updated dependencies/plugins; plus junit updates (#173)

* updated dependencies/plugins; plus junit updates * Java 8 doesn't build in Github due to a dependency. Use 11 instead. * @disabled ignored without plugin
KnowledgeCaptureAndDiscovery · Apr 15, 2024 · 306efa6 · 306efa6
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diff --git a/.github/workflows/build.yaml b/.github/workflows/build.yaml
@@ -12,16 +12,16 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        java: [ '8', '11', '13', '15' ]
+        java: ["11", "17", "21"]
     name: Java ${{ matrix.Java }}
     steps:
       - uses: actions/checkout@v3
       - name: Setup java
         uses: actions/setup-java@v3
         with:
-          distribution: 'adopt'
+          distribution: "adopt"
           java-version: ${{ matrix.java }}
       - name: Build with Maven
-        run: mvn -B package --file pom.xml     
+        run: mvn -B package --file pom.xml
       - name: Test with Maven
-        run: mvn -B test --file pom.xml
+        run: mvn -B test --file pom.xml
diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
 
 OBA reads ontologies (OWL) and generates an OpenAPI Specification (OAS). Using this definition, OBA creates a REST API server automatically.
 
-![Diagram](docs/figures/oba.svg) 
+![Diagram](docs/figures/oba.svg)
 
 ## Quickstart
 
@@ -11,6 +11,11 @@ There are two option to run OBA:
 1. Download the binary.
 2. Build the binary from the repository.
 
+### Pre-requisites
+
+Due to recent versions of the OpenAPI generator being built with Java 11, you will need Java 11 or higher to run OBA v3.7.0. The current recommended distribution of Java 11+ JDKs (and "JREs") is at [Adoptium's releases page](https://adoptium.net/temurin/releases/?version=11).
+
+Java versions higher than 11 are also available to use. Java 11 is simply the minimum version.
 
 ### Downloading binary
 
@@ -37,6 +42,7 @@ Congratulations! You have generated an Open Api Specification.
 For instructions on using OBA to create your API server, go to the [documentation](https://oba.readthedocs.io/en/latest/)
 
 ## Citation
+
 Please cite our work as follows:
 
 ```

diff --git a/pom.xml b/pom.xml
@@ -6,97 +6,107 @@
     <packaging>jar</packaging>
     <groupId>edu.isi.oba</groupId>
     <artifactId>oba</artifactId>
-    <version>3.6.1</version>
+    <version>3.7.0</version>
     <name>core</name>
     <url>https://github.com/KnowledgeCaptureAndDiscovery/OBA</url>
 
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-        <maven.compiler.source>1.8</maven.compiler.source>
-        <maven.compiler.target>1.8</maven.compiler.target>
-        <jdk.version>1.8</jdk.version>
-        <maven-shade-plugin.version>3.1.1</maven-shade-plugin.version>
+        <maven.compiler.release>11</maven.compiler.release>
+        <jdk.version>11</jdk.version>
+        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-shade-plugin -->
+        <maven-shade-plugin.version>3.5.2</maven-shade-plugin.version>
     </properties>
 
     <dependencies>
         <!-- https://mvnrepository.com/artifact/org.json/json -->
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
-            <version>20190722</version>
+            <version>20240303</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/org.junit.jupiter/junit-jupiter-api -->
         <dependency>
-            <groupId>com.github.jsonld-java</groupId>
-            <artifactId>jsonld-java</artifactId>
-            <version>0.11.1</version>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter-api</artifactId>
+            <version>5.10.2</version>
+            <scope>test</scope>
         </dependency>
 
-
-        <!-- logging (Removed because it's not used) -->
-        <!-- https://mvnrepository.com/artifact/org.slf4j/jcl-over-slf4j -->
-        <!--
+        <!-- https://mvnrepository.com/artifact/io.swagger/swagger-compat-spec-parser -->
         <dependency>
-            <groupId>log4j</groupId>
-            <artifactId>log4j</artifactId>
-            <version>1.2.17</version>
+            <groupId>io.swagger</groupId>
+            <artifactId>swagger-compat-spec-parser</artifactId>
+            <version>1.0.70</version>
         </dependency>
-
+        <!-- https://mvnrepository.com/artifact/io.swagger.core.v3/swagger-models -->
+        <dependency>
+            <groupId>io.swagger.core.v3</groupId>
+            <artifactId>swagger-models</artifactId>
+            <version>2.2.21</version>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/io.swagger.parser.v3/swagger-parser -->
+        <dependency>
+            <groupId>io.swagger.parser.v3</groupId>
+            <artifactId>swagger-parser</artifactId>
+            <version>2.1.21</version>
+        </dependency>
+        <!-- https://mvnrepository.com/artifact/io.swagger.parser.v3/swagger-parser-core -->
         <dependency>
-            <groupId>org.slf4j</groupId>
-            <artifactId>slf4j-simple</artifactId>
-            <version>1.7.28</version>
+            <groupId>io.swagger.parser.v3</groupId>
+            <artifactId>swagger-parser-core</artifactId>
+            <version>2.1.21</version>
         </dependency>
-        -->
 
+        <!-- https://mvnrepository.com/artifact/org.openapitools/openapi-generator -->
         <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <version>4.13.1</version>
-            <scope>test</scope>
+            <groupId>org.openapitools</groupId>
+            <artifactId>openapi-generator</artifactId>
+            <version>7.4.0</version>
         </dependency>
+
+        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-api -->
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-api</artifactId>
-            <version>5.1.10</version>
+            <version>5.5.0</version>
         </dependency>
+        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-apibinding -->
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-apibinding</artifactId>
-            <version>5.1.10</version>
-        </dependency>
-        <!-- https://mvnrepository.com/artifact/org.openapitools/openapi-generator -->
-        <dependency>
-            <groupId>org.openapitools</groupId>
-            <artifactId>openapi-generator</artifactId>
-            <version>4.0.0</version>
-            <!-- <version>4.3.1</version>-->
+            <version>5.5.0</version>
         </dependency>
+        <!-- https://mvnrepository.com/artifact/net.sourceforge.owlapi/owlapi-impl -->
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
-            <artifactId>owlapi-compatibility</artifactId>
-            <version>5.1.10</version>
+            <artifactId>owlapi-impl</artifactId>
+            <version>5.5.0</version>
         </dependency>
+
         <!-- https://mvnrepository.com/artifact/org.yaml/snakeyaml -->
         <dependency>
             <groupId>org.yaml</groupId>
             <artifactId>snakeyaml</artifactId>
-            <version>1.25</version>
-        </dependency>
-        <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-dependency-plugin -->
-        <dependency>
-            <groupId>org.apache.maven.plugins</groupId>
-            <artifactId>maven-dependency-plugin</artifactId>
-            <version>3.1.1</version>
+            <version>2.2</version>
         </dependency>
+
         <!-- https://mvnrepository.com/artifact/commons-cli/commons-cli -->
         <dependency>
             <groupId>commons-cli</groupId>
             <artifactId>commons-cli</artifactId>
-            <version>1.3.1</version>
+            <version>1.6.0</version>
         </dependency>
 
+        <!-- https://mvnrepository.com/artifact/com.fasterxml.jackson.core/jackson-core -->
+        <!-- "Unused dependency" - but it is called via SerializerUtils from org.openapitools/openapi-generator and throws an error if not included explicitly -->
+        <dependency>
+            <groupId>com.fasterxml.jackson.core</groupId>
+            <artifactId>jackson-core</artifactId>
+            <version>2.17.0</version>
+        </dependency>
     </dependencies>
 
     <build>
@@ -106,26 +116,35 @@
             </resource>
         </resources>
         <plugins>
+            <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-eclipse-plugin -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-eclipse-plugin</artifactId>
-                <version>2.9</version>
+                <version>2.10</version>
                 <configuration>
                     <downloadSources>true</downloadSources>
                     <downloadJavadocs>false</downloadJavadocs>
                 </configuration>
             </plugin>
 
+            <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-compiler-plugin -->
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>2.3.2</version>
+                <version>3.13.0</version>
                 <configuration>
                     <source>${jdk.version}</source>
                     <target>${jdk.version}</target>
                 </configuration>
             </plugin>
 
+            <!-- https://mvnrepository.com/artifact/org.apache.maven.plugins/maven-surefire-plugin -->
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.2.5</version>
+            </plugin>
+
             <!-- Make this jar executable -->
             <plugin>
                 <artifactId>maven-assembly-plugin</artifactId>

diff --git a/src/main/java/edu/isi/oba/ObaUtils.java b/src/main/java/edu/isi/oba/ObaUtils.java
@@ -1,33 +1,38 @@
 package edu.isi.oba;
 
+import static edu.isi.oba.Oba.logger;
 import edu.isi.oba.config.YamlConfig;
-import org.apache.commons.cli.*;
-import org.json.JSONException;
-import org.json.JSONObject;
-import org.yaml.snakeyaml.Yaml;
-import org.yaml.snakeyaml.constructor.Constructor;
 
 import java.io.*;
-import java.nio.file.Files;
-import java.nio.file.StandardCopyOption;
-import java.util.logging.Level;
-import java.util.zip.ZipEntry;
-import java.util.zip.ZipInputStream;
-
-import static edu.isi.oba.Oba.logger;
 import java.net.HttpURLConnection;
 import java.net.URL;
+import java.nio.file.Files;
 import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 import java.util.Optional;
+import java.util.logging.Level;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.apache.commons.cli.*;
+
+import org.json.JSONException;
+import org.json.JSONObject;
+
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLAnnotation;
 import org.semanticweb.owlapi.model.OWLEntity;
 import org.semanticweb.owlapi.model.OWLLiteral;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.search.EntitySearcher;
+
+import org.yaml.snakeyaml.LoaderOptions;
+import org.yaml.snakeyaml.Yaml;
+import org.yaml.snakeyaml.constructor.Constructor;
+
 import uk.ac.manchester.cs.owl.owlapi.OWLAnnotationPropertyImpl;
 
 public class ObaUtils {
@@ -180,7 +185,7 @@ public static String get_config_yaml(String[] args) {
     }
 
     public static YamlConfig get_yaml_data(String config_yaml) {
-        Constructor constructor = new Constructor(YamlConfig.class);
+        Constructor constructor = new Constructor(YamlConfig.class, new LoaderOptions());
         Yaml yaml = new Yaml(constructor);
 
         InputStream config_input = null;

diff --git a/src/main/java/edu/isi/oba/Serializer.java b/src/main/java/edu/isi/oba/Serializer.java
@@ -1,20 +1,17 @@
 package edu.isi.oba;
 
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.util.*;
 
 import io.swagger.parser.OpenAPIParser;
 import io.swagger.v3.oas.models.*;
 import io.swagger.v3.oas.models.security.SecurityScheme;
-
 import io.swagger.v3.parser.core.models.ParseOptions;
 import io.swagger.v3.parser.core.models.SwaggerParseResult;
-import org.openapitools.codegen.serializer.SerializerUtils;
 
-import java.io.BufferedWriter;
-import java.io.File;
-import java.io.FileWriter;
-import java.io.IOException;
-import java.nio.file.Files;
-import java.util.*;
+import org.openapitools.codegen.serializer.SerializerUtils;
 
 class Serializer {
   //TODO: validate the yaml