Merge pull request #9 from ebremer/develop

code cleanup
halcyon-project · May 24, 2023 · 4c053c8 · 4c053c8
2 parents cc4d219 + 495184a
commit 4c053c8
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Showing 78 changed files with 95 additions and 24,623 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>0.3.1</version>
+  <version>0.4.0</version>
   <description>A whole slide image annotation, management, and visualization system</description>
   <issueManagement>
     <system>github</system>
@@ -94,6 +94,15 @@
           </javaOptions>
         </configuration>
       </plugin>
+      <plugin>
+        <artifactId>maven-compiler-plugin</artifactId>
+        <version>3.11.0</version>
+        <configuration>
+          <compilerArgs>
+            <arg>--enable-preview</arg>
+          </compilerArgs>
+        </configuration>
+      </plugin>
     </plugins>
   </build>
   <profiles>
@@ -170,6 +179,15 @@
           </resource>
         </resources>
         <plugins>
+          <plugin>
+            <artifactId>maven-dependency-plugin</artifactId>
+            <version>3.5.0</version>
+            <configuration>
+              <usedDependencies>
+                <dependency>org.apache.jena:jena-tdb2</dependency>
+              </usedDependencies>
+            </configuration>
+          </plugin>
           <plugin>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-maven-plugin</artifactId>
@@ -774,7 +792,7 @@
     <dependency>
       <groupId>com.ebremer</groupId>
       <artifactId>BeakGraph</artifactId>
-      <version>0.2.0</version>
+      <version>0.3.1</version>
       <scope>provided</scope>
     </dependency>
     <dependency>
@@ -907,7 +925,7 @@
     <titanium-json-ld.ver>1.3.0</titanium-json-ld.ver>
     <maven.compiler.target>17</maven.compiler.target>
     <hilbert.ver>0.2.2</hilbert.ver>
-    <beakgraph.version>0.2.0</beakgraph.version>
+    <beakgraph.version>0.3.1</beakgraph.version>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
     <commons-pool2.ver>2.11.1</commons-pool2.ver>
     <keycloak.ver>18.0.2</keycloak.ver>

diff --git a/nbactions-ingestjar.xml b/nbactions-ingestjar.xml
@@ -13,8 +13,8 @@
                 <exec.longClasspath>true</exec.longClasspath>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.executable>java</exec.executable>
-                <exec.vmArgs>-Xmx60G -Xms60G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview</exec.vmArgs>
-                <exec.appArgs></exec.appArgs>
+                <exec.vmArgs>-Xmx30G -Xms30G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview  -Darrow.memory.debug.allocator=true</exec.vmArgs>
+                <exec.appArgs>-v -src "D:\halcyon\features\src2" -dest "D:\halcyon\features\dest"</exec.appArgs>
                 <exec.mainClass>com.ebremer.halcyon.converters.Ingest</exec.mainClass>
             </properties>
         </action>
@@ -32,8 +32,8 @@
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
-                <exec.vmArgs>-Xmx60G -Xms60G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
-                <exec.appArgs></exec.appArgs>
+                <exec.vmArgs>-Xmx30G -Xms30G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview  -Darrow.memory.debug.allocator=true -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
+                <exec.appArgs>-v -src "D:\halcyon\features\src2" -dest "D:\halcyon\features\dest"</exec.appArgs>
                 <exec.mainClass>com.ebremer.halcyon.converters.Ingest</exec.mainClass>
             </properties>
         </action>
@@ -50,8 +50,8 @@
                 <exec.longClasspath>true</exec.longClasspath>
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.executable>java</exec.executable>
-                <exec.vmArgs>-Xmx60G -Xms60G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview</exec.vmArgs>
-                <exec.appArgs></exec.appArgs>
+                <exec.vmArgs>-Xmx30G -Xms30G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview  -Darrow.memory.debug.allocator=true</exec.vmArgs>
+                <exec.appArgs>-v -src "D:\halcyon\features\src2" -dest "D:\halcyon\features\dest"</exec.appArgs>
                 <exec.mainClass>com.ebremer.halcyon.converters.Ingest</exec.mainClass>
             </properties>
         </action>

diff --git a/pom.xml b/pom.xml
@@ -3,15 +3,15 @@
     <modelVersion>4.0.0</modelVersion>
     <groupId>com.ebremer</groupId>
     <artifactId>Halcyon</artifactId>
-    <version>0.3.1</version>
+    <version>0.4.0</version>
     <packaging>jar</packaging>
     <name>Halcyon</name>
     <description>A whole slide image annotation, management, and visualization system</description>
 
     <licenses>
         <license>
             <name>MIT License</name>
-            <url>https://github.com/ebremer/Halcyon/blob/master/LICENSE</url>
+            <url>https://github.com/halcyon-project/Halcyon/blob/master/LICENSE</url>
         </license>
     </licenses>
 
@@ -50,6 +50,14 @@
           <timezone>America/New_York</timezone>
           <organization>Stony Brook University - Biomedical Informatics</organization>
         </developer>
+        <developer>
+          <id>fwang</id>
+          <name>Feiqiao Wang</name>
+          <email>feiqiao.wang@stonybrook.edu</email>
+          <roles><role>developer</role></roles>
+          <timezone>America/New_York</timezone>
+          <organization>Stony Brook University - Biomedical Informatics</organization>
+        </developer>
     </developers>
 
     <organization>
@@ -77,7 +85,7 @@
         <resteasy.version>4.7.4.Final</resteasy.version>
         <infinispan.version>13.0.12.Final</infinispan.version>
         <jgroups.version>4.2.21.Final</jgroups.version>
-        <beakgraph.version>0.2.0</beakgraph.version>
+        <beakgraph.version>0.3.1</beakgraph.version>
     </properties>
 
     <parent>
@@ -174,6 +182,15 @@
                         <groupId>org.panteleyev</groupId>
                         <artifactId>jpackage-maven-plugin</artifactId>
                         <version>1.6.0</version>
+                        <configuration>
+                            <winMenu>true</winMenu>
+                            <winShortcutPrompt>true</winShortcutPrompt>
+                            <winDirChooser>true</winDirChooser>
+                            <winConsole>true</winConsole>
+                            <winHelpUrl>https://github.com/ebremer/Halcyon</winHelpUrl>
+                            <winUpdateUrl>https://github.com/ebremer/Halcyon</winUpdateUrl>
+                            <type>MSI</type>
+                        </configuration>
                     </plugin>
                 </plugins>
             </build>
@@ -192,30 +209,14 @@
                         <artifactId>jpackage-maven-plugin</artifactId>
                         <version>1.6.0</version>
                         <configuration>
-                            <name>Halcyon</name>
-                            <appVersion>${project.version}</appVersion>
-                            <vendor>Wing-n-Beak LLC</vendor>
-                            <copyright>Copyright 2022 Erich Bremer - Stony Brook University</copyright>
-                            <licenseFile>LICENSE</licenseFile>
-                            <input>target</input>
-                            <mainJar>Halcyon-0.3.1.jar</mainJar>
-                            <verbose>true</verbose>
-                            <description>Whole Slide Imaging and Feature Management</description>
-                            <installDir>\Halcyon</installDir>
-                            <icon>src\main\resources\META-INF\halcyon.ico</icon>
-                            <destination>target/dist</destination>
-                            <type>dmg</type>
-                            <javaOptions>
-                                <option>--enable-preview</option>
-                                <option>-Dfile.encoding=UTF-8</option>
-                            </javaOptions>
+                            <type>DMG</type>
                         </configuration>
                     </plugin>
                 </plugins>
             </build>
         </profile>
         <profile>
-            <id>linux-installer</id>
+            <id>ubuntu-installer</id>
             <activation>
                 <os>
                     <family>linux</family>
@@ -227,6 +228,9 @@
                         <groupId>org.panteleyev</groupId>
                         <artifactId>jpackage-maven-plugin</artifactId>
                         <version>1.6.0</version>
+                        <configuration>
+                            <type>DEB</type>
+                        </configuration>
                     </plugin>
                 </plugins>
             </build>
@@ -235,6 +239,16 @@
             <id>server</id>
             <build>
                 <plugins>
+                    <plugin>
+                        <!-- mvn dependency:analyze -->
+                        <artifactId>maven-dependency-plugin</artifactId>
+                        <configuration>
+                            <usedDependencies>
+                                <dependency>org.apache.jena:jena-tdb2</dependency>
+                            </usedDependencies>
+                        </configuration>
+                        <version>3.5.0</version>
+                    </plugin>
                     <plugin>
                         <groupId>org.springframework.boot</groupId>
                         <artifactId>spring-boot-maven-plugin</artifactId>
@@ -581,28 +595,31 @@
                     <name>Halcyon</name>
                     <appVersion>${project.version}</appVersion>
                     <vendor>Wing-n-Beak LLC</vendor>
-                    <copyright>Copyright 2022 Erich Bremer - Stony Brook University</copyright>
+                    <copyright>Copyright 2021-2023 Erich Bremer - Stony Brook University</copyright>
                     <licenseFile>LICENSE</licenseFile>
                     <input>target</input>
-                    <mainJar>Halcyon-0.2.0.jar</mainJar>
+                    <mainJar>Halcyon-${project.version}.jar</mainJar>
                     <verbose>true</verbose>
-                    <winMenu>true</winMenu>
-                    <winShortcutPrompt>true</winShortcutPrompt>
-                    <winDirChooser>true</winDirChooser>
-                    <winConsole>true</winConsole>
-                    <winHelpUrl>https://github.com/ebremer/Halcyon</winHelpUrl>
-                    <winUpdateUrl>https://github.com/ebremer/Halcyon</winUpdateUrl>
                     <description>Whole Slide Imaging and Feature Management</description>
                     <installDir>\Halcyon</installDir>
                     <icon>src\main\resources\META-INF\halcyon.ico</icon>
                     <destination>target/dist</destination>
-                    <type>MSI</type>
                     <javaOptions>
                         <option>--enable-preview</option>
                         <option>-Dfile.encoding=UTF-8</option>
                     </javaOptions>
                 </configuration>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-compiler-plugin</artifactId>
+                <version>3.11.0</version>
+                <configuration>
+                    <compilerArgs>
+                        <arg>--enable-preview</arg>
+                    </compilerArgs>
+                </configuration>
+            </plugin>
         </plugins>
     </build>
     <dependencies>

diff --git a/src/main/java/com/ebremer/halcyon/EmbeddedSpringKeycloakAutoConfiguration.java b/src/main/java/com/ebremer/halcyon/EmbeddedSpringKeycloakAutoConfiguration.java
@@ -1,7 +1,3 @@
-/*
- * Click nbfs://nbhost/SystemFileSystem/Templates/Licenses/license-default.txt to change this license
- * Click nbfs://nbhost/SystemFileSystem/Templates/Classes/Class.java to edit this template
- */
 package com.ebremer.halcyon;
 
 import com.github.thomasdarimont.keycloak.embedded.EmbeddedKeycloakConfig;

diff --git a/src/main/java/com/ebremer/halcyon/FL/FL.java b/src/main/java/com/ebremer/halcyon/FL/FL.java
@@ -12,7 +12,6 @@
 import com.ebremer.halcyon.Standard;
 import com.ebremer.halcyon.hilbert.HilbertSpace;
 import com.ebremer.halcyon.hsPolygon;
-import com.ebremer.ns.CSVW;
 import com.ebremer.ns.EXIF;
 import com.ebremer.ns.HAL;
 import com.ebremer.ns.IIIF;
@@ -295,7 +294,6 @@ public String GetImageInfo(String xurl) {
             Model mm = ModelFactory.createDefaultModel();
             mm.setNsPrefix("so", SchemaDO.NS);
             mm.setNsPrefix("hal", HAL.NS);
-            mm.setNsPrefix("csvw", CSVW.NS);
             mm.setNsPrefix("iiif", IIIF.getURI());
             mm.setNsPrefix("doap", DOAP.getURI());
             Resource s = ResourceFactory.createResource(modbase);

diff --git a/src/main/java/com/ebremer/halcyon/HalcyonSettings.java b/src/main/java/com/ebremer/halcyon/HalcyonSettings.java
@@ -53,7 +53,7 @@ public class HalcyonSettings {
     private static final int DEFAULTSPARQLPORT = 8887;
     private final Property SPARQLPORT;
     private final Property MULTIVIEWERLOCATION;
-    public static final String VERSION = "0.3.1";
+    public static final String VERSION = "0.4.0";
     public static Resource HALCYONAGENT = ResourceFactory.createResource(HAL.NS+"/VERSION/"+VERSION);
     private static final String MasterSettingsLocation = "settings.ttl";
     private Resource Master;

diff --git a/src/main/java/com/ebremer/halcyon/INIT.java b/src/main/java/com/ebremer/halcyon/INIT.java
@@ -93,6 +93,9 @@ public void CreateDefaultSettingsFile(File file, Model m) {
     }
 
     public void init() {
+
+        // Setup Keycloak initialization files
+
         if (!(new File("data").exists())) {
             if (!(new File("keycloak-realm-config.json").exists())) {
                 dump("keycloak-realm-config.json");

diff --git a/src/main/java/com/ebremer/halcyon/PathFinder.java b/src/main/java/com/ebremer/halcyon/PathFinder.java
@@ -1,7 +1,3 @@
-/*
- * Click nbfs://nbhost/SystemFileSystem/Templates/Licenses/license-default.txt to change this license
- * Click nbfs://nbhost/SystemFileSystem/Templates/Classes/Class.java to edit this template
- */
 package com.ebremer.halcyon;
 
 import com.ebremer.halcyon.filesystem.StorageLocation;