Merge pull request #201 from Wimmics/development

Merge development changes to doc_development

Author: AnnaBobasheva

.github/workflows/sphinx.yml

@@ -9,10 +9,10 @@ jobs:
       contents: write
     steps:
 
-    - name: Checkout doc_development branch
+    - name: Checkout development branch
       uses: actions/checkout@v4
       with:
-        ref: doc_development
+        ref: development
 
     - name: Build Sphinx Docs
       uses: ammaraskar/sphinx-action@master
@@ -29,7 +29,7 @@ jobs:
 
     - name: Deploy
       uses: peaceiris/actions-gh-pages@v3
-      if: github.ref == 'refs/heads/doc_development'
+      if: github.ref == 'refs/heads/development'
       with:
         github_token: ${{ secrets.GITHUB_TOKEN }}
         publish_dir: docs/build/html

corese-command/pom.xml

@@ -16,29 +16,46 @@
 
   <dependencies>
 
-    <dependency>
-      <groupId>junit</groupId>
-      <artifactId>junit</artifactId>
-      <version>4.13.2</version>
-      <scope>test</scope>
-    </dependency>
-
+    <!-- CLI Interface -->
     <dependency>
       <groupId>info.picocli</groupId>
       <artifactId>picocli</artifactId>
-      <version>4.7.4</version>
+      <version>4.7.6</version>
     </dependency>
 
+    <!-- Corese -->
     <dependency>
       <groupId>${project.parent.groupId}</groupId>
       <artifactId>corese-core</artifactId>
     </dependency>
 
+    <!-- Unit Test -->
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-api</artifactId>
+      <version>5.11.0-M1</version>
+      <scope>test</scope>
+    </dependency>
     <dependency>
-      <groupId>jakarta.activation</groupId>
-      <artifactId>jakarta.activation-api</artifactId>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter-engine</artifactId>
+      <version>5.11.0-M1</version>
+      <scope>test</scope>
     </dependency>
 
+    <!-- Mock HTTPS Server for Test -->
+    <dependency>
+      <groupId>org.wiremock</groupId>
+      <artifactId>wiremock</artifactId>
+      <version>3.8.0</version>
+      <scope>test</scope>
+    </dependency>
+    <dependency>
+      <groupId>org.assertj</groupId>
+      <artifactId>assertj-core</artifactId>
+      <version>3.26.3</version>
+      <scope>test</scope>
+    </dependency>
 
   </dependencies>
 

corese-command/src/main/java/fr/inria/corese/command/App.java

@@ -1,23 +1,44 @@
 package fr.inria.corese.command;
 
-import fr.inria.corese.command.programs.canonicalize;
+import fr.inria.corese.command.programs.Canonicalize;
 import fr.inria.corese.command.programs.Convert;
 import fr.inria.corese.command.programs.RemoteSparql;
 import fr.inria.corese.command.programs.Shacl;
 import fr.inria.corese.command.programs.Sparql;
+import picocli.AutoComplete.GenerateCompletion;
 import picocli.CommandLine;
 import picocli.CommandLine.Command;
+import picocli.CommandLine.Help.Ansi.Style;
+import picocli.CommandLine.Help.ColorScheme;
 
 @Command(name = "Corese-command", version = App.version, mixinStandardHelpOptions = true, subcommands = {
-        Convert.class, Sparql.class, Shacl.class, RemoteSparql.class, canonicalize.class
+        Convert.class, Sparql.class, Shacl.class, RemoteSparql.class, Canonicalize.class, GenerateCompletion.class
 })
 
 public final class App implements Runnable {
 
     public final static String version = "4.5.1";
 
     public static void main(String[] args) {
-        int exitCode = new CommandLine(new App()).execute(args);
+        // Define the color scheme
+        ColorScheme colorScheme = new ColorScheme.Builder()
+                .commands(Style.bold) // Commands in blue
+                .options(Style.fg_yellow) // Options in yellow
+                .parameters(Style.fg_cyan, Style.bold) // Parameters in cyan and bold
+                .optionParams(Style.italic, Style.fg_cyan) // Option parameters in italic
+                .errors(Style.fg_red, Style.bold) // Errors in red and bold
+                .stackTraces(Style.italic) // Stack traces in italic
+                .applySystemProperties() // Apply system properties for colors
+                .build();
+
+        CommandLine commandLine = new CommandLine(new App()).setColorScheme(colorScheme);
+
+        // Hide the generate-completion command
+        CommandLine gen = commandLine.getSubcommands().get("generate-completion");
+        gen.getCommandSpec().usageMessage().hidden(true);
+
+        // Execute the command
+        int exitCode = commandLine.execute(args);
         System.exit(exitCode);
     }
 

corese-command/src/main/java/fr/inria/corese/command/programs/AbstractCommand.java

@@ -0,0 +1,85 @@
+package fr.inria.corese.command.programs;
+
+import java.nio.file.Path;
+import java.util.Optional;
+import java.util.concurrent.Callable;
+
+import fr.inria.corese.command.App;
+import fr.inria.corese.command.utils.ConfigManager;
+import fr.inria.corese.command.utils.exporter.rdf.RdfDataExporter;
+import fr.inria.corese.core.util.Property;
+import fr.inria.corese.core.util.Property.Value;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Model.CommandSpec;
+import picocli.CommandLine.Option;
+import picocli.CommandLine.Spec;
+
+/**
+ * Abstract class for all commands.
+ * 
+ * This class provides common options and methods for all commands.
+ */
+@Command(version = App.version)
+public abstract class AbstractCommand implements Callable<Integer> {
+
+    ///////////////
+    // Constants //
+    ///////////////
+
+    // Exit codes
+    protected final int ERROR_EXIT_CODE_SUCCESS = 0;
+    protected final int ERROR_EXIT_CODE_ERROR = 1;
+
+    /////////////
+    // Options //
+    /////////////
+
+    @Option(names = { "-o",
+            "--output-data" }, description = "Specifies the output file path. If not provided, the result will be written to standard output.", arity = "0..1", fallbackValue = RdfDataExporter.DEFAULT_OUTPUT)
+    protected Path output;
+
+    @Option(names = { "-c", "--config",
+            "--init" }, description = "Specifies the path to a configuration file. If not provided, the default configuration file will be used.", required = false)
+    private Path configFilePath;
+
+    @Option(names = { "-v",
+            "--verbose" }, description = "Enables verbose mode, printing more information about the execution of the command.", negatable = true)
+    protected boolean verbose = false;
+
+    @Option(names = { "-w",
+            "--owl-import" }, description = "Disables the automatic importation of ontologies specified in 'owl:imports' statements. When this flag is set, the application will not fetch and include referenced ontologies. Default is '${DEFAULT-VALUE}'.", required = false, defaultValue = "false", negatable = true)
+    private boolean noOwlImport;
+
+    ////////////////
+    // Properties //
+    ////////////////
+
+    // Command specification
+    @Spec
+    protected CommandSpec spec;
+
+    // Output
+    protected Boolean outputToFileIsDefault = false;
+
+    /////////////
+    // Methods //
+    /////////////
+
+    @Override
+    public Integer call() {
+
+        // Load configuration file
+        Optional<Path> configFilePath = Optional.ofNullable(this.configFilePath);
+        if (configFilePath.isPresent()) {
+            ConfigManager.loadFromFile(configFilePath.get(), this.spec, this.verbose);
+        } else {
+            ConfigManager.loadDefaultConfig(this.spec, this.verbose);
+        }
+
+        // Set owl import
+        Property.set(Value.DISABLE_OWL_AUTO_IMPORT, this.noOwlImport);
+
+        return 0;
+    }
+
+}

corese-command/src/main/java/fr/inria/corese/command/programs/AbstractInputCommand.java

@@ -0,0 +1,42 @@
+package fr.inria.corese.command.programs;
+
+import java.nio.file.Path;
+
+import picocli.CommandLine.Option;
+
+public abstract class AbstractInputCommand extends AbstractCommand {
+
+    @Option(names = { "-i",
+            "--input-data" }, description = "Specifies the path or URL of the input RDF data. Multiple values are allowed.", arity = "1...")
+    protected String[] inputsRdfData;
+
+    @Option(names = { "-R",
+            "--recursive" }, description = "If set to true and an input is a directory, all files in the directory will be loaded recursively. Default value: ${DEFAULT-VALUE}.", defaultValue = "false")
+    protected boolean recursive = false;
+
+    @Override
+    public Integer call() {
+        super.call();
+
+        // Check input values
+        this.checkInputValues();
+
+        return 0;
+    }
+
+    /**
+     * Check if the input values are correct.
+     *
+     * @throws IllegalArgumentException if input path is same as output path.
+     */
+    private void checkInputValues() throws IllegalArgumentException {
+        if (this.inputsRdfData != null && this.output != null) {
+            for (String input : this.inputsRdfData) {
+                if (Path.of(input).compareTo(this.output) == 0) {
+                    throw new IllegalArgumentException("Input path cannot be same as output path: " + input);
+                }
+            }
+        }
+    }
+
+}

corese-command/src/main/java/fr/inria/corese/command/programs/Canonicalize.java

@@ -0,0 +1,46 @@
+package fr.inria.corese.command.programs;
+
+import fr.inria.corese.command.utils.exporter.rdf.EnumCanonicAlgo;
+import fr.inria.corese.command.utils.exporter.rdf.RdfDataCanonicalizer;
+import fr.inria.corese.command.utils.loader.rdf.EnumRdfInputFormat;
+import fr.inria.corese.command.utils.loader.rdf.RdfDataLoader;
+import fr.inria.corese.core.Graph;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Option;
+
+@Command(name = "canonicalize", description = "Canonicalize an RDF file to a specific format.", mixinStandardHelpOptions = true)
+public class Canonicalize extends AbstractInputCommand {
+
+    @Option(names = { "-f", "-if",
+            "--input-format" }, description = "Specifies the RDF serialization format of the input file. Available options are: :@|fg(225) ${COMPLETION-CANDIDATES}|@.")
+    private EnumRdfInputFormat inputFormat;
+
+    @Option(names = { "-a", "-ca", "-r", "-of",
+            "--canonical-algo" }, required = true, description = "Specifies the canonicalization algorithm to be applied to the input file. Available options are: :@|fg(225) ${COMPLETION-CANDIDATES}|@. The default algorithm is ${DEFAULT-VALUE}.", defaultValue = "rdfc-1.0")
+    private EnumCanonicAlgo canonicalAlgo;
+
+    public Canonicalize() {
+    }
+
+    @Override
+    public Integer call() {
+
+        super.call();
+
+        try {
+            // Load the input file(s)
+            RdfDataLoader loader = new RdfDataLoader(this.spec, this.verbose);
+            Graph graph = loader.load(this.inputsRdfData, this.inputFormat, this.recursive);
+
+            // Canonicalize and export the graph
+            RdfDataCanonicalizer rdfCanonicalizer = new RdfDataCanonicalizer(this.spec, this.verbose, this.output);
+            rdfCanonicalizer.export(graph, this.canonicalAlgo);
+
+            return this.ERROR_EXIT_CODE_SUCCESS;
+        } catch (IllegalArgumentException e) {
+            this.spec.commandLine().getErr().println("Error: " + e.getMessage());
+            return this.ERROR_EXIT_CODE_ERROR;
+        }
+    }
+
+}