasy-jaxb-provider</artifactId>
-			<version>3.0.8.Final</version>
 		</dependency>
         <dependency>
             <groupId>edu.harvard.hms.dbmi.avillach</groupId>
@@ -55,7 +52,6 @@
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.7</version>
         </dependency>
 		<dependency>
 			<groupId>org.hibernate.javax.persistence</groupId>