ont-converter: ontapi-1.4.0-snapshot

sszuev · Sep 12, 2018 · 53fc7b6 · 53fc7b6
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diff --git a/README.md b/README.md
@@ -1,8 +1,11 @@
 # Ontology Converter v1.0
 
-## A simple command-line utility to convert any rdf graph to OWL2-DL ontology.
-This is a kind of [ONT-API](https://github.com/avicomp/ont-api) extension, without a claim. Can work both with single ontology file source and with directory containing dependent or independent sources. 
-The utility automatically transforms the source RDF Graph to the OWL2 DL syntax according to the inner rules and command-line options. For example, if there is no `owl:Ontology` section inside rdf-graph, which is required by OWL, an anonymous ontology header will be generated. 
+## A simple command-line utility to convert any RDF graph to OWL2-DL ontology.
+This is a kind of [ONT-API](https://github.com/avicomp/ont-api) extension with intentionally straightforward realisation.
+Can work both with single ontology file source and with directory containing dependent or independent sources. 
+The utility automatically transforms the source RDF Graph to the OWL2 DL syntax according to the internal rules and command-line options. 
+For example, if there is no `owl:Ontology` section inside rdf-graph, which is required by OWL, an anonymous ontology header will be generated. 
+This is a tool, not a library, and, therefore, it is available only in the form of code and prebuilt jar (see [/releases](https://github.com/sszuev/ont-converter/releases)).
 
 ### Usage: `java -jar ont-converter.jar [-f] [-h] -i <path> [-if <format>] -o <path> -of <format> [-p <0|1|2>] [-r] [-s] [-v] [-w]`
 
@@ -114,5 +117,8 @@ where
 * java1.8
 * maven to build (`mvn package`)
 
+### Issues:
+In case of any issue (for example the program hangs), please report it into the [/ont-converter/issues](https://github.com/sszuev/ont-converter/issues) page, but only if you really sure that the problem is in the program, not in the underlying API. Otherwise please refer to the [/ont-api/issues](https://github.com/avicomp/ont-api/issues) page.
+
  ### Dependencies:
- [ONT-API](https://github.com/avicomp/ont-api) (__version 1.1.0-SNAPSHOT__)
+ [ONT-API](https://github.com/avicomp/ont-api) (__version 1.4.0-SNAPSHOT__)
diff --git a/pom.xml b/pom.xml
@@ -13,6 +13,10 @@
         <maven.compiler.source>1.8</maven.compiler.source>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <skipTests>true</skipTests>
+        <version.ontapi>1.4.0-SNAPSHOT</version.ontapi>
+        <version.jena>3.8.0</version.jena>
+        <version.owlapi>5.1.7</version.owlapi>
+        <version.slf4j>1.7.25</version.slf4j>
     </properties>
 
     <repositories>
@@ -32,27 +36,27 @@
         <dependency>
             <groupId>ru.avicomp</groupId>
             <artifactId>ontapi</artifactId>
-            <version>1.1.0-SNAPSHOT</version>
+            <version>${version.ontapi}</version>
         </dependency>
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-csv</artifactId>
-            <version>3.6.0</version>
+            <version>${version.jena}</version>
         </dependency>
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-parsers</artifactId>
-            <version>5.1.4</version>
+            <version>${version.owlapi}</version>
         </dependency>
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-rio</artifactId>
-            <version>5.1.4</version>
+            <version>${version.owlapi}</version>
         </dependency>
         <dependency>
             <groupId>net.sourceforge.owlapi</groupId>
             <artifactId>owlapi-oboformat</artifactId>
-            <version>5.1.4</version>
+            <version>${version.owlapi}</version>
         </dependency>
         <dependency>
             <groupId>org.topbraid</groupId>
@@ -69,10 +73,15 @@
             <artifactId>commons-lang</artifactId>
             <version>2.6</version>
         </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+            <version>${version.slf4j}</version>
+        </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-log4j12</artifactId>
-            <version>1.7.22</version>
+            <version>${version.slf4j}</version>
         </dependency>
     </dependencies>
 

diff --git a/src/main/java/com/github/sszuev/Args.java b/src/main/java/com/github/sszuev/Args.java
@@ -5,9 +5,8 @@
 import org.apache.commons.lang.ArrayUtils;
 import org.apache.commons.lang3.StringUtils;
 import ru.avicomp.ontapi.OntFormat;
-import ru.avicomp.ontapi.jena.impl.configuration.Configurable;
-import ru.avicomp.ontapi.jena.impl.configuration.OntModelConfig;
-import ru.avicomp.ontapi.jena.impl.configuration.OntPersonality;
+import ru.avicomp.ontapi.jena.impl.conf.OntModelConfig;
+import ru.avicomp.ontapi.jena.impl.conf.OntPersonality;
 
 import java.io.IOException;
 import java.io.PrintWriter;
@@ -32,12 +31,20 @@ public class Args {
     private static final int READ_WRITE_COL_LENGTH = 13;
     private final Path input, output;
     private final OntFormat outFormat, inFormat;
-    private final Configurable.Mode personality;
+    private final OntModelConfig.StdMode personality;
     private final boolean spin, force, refine, verbose, webAccess;
     private boolean outDir, inDir;
 
-    private Args(Path input, Path output, OntFormat outFormat, OntFormat inFormat, Configurable.Mode personality,
-                 boolean spin, boolean force, boolean clear, boolean verbose, boolean webAccess) {
+    private Args(Path input,
+                 Path output,
+                 OntFormat outFormat,
+                 OntFormat inFormat,
+                 OntModelConfig.StdMode personality,
+                 boolean spin,
+                 boolean force,
+                 boolean clear,
+                 boolean verbose,
+                 boolean webAccess) {
         this.input = input;
         this.output = output;
         this.outFormat = outFormat;
@@ -67,7 +74,7 @@ public static Args parse(String... args) throws IOException, IllegalArgumentExce
         // parse
         OntFormat outputFormat = parseOutputFormat(cmd);
         OntFormat inputFormat = parseInputFormat(cmd);
-        Configurable.Mode mode = parsePersonalities(cmd);
+        OntModelConfig.StdMode mode = parsePersonalities(cmd);
 
         Path in = Paths.get(cmd.getOptionValue(Opts.INPUT.longName)).toRealPath();
         Path out = Paths.get(cmd.getOptionValue(Opts.OUTPUT.longName));
@@ -111,13 +118,14 @@ private static OntFormat parseOutputFormat(CommandLine cmd) {
         return res;
     }
 
-    private static Configurable.Mode parsePersonalities(CommandLine cmd) {
+    private static OntModelConfig.StdMode parsePersonalities(CommandLine cmd) {
         if (!cmd.hasOption(Opts.PUNNING.longName)) {
-            return Configurable.Mode.LAX;
+            return OntModelConfig.StdMode.LAX;
         }
         String val = cmd.getOptionValue(Opts.PUNNING.longName);
+        OntModelConfig.StdMode[] values = OntModelConfig.StdMode.values();
         try {
-            return Configurable.Mode.values()[Configurable.Mode.values().length - Integer.parseInt(val)];
+            return values[values.length - Integer.parseInt(val)];
         } catch (NumberFormatException | IndexOutOfBoundsException e) {
             throw new IllegalArgumentException("Wrong --" + Opts.PUNNING.longName + ":" + val, e);
         }
@@ -129,7 +137,8 @@ private static String help(Options opts, boolean usage) {
             sb.append("A simple command-line utility to convert any rdf graph to OWL2-DL ontology.").append("\n");
         }
         StringWriter sw = new StringWriter();
-        new HelpFormatter().printHelp(new PrintWriter(sw), 74, "java -jar " + JAR_NAME, "options:", opts, 1, 3, null, true);
+        new HelpFormatter().printHelp(new PrintWriter(sw), 74, "java -jar " + JAR_NAME,
+                "options:", opts, 1, 3, null, true);
         sb.append(sw);
         if (usage) {
             sb.append("Full list of supported formats:").append("\n");

diff --git a/src/main/java/com/github/sszuev/Main.java b/src/main/java/com/github/sszuev/Main.java
@@ -103,7 +103,9 @@ private static void processDir(Args args) throws IOException, OntApiException {
         }
     }
 
-    private static OWLOntologyID load(OntologyManager manager, OWLOntologyDocumentSource source, boolean ignoreErrors) throws OntApiException {
+    private static OWLOntologyID load(OntologyManager manager,
+                                      OWLOntologyDocumentSource source,
+                                      boolean ignoreErrors) throws OntApiException {
         try {
             OWLOntology o = Managers.loadOntology(manager, source);
             return o.getOntologyID();

diff --git a/src/main/java/com/github/sszuev/spin/SpinTransform.java b/src/main/java/com/github/sszuev/spin/SpinTransform.java
@@ -88,7 +88,7 @@ public void perform() {
                     .map(Statement::getObject)
                     .filter(RDFNode::isURIResource)
                     .map(RDFNode::asResource)
-                    .findFirst().orElseThrow(OntJenaException.supplier("No type for " + literal));
+                    .findFirst().orElseThrow(() -> new OntJenaException("No type for " + literal));
             Set<Statement> remove = Models.getAssociatedStatements(query);
             remove.stream()
                     .filter(s -> !(RDF.type.equals(s.getPredicate()) && type.equals(s.getObject())))

diff --git a/src/main/java/com/github/sszuev/utils/Formats.java b/src/main/java/com/github/sszuev/utils/Formats.java
@@ -1,24 +1,23 @@
 package com.github.sszuev.utils;
 
-import java.util.List;
-import java.util.Objects;
-import java.util.Optional;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
 import org.apache.jena.lang.csv.ReaderRIOTFactoryCSV;
 import org.apache.jena.riot.Lang;
 import org.apache.jena.riot.RDFParserRegistry;
 import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLDocumentFormat;
 import org.semanticweb.owlapi.model.OWLOntology;
-
 import ru.avicomp.ontapi.OntFormat;
 
+import java.util.List;
+import java.util.Objects;
+import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
 /**
  * Utils to work with {@link OntFormat format}s.
- *
+ * <p>
  * Created by @szuev on 11.01.2018.
  */
 @SuppressWarnings("WeakerAccess")
@@ -40,6 +39,7 @@ public static OntFormat find(String key) {
 
     /**
      * Returns format aliases
+     *
      * @param f {@link OntFormat}, not null
      * @return List of stings corresponding specified format.
      */
@@ -52,6 +52,7 @@ public static List<String> aliases(OntFormat f) {
     /**
      * Registers {@link Lang#CSV} in jena system.
      * This operation enables {@link OntFormat#CSV} for reading operations.
+     *
      * @see #unregisterJenaCSV()
      */
     public static void registerJenaCSV() {
@@ -61,6 +62,7 @@ public static void registerJenaCSV() {
 
     /**
      * unregisters csv format
+     *
      * @see #registerJenaCSV()
      */
     public static void unregisterJenaCSV() {
@@ -69,6 +71,7 @@ public static void unregisterJenaCSV() {
 
     /**
      * Determines is the specified resource can be treated as csv-file.
+     *
      * @param iri {@link IRI}
      * @return true if the resource has extension '.csv'
      */

diff --git a/src/main/java/com/github/sszuev/utils/IRIs.java b/src/main/java/com/github/sszuev/utils/IRIs.java
@@ -1,5 +1,14 @@
 package com.github.sszuev.utils;
 
+import org.apache.commons.io.FilenameUtils;
+import org.semanticweb.owlapi.io.FileDocumentSource;
+import org.semanticweb.owlapi.io.IRIDocumentSource;
+import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyID;
+import ru.avicomp.ontapi.OntFormat;
+
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.Path;
@@ -11,19 +20,9 @@
 import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
-import org.apache.commons.io.FilenameUtils;
-import org.semanticweb.owlapi.io.FileDocumentSource;
-import org.semanticweb.owlapi.io.IRIDocumentSource;
-import org.semanticweb.owlapi.io.OWLOntologyDocumentSource;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyID;
-
-import ru.avicomp.ontapi.OntFormat;
-
 /**
  * The helper to work with {@link IRI}s, usually related to local files.
- *
+ * <p>
  * Created by @szuev on 15.01.2018.
  */
 public class IRIs {
@@ -41,6 +40,7 @@ public static boolean hasExtension(String extension, IRI iri) {
 
     /**
      * Returns all files from a directory, most deep go first, empty files are excluded
+     *
      * @param dir {@link Path}, the directory (but can be file also)
      * @return List of {@link IRI}s
      * @throws IOException if any i/o error occurs.
@@ -52,7 +52,8 @@ public static List<IRI> getFiles(Path dir) throws IOException {
 
     /**
      * Walks through directory, the output stream are sorted in descending order of file depth
-     * @param dir {@link Path}
+     *
+     * @param dir    {@link Path}
      * @param holder {@link IOException} to collect any internal (file-specified) exceptions
      * @return Stream of {@link IRI}s
      * @throws IOException if i/o error occurs when read directory
@@ -85,8 +86,9 @@ public static Stream<IRI> walk(Path dir, IOException holder) throws IOException
 
     /**
      * Creates a document-source from iri and format
+     *
      * @param document {@link IRI}, not null
-     * @param format {@link OntFormat}, nullable
+     * @param format   {@link OntFormat}, nullable
      * @return {@link OWLOntologyDocumentSource}
      */
     public static OWLOntologyDocumentSource toSource(IRI document, OntFormat format) {