Merge pull request #142 from imas/jena4

upgrade depends libraries (jena 4.5)
imas · May 11, 2022 · 0a68a28 · 0a68a28
2 parents c0d57f9 + bc9db80
commit 0a68a28
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Showing 7 changed files with 94 additions and 75 deletions.
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -17,10 +17,10 @@ jobs:
       - name: Prepare git
         run: git config --global core.autocrlf false
       - uses: actions/checkout@v2
-      - uses: actions/setup-java@v2
+      - uses: actions/setup-java@v3
         with:
           distribution: 'adopt'
-          java-version: '8'
+          java-version: '11'
       - uses: actions/setup-node@v1
         with:
           node-version: '12'

diff --git a/build.gradle b/build.gradle
@@ -4,33 +4,33 @@ plugins {
     id 'pmd'
     id 'jacoco'
     id 'com.github.johnrengelman.shadow' version '4.0.3'
-    id 'com.github.spotbugs' version '4.0.5'
+    id 'com.github.spotbugs' version '4.7.0'
 }
 java {
-    sourceCompatibility = JavaVersion.VERSION_1_8
-    targetCompatibility = JavaVersion.VERSION_1_8
+    sourceCompatibility = JavaVersion.VERSION_11
+    targetCompatibility = JavaVersion.VERSION_11
 }
 
 repositories {
     mavenCentral()
 }
 dependencies {
-    implementation 'org.apache.jena:jena-arq:3.4.0'
-    implementation 'commons-cli:commons-cli:1.4'
+    implementation 'org.apache.jena:jena-arq:4.5.0'
+    implementation 'commons-cli:commons-cli:1.5.0'
     implementation 'org.jline:jline:3.21.0'
-    implementation 'org.yaml:snakeyaml:1.23'
-    implementation 'org.codehaus.groovy:groovy:3.0.0-rc-3'
+    implementation 'org.yaml:snakeyaml:1.30'
+    implementation 'org.codehaus.groovy:groovy:3.0.10'
     implementation 'org.slf4j:slf4j-log4j12:1.7.25'
-    implementation 'org.thymeleaf:thymeleaf:3.0.11.RELEASE'
+    implementation 'org.thymeleaf:thymeleaf:3.0.15.RELEASE'
     implementation 'nz.net.ultraq.thymeleaf:thymeleaf-layout-dialect:2.2.2'
-    implementation 'org.reflections:reflections:0.9.11'
+    implementation 'org.reflections:reflections:0.10.2'
     implementation 'com.github.albfernandez:juniversalchardet:2.3.0'
-    implementation 'org.eclipse.lsp4j:org.eclipse.lsp4j:0.8.1'
-    implementation group: 'org.topbraid', name: 'shacl', version: '1.3.0'
+    implementation 'org.eclipse.lsp4j:org.eclipse.lsp4j:0.12.0'
+    implementation 'org.topbraid:shacl:1.3.0'
 
     compileOnly 'net.jcip:jcip-annotations:1.0'
-    compileOnly 'com.github.spotbugs:spotbugs:4.0.2'
-    compileOnly 'com.github.spotbugs:spotbugs-annotations:4.0.2'
+    compileOnly 'com.github.spotbugs:spotbugs:4.7.0'
+    compileOnly 'com.github.spotbugs:spotbugs-annotations:4.7.0'
 
     testImplementation 'junit:junit:4.+'
     testImplementation 'org.hamcrest:hamcrest-all:1.3'
@@ -62,7 +62,7 @@ pmd {
     ]
 }
 spotbugs {
-    toolVersion = '4.0.2'
+    toolVersion = '4.2.1'
 }
 jacocoTestCoverageVerification {
     violationRules {
@@ -75,8 +75,8 @@ jacocoTestCoverageVerification {
 }
 tasks.withType(Checkstyle) {
     reports {
-        xml.enabled = false
-        html.enabled = true
+        xml.enabled(false)
+        html.enabled(true)
     }
 }
 tasks.withType(com.github.spotbugs.snom.SpotBugsTask) {

diff --git a/jitpack.yml b/jitpack.yml
@@ -0,0 +1,3 @@
+before_install:
+  - sdk install java 11.0.10-open
+  - sdk use java 11.0.10-open
diff --git a/src/main/java/com/github/imas/rdflint/parser/RdflintParserBuilder.java b/src/main/java/com/github/imas/rdflint/parser/RdflintParserBuilder.java
@@ -72,7 +72,7 @@ public RdflintParser build() {
     if (this.lang == Lang.RDFXML) {
       return new RdflintParserRdfxml(this.body, this.validators, this.base);
     }
-    return new RdflintParserTurtle(this.body, this.validators);
+    return new RdflintParserTurtle(this.body, this.validators, this.base);
   }
 
 }
diff --git a/src/main/java/com/github/imas/rdflint/parser/RdflintParserRdfxml.java b/src/main/java/com/github/imas/rdflint/parser/RdflintParserRdfxml.java
@@ -21,6 +21,8 @@
 import org.apache.jena.graph.Node;
 import org.apache.jena.graph.NodeFactory;
 import org.apache.jena.graph.Triple;
+import org.apache.jena.irix.IRIs;
+import org.apache.jena.irix.SetupJenaIRI;
 import org.apache.jena.rdf.model.RDFErrorHandler;
 import org.apache.jena.rdfxml.xmlinput.ALiteral;
 import org.apache.jena.rdfxml.xmlinput.ARP;
@@ -35,10 +37,9 @@
 import org.apache.jena.riot.RiotException;
 import org.apache.jena.riot.RiotParseException;
 import org.apache.jena.riot.SysRIOT;
-import org.apache.jena.riot.checker.CheckerLiterals;
 import org.apache.jena.riot.lang.ReaderRIOTRDFXML;
+import org.apache.jena.riot.system.Checker;
 import org.apache.jena.riot.system.ErrorHandler;
-import org.apache.jena.riot.system.IRIResolver;
 import org.apache.jena.riot.system.StreamRDF;
 import org.apache.jena.riot.system.StreamRDFLib;
 import org.apache.jena.sparql.util.Context;
@@ -52,16 +53,16 @@ public class RdflintParserRdfxml extends RdflintParser {
 
   String text;
   List<RdfValidator> validators;
-  String baseUri;
+  String base;
 
   /**
    * constructor.
    */
-  public RdflintParserRdfxml(String text, List<RdfValidator> validators, String baseUri) {
+  public RdflintParserRdfxml(String text, List<RdfValidator> validators, String base) {
     super();
     this.text = text;
-    this.baseUri = baseUri;
     this.validators = validators;
+    this.base = base;
   }
 
   @Override
@@ -76,9 +77,9 @@ public void parse(Graph g, List<LintProblem> problems) {
 
     ContentType ct = Lang.RDFXML.getContentType();
     InputStream validateIn = new ByteArrayInputStream(this.text.getBytes(StandardCharsets.UTF_8));
-    try {
-      reader.read(validateIn, baseUri, ct, StreamRDFLib.graph(g), context);
 
+    try {
+      reader.read(validateIn, this.base, ct, StreamRDFLib.graph(g), context);
       if (!parseProblemList.isEmpty()) {
         problems.addAll(parseProblemList);
         return;
@@ -107,7 +108,8 @@ public void parse(Graph g, List<LintProblem> problems) {
   static class ReaderRIOTRDFXML2 // SUPPRESS CHECKSTYLE AbbreviationAsWord
       extends ReaderRIOTRDFXML { // SUPPRESS CHECKSTYLE AbbreviationAsWord
 
-    List<LintProblem> diagnosticList;
+    private final List<RdfValidator> models;
+    private final List<LintProblem> diagnosticList;
 
     public ReaderRIOTRDFXML2(ErrorHandler errorHandler, List<RdfValidator> models) {
       super(errorHandler);
@@ -116,36 +118,26 @@ public ReaderRIOTRDFXML2(ErrorHandler errorHandler, List<RdfValidator> models) {
       this.diagnosticList = new LinkedList<>();
     }
 
+    public List<LintProblem> getDiagnosticList() {
+      return this.diagnosticList;
+    }
+
     private ARP arp = new ARP();
     private InputStream input = null; // NOPMD
     private Reader reader = null; // NOPMD
     private String xmlBase;
     private String filename;
     private StreamRDF sink;
     private ErrorHandler errorHandler;
-    private List<RdfValidator> models;
     private Context context;
 
-    public List<LintProblem> getDiagnosticList() {
-      return this.diagnosticList;
-    }
-
-    /**
-     * Sort out the base URI for RDF/XML parsing.
-     */
-    private static String baseURI_RDFXML( // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
-        String baseIRI) { // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
-      if (baseIRI == null) {
-        return SysRIOT.chooseBaseIRI();
-      } else {
-        // This normalizes the URI.
-        return SysRIOT.chooseBaseIRI(baseIRI);
-      }
-    }
-
     @Override
-    public void read(InputStream in, String baseURI, // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
-        ContentType ct, StreamRDF output, Context context) {
+    public void read(
+        InputStream in,
+        String baseURI, // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
+        ContentType ct,
+        StreamRDF output,
+        Context context) {
       this.input = in;
       this.xmlBase = baseURI_RDFXML(baseURI);
       this.filename = baseURI;
@@ -155,8 +147,12 @@ public void read(InputStream in, String baseURI, // SUPPRESS CHECKSTYLE Abbrevia
     }
 
     @Override
-    public void read(Reader reader, String baseURI, // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
-        ContentType ct, StreamRDF output, Context context) {
+    public void read(
+        Reader reader,
+        String baseURI, // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
+        ContentType ct,
+        StreamRDF output,
+        Context context) {
       this.reader = reader;
       this.xmlBase = baseURI_RDFXML(baseURI);
       this.filename = baseURI;
@@ -165,6 +161,9 @@ public void read(Reader reader, String baseURI, // SUPPRESS CHECKSTYLE Abbreviat
       parse();
     }
 
+    // RDF 1.1 is based on URIs/IRIs, where space are not allowed.
+    // RDF 1.0 (and RDF/XML) was based on "RDF URI References" which did allow spaces.
+
     // Use with TDB requires this to be "true" - it is set by InitTDB.
     public static boolean RiotUniformCompatibility = false; // NOPMD
     // Warnings in ARP that should be errors to be compatible with
@@ -183,7 +182,8 @@ public void read(Reader reader, String baseURI, // SUPPRESS CHECKSTYLE Abbreviat
     private static boolean errorForSpaceInURI = true;
 
     // Extracted from org.apache.jena.rdfxml.xmlinput.JenaReader
-    private void oneProperty(ARPOptions options, // SUPPRESS CHECKSTYLE ParameterName
+    private void oneProperty(
+        ARPOptions options,
         String pName, // SUPPRESS CHECKSTYLE ParameterName
         Object value) {
       if (!pName.startsWith("ERR_") && !pName.startsWith("IGN_") && !pName.startsWith("WARN_")) {
@@ -244,15 +244,15 @@ public void parse() {
       }
 
       if (JenaRuntime.isRDF11) {
-        arp.getOptions().setIRIFactory(IRIResolver.iriFactory());
+        arp.getOptions().setIRIFactory(SetupJenaIRI.iriFactory_RDFXML());
       }
 
       if (context != null) {
         Map<String, Object> properties = null;
         try {
           @SuppressWarnings("unchecked")
-          Map<String, Object> p = (Map<String, Object>) (context
-              .get(SysRIOT.sysRdfReaderProperties));
+          Map<String, Object> p = (Map<String, Object>) (context.get(
+              SysRIOT.sysRdfReaderProperties));
           properties = p;
         } catch (Throwable ex) {
           Log.warn(this, "Problem accessing the RDF/XML reader properties: properties ignored", ex);
@@ -269,32 +269,42 @@ public void parse() {
         } else {
           arp.load(input, xmlBase);
         }
+      } catch (IOException e) {
+        errorHandler.error(filename + ": " + ParseException.formatMessage(e), -1, -1); // NOPMD
       } catch (SAXParseException e) {
         // already reported.
-      } catch (IOException | SAXException | RiotParseException ex) {
-        errorHandler.error(filename + ": " + ParseException.formatMessage(ex), // NOPMD
-            arp.getLocator().getLineNumber(),
-            arp.getLocator().getColumnNumber());
+      } catch (SAXException sax) {
+        errorHandler.error(filename + ": " + ParseException.formatMessage(sax), -1, -1); // NOPMD
       }
       sink.finish();
     }
 
+    /**
+     * Sort out the base URI for RDF/XML parsing.
+     */
+    private static String baseURI_RDFXML(  // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
+        String baseIRI) {  // SUPPRESS CHECKSTYLE AbbreviationAsWordInName
+      if (baseIRI == null) {
+        return IRIs.getBaseStr();
+      } else {
+        return IRIs.toBase(baseIRI);
+      }
+    }
+
     private static class HandlerSink extends ARPSaxErrorHandler implements StatementHandler,
         NamespaceHandler {
 
       private StreamRDF output;
       private ErrorHandler riotErrorHandler;
-      private CheckerLiterals checker;
       private ARP arp;
       private List<RdfValidator> models;
       private List<LintProblem> diagnosticList;
 
       HandlerSink(StreamRDF output, ErrorHandler errHandler, ARP arp,
           List<RdfValidator> models, List<LintProblem> diagnosticList) {
-        super(new ErrorHandlerBridge(errHandler));
+        super(new ReaderRIOTRDFXML2.ErrorHandlerBridge(errHandler));
         this.output = output;
         this.riotErrorHandler = errHandler;
-        this.checker = new CheckerLiterals(errHandler);
         this.arp = arp;
         this.models = models;
         this.diagnosticList = diagnosticList;
@@ -356,10 +366,8 @@ private Node convert(AResource r) {
               int i = uriStr.indexOf(' ');
               String s = uriStr.substring(0, i);
               String msg = String.format("Bad character in IRI (space): <%s[space]...>", s);
-              int line = arp.getLocator().getLineNumber();
-              int col = arp.getLocator().getColumnNumber();
-              riotErrorHandler.error(msg, line, col);// NOPMD
-              throw new RiotParseException(msg, line, col);
+              riotErrorHandler.error(msg, -1, -1);
+              throw new RiotParseException(msg, -1, -1);
             }
           }
           return NodeFactory.createURI(uriStr);
@@ -379,11 +387,11 @@ private Triple convert(AResource s, AResource p, AResource o) {
       }
 
       private Triple convert(AResource s, AResource p, ALiteral o) {
-        Node object = convert(o);
-        checker.check(object,
+        Node literal = convert(o);
+        Checker.checkLiteral(literal, riotErrorHandler,
             arp.getLocator().getLineNumber(),
             arp.getLocator().getColumnNumber());
-        return Triple.create(convert(s), convert(p), object);
+        return Triple.create(convert(s), convert(p), literal);
       }
 
       @Override
@@ -431,7 +439,6 @@ private static Pair<Integer, Integer> getLineCol(Exception e) {
         }
       }
     }
-
   }
 
 }
diff --git a/src/main/java/com/github/imas/rdflint/parser/RdflintParserTurtle.java b/src/main/java/com/github/imas/rdflint/parser/RdflintParserTurtle.java
@@ -12,6 +12,7 @@
 import org.apache.jena.graph.Graph;
 import org.apache.jena.graph.Node;
 import org.apache.jena.graph.Triple;
+import org.apache.jena.irix.IRIxResolver;
 import org.apache.jena.query.ARQ;
 import org.apache.jena.riot.Lang;
 import org.apache.jena.riot.RDFParserRegistry;
@@ -20,7 +21,6 @@
 import org.apache.jena.riot.RiotParseException;
 import org.apache.jena.riot.system.ErrorHandler;
 import org.apache.jena.riot.system.FactoryRDF;
-import org.apache.jena.riot.system.IRIResolver;
 import org.apache.jena.riot.system.ParserProfileStd;
 import org.apache.jena.riot.system.PrefixMap;
 import org.apache.jena.riot.system.PrefixMapFactory;
@@ -40,7 +40,7 @@ static class RdflintParseProfile extends ParserProfileStd {
     List<LintProblem> diagnosticList;
     List<RdfValidator> validationModels;
 
-    public RdflintParseProfile(FactoryRDF factory, ErrorHandler errorHandler, IRIResolver resolver,
+    public RdflintParseProfile(FactoryRDF factory, ErrorHandler errorHandler, IRIxResolver resolver,
         PrefixMap prefixMap, Context context, boolean checking, boolean strictMode,
         List<RdfValidator> validationModels, List<LintProblem> diagnosticList) {
       super(factory, errorHandler, resolver, prefixMap, context, checking, strictMode);
@@ -101,14 +101,16 @@ public Node create(Node currentGraph, Token token) {
 
   String text;
   List<RdfValidator> validators;
+  String base;
 
   /**
    * constructor.
    */
-  public RdflintParserTurtle(String text, List<RdfValidator> validators) {
+  public RdflintParserTurtle(String text, List<RdfValidator> validators, String base) {
     super();
     this.text = text;
     this.validators = validators;
+    this.base = base;
   }
 
   @Override
@@ -118,8 +120,8 @@ public void parse(Graph g, List<LintProblem> problems) {
     try {
       // validation
       FactoryRDF factory = RiotLib.factoryRDF();
-      IRIResolver resolver = IRIResolver.create();
-      PrefixMap prefixMap = PrefixMapFactory.createForInput();
+      IRIxResolver resolver = IRIxResolver.create().base(this.base).build();
+      PrefixMap prefixMap = PrefixMapFactory.create();
       Context context = new Context();
       boolean checking = true;
       boolean strict = false;