From 760b9b12d26e1abac32df022c87f5c23659654ba Mon Sep 17 00:00:00 2001
From: snyk-bot <snyk-bot@snyk.io>
Date: Sat, 31 Aug 2024 09:14:58 +0000
Subject: [PATCH 1/2] fix: upgrade org.mongodb:mongodb-driver-reactivestreams
 from 4.11.2 to 4.11.3

Snyk has created this PR to upgrade org.mongodb:mongodb-driver-reactivestreams from 4.11.2 to 4.11.3.

See this package in maven:
org.mongodb:mongodb-driver-reactivestreams

See this project in Snyk:
https://app.snyk.io/org/brambg/project/505c5a7f-784c-4b50-9a6a-22fc806fb68e?utm_source=github&utm_medium=referral&page=upgrade-pr
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 1d02f12..84b018a 100644
--- a/pom.xml
+++ b/pom.xml
@@ -57,7 +57,7 @@
         <kotlinx-coroutines-core.version>1.8.1</kotlinx-coroutines-core.version>
         <log4j.version>1.2.17</log4j.version>
         <log4j-api-kotlin.version>1.5.0</log4j-api-kotlin.version>
-        <mongodb.version>4.11.2</mongodb.version>
+        <mongodb.version>4.11.3</mongodb.version>
         <mordant.version>2.7.2</mordant.version>
         <problem.version>0.27.1</problem.version>
         <protobuf.version>3.25.4</protobuf.version>

From 3859316f3a8508de898cfccc846116e0a62bcd0e Mon Sep 17 00:00:00 2001
From: Bram Buitendijk <bram.buitendijk@di.huc.knaw.nl>
Date: Tue, 3 Sep 2024 14:06:31 +0200
Subject: [PATCH 2/2] update some dependency versions; fix
 nullpointerexception; fixes #171

---
 client/pom.xml                                |  7 +++++
 common/pom.xml                                |  6 +++-
 pom.xml                                       | 29 ++++++++++---------
 .../knaw/huc/annorepo/AnnoRepoApplication.kt  |  2 +-
 .../knaw/huc/annorepo/dao/ARContainerDAO.kt   |  2 +-
 5 files changed, 29 insertions(+), 17 deletions(-)

diff --git a/client/pom.xml b/client/pom.xml
index fd8cb39..7df6cd5 100644
--- a/client/pom.xml
+++ b/client/pom.xml
@@ -169,5 +169,12 @@
             <url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
         </license>
     </licenses>
+    <repositories>
+        <repository>
+            <id>maven_central</id>
+            <name>Maven Central</name>
+            <url>https://repo.maven.apache.org/maven2/</url>
+        </repository>
+    </repositories>
 
 </project>
diff --git a/common/pom.xml b/common/pom.xml
index eb0c068..9688504 100644
--- a/common/pom.xml
+++ b/common/pom.xml
@@ -41,7 +41,11 @@
             <artifactId>log4j-api-kotlin</artifactId>
             <version>${log4j-api-kotlin.version}</version>
         </dependency>
-
+        <dependency>
+            <groupId>org.apache.logging.log4j</groupId>
+            <artifactId>log4j-core</artifactId>
+            <version>${log4j-core.version}</version>
+        </dependency>
         <!-- protobuf/grpc -->
         <dependency>
             <groupId>com.google.protobuf</groupId>
diff --git a/pom.xml b/pom.xml
index 84b018a..80c97c6 100644
--- a/pom.xml
+++ b/pom.xml
@@ -38,17 +38,17 @@
 
         <annotations-api.version>6.0.53</annotations-api.version>
         <arrow-core.version>1.2.4</arrow-core.version>
-        <dropwizard-jobs.version>5.1.4</dropwizard-jobs.version>
+        <dropwizard-jobs.version>6.0.1</dropwizard-jobs.version>
         <dropwizard-swagger-ui.version>4.6.2</dropwizard-swagger-ui.version>
         <dropwizard-swagger.version>4.0.5-1</dropwizard-swagger.version>
         <dropwizard.version>4.0.7</dropwizard.version>
         <grpc.kotlin.version>1.4.1</grpc.kotlin.version>
         <grpc.version>1.66.0</grpc.version>
         <jackson-annotations.version>2.17.2</jackson-annotations.version>
-        <jackson-databind.version>2.13.4.1</jackson-databind.version>
+        <jackson-databind.version>2.17.2</jackson-databind.version>
         <jackson-module-kotlin.version>2.17.2</jackson-module-kotlin.version>
         <jakarta.json.version>2.0.1</jakarta.json.version>
-        <jakarta.ws.rs-api.version>3.1.0</jakarta.ws.rs-api.version>
+        <jakarta.ws.rs-api.version>4.0.0</jakarta.ws.rs-api.version>
         <jaxb-api.version>2.3.1</jaxb-api.version>
         <jena.version>4.10.0</jena.version>
         <json.version>20231013</json.version>
@@ -57,28 +57,29 @@
         <kotlinx-coroutines-core.version>1.8.1</kotlinx-coroutines-core.version>
         <log4j.version>1.2.17</log4j.version>
         <log4j-api-kotlin.version>1.5.0</log4j-api-kotlin.version>
-        <mongodb.version>4.11.3</mongodb.version>
+        <log4j-core.version>2.22.1</log4j-core.version>
+        <mongodb.version>4.11.0</mongodb.version>
         <mordant.version>2.7.2</mordant.version>
         <problem.version>0.27.1</problem.version>
-        <protobuf.version>3.25.4</protobuf.version>
-        <slf4j.version>2.0.9</slf4j.version>
+        <protobuf.version>4.28.0</protobuf.version>
+        <slf4j.version>2.0.13</slf4j.version>
         <swagger-annotations.version>1.6.6</swagger-annotations.version>
         <titanium-json-ld.version>1.4.1</titanium-json-ld.version>
 
         <!-- test dependencies -->
-        <assertj-core.version>3.24.2</assertj-core.version>
+        <assertj-core.version>3.26.3</assertj-core.version>
         <h2.version>2.2.224</h2.version>
-        <jsonassert.version>1.5.0</jsonassert.version>
-        <json-path.version>2.8.0</json-path.version>
-        <json-unit-assertj.version>3.2.2</json-unit-assertj.version>
-        <junit-jupiter.version>5.10.0</junit-jupiter.version>
-        <mockito-kotlin.version>5.1.0</mockito-kotlin.version>
-        <mockito.version>5.6.0</mockito.version>
+        <jsonassert.version>1.5.3</jsonassert.version>
+        <json-path.version>2.9.0</json-path.version>
+        <json-unit-assertj.version>3.2.7</json-unit-assertj.version>
+        <junit-jupiter.version>5.11.0</junit-jupiter.version>
+        <mockito-kotlin.version>5.4.0</mockito-kotlin.version>
+        <mockito.version>5.13.0</mockito.version>
         <mockk.version>1.12.5</mockk.version>
 
         <!-- maven plugin dependencies -->
         <another-protobuf-maven-plugin.version>2.1.0</another-protobuf-maven-plugin.version>
-        <dokka.version>1.7.20</dokka.version>
+        <dokka.version>1.9.20</dokka.version>
         <grpc-bridge.version>1.0.0.Alpha2</grpc-bridge.version>
         <joda-time.version>2.12.7</joda-time.version>
         <maven-compiler-plugin.version>3.11.0</maven-compiler-plugin.version>
diff --git a/server/src/main/kotlin/nl/knaw/huc/annorepo/AnnoRepoApplication.kt b/server/src/main/kotlin/nl/knaw/huc/annorepo/AnnoRepoApplication.kt
index 50f8b0b..9913d86 100644
--- a/server/src/main/kotlin/nl/knaw/huc/annorepo/AnnoRepoApplication.kt
+++ b/server/src/main/kotlin/nl/knaw/huc/annorepo/AnnoRepoApplication.kt
@@ -85,7 +85,7 @@ class AnnoRepoApplication : Application<AnnoRepoConfiguration?>() {
 
     private fun getJobsBundle(): ConfiguredBundle<in AnnoRepoConfiguration?> {
         val expiredChoresCleanerJob = ExpiredChoresCleanerJob()
-        return JobsBundle(expiredChoresCleanerJob)
+        return JobsBundle(listOf(expiredChoresCleanerJob))
     }
 
     @OptIn(ExperimentalStdlibApi::class)
diff --git a/server/src/main/kotlin/nl/knaw/huc/annorepo/dao/ARContainerDAO.kt b/server/src/main/kotlin/nl/knaw/huc/annorepo/dao/ARContainerDAO.kt
index d0a7e29..96cedcf 100644
--- a/server/src/main/kotlin/nl/knaw/huc/annorepo/dao/ARContainerDAO.kt
+++ b/server/src/main/kotlin/nl/knaw/huc/annorepo/dao/ARContainerDAO.kt
@@ -39,7 +39,7 @@ class ARContainerDAO(configuration: AnnoRepoConfiguration, client: MongoClient)
     }
 
     override fun getAnnotationFields(containerName: String): SortedMap<String, Int> =
-        getContainerMetadata(containerName)!!.fieldCounts.toSortedMap()
+        getContainerMetadata(containerName)?.fieldCounts?.toSortedMap() ?: emptyMap<String, Int>().toSortedMap()
 
     override fun getContainerMetadataCollection(): MongoCollection<ContainerMetadata> =
         mdb.getCollection<ContainerMetadata>(ARConst.CONTAINER_METADATA_COLLECTION)