#1 - Added content encoding support

build.sbt

@@ -86,6 +86,8 @@ lazy val oni = project
             circeGeneric,
             circeParser,
             commonsCodec,
+            helidonEncodingDeflate,
+            helidonEncodingGzip,
             hibernateCore,
             hibernateEnvers,
             hibernateHikari,

it/src/main/scala/org/mbari/oni/jpa/entities/TestEntityFactory.scala

@@ -157,8 +157,7 @@ object TestEntityFactory:
             entity.setRankLevel(Strings.random(6))
             entity.setRankName(Strings.random(12))
 
-        if random.nextBoolean() then
-            entity.setAphiaId(random.nextLong(100000000))
+        if random.nextBoolean() then entity.setAphiaId(random.nextLong(100000000))
 
         // DON'T DO THIS. The ID should be assigned by the database. Otherwise inserts will fail.
 //        entity.setId(nextConceptId.incrementAndGet())

it/src/main/scala/org/mbari/oni/services/ConceptServiceSuite.scala

@@ -274,7 +274,6 @@ trait ConceptServiceSuite extends DatabaseFunSuite with UserAuthMixin:
             yield updatedChild
         )
 
-
         attempt match
             case Left(e)      =>
                 fail("Failed to update")
@@ -292,7 +291,8 @@ trait ConceptServiceSuite extends DatabaseFunSuite with UserAuthMixin:
     test("update parent") {
 
         val root       = TestEntityFactory.buildRoot(3)
-        val grandChild = root.getChildConcepts
+        val grandChild = root
+            .getChildConcepts
             .iterator()
             .next()
             .getChildConcepts
@@ -330,8 +330,9 @@ trait ConceptServiceSuite extends DatabaseFunSuite with UserAuthMixin:
     }
 
     test("update (parent multiple times)") {
-        val root = TestEntityFactory.buildRoot(5)
-        val grandChild = root.getChildConcepts
+        val root         = TestEntityFactory.buildRoot(5)
+        val grandChild   = root
+            .getChildConcepts
             .iterator()
             .next()
             .getChildConcepts
@@ -344,30 +345,28 @@ trait ConceptServiceSuite extends DatabaseFunSuite with UserAuthMixin:
 
         val attempt = runWithUserAuth(user =>
             for
-                rootEntity <- conceptService.init(root)
-                grandChildEntity <- Right(grandChild)
-                updatedGrandChild1 <- conceptService.update( grandChildEntity.getName, update1, user.username)
-                updatedGrandChild2 <- conceptService.update( grandChildEntity.getName, update2, user.username)
-
+                rootEntity         <- conceptService.init(root)
+                grandChildEntity   <- Right(grandChild)
+                updatedGrandChild1 <- conceptService.update(grandChildEntity.getName, update1, user.username)
+                updatedGrandChild2 <- conceptService.update(grandChildEntity.getName, update2, user.username)
             yield updatedGrandChild2
         )
 
         attempt match
-            case Left(e) =>
+            case Left(e)           =>
                 fail("Failed to update")
             case Right(grandChild) =>
                 conceptService.findParentByChildName(grandChild.name) match
-                    case Left(e) =>
+                    case Left(e)      =>
                         fail("Failed to find parent")
                     case Right(found) =>
                         assertEquals(found.name, childsParent.getName)
                 historyService.findByConceptName(grandChild.name) match
-                    case Left(e) =>
+                    case Left(e)      =>
                         fail("Failed to find history")
                     case Right(found) =>
                         assertEquals(found.size, 2)
 
-
     }
 
     test("delete") {

oni/src/docs/_docs/development/development.md

@@ -17,3 +17,4 @@ This is a normal [sbt](https://www.scala-sbt.org) project. You can compile code
 Documentation can be added as markdown files in `docs` and will be included automatically when you run `scaladoc`.
 
 When updating SBT version, make sure to update the devcontainer image in [devcontainer.json](.devcontainer/devcontainer.json). It's versions are `eclipse-temurin-<java.version>_<sbt.version>_<scala.version>`
+

oni/src/docs/_docs/development/nima.md

@@ -0,0 +1,32 @@
+# nima
+
+Oni uses Helidon's Webserver (aka Nima) to serve the web application.
+
+## Supporting gzip
+
+From [Slack](https://helidon.slack.com/archives/CCS216A5A/p1719928229654769?thread_ts=1719792358.413759&cid=CCS216A5A)
+
+ne way (and probably the easiest way) would be to simply add the following dependencies. These will be automatically discovered and used. It is not needed to do anything else.
+
+```xml
+<!-- gzip -->
+<dependency>
+    <groupId>io.helidon.http.encoding</groupId>
+    <artifactId>helidon-http-encoding-gzip</artifactId>
+</dependency>
+<!-- deflate -->
+<dependency>
+    <groupId>io.helidon.http.encoding</groupId>
+    <artifactId>helidon-http-encoding-deflate</artifactId>
+</dependency>
+```
+
+Other way, if you would not want it to be automatically discovered and you would want to do it programatically yourselft would be to use something like this:
+
+```java
+WebServer.builder()
+    .contentEncoding(encodingBuilder -> encodingBuilder.contentEncodingsDiscoverServices(false)
+    .addContentEncoding(GzipEncoding.create())
+    .addContentEncoding(DeflateEncoding.create()))
+```
+But even for that you need the above dependencies.

oni/src/main/java/org/mbari/oni/VARSException.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni;

oni/src/main/java/org/mbari/oni/domain/BasicConceptNode.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/ConceptNameTypes.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/ConceptNode.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/ConceptTypes.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/History.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/ILink.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/LinkComparator.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/LinkNameAndValueComparator.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/LinkNameComparator.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/LinkNode.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/LinkUtilities.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/MediaNode.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/MediaTypes.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/Msg.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/NamedMedia.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/PhylogenyNode.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/domain/UserAccountRoles.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.domain;

oni/src/main/java/org/mbari/oni/etc/jdk/IgnoreCaseToStringComparator.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.etc.jdk;

oni/src/main/java/org/mbari/oni/etc/jdk/Logging.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.etc.jdk;

oni/src/main/java/org/mbari/oni/etc/jdk/Preconditions.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.etc.jdk;

oni/src/main/java/org/mbari/oni/jpa/IPersistentObject.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa;

oni/src/main/java/org/mbari/oni/jpa/KeyNullifier.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa;

oni/src/main/java/org/mbari/oni/jpa/TransactionLogger.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa;

oni/src/main/java/org/mbari/oni/jpa/URIConverter.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa;

oni/src/main/java/org/mbari/oni/jpa/VARSPersistenceException.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa;

oni/src/main/java/org/mbari/oni/jpa/entities/ConceptEntity.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa.entities;

oni/src/main/java/org/mbari/oni/jpa/entities/ConceptMetadataEntity.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa.entities;

oni/src/main/java/org/mbari/oni/jpa/entities/ConceptNameEntity.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa.entities;

oni/src/main/java/org/mbari/oni/jpa/entities/EntityUtilities.java

@@ -2,7 +2,7 @@
  * Copyright (c) Monterey Bay Aquarium Research Institute 2024
  *
  * oni code is non-public software. Unauthorized copying of this file,
- * via any medium is strictly prohibited. Proprietary and confidential. 
+ * via any medium is strictly prohibited. Proprietary and confidential.
  */
 
 package org.mbari.oni.jpa.entities;