maven plugin for RDF ontology to SQL translation

.settings/

.classpath

.project

target/

<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>

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);

		}

	}

}

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();

	}

}

# 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