Merge pull request #13 from ebremer/develop

Develop
halcyon-project · Jun 6, 2023 · 8a72d8b · 8a72d8b
2 parents 7e9b472 + 387bb10
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diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 # Halcyon specific files
 /*.ttl
 /keycloak.json
+/keycloak-realm-config.json
 
 # Compiled class file
 *.class
@@ -35,4 +36,5 @@ hs_err_pid*
 target/*
 data/*
 dist/*
+tdb2/*
 
diff --git a/README.md b/README.md
@@ -33,74 +33,6 @@ mvn -Pwindows-installer jpackage:jpackage
 
 ## SSL:
 
-[How to enable HTTPS in a Spring Boot Java application](https://www.thomasvitale.com/https-spring-boot-ssl-certificate/)
-
-```sh
-keytool -genkeypair -alias halcyon -keyalg RSA -keysize 4096 -storetype PKCS12 -keystore halcyon.p12 -validity 3650 -storepass password
-```
-
-### Private key (seems the same as above, will test)
-
-```sh
-keytool -genkey -keyalg RSA -alias selfsigned -keystore halcyon.jks -storepass password -validity 360 -keysize 2048
-```
-
-### See also:
-
-[How set up Spring Boot to run HTTPS / HTTP ports](https://stackoverflow.com/questions/30896234/how-set-up-spring-boot-to-run-https-http-ports/49740689)
-
-
-## Migrations to p12
-
-```sh
-keytool -importkeystore -srckeystore cacerts -destkeystore cacerts -deststoretype pkcs12
-
-keytool -delete -noprompt -alias halcyon  -keystore cacerts.p12 -storepass changeit
-```
-
-### Export key:
-
-```sh
-keytool -export -keystore cacerts.p12 -alias halcyon -file halcyon.cer
-```
-
-### Import key
-
-```sh
-keytool -import -alias halcyon -keystore C:\bin\graalvm\lib\security\cacerts -file erich-bremer.pem
-```
-
-### Convert apache key to right format:
-
-```sh
-openssl pkcs12 -export -in [<em>filename-certificate</em>] -inkey [<em>filename-key</em>] -name [<em>host</em>] -out [<em>filename-new</em>-PKCS-12.p12]
-```
-
-[Import an existing SSL certificate and private key for Wowza Streaming Engine](https://www.wowza.com/docs/how-to-import-an-existing-ssl-certificate-and-private-key#:~:text=You%20can't%20directly%20import,12%20file%20into%20your%20keystore.)
-
-
-## Importing new/renewal PEM certs into certificate store
-
-```sh
-openssl pkcs12 -export -in wow.fullchain -inkey atoz2022.key  -name shared > server.p12
-
-keytool -importkeystore -srckeystore server.p12 -destkeystore cacerts.p12 -srcstoretype pkcs12 -alias shared
-```
-
-## Extra
-
-```sh
-keytool -import -alias sbu -keystore cacerts.p12 -trustcacerts -file inter.crt
-keytool -list -v -keystore cacerts.p12
-keytool -list -v -keystore cacerts.p12
-keytool -list -v -keystore cacerts.p12 | more
-keytool -import -alias sbu -keystore cacerts.p12 -trustcacerts -file inter.crt
-keytool -import -alias sbu -keystore /home/bremer/graalvm/lib/security/cacerts -trustcacerts -file inter.crt
-keytool -list -v -keystore cacerts.p12
-keytool -list -v -keystore cacerts.p12 | grep alias
-keytool -list -v -keystore cacerts.p12 | grep Alias
-keytool -list -v -keystore cacerts.p12 | grep Alias | more
-keytool -list -v -keystore cacerts.p12 | grep atoz
-keytool -importkeystore -deststorepass changeit -destkeystore cacerts.p12 -srckeystore atoz.p12 -srcstoretype PKCS12
-keytool -list -v -keystore cacerts.p12 | grep atoz
-```
+openssl req -new -newkey rsa:2048 -nodes -keyout beak.key -out beak.csr
+openssl pkcs12 -export -in beak.crt -inkey beak.key -name Halcyon -out beak.p12
+keytool -importkeystore -deststorepass changeit -destkeystore cacerts -srckeystore beak.p12 -srcstoretype PKCS12
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>0.4.1</version>
+  <version>0.4.2</version>
   <description>A whole slide image annotation, management, and visualization system</description>
   <issueManagement>
     <system>github</system>
@@ -793,7 +793,7 @@
     <dependency>
       <groupId>com.ebremer</groupId>
       <artifactId>BeakGraph</artifactId>
-      <version>0.3.2</version>
+      <version>0.4.0</version>
       <scope>provided</scope>
     </dependency>
     <dependency>
@@ -926,7 +926,7 @@
     <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>0.3.2</beakgraph.version>
+    <beakgraph.version>0.4.0</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
@@ -14,7 +14,7 @@
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.executable>java</exec.executable>
                 <exec.vmArgs>-Xmx30G -Xms30G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview  -Darrow.memory.debug.allocator=true</exec.vmArgs>
-                <exec.appArgs>-v -src "D:\halcyon\features\src2" -dest "D:\halcyon\features\dest"</exec.appArgs>
+                <exec.appArgs>-v -src "D:\halcyon\features\src3" -dest "D:\halcyon\features\dest5"</exec.appArgs>
                 <exec.mainClass>com.ebremer.halcyon.converters.Ingest</exec.mainClass>
             </properties>
         </action>
@@ -33,7 +33,7 @@
                 <exec.executable>java</exec.executable>
                 <jpda.listen>true</jpda.listen>
                 <exec.vmArgs>-Xmx30G -Xms30G --add-opens=java.base/java.nio=ALL-UNNAMED --enable-preview  -Darrow.memory.debug.allocator=true -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
-                <exec.appArgs>-v -src "D:\halcyon\features\src2" -dest "D:\halcyon\features\dest"</exec.appArgs>
+                <exec.appArgs>-v -src "D:\halcyon\features\src3" -dest "D:\halcyon\features\dest5"</exec.appArgs>
                 <exec.mainClass>com.ebremer.halcyon.converters.Ingest</exec.mainClass>
             </properties>
         </action>
@@ -51,7 +51,7 @@
                 <exec.args>${exec.vmArgs} -classpath %classpath ${exec.mainClass} ${exec.appArgs}</exec.args>
                 <exec.executable>java</exec.executable>
                 <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.appArgs>-v -src "D:\halcyon\features\src3" -dest "D:\halcyon\features\dest5"</exec.appArgs>
                 <exec.mainClass>com.ebremer.halcyon.converters.Ingest</exec.mainClass>
             </properties>
         </action>

diff --git a/nbactions-server.xml b/nbactions-server.xml
@@ -15,7 +15,7 @@
                 <exec.executable>java</exec.executable>
                 <exec.vmArgs>-Xmx45G  -Xms45G --add-opens java.base/java.nio=ALL-UNNAMED --enable-preview</exec.vmArgs>
                 <exec.appArgs></exec.appArgs>
-                <exec.mainClass>com.ebremer.halcyon.imagebox.Main</exec.mainClass>
+                <exec.mainClass>com.ebremer.halcyon.server.Main</exec.mainClass>
             </properties>
         </action>
         <action>
@@ -34,7 +34,7 @@
                 <jpda.listen>true</jpda.listen>
                 <exec.vmArgs>-Xmx45G  -Xms45G --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.mainClass>com.ebremer.halcyon.imagebox.Main</exec.mainClass>
+                <exec.mainClass>com.ebremer.halcyon.server.Main</exec.mainClass>
             </properties>
         </action>
         <action>
@@ -51,7 +51,7 @@
                 <exec.executable>java</exec.executable>
                 <exec.vmArgs>-Xmx45G  -Xms45G --add-opens java.base/java.nio=ALL-UNNAMED --enable-preview</exec.vmArgs>
                 <exec.appArgs></exec.appArgs>
-                <exec.mainClass>com.ebremer.halcyon.imagebox.Main</exec.mainClass>
+                <exec.mainClass>com.ebremer.halcyon.server.Main</exec.mainClass>
             </properties>
         </action>
         <action>

diff --git a/nbactions.xml b/nbactions.xml
@@ -15,7 +15,7 @@
                 <exec.executable>java</exec.executable>
                 <exec.vmArgs>-Xmx50G -Xms50G --add-opens=java.base/java.nio=ALL-UNNAMED</exec.vmArgs>
                 <exec.appArgs></exec.appArgs>
-                <exec.mainClass>is.halcyon.imagebox.Main</exec.mainClass>
+                <exec.mainClass>com.ebremer.halcyon.imagebox.Main</exec.mainClass>
             </properties>
         </action>
         <action>
@@ -34,7 +34,7 @@
                 <jpda.listen>true</jpda.listen>
                 <exec.vmArgs>-Xmx50G -Xms50G --add-opens=java.base/java.nio=ALL-UNNAMED -agentlib:jdwp=transport=dt_socket,server=n,address=${jpda.address}</exec.vmArgs>
                 <exec.appArgs></exec.appArgs>
-                <exec.mainClass>is.halcyon.imagebox.Main</exec.mainClass>
+                <exec.mainClass>com.ebremer.halcyon.imagebox.Main</exec.mainClass>
             </properties>
         </action>
         <action>
@@ -52,7 +52,7 @@
                 <exec.executable>java</exec.executable>
                 <exec.vmArgs>-Xmx50G -Xms50G --add-opens=java.base/java.nio=ALL-UNNAMED</exec.vmArgs>
                 <exec.appArgs></exec.appArgs>
-                <exec.mainClass>is.halcyon.imagebox.Main</exec.mainClass>
+                <exec.mainClass>com.ebremer.halcyon.imagebox.Main</exec.mainClass>
             </properties>
         </action>
         <action>