maven plugin for RDF ontology to SQL translation

histream-maven-plugin/.gitignore

+.settings/
+.classpath
+.project
+target/

histream-maven-plugin/pom.xml

+<project>
+	<modelVersion>4.0.0</modelVersion>
+
+	<groupId>de.sekmi.histream.maven</groupId>
+	<artifactId>histream-maven-plugin</artifactId>
+	<version>0.9-SNAPSHOT</version>
+	<packaging>maven-plugin</packaging>
+
+	<name>HIStream maven plugin</name>
+
+	<build>
+		<plugins>
+		<!-- use new plugin plugin. default 3.2 will not work with java 8 -->
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-plugin-plugin</artifactId>
+				<version>3.4</version>
+			</plugin>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.5.1</version>
+				<configuration>
+					<source>1.8</source>
+					<target>1.8</target>
+				</configuration>
+			</plugin>
+
+		</plugins>
+	</build>
+	<dependencies>
+		<!-- functional dependencies -->
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-i2b2</artifactId>
+			<version>0.9-SNAPSHOT</version>
+		</dependency>
+		<dependency>
+			<groupId>de.sekmi.histream</groupId>
+			<artifactId>histream-skos</artifactId>
+			<version>0.9-SNAPSHOT</version>
+		</dependency>
+
+		<!-- maven plugin dependencies -->
+		<dependency>
+			<groupId>org.apache.maven</groupId>
+			<artifactId>maven-plugin-api</artifactId>
+			<version>3.3.9</version>
+		</dependency>
+		<!-- https://mvnrepository.com/artifact/org.apache.maven.shared/file-management -->
+		<dependency>
+		    <groupId>org.apache.maven.shared</groupId>
+		    <artifactId>file-management</artifactId>
+		    <version>3.0.0</version>
+		</dependency>
+
+		<!-- dependencies to annotations -->
+		<dependency>
+			<groupId>org.apache.maven.plugin-tools</groupId>
+			<artifactId>maven-plugin-annotations</artifactId>
+			<version>3.4</version>
+			<scope>provided</scope>
+		</dependency>
+
+		<!-- testing -->
+		<dependency>
+			<groupId>junit</groupId>
+			<artifactId>junit</artifactId>
+			<version>4.12</version>
+			<scope>test</scope>
+		</dependency>
+	</dependencies>
+</project>

histream-maven-plugin/src/main/java/de/sekmi/histream/maven/OntologyMojo.java

+package de.sekmi.histream.maven;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Locale;
+import java.util.Map;
+import java.util.Objects;
+import java.util.Properties;
+
+import org.apache.maven.plugin.AbstractMojo;
+import org.apache.maven.plugin.MojoExecutionException;
+import org.apache.maven.plugin.MojoFailureException;
+import org.apache.maven.plugins.annotations.Mojo;
+import org.apache.maven.plugins.annotations.Parameter;
+import org.apache.maven.project.MavenProject;
+import org.apache.maven.shared.model.fileset.FileSet;
+import org.apache.maven.shared.model.fileset.util.FileSetManager;
+import org.openrdf.repository.RepositoryException;
+
+import de.sekmi.histream.i2b2.ont.SQLGenerator;
+import de.sekmi.histream.ontology.OntologyException;
+import de.sekmi.histream.ontology.skos.Store;
+
+@Mojo(name="ontology")
+public class OntologyMojo extends AbstractMojo {	
+	@Parameter(required=true)
+	FileSet source;
+
+	/**
+	 * Destination for the generated resources. 
+	 * Defaults to {@code ${project.build.directory}/generated-resources/sql/}
+	 */
+	@Parameter(required=false, defaultValue="${project.build.directory}/generated-resources/sql")
+	File destination;
+	
+	/**
+	 * Overwrite existing files in the destination
+	 */
+	@Parameter
+	boolean overwrite;
+
+	@Parameter
+	Properties properties;
+
+	@Parameter(defaultValue="${project}", readonly=true, required=true)
+	MavenProject project;
+
+	private void logWarning(String message){
+		getLog().warn(message);
+	}
+	private List<File> getSourceFiles(){
+		// read source files
+		Objects.requireNonNull(source);
+		FileSetManager fsm = new FileSetManager();
+		String[] files = fsm.getIncludedFiles(source);
+		String base = source.getDirectory();
+		List<File> list = new ArrayList<>(files.length);
+		for( int i=0; i<files.length; i++ ){
+			list.add(new File(base, files[i]));
+		}
+		return list;
+	}
+	private Map<String,String> loadConfiguration(){
+		Map<String,String> map = new HashMap<>();
+		if( properties != null ){
+			for( String name : properties.stringPropertyNames() ){
+				map.put(name, properties.getProperty(name));
+			}
+		}
+		if( !map.containsKey("meta.sourcesystem_cd") ){
+			// use artifact id
+			this.getLog().warn("Using project artifact id for missing property meta.sourcesystem_cd");
+			map.put("meta.sourcesystem_cd", project.getArtifactId());
+		}
+		// language
+		if( !map.containsKey("ont.language") ){
+			this.getLog().warn("Using system default language for missing property ont.language: "+Locale.getDefault().getLanguage());
+			map.put("ont.language", Locale.getDefault().getLanguage());
+		}
+		// TODO use defaults for missing properties meta.table, etc
+		return map;
+	}
+	@Override
+	public void execute() throws MojoExecutionException, MojoFailureException {
+		// copy properties to string map
+		Map<String,String> map = loadConfiguration();
+		// create destination directories if not existing
+		try {
+			Files.createDirectories(destination.toPath());
+		} catch (IOException e) {
+			throw new MojoExecutionException("Unable to create destination directory: "+destination, e);
+		}
+		Path metaSQL = new File(destination, "meta.sql").toPath();
+		Path dataSQL = new File(destination, "data.sql").toPath();
+
+		// load ontology
+		Store store;
+		try {
+			store = new Store(getSourceFiles(), null);
+		} catch (RepositoryException | IOException e) {
+			throw new MojoExecutionException("Unable to load ontology", e);
+		}
+		
+		try {
+			SQLGenerator gen = new SQLGenerator(metaSQL, dataSQL, map, overwrite);
+			gen.setWarningHandler(this::logWarning);
+			gen.writeOntologySQL(store);
+			gen.close();
+			store.close();
+		} catch (IOException | SQLException | OntologyException e) {
+			throw new MojoExecutionException("Ontology to SQL transformation failed", e);
+		}
+	}
+
+}

histream-maven-plugin/src/test/java/de/sekmi/histream/maven/TestOntologyMojo.java

+package de.sekmi.histream.maven;
+
+import java.io.File;
+import java.io.InputStream;
+import java.net.URL;
+import java.util.Collections;
+import java.util.Properties;
+
+import org.apache.maven.shared.model.fileset.FileSet;
+import org.junit.Assert;
+import org.junit.Test;
+
+public class TestOntologyMojo {
+
+	@Test
+	public void expectSuccessfulExecution() throws Exception{
+		URL ttl = getClass().getResource("/skos-aktin-cda.ttl");
+		File source = new File(ttl.toURI());
+		Assert.assertTrue(source.isFile());
+		OntologyMojo mojo = new OntologyMojo();
+		mojo.source = new FileSet();
+		mojo.source.setDirectory(source.getParent());
+		mojo.source.addInclude(source.getName());
+		mojo.destination = new File("target/");
+		mojo.properties = new Properties();
+		mojo.overwrite = true;
+		try( InputStream in = getClass().getResourceAsStream("/ontology.properties") ){
+			mojo.properties.load(in);			
+		}
+				
+		mojo.execute();
+	}
+}

histream-maven-plugin/src/test/resources/ontology.properties

+# metadata table
+meta.table=i2b2metadata.i2b2
+# metadata table access
+meta.access=i2b2metadata.table_access
+meta.basepath=\\i2b2\\
+# Before each import, data for this sourcesystem_cd will be deleted
+meta.sourcesystem_cd=test
+
+data.concept.table=i2b2demodata.concept_dimension
+
+
+# language to use for accessing ontology
+ont.language=DE