Major dependency updates

.github/workflows/build.yaml

@@ -0,0 +1,11 @@
+name: Build
+on: [push, pull_request]
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: epimorphics/github-actions/maven-build@v17
+        with:
+          java-version: '21'
+          aws-access-key-id: ${{ secrets.DEPLOY_MAVEN_PRIVATE_S3_USERNAME }}
+          aws-secret-access-key: ${{ secrets.DEPLOY_MAVEN_PRIVATE_S3_PASSWORD }}

pom.xml

@@ -3,7 +3,7 @@
   <groupId>com.epimorphics</groupId>
   <artifactId>sapi</artifactId>
   <packaging>pom</packaging>
-  <version>2.3.16-SNAPSHOT</version>
+  <version>4.0.0-SNAPSHOT</version>
   <name>sapi</name>
   <description>Simple API</description>
 
@@ -14,8 +14,9 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
-      <appbase.version>3.1.14</appbase.version>
-      <jersey.version>2.25.1</jersey.version>
+      <appbase.version>4.0.0</appbase.version>
+      <jersey.version>3.1.11</jersey.version>
+    <tomcat.version>11.0.12</tomcat.version>
   </properties>
 
   <repositories>
@@ -79,10 +80,9 @@
   <dependencies>
 
     <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.13.1</version>
-      <type>jar</type>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-api</artifactId>
+      <version>5.13.2</version>
       <scope>test</scope>
     </dependency>
 
@@ -105,7 +105,17 @@
         <version>${jersey.version}</version>
     </dependency>
 
-
+    <dependency>
+      <groupId>org.glassfish.jersey.inject</groupId>
+      <artifactId>jersey-hk2</artifactId>
+      <version>${jersey.version}</version>
+    </dependency>
+
+    <dependency>
+      <groupId>jakarta.activation</groupId>
+      <artifactId>jakarta.activation-api</artifactId>
+      <version>2.1.4</version>
+    </dependency>
   </dependencies>
 
   <modules>
@@ -121,8 +131,8 @@
         <artifactId>maven-compiler-plugin</artifactId>
         <version>3.14.1</version>
         <configuration>
-          <source>1.8</source>
-          <target>1.8</target>
+          <source>21</source>
+          <target>21</target>
         </configuration>
       </plugin>
 
@@ -146,6 +156,17 @@
         <artifactId>maven-release-plugin</artifactId>
         <version>3.1.1</version>
       </plugin>
+
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <version>3.5.4</version>
+        <configuration>
+          <properties>
+            <excludeTags>slow</excludeTags>
+          </properties>
+        </configuration>
+      </plugin>
     </plugins>
 
     <extensions>

sapi-app/pom.xml

@@ -5,16 +5,17 @@
   <name>sapi-app</name>
   <description>Simple API application</description>
 
-  <properties>
-    <tomcat.version>9.0.113</tomcat.version>
-  </properties>
+  <parent>
+    <groupId>com.epimorphics</groupId>
+    <artifactId>sapi</artifactId>
+    <version>4.0.0-SNAPSHOT</version>
+  </parent>
 
   <dependencies>
-
     <dependency>
     	<groupId>com.epimorphics</groupId>
       <artifactId>sapi-lib</artifactId>
-      <version>2.3.16-SNAPSHOT</version>
+      <version>4.0.0-SNAPSHOT</version>
     </dependency>
 
     <dependency>
@@ -33,10 +34,4 @@
 
   </dependencies>
 
-  <parent>
-	  <groupId>com.epimorphics</groupId>
-    <artifactId>sapi</artifactId>
-    <version>2.3.16-SNAPSHOT</version>
-  </parent>
-
 </project>

sapi-app/src/main/java/com/epimorphics/simpleAPI/app/webapi/DefaultHandler.java

@@ -9,12 +9,12 @@
  *****************************************************************/
 
 
-import javax.ws.rs.Consumes;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
+import jakarta.ws.rs.Consumes;
+import jakarta.ws.rs.GET;
+import jakarta.ws.rs.POST;
+import jakarta.ws.rs.Path;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response;
 
 import com.epimorphics.simpleAPI.webapi.EndpointsBase;
 
@@ -31,4 +31,4 @@ public Response handleDefaultJson() {
     public Response handleDefault(String body) {
         return defaultResponse(body);
     }
-}
+}

sapi-doctool/pom.xml

@@ -4,13 +4,19 @@
   <packaging>jar</packaging>
   <name>sapi-doctool</name>
   <description>Documentation tooling for sapi</description>
-
+
+  <parent>
+    <groupId>com.epimorphics</groupId>
+    <artifactId>sapi</artifactId>
+    <version>4.0.0-SNAPSHOT</version>
+  </parent>
+
   <dependencies>
 
     <dependency>
     	<groupId>com.epimorphics</groupId>
       <artifactId>sapi-lib</artifactId>
-      <version>2.3.16-SNAPSHOT</version>
+      <version>4.0.0-SNAPSHOT</version>
     </dependency>
 
     <dependency>
@@ -21,12 +27,6 @@
 
   </dependencies>
 
-  <parent>
-	  <groupId>com.epimorphics</groupId>
-    <artifactId>sapi</artifactId>
-    <version>2.3.16-SNAPSHOT</version>
-  </parent>
-
   <build>
     <plugins>
 

sapi-lib/pom.xml

@@ -5,15 +5,17 @@
   <name>sapi-lib</name>
   <description>Simple API library</description>
 
-  <properties>
-    <tomcat.version>9.0.113</tomcat.version>
-  </properties>
+  <parent>
+    <groupId>com.epimorphics</groupId>
+    <artifactId>sapi</artifactId>
+    <version>4.0.0-SNAPSHOT</version>
+  </parent>
 
   <dependencies>
     <dependency>
-      <groupId>javax.servlet</groupId>
-      <artifactId>javax.servlet-api</artifactId>
-      <version>3.1.0</version>
+      <groupId>jakarta.servlet</groupId>
+      <artifactId>jakarta.servlet-api</artifactId>
+      <version>6.0.0</version>
       <scope>provided</scope>
     </dependency>
 
@@ -30,12 +32,31 @@
       <scope>provided</scope>
     </dependency>
 
-  </dependencies>
+    <dependency>
+      <groupId>com.github.jsonld-java</groupId>
+      <artifactId>jsonld-java</artifactId>
+      <version>0.13.6</version>
+    </dependency>
 
-  <parent>
-    <groupId>com.epimorphics</groupId>
-    <artifactId>sapi</artifactId>
-    <version>2.3.16-SNAPSHOT</version>
-  </parent>
+    <dependency>
+      <groupId>commons-codec</groupId>
+      <artifactId>commons-codec</artifactId>
+      <version>1.19.0</version>
+    </dependency>
+
+    <dependency>
+      <groupId>ch.qos.logback</groupId>
+      <artifactId>logback-classic</artifactId>
+      <version>1.5.21</version>
+      <scope>test</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>org.slf4j</groupId>
+      <artifactId>slf4j-api</artifactId>
+      <version>2.0.17</version>
+    </dependency>
+
+  </dependencies>
 
 </project>

sapi-lib/src/main/java/com/epimorphics/simpleAPI/containers/Container.java

@@ -14,11 +14,11 @@
 import java.io.InputStream;
 import java.util.UUID;
 
-import javax.ws.rs.core.HttpHeaders;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response.Status;
+import com.epimorphics.appbase.data.DatasetAccessor;
+import jakarta.ws.rs.core.HttpHeaders;
+import jakarta.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.Response.Status;
 
-import org.apache.jena.query.DatasetAccessor;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
 import org.apache.jena.rdf.model.Property;

sapi-lib/src/main/java/com/epimorphics/simpleAPI/core/API.java

@@ -14,9 +14,9 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.core.UriInfo;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.core.UriInfo;
 
 import org.apache.jena.rdf.model.Property;
 import org.apache.jena.rdf.model.Resource;

sapi-lib/src/main/java/com/epimorphics/simpleAPI/core/SpecMonitor.java

@@ -15,8 +15,8 @@
 import java.util.HashMap;
 import java.util.Map;
 
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.core.UriInfo;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.core.UriInfo;
 
 import com.epimorphics.appbase.monitor.ConfigMonitor;
 import com.epimorphics.simpleAPI.endpoints.EndpointSpec;

sapi-lib/src/main/java/com/epimorphics/simpleAPI/endpoints/impl/SparqlEndpointSpec.java

@@ -9,7 +9,7 @@
 
 package com.epimorphics.simpleAPI.endpoints.impl;
 
-import javax.ws.rs.NotFoundException;
+import jakarta.ws.rs.NotFoundException;
 
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;

sapi-lib/src/main/java/com/epimorphics/simpleAPI/jsonld/JsonLDJenaTripleCallBack.java

@@ -68,7 +68,7 @@ public Object call(RDFDataset dataset) {
                     Node s = createNode(t, "subject") ;
                     Node p = createNode(t, "predicate") ;
                     Node o = createNode(t, "object") ;
-                    model.getGraph().add( new Triple(s,p,o) );
+                    model.getGraph().add( Triple.create(s,p,o) );
                 }
             } 
         }

sapi-lib/src/main/java/com/epimorphics/simpleAPI/jsonld/JsonLDUtil.java

@@ -26,7 +26,7 @@
 import java.io.InputStream;
 import java.util.Map;
 
-import javax.ws.rs.core.MediaType;
+import jakarta.ws.rs.core.MediaType;
 
 import org.apache.jena.rdf.model.Model;
 

sapi-lib/src/main/java/com/epimorphics/simpleAPI/query/impl/SparqlDataSource.java

@@ -9,7 +9,7 @@
 
 package com.epimorphics.simpleAPI.query.impl;
 
-import javax.ws.rs.NotFoundException;
+import jakarta.ws.rs.NotFoundException;
 
 import org.apache.jena.graph.Graph;
 import org.apache.jena.rdf.model.Model;

sapi-lib/src/main/java/com/epimorphics/simpleAPI/requests/Call.java

@@ -27,9 +27,9 @@
 import org.slf4j.LoggerFactory;
 import org.slf4j.MDC;
 
-import javax.ws.rs.NotFoundException;
-import javax.ws.rs.WebApplicationException;
-import javax.ws.rs.core.Response.Status;
+import jakarta.ws.rs.NotFoundException;
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.Response.Status;
 import java.util.List;
 import java.util.function.Function;
 
@@ -170,7 +170,7 @@ public ResultOrStream getResults() throws WebApiException {
             return getResults(query);
         } catch (QueryExceptionHTTP e) {
             // Retry before reporting error?
-            if (e.getResponseCode() >= 500) {
+            if (e.getStatusCode() >= 500) {
                 log.warn("Sparql query execution failed, retrying");
                 try {
                     Thread.sleep(3000);  // TODO make configurable
@@ -192,7 +192,7 @@ public ResultOrStream getResults() throws WebApiException {
     public void returnError(Exception e) throws WebApiException, WebApplicationException {
         if (e instanceof QueryExceptionHTTP) {
             // Maybe a bad query, a timeout, or dead fuseki
-            int status = ((QueryExceptionHTTP)e).getResponseCode();
+            int status = ((QueryExceptionHTTP)e).getStatusCode();
             if (status == 503) {
                 // Fuseki returns 503 when queries time out
                 returnError(status, "Query timed out");

sapi-lib/src/main/java/com/epimorphics/simpleAPI/requests/Request.java

@@ -18,10 +18,11 @@
 import java.util.Map;
 import java.util.Set;
 
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.core.MultivaluedMap;
-import javax.ws.rs.core.Response.Status;
-import javax.ws.rs.core.UriInfo;
+import jakarta.servlet.http.HttpServletRequest;
+import jakarta.ws.rs.core.MultivaluedHashMap;
+import jakarta.ws.rs.core.MultivaluedMap;
+import jakarta.ws.rs.core.Response.Status;
+import jakarta.ws.rs.core.UriInfo;
 
 import org.apache.jena.atlas.json.JSON;
 import org.apache.jena.atlas.json.JsonObject;

sapi-lib/src/main/java/com/epimorphics/simpleAPI/requests/RequestCheck.java

@@ -12,7 +12,7 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.ws.rs.core.Response.Status;
+import jakarta.ws.rs.core.Response.Status;
 
 import org.apache.jena.atlas.json.JsonObject;
 

sapi-lib/src/main/java/com/epimorphics/simpleAPI/requests/SortRequestProcessor.java

@@ -9,7 +9,7 @@
 
 package com.epimorphics.simpleAPI.requests;
 
-import javax.ws.rs.core.Response.Status;
+import jakarta.ws.rs.core.Response.Status;
 
 import com.epimorphics.appbase.webapi.WebApiException;
 import com.epimorphics.simpleAPI.endpoints.EndpointSpec;