Merge branch 'main' into error_improvements

Author: mergify[bot]

.github/workflows/ci-build.yml

@@ -19,15 +19,15 @@ jobs:
           repository: ${{ github.event.pull_request.head.repo.full_name }}
 
       - name: Restore dependency cache
-        uses: actions/cache@v3.3.2
+        uses: actions/cache@v4.0.0
         with:
           path: ~/.m2/repository
           key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}
           restore-keys: |
             ${{ runner.os }}-maven-
 
       - name: Set up Java
-        uses: actions/setup-java@v3
+        uses: actions/setup-java@v4
         with:
           distribution: 'adopt'
           java-version: '17'

.github/workflows/codeql-analysis.yml

@@ -18,21 +18,21 @@ jobs:
       uses: actions/checkout@v4
 
     - name: Set up Java
-      uses: actions/setup-java@v3
+      uses: actions/setup-java@v4
       with:
         distribution: 'adopt'
         java-version: '17'
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: javascript, java
 
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 https://git.io/JvXDl
@@ -46,4 +46,4 @@ jobs:
     #   make release
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

Dockerfile

@@ -1,4 +1,4 @@
-FROM maven:3-eclipse-temurin-17-alpine AS build-licensee
+FROM docker.io/library/maven:3-eclipse-temurin-17-alpine AS build-licensee
 
 RUN apk add --update \
   alpine-sdk \
@@ -10,7 +10,7 @@ RUN apk add --update \
 RUN gem install licensee
 
 
-FROM maven:3-eclipse-temurin-17-alpine
+FROM docker.io/library/maven:3-eclipse-temurin-17-alpine
 MAINTAINER Stian Soiland-Reyes <[email protected]>
 
 # Build-time metadata as defined at https://github.com/opencontainers/image-spec/blob/main/annotations.md
@@ -29,8 +29,8 @@ LABEL org.opencontainers.image.created=$BUILD_DATE \
 RUN apk add --update \
   graphviz \
   ttf-freefont \
-  py3-pip \
   gcc \
+  pipx \
   python3-dev \
   libc-dev \
   nodejs \
@@ -43,9 +43,9 @@ RUN apk add --update \
   heimdal \
   && rm -rf /var/cache/apk/*
 
-#wheel needed by ruamel.yaml for some reason
-RUN pip3 install -U wheel setuptools pip
-RUN pip3 install cwltool
+ENV PATH="/root/.local/bin:${PATH}"
+
+RUN pipx install cwltool
 
 RUN cwltool --version
 

pom.xml

@@ -15,7 +15,7 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>2.6.7</version>
+    <version>2.7.18</version>
     <relativePath/>
   </parent>
 
@@ -26,7 +26,7 @@
     <jena.version>4.10.0</jena.version>
     <!-- BEGIN should correspond to https://repo1.maven.org/maven2/org/apache/jena/jena/3.9.0/jena-3.9.0.pom -->
     <ver.jsonldjava>0.13.6</ver.jsonldjava>
-    <ver.jackson>2.16.0</ver.jackson>
+    <ver.jackson>2.16.1</ver.jackson>
     <!-- END -->
     <log4j2.version>2.17.0</log4j2.version>
   </properties>
@@ -84,7 +84,7 @@
     <dependency>
       <groupId>org.liquibase</groupId>
       <artifactId>liquibase-core</artifactId>
-      <version>4.25.0</version>
+      <version>4.25.1</version>
     </dependency>
     <!-- Postgres -->
     <dependency>
@@ -149,7 +149,7 @@
     <dependency>
       <groupId>commons-io</groupId>
       <artifactId>commons-io</artifactId>
-      <version>2.15.0</version>
+      <version>2.15.1</version>
     </dependency>
     <!-- For JSR-303, javax.validation -->
     <dependency>
@@ -171,13 +171,13 @@
     <dependency>
       <groupId>org.testcontainers</groupId>
       <artifactId>junit-jupiter</artifactId>
-      <version>1.19.2</version>
+      <version>1.19.3</version>
       <scope>test</scope>
     </dependency>
     <dependency>
       <groupId>org.testcontainers</groupId>
       <artifactId>postgresql</artifactId>
-      <version>1.19.2</version>
+      <version>1.19.4</version>
       <scope>test</scope>
     </dependency>
     <!-- We use mockito-inline as it supports mocking static methods -->
@@ -223,7 +223,7 @@
       <plugin>
           <groupId>com.spotify.fmt</groupId>
           <artifactId>fmt-maven-plugin</artifactId>
-          <version>2.21.1</version>
+          <version>2.22.1</version>
           <executions>
               <execution>
                   <goals>