Upgrade dependencies

pom.xml

@@ -13,6 +13,7 @@
 
   <properties>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <junit.jupiter.version>5.14.1</junit.jupiter.version>
   </properties>
 
   <repositories>
@@ -36,15 +37,19 @@
     </repository>
 
     <repository>
-      <releases>
-        <enabled>true</enabled>
-      </releases>
-      <snapshots>
-        <enabled>true</enabled>
-      </snapshots>
-      <id>epi-public-repo</id>
-      <name>Epimorphics Public Repository</name>
-      <url>https://repository.epimorphics.com</url>
+      <id>epi-public-s3-release</id>
+      <name>Epimorphics S3 release repository</name>
+      <url>https://epi-repository.s3-eu-west-1.amazonaws.com/release</url>
+      <releases><enabled>true</enabled></releases>
+      <snapshots><enabled>false</enabled></snapshots>
+    </repository>
+
+    <repository>
+      <id>epi-public-s3-snapshot</id>
+      <name>Epimorphics S3 snapshot repository</name>
+      <url>https://epi-repository.s3-eu-west-1.amazonaws.com/snapshot</url>
+      <releases><enabled>false</enabled></releases>
+      <snapshots><enabled>true</enabled></snapshots>
     </repository>
 
   </repositories>
@@ -70,15 +75,26 @@
 
   <dependencies>
     <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.13.1</version>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-api</artifactId>
+        <version>${junit.jupiter.version}</version>
       <scope>test</scope>
-    </dependency> 
+    </dependency>
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-engine</artifactId>
+      <version>${junit.jupiter.version}</version>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>com.epimorphics</groupId>
       <artifactId>appbase</artifactId>
-      <version>3.1.14</version>
+      <version>4.0.0</version>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-lang3</artifactId>
+      <version>3.20.0</version>
     </dependency>
     <dependency>
       <groupId>org.apache.commons</groupId>
@@ -88,31 +104,36 @@
     <dependency>
         <groupId>joda-time</groupId>
         <artifactId>joda-time</artifactId>
-        <version>2.3</version>
+        <version>2.14.0</version>
     </dependency>
     <dependency>
       <groupId>org.yaml</groupId>
       <artifactId>snakeyaml</artifactId>
-      <version>2.4</version>
+      <version>2.5</version>
     </dependency>
   </dependencies>
 
   <build>
     <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-plugin</artifactId>
+        <version>3.5.4</version>
+      </plugin>
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-compiler-plugin</artifactId>
-        <version>3.3</version>
+        <version>3.14.1</version>
         <configuration>
-          <source>1.8</source>
-          <target>1.8</target>
+          <source>21</source>
+          <target>21</target>
         </configuration>
       </plugin>
 
      <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-scm-plugin</artifactId>
-        <version>1.9.4</version>
+        <version>2.2.1</version>
         <configuration>
           <connectionType>developerConnection</connectionType>
         </configuration>
@@ -121,13 +142,13 @@
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-release-plugin</artifactId>
-        <version>2.5.2</version>
+        <version>3.3.0</version>
       </plugin>
 
       <plugin>
         <groupId>org.apache.maven.plugins</groupId>
         <artifactId>maven-shade-plugin</artifactId>
-        <version>2.4.1</version>
+        <version>3.6.1</version>
         <configuration>
           <filters>
             <filter>

src/main/java/com/epimorphics/dclib/Main.java

@@ -213,7 +213,7 @@ public Boolean call()  {
                     String filebasename = NameUtils.removeExtension(filename);
                     dc.getGlobalEnv().put(ConverterProcess.FILE_NAME, filename);
                     dc.getGlobalEnv().put(ConverterProcess.FILE_BASE_NAME, filebasename);
-                    InputStream is = new BOMInputStream( new FileInputStream(dataFileF) );
+                    InputStream is = BOMInputStream.builder().setInputStream( new FileInputStream(dataFileF) ).get();
 
                     ConverterProcess process = new ConverterProcess(dc, is);
                     process.setDebug( args.isDebug() );

src/main/java/com/epimorphics/dclib/framework/ConverterProcess.java

@@ -13,6 +13,7 @@
 import java.io.InputStream;
 import java.util.Map.Entry;
 
+import com.opencsv.exceptions.CsvValidationException;
 import org.apache.commons.collections.map.LRUMap;
 import org.apache.jena.riot.RDFDataMgr;
 import org.apache.jena.riot.system.StreamRDF;
@@ -221,6 +222,8 @@ public boolean process() {
 
         } catch (IOException e) {
             messageReporter.reportError("Problem reading next line of source");
+        } catch (CsvValidationException csvve) {
+            messageReporter.reportError("The CSV content was invalid: " + csvve.getMessage());
         } finally {
             current.set(null);
         }
@@ -291,7 +294,7 @@ public BindingEnv peekRow() {
         }
     }
 
-    protected void preprocess() throws IOException {        
+    protected void preprocess() throws IOException, CsvValidationException {
         Node dataset = NodeFactory.createBlankNode();
 
         Object baseURI = env.get(BASE_OBJECT_NAME);
@@ -332,7 +335,7 @@ protected void preprocess() throws IOException {
                             try {
                                 Node prop = new Pattern(peekRow[1], dataContext).evaluateAsURINode(env, this, -1);
                                 Node value = new Pattern(peekRow[2], dataContext).evaluateAsNode(env, this, -1);
-                                getOutputStream().triple( new Triple(dataset, prop, value) );
+                                getOutputStream().triple(Triple.create(dataset, prop, value));
                             } catch (Exception e) {
                                 messageReporter.report("Failed to process metadata row: " + e, dataSource.getLineNumber());
                             }

src/main/java/com/epimorphics/dclib/framework/ConverterService.java

@@ -15,6 +15,7 @@
 import java.io.InputStream;
 
 import org.apache.commons.io.input.BOMInputStream;
+import org.apache.jena.riot.RDFDataMgr;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -50,7 +51,7 @@ public class ConverterService extends ComponentBase {
     public ConverterService(String defaultPrefixes) {
         dc = new DataContext();
         dc.getGlobalEnv().put(ConverterProcess.BASE_OBJECT_NAME, DEFAULT_BASE_URI);
-        PrefixMapping prefixes = FileManager.get().loadModel(defaultPrefixes);
+        PrefixMapping prefixes = RDFDataMgr.loadModel(defaultPrefixes);
         if (prefixes != null) {
             dc.setPrefixes(prefixes);
         } else {
@@ -64,7 +65,7 @@ public ConverterService(String defaultPrefixes) {
      * all qnames in templates.
      */
     public void setPrefixFile(String prefixes) {
-        PrefixMapping pref = FileManager.get().loadModel(prefixes);
+        PrefixMapping pref = RDFDataMgr.loadModel(prefixes);
         dc.setPrefixes(pref);
     }
 
@@ -147,7 +148,7 @@ public Model simpleConvert(String templateFile, String dataFile, ProgressMonitor
         String filebasename = NameUtils.removeExtension(filename);
         put(ConverterProcess.FILE_NAME, filename);
         put(ConverterProcess.FILE_BASE_NAME, filebasename);
-        InputStream is = new BOMInputStream( new FileInputStream(dataFileF) );
+        InputStream is = BOMInputStream.builder().setInputStream( new FileInputStream(dataFileF) ).get();
 
         ConverterProcess process = new ConverterProcess(dc, is);
         process.setDebug(debug);

src/main/java/com/epimorphics/dclib/framework/LocatorHTTP.java

@@ -27,7 +27,7 @@
 package com.epimorphics.dclib.framework ;
 
 import org.apache.jena.atlas.web.TypedInputStream ;
-import org.apache.jena.riot.web.HttpOp ;
+import org.apache.jena.http.HttpOp;
 import org.slf4j.Logger ;
 import org.slf4j.LoggerFactory ;
 
@@ -47,7 +47,7 @@ public LocatorHTTP() {
     @Override
     public TypedInputStream performOpen(String uri) {
         if ( uri.startsWith("http://") || uri.startsWith("https://") )
-            return HttpOp.execHttpGet(uri, acceptHeader) ;
+            return HttpOp.httpGet(uri, acceptHeader) ;
         return null ;
     }
 

src/main/java/com/epimorphics/dclib/framework/Pattern.java

@@ -12,11 +12,13 @@
 import java.util.ArrayList;
 import java.util.List;
 
-import javax.ws.rs.NotSupportedException;
+import jakarta.ws.rs.NotSupportedException;
 
 import org.apache.commons.jexl2.Expression;
 import org.apache.commons.jexl2.JexlEngine;
 import org.apache.commons.jexl2.Script;
+import org.apache.jena.datatypes.xsd.XSDDatatype;
+import org.apache.jena.vocabulary.XSD;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -225,11 +227,11 @@ public Node asNode(Object result) {
         } else if (result instanceof RDFNodeWrapper) {
             return ((RDFNodeWrapper)result).asRDFNode().asNode();
         } else if (result instanceof String) {
-            return NodeFactory.createLiteral( (String)result );
+            return NodeFactory.createLiteralString( (String)result );
         } else if (result instanceof Number) {
             return ValueNumber.nodeFromNumber( (Number)result );
         } else if (result instanceof Boolean) {
-            return NodeFactory.createLiteral( LiteralLabelFactory.createTypedLiteral(result) );
+            return NodeFactory.createLiteralDT(result.toString(), XSDDatatype.XSDboolean);
         } else if (result instanceof Value) {
             return ((Value)result).asNode();
         } else {

src/main/java/com/epimorphics/dclib/sources/CSVInput.java

@@ -15,11 +15,13 @@
 import java.io.InputStreamReader;
 import java.nio.charset.StandardCharsets;
 
+import com.opencsv.CSVParser;
+import com.opencsv.CSVParserBuilder;
+import com.opencsv.CSVReader;
+import com.opencsv.CSVReaderBuilder;
+import com.opencsv.exceptions.CsvValidationException;
 import org.apache.commons.io.input.BOMInputStream;
 
-import au.com.bytecode.opencsv.CSVParser;
-import au.com.bytecode.opencsv.CSVReader;
-
 import com.epimorphics.dclib.framework.BindingEnv;
 import com.epimorphics.util.EpiException;
 import com.epimorphics.util.NameUtils;
@@ -35,12 +37,12 @@ public class CSVInput {
     protected boolean hasPreamble = false;
     protected String[] peekRow;
 
-    public CSVInput(String filename) throws IOException {
-        this( new BOMInputStream( new FileInputStream(filename) ) );
+    public CSVInput(String filename) throws IOException, CsvValidationException {
+        this(BOMInputStream.builder().setInputStream( new FileInputStream(filename) ).get());
     }
 
-    public CSVInput(InputStream ins) throws IOException {
-        in = new CSVReader( new InputStreamReader(ins, StandardCharsets.UTF_8), CSVParser.DEFAULT_SEPARATOR, CSVParser.DEFAULT_QUOTE_CHARACTER, '\0' );
+    public CSVInput(InputStream ins) throws IOException, CsvValidationException {
+        in = new CSVReaderBuilder(new InputStreamReader(ins, StandardCharsets.UTF_8)).build();
 
         String[] headerLine = in.readNext();
         if (headerLine == null) {
@@ -72,7 +74,7 @@ private String safeColName(String col) {
      * Return a look ahead to the next row.
      * Repeat calls do not advance to further rows, 
      */
-    public String[] getPeekRow() throws IOException {
+    public String[] getPeekRow() throws IOException, CsvValidationException {
         if (peekRow == null) {
             peekRow = in.readNext();
         }
@@ -83,7 +85,7 @@ public String[] getPeekRow() throws IOException {
      * Advances to the next row after a prior peek.
      * Returns true if a new peek was available.
      */
-    public boolean advancePeek() throws IOException {
+    public boolean advancePeek() throws IOException, CsvValidationException {
         peekRow = in.readNext();
         lineNumber++;
         return peekRow != null;
@@ -96,7 +98,7 @@ public boolean advancePeek() throws IOException {
      * If there have been any peek rows then returns an env based
      * on the last peeked row.
      */
-    public BindingEnv nextRow() throws IOException {
+    public BindingEnv nextRow() throws IOException, CsvValidationException {
         if (in != null) {
             String[] rowValues = (peekRow != null) ? peekRow : in.readNext();
             lineNumber++;

src/main/java/com/epimorphics/dclib/sources/CSVMapSource.java

@@ -11,6 +11,7 @@
 
 import java.io.IOException;
 
+import com.opencsv.exceptions.CsvValidationException;
 import org.apache.jena.atlas.json.JsonObject;
 
 import com.epimorphics.dclib.framework.BindingEnv;
@@ -39,7 +40,7 @@ public static boolean isSpec(JsonObject spec) {
         return false;
     }
 
-    public CSVMapSource(JsonObject spec, ConverterProcess config) throws IOException {
+    public CSVMapSource(JsonObject spec, ConverterProcess config) throws IOException, CsvValidationException {
         super(spec);
         String keyCol = getField(JSONConstants.KEY, "key");
         String valueCol = getField(JSONConstants.VALUE, "value");
@@ -76,7 +77,7 @@ private Node asNode(boolean isURI, String value) {
         if (isURI) {
             return NodeFactory.createURI(value);
         } else {
-            return NodeFactory.createLiteral(value);
+            return NodeFactory.createLiteralString(value);
         }
     }
 }

src/main/java/com/epimorphics/dclib/sources/LexIndex.java

@@ -16,6 +16,7 @@
 import java.util.regex.Pattern;
 
 import org.apache.commons.lang3.StringUtils;
+import org.apache.commons.text.similarity.LevenshteinDistance;
 import org.apache.jena.util.OneToManyMap;
 
 /**
@@ -25,6 +26,7 @@
  * @author <a href="mailto:dave@epimorphics.com">Dave Reynolds</a>
  */
 public class LexIndex<T> {
+    private static final LevenshteinDistance levDist = LevenshteinDistance.getDefaultInstance();
     protected OneToManyMap<String, Record> table = new OneToManyMap<>();
 
     /**
@@ -48,11 +50,11 @@ public T lookup(String key) {
             // There is a result but is there more than one
             if (i.hasNext()) {
                 // Yes, so search for best
-                int bestDist = StringUtils.getLevenshteinDistance(key, match.key);
+                int bestDist = levDist.apply(key, match.key);
                 Record best = match;
                 while (i.hasNext()) {
                     match = i.next();
-                    int dist = StringUtils.getLevenshteinDistance(key, match.key);
+                    int dist = levDist.apply(key, match.key);
                     if (dist < bestDist) {
                         bestDist = dist;
                         best = match;

src/main/java/com/epimorphics/dclib/sources/MapSourceFactory.java

@@ -11,14 +11,15 @@
 
 import java.io.IOException;
 
+import com.opencsv.exceptions.CsvValidationException;
 import org.apache.jena.atlas.json.JsonObject;
 
 import com.epimorphics.dclib.framework.ConverterProcess;
 import com.epimorphics.dclib.framework.MapSource;
 
 public class MapSourceFactory {
 
-    public static MapSource sourceFrom(JsonObject spec, ConverterProcess proc) throws IOException {
+    public static MapSource sourceFrom(JsonObject spec, ConverterProcess proc) throws IOException, CsvValidationException {
         if (CSVMapSource.isSpec(spec)) {
             return new CSVMapSource(spec, proc);
         } else if (RDFMapSource.isSpec(spec)) {