Merge pull request #6 from ebremer/develop

Bump Jena 4.6.1 --> 4.8.0
halcyon-project · May 2, 2023 · f5ec4a3 · f5ec4a3
2 parents 21518a0 + 9a5ca52
commit f5ec4a3
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Showing 18 changed files with 315 additions and 180 deletions.
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -10,7 +10,7 @@
   <groupId>com.ebremer</groupId>
   <artifactId>Halcyon</artifactId>
   <name>Halcyon</name>
-  <version>0.1.0</version>
+  <version>0.2.1</version>
   <description>A whole slide image annotation, management, and visualization system</description>
   <issueManagement>
     <system>github</system>
@@ -75,7 +75,7 @@
           <copyright>Copyright 2022 Erich Bremer - Stony Brook University</copyright>
           <licenseFile>LICENSE</licenseFile>
           <input>target</input>
-          <mainJar>Halcyon-0.0.0.jar</mainJar>
+          <mainJar>Halcyon-0.2.0.jar</mainJar>
           <verbose>true</verbose>
           <winMenu>true</winMenu>
           <winShortcutPrompt>true</winShortcutPrompt>
@@ -167,7 +167,7 @@
           </plugin>
           <plugin>
             <artifactId>maven-enforcer-plugin</artifactId>
-            <version>3.1.0</version>
+            <version>3.2.1</version>
             <configuration>
               <rules>
                 <dependencyConvergence />
@@ -218,7 +218,7 @@
         <plugins>
           <plugin>
             <artifactId>maven-enforcer-plugin</artifactId>
-            <version>3.1.0</version>
+            <version>3.2.1</version>
             <configuration>
               <rules>
                 <dependencyConvergence />
@@ -228,7 +228,7 @@
           <plugin>
             <groupId>org.springframework.experimental</groupId>
             <artifactId>spring-aot-maven-plugin</artifactId>
-            <version>0.12.1</version>
+            <version>0.12.2</version>
             <executions>
               <execution>
                 <id>generate</id>
@@ -241,7 +241,7 @@
           <plugin>
             <groupId>org.graalvm.buildtools</groupId>
             <artifactId>native-maven-plugin</artifactId>
-            <version>0.9.13</version>
+            <version>0.9.20</version>
             <extensions>true</extensions>
             <executions>
               <execution>
@@ -295,7 +295,7 @@
         <dependency>
           <groupId>org.springframework.experimental</groupId>
           <artifactId>spring-native</artifactId>
-          <version>0.12.1</version>
+          <version>0.12.2</version>
         </dependency>
       </dependencies>
     </profile>
@@ -306,7 +306,7 @@
           <plugin>
             <groupId>org.graalvm.buildtools</groupId>
             <artifactId>native-maven-plugin</artifactId>
-            <version>0.9.19</version>
+            <version>0.9.21</version>
             <extensions>true</extensions>
             <executions>
               <execution>
@@ -324,11 +324,16 @@
               <skipNativeBuild>true</skipNativeBuild>
               <skipNativeTests>true</skipNativeTests>
               <verbose>true</verbose>
+              <jvmArgs>
+                <arg>--add-opens=java.base/java.nio=ALL-UNNAMED</arg>
+                <arg>--enable-preview</arg>
+              </jvmArgs>
               <buildArgs>
                 <buildArg>--no-fallback</buildArg>
                 <buildArg>-H:ConfigurationFileDirectories=ingestconfig</buildArg>
                 <buildArg>--enable-url-protocols=https</buildArg>
                 <buildArg>-H:+AddAllCharsets</buildArg>
+                <buildArg>--static</buildArg>
               </buildArgs>
             </configuration>
           </plugin>
@@ -633,6 +638,12 @@
       <version>4.6.1</version>
       <scope>provided</scope>
     </dependency>
+    <dependency>
+      <groupId>org.apache.jena</groupId>
+      <artifactId>jena-querybuilder</artifactId>
+      <version>4.6.1</version>
+      <scope>provided</scope>
+    </dependency>
     <dependency>
       <groupId>org.apache.jena</groupId>
       <artifactId>jena-permissions</artifactId>
@@ -730,7 +741,61 @@
     <dependency>
       <groupId>com.ebremer</groupId>
       <artifactId>BeakGraph</artifactId>
-      <version>0.0.0</version>
+      <version>0.1.0</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.shiro</groupId>
+      <artifactId>shiro-core</artifactId>
+      <version>1.11.0</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.shiro</groupId>
+      <artifactId>shiro-web</artifactId>
+      <version>1.11.0</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>com.jcabi</groupId>
+      <artifactId>jcabi-aspects</artifactId>
+      <version>0.24.1</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.jena</groupId>
+      <artifactId>jena-tdb</artifactId>
+      <version>4.6.1</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>io.jsonwebtoken</groupId>
+      <artifactId>jjwt-api</artifactId>
+      <version>0.11.5</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>io.jsonwebtoken</groupId>
+      <artifactId>jjwt-impl</artifactId>
+      <version>0.11.5</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>io.jsonwebtoken</groupId>
+      <artifactId>jjwt-jackson</artifactId>
+      <version>0.11.5</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.projectlombok</groupId>
+      <artifactId>lombok</artifactId>
+      <version>1.18.26</version>
+      <scope>provided</scope>
+    </dependency>
+    <dependency>
+      <groupId>com.beust</groupId>
+      <artifactId>jcommander</artifactId>
+      <version>1.82</version>
       <scope>provided</scope>
     </dependency>
   </dependencies>
@@ -815,7 +880,7 @@
     <wicket.ver>9.12.0</wicket.ver>
     <infinispan.version>13.0.12.Final</infinispan.version>
     <embeddedkeycloak.ver>8.0.0</embeddedkeycloak.ver>
-    <dcm4che.ver>5.29.1</dcm4che.ver>
+    <dcm4che.ver>5.29.2</dcm4che.ver>
     <jgroups.version>4.2.21.Final</jgroups.version>
     <titanium-json-ld.ver>1.3.0</titanium-json-ld.ver>
     <maven.compiler.target>17</maven.compiler.target>

diff --git a/ingestconfig/jni-config.json b/ingestconfig/jni-config.json
@@ -3,20 +3,6 @@
   "name":"java.lang.Boolean",
   "methods":[{"name":"getBoolean","parameterTypes":["java.lang.String"] }]
 },
-{
-  "name":"java.lang.ClassLoader",
-  "methods":[
-    {"name":"getPlatformClassLoader","parameterTypes":[] }, 
-    {"name":"loadClass","parameterTypes":["java.lang.String"] }
-  ]
-},
-{
-  "name":"jdk.internal.loader.ClassLoaders$PlatformClassLoader"
-},
-{
-  "name":"org.graalvm.jniutils.JNIExceptionWrapperEntryPoints",
-  "methods":[{"name":"getClassName","parameterTypes":["java.lang.Class"] }]
-},
 {
   "name":"sun.management.VMManagementImpl",
   "fields":[

diff --git a/ingestconfig/proxy-config.json b/ingestconfig/proxy-config.json
@@ -1,5 +1,2 @@
 [
-  {
-    "interfaces":["org.apache.http.client.methods.CloseableHttpResponse"]}
-
 ]