Add infer command

build.gradle

@@ -60,11 +60,13 @@ task jacocoRootReport(type: JacocoReport, group: 'Coverage reports') {
         "${projectDir}/cli/build/classes/java/main",
         "${projectDir}/diagram/build/classes/java/main",
         "${projectDir}/write/build/classes/java/main",
+        "${projectDir}/infer/build/classes/java/main",
     ]
     sourceDirectories.from = [
         "${projectDir}/cli/src/main/java",
         "${projectDir}/diagram/src/main/java",
         "${projectDir}/write/src/main/java",
+        "${projectDir}/infer/src/main/java",
     ]
 
     executionData fileTree(project.rootDir.absolutePath).include("**/build/jacoco/*.exec")
@@ -79,6 +81,7 @@ task jacocoRootReport(type: JacocoReport, group: 'Coverage reports') {
     dependsOn ':cli:test'
     dependsOn ':diagram:test'
     dependsOn ':write:test'
+    dependsOn ':infer:test'
 }
 
 defaultTasks 'test', 'shadowJar'

cli/build.gradle

@@ -37,6 +37,7 @@ apply from: file("${rootDir}/dependencies.gradle")
 dependencies {
     implementation project(':diagram')
     implementation project(':write')
+    implementation project(':infer')
     implementation(deps.owlapi) {
         exclude group: 'org.slf4j', module: 'slf4j-simple'
     }

cli/src/main/java/de/atextor/owlcli/OWLCLI.java

@@ -80,7 +80,11 @@ private static void printError( final CommandLine commandLine, final Exception e
 
     public static void main( final String[] args ) {
         LogManager.getLogManager().reset();
-        final List<AbstractCommand> commands = List.of( new OWLCLIDiagramCommand(), new OWLCLIWriteCommand() );
+        final List<AbstractCommand> commands = List.of(
+            new OWLCLIDiagramCommand(),
+            new OWLCLIWriteCommand(),
+            new OWLCLIInferCommand()
+        );
         final CommandLine cmd = commands.foldLeft( new OWLCLI().commandLine, CommandLine::addSubcommand )
             .setParameterExceptionHandler( PARAMETER_EXCEPTION_HANDLER )
             .setExecutionExceptionHandler( EXECUTION_EXCEPTION_HANDLER )

cli/src/main/java/de/atextor/owlcli/OWLCLIInferCommand.java

@@ -0,0 +1,91 @@
+/*
+ * Copyright 2021 Andreas Textor
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package de.atextor.owlcli;
+
+import de.atextor.owlcli.infer.Configuration;
+import de.atextor.owlcli.infer.Inferrer;
+import de.atextor.turtle.formatter.FormattingStyle;
+import org.apache.jena.rdf.model.Property;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.ResourceFactory;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import picocli.CommandLine;
+
+import java.net.MalformedURLException;
+import java.net.URI;
+import java.net.URL;
+import java.text.DecimalFormat;
+import java.text.NumberFormat;
+import java.util.Map;
+import java.util.Set;
+import java.util.function.BiFunction;
+import java.util.stream.Collectors;
+
+@CommandLine.Command( name = "infer",
+    description = "Runs an OWL reasoner on an ontology",
+    descriptionHeading = "%n@|bold Description|@:%n%n",
+    parameterListHeading = "%n@|bold Parameters|@:%n",
+    optionListHeading = "%n@|bold Options|@:%n",
+    footer = "%nSee the online documentation for details:%n" +
+        "https://atextor.de/owl-cli/main/" + OWLCLIConfig.VERSION + "/usage.html#infer-command"
+)
+public class OWLCLIInferCommand extends AbstractCommand implements Runnable {
+    private static final Logger LOG = LoggerFactory.getLogger( OWLCLIInferCommand.class );
+
+    private static final Configuration config = Inferrer.DEFAULT_CONFIGURATION;
+
+    @CommandLine.Mixin
+    LoggingMixin loggingMixin;
+
+    @CommandLine.Parameters( paramLabel = "INPUT", description = "File name, URL, or - for stdin", arity = "1",
+        index = "0" )
+    private String input;
+
+    @CommandLine.Parameters( paramLabel = "OUTPUT",
+        description = "File name or - for stdout. If left out, output is written to stdout.",
+        arity = "0..1", index = "1" )
+    private String output;
+
+    @Override
+    public void run() {
+        final Configuration.ConfigurationBuilder configurationBuilder = Configuration.builder();
+
+        final Inferrer inferrer = new Inferrer();
+
+        if ( input.toLowerCase().startsWith( "http:" ) || input.toLowerCase().startsWith( "https:" ) ) {
+            final Configuration configuration = configurationBuilder.build();
+            try {
+                final URL inputUrl = new URL( input );
+                openOutput( input, output != null ? output : "-", "ttl" )
+                    .map( outputStream -> inferrer.infer( inputUrl, outputStream, configuration ) )
+                    .onFailure( throwable -> exitWithErrorMessage( LOG, loggingMixin, throwable ) );
+                return;
+            } catch ( final MalformedURLException exception ) {
+                exitWithErrorMessage( LOG, loggingMixin, exception );
+            }
+        }
+
+        openInput( input ).flatMap( inputStream -> {
+                final Configuration configuration = configurationBuilder.build();
+                return openOutput( input, output != null ? output : "-", "ttl" )
+                    .flatMap( outputStream -> inferrer.infer( inputStream, outputStream, configuration ) );
+            }
+        ).onFailure( throwable -> exitWithErrorMessage( LOG, loggingMixin, throwable ) );
+    }
+}

infer/build.gradle

@@ -0,0 +1,63 @@
+/*
+ * Copyright 2021 Andreas Textor
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+plugins {
+    id 'java'
+    id 'jacoco'
+    id 'io.freefair.lombok'
+    id 'com.adarshr.test-logger'
+}
+
+repositories {
+    maven { url 'https://jitpack.io' }
+}
+
+apply from: file("${rootDir}/dependencies.gradle")
+dependencies {
+    implementation(deps.jena)
+    implementation(deps.jena_core)
+    implementation(deps.slf4j_api)
+    implementation(deps.turtle_formatter)
+    implementation(deps.vavr)
+
+    // Test
+    testImplementation(deps.junit_jupiter_api)
+    testImplementation(deps.assertj)
+    testImplementation(deps.jqwik)
+    testRuntimeOnly(deps.junit_jupiter_engine)
+}
+
+compileJava {
+    sourceCompatibility = 17
+    targetCompatibility = 17
+}
+
+compileTestJava {
+    sourceCompatibility = 17
+    targetCompatibility = 17
+}
+
+test {
+    useJUnitPlatform()
+    maxHeapSize = '1G'
+    ignoreFailures = false
+    failFast = true
+
+    filter {
+        includeTestsMatching "*Test"
+    }
+}
+

infer/src/main/java/de/atextor/owlcli/infer/Configuration.java

@@ -0,0 +1,25 @@
+/*
+ * Copyright 2021 Andreas Textor
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package de.atextor.owlcli.infer;
+
+import lombok.Builder;
+
+@Builder
+public class Configuration {
+    @Builder.Default
+    public boolean test = true;
+}

infer/src/main/java/de/atextor/owlcli/infer/Inferrer.java

@@ -0,0 +1,61 @@
+/*
+ * Copyright 2021 Andreas Textor
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package de.atextor.owlcli.infer;
+
+import io.vavr.control.Try;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import java.io.ByteArrayInputStream;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.net.HttpURLConnection;
+import java.net.URL;
+import java.net.http.HttpClient;
+import java.net.http.HttpRequest;
+import java.net.http.HttpResponse;
+
+public class Inferrer {
+    public static final Configuration DEFAULT_CONFIGURATION = Configuration.builder().build();
+
+    private static final Logger LOG = LoggerFactory.getLogger( Inferrer.class );
+
+    public Try<Void> infer( final URL inputUrl, final OutputStream output, final Configuration configuration ) {
+        try {
+            final HttpClient client = HttpClient.newBuilder()
+                .followRedirects( HttpClient.Redirect.ALWAYS )
+                .build();
+            final HttpRequest request = HttpRequest.newBuilder()
+                .uri( inputUrl.toURI() )
+                .build();
+            final HttpResponse<String> response = client.send( request, HttpResponse.BodyHandlers.ofString() );
+            if ( response.statusCode() == HttpURLConnection.HTTP_OK ) {
+                final ByteArrayInputStream inputStream = new ByteArrayInputStream( response.body().getBytes() );
+                return infer( inputStream, output, configuration );
+            }
+            return Try.failure( new RuntimeException( "Got unexpected HTTP response: " + response.statusCode() ) );
+        } catch ( final Exception exception ) {
+            LOG.debug( "Failure during reading from URL: {}", inputUrl );
+            return Try.failure( exception );
+        }
+    }
+
+    public Try<Void> infer( final InputStream input, final OutputStream output, final Configuration configuration ) {
+        return Try.success( null );
+    }
+}

infer/src/test/java/de/atextor/owlcli/infer/InferrerTest.java

@@ -0,0 +1,28 @@
+/*
+ * Copyright 2021 Andreas Textor
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package de.atextor.owlcli.infer;
+
+import org.junit.jupiter.api.Test;
+
+public class InferrerTest {
+    private final Inferrer writer = new Inferrer();
+
+    @Test
+    public void testFoo() {
+
+    }
+}

settings.gradle

@@ -17,5 +17,6 @@
 rootProject.name = 'owl-cli'
 include ':diagram'
 include ':write'
+include ':infer'
 include ':cli'
 include ':docs'